[vistrails] 03/06: upstream vistrails-src-2.1.4-269e4808eca3
Alastair McKinstry
mckinstry at moszumanska.debian.org
Mon Jun 8 14:37:12 UTC 2015
This is an automated email from the git hooks/post-receive script.
mckinstry pushed a commit to branch master
in repository vistrails.
commit e11f3ffbfd63d0700f8bb6f3e9b0d0686fbe0b52
Author: Alastair McKinstry <mckinstry at debian.org>
Date: Mon Jun 8 14:05:08 2015 +0100
upstream vistrails-src-2.1.4-269e4808eca3
---
RELEASE | 57 +-
contrib/NumSciPy/Array.py | 250 -
contrib/NumSciPy/ArrayAccess.py | 342 -
contrib/NumSciPy/ArrayConvert.py | 151 -
contrib/NumSciPy/ArrayIO.py | 364 -
contrib/NumSciPy/ArrayInterpolate.py | 152 -
contrib/NumSciPy/ArrayOperations.py | 632 -
contrib/NumSciPy/ArrayPlot.py | 638 -
contrib/NumSciPy/ArrayUtilities.py | 254 -
contrib/NumSciPy/DSP.py | 369 -
contrib/NumSciPy/EnsembleOrdering.py | 297 -
contrib/NumSciPy/Filters.py | 185 -
contrib/NumSciPy/Imaging.py | 193 -
contrib/NumSciPy/Matrix.py | 107 -
contrib/NumSciPy/MatrixUtilities.py | 93 -
contrib/NumSciPy/Stockwell.py | 763 -
contrib/NumSciPy/__init__.py | 276 -
contrib/NumSciPy/smt.py | 40 -
contrib/ParaView/PVBase.py | 53 -
contrib/ParaView/__init__.py | 22 -
contrib/ParaView/configuration.py | 7 -
contrib/ParaView/contour.vt | Bin 463580 -> 0 bytes
contrib/ParaView/init.py | 185 -
contrib/ParaView/pv.vt | Bin 30902 -> 0 bytes
contrib/ParaView/pvcell.py | 83 -
contrib/ParaView/pvconfig.py | 89 -
contrib/SCIRun/__init__.py | 9001 --
contrib/SCIRun/cm2viewcell.py | 285 -
contrib/SCIRun/renderbase.py | 10 -
contrib/SCIRun/viewercell.py | 289 -
contrib/SciPy/DSP.py | 150 -
contrib/SciPy/Filters.py | 118 -
contrib/SciPy/MatlabReader.py | 51 -
contrib/SciPy/Matrix.py | 121 -
contrib/SciPy/MatrixConvert.py | 150 -
contrib/SciPy/MatrixInfo.py | 45 -
contrib/SciPy/MatrixOperations.py | 139 -
contrib/SciPy/SciPy.py | 36 -
contrib/SciPy/__init__.py | 226 -
contrib/TetGenBridge/CreateTestSurf.py | 102 -
contrib/TetGenBridge/Makefile | 19 -
contrib/TetGenBridge/TetGen.py | 313 -
contrib/TetGenBridge/__init__.py | 90 -
contrib/TetGenBridge/pill.nodes | 150 -
contrib/TetGenBridge/pill.tri | 295 -
contrib/TetGenBridge/tetgen.i | 284 -
contrib/cdat/NOTES | 17 -
contrib/cdat/__init__.py | 10094 --
contrib/cdat/cdat.sip | 36 -
contrib/cdat/cdat.vt | Bin 2948 -> 0 bytes
contrib/cdat/cdat_cell.py | 291 -
contrib/cdat/cdat_window.py | 2356 -
contrib/cdat/configure.py | 72 -
contrib/cdat/graphics_method_controller.py | 1624 -
contrib/cdat/gui_controller.py | 350 -
contrib/cdat/pyqtscripting.sbf | 3 -
contrib/cdat/quickplot.py | 50 -
contrib/cdat/scripts/cdat_domain.py | 289 -
contrib/cdat/scripts/cdatwindow_init_inc.py | 85 -
contrib/cdat/scripts/gen_init.py | 267 -
contrib/cdat/scripts/init_inc.py | 49 -
contrib/cdat/scripts/old_cdat_init.py | 447 -
contrib/cdat/scripts/parse_cdat_xml_file.py | 165 -
contrib/cdat/scripts/xml/canvas.xml | 2747 -
contrib/cdat/scripts/xml/cdms2.xml | 26 -
contrib/cdat/scripts/xml/cdmsFile.xml | 23 -
contrib/edu_utah_sci_cscheid_macet/MANIFEST | 1 -
contrib/edu_utah_sci_cscheid_macet/__init__.py | 125 -
contrib/edu_utah_sci_cscheid_metro/MANIFEST | 2 -
contrib/edu_utah_sci_cscheid_metro/__init__.py | 158 -
contrib/edu_utah_sci_cscheid_teem/__init__.py | 909 -
contrib/edu_utah_sci_cscheid_teem/examples.vt | Bin 52295 -> 0 bytes
.../edu_utah_sci_eranders_proteindatabank/PDB.py | 144 -
.../__init__.py | 68 -
contrib/edu_utah_sci_vgc_afront/MANIFEST | 1 -
contrib/edu_utah_sci_vgc_afront/__init__.py | 143 -
contrib/itk/FeatureExtractionFilters.py | 208 -
contrib/itk/GradientFilters.py | 84 -
contrib/itk/ITK.py | 166 -
contrib/itk/Image.py | 64 -
contrib/itk/ImageReader.py | 169 -
contrib/itk/IntensityFilters.py | 343 -
contrib/itk/NeighborhoodFilters.py | 210 -
contrib/itk/PixelType.py | 71 -
contrib/itk/SegmentationFilters.py | 319 -
contrib/itk/SelectionFilters.py | 231 -
contrib/itk/SmoothingFilters.py | 558 -
contrib/itk/ThresholdFilters.py | 110 -
contrib/itk/__init__.py | 179 -
contrib/itk/filter_generator.py | 170 -
contrib/itk/itk_test_example.py | 42 -
contrib/meshutils.py | 104 -
contrib/mobile/__init__.py | 365 -
contrib/pc3/__init__.py | 420 -
contrib/pc3/info/__init__.py | 1 -
contrib/pc3/info/ipaw/__init__.py | 1 -
contrib/pc3/info/ipaw/pc3/LoadAppLogic.py | 441 -
contrib/pc3/info/ipaw/pc3/LoadConstants.py | 19 -
contrib/pc3/info/ipaw/pc3/LoadSql.py | 147 -
contrib/pc3/info/ipaw/pc3/LoadWorkflow.py | 112 -
contrib/pc3/info/ipaw/pc3/__init__.py | 1 -
contrib/pc3/workflow.vt | Bin 8944 -> 0 bytes
contrib/pc3/workflow_ifs.vt | Bin 23612 -> 0 bytes
contrib/pc3/workflow_log.xml | 74 -
contrib/pc3/workflow_log_err.xml | 49 -
contrib/pc3/workflow_opm.xml | 1379 -
contrib/pc3/workflow_opm_err.xml | 756 -
contrib/pc3/workflow_reg.xml | 330 -
contrib/pc3/workflow_vt.xml | 1153 -
contrib/pc3/workflow_wf.xml | 169 -
contrib/poissonrecon.py | 101 -
contrib/provenance/__init__.py | 274 -
contrib/provenance2/__init__.py | 366 -
contrib/sahm/ColorBreaks.csv | 18 -
contrib/sahm/Images/BinMap.png | Bin 2627 -> 0 bytes
contrib/sahm/Images/BlackPoints.png | Bin 11389 -> 0 bytes
contrib/sahm/Images/GreenPoints.png | Bin 16370 -> 0 bytes
contrib/sahm/Images/MesMap.png | Bin 47294 -> 0 bytes
contrib/sahm/Images/ModMap.png | Bin 23896 -> 0 bytes
contrib/sahm/Images/ProbMap.png | Bin 377 -> 0 bytes
contrib/sahm/Images/RedPoints.png | Bin 17243 -> 0 bytes
contrib/sahm/Images/ResMap.png | Bin 7869 -> 0 bytes
contrib/sahm/Images/icons.pptx | Bin 79659 -> 0 bytes
contrib/sahm/SahmOutputViewer.py | 494 -
contrib/sahm/SahmSpatialOutputViewer.py | 483 -
contrib/sahm/SahmSpatialViewerCell.py | 89 -
contrib/sahm/SahmViewerCell.py | 72 -
contrib/sahm/SelectPredictorsLayers.py | 428 -
contrib/sahm/__init__.py | 14 -
contrib/sahm/enum_modules.py | 11 -
contrib/sahm/enum_widget.py | 44 -
contrib/sahm/init.py | 1788 -
contrib/sahm/layers.csv | 820 -
contrib/sahm/layers.exampledata.csv | 6 -
contrib/sahm/maxent.csv | 33 -
contrib/sahm/pySAHM/FieldDataQuery.py | 385 -
contrib/sahm/pySAHM/MDSBuilder.py | 473 -
contrib/sahm/pySAHM/MaxentRunner.py | 319 -
contrib/sahm/pySAHM/PARC.py | 776 -
contrib/sahm/pySAHM/RasterFormatConverter.py | 204 -
.../sahm/pySAHM/Resources/Docs/SAHM User Help.docx | Bin 907362 -> 0 bytes
.../sahm/pySAHM/Resources/R_Modules/AppendOut.r | 170 -
.../pySAHM/Resources/R_Modules/CompileOutput.r | 12 -
.../Resources/R_Modules/CrossValidationSplit.r | 99 -
.../sahm/pySAHM/Resources/R_Modules/EvalStats.r | 25 -
.../Resources/R_Modules/EvalStatsHelperFcts.r | 122 -
.../pySAHM/Resources/R_Modules/EvaluationStats.r | 436 -
.../pySAHM/Resources/R_Modules/FIT_BRT_pluggable.r | 2505 -
.../pySAHM/Resources/R_Modules/FIT_GLM_pluggable.r | 775 -
.../Resources/R_Modules/FIT_MARS_pluggable.r | 1697 -
.../pySAHM/Resources/R_Modules/FIT_RF_pluggable.r | 649 -
.../sahm/pySAHM/Resources/R_Modules/FunctionCall.r | 87 -
.../pySAHM/Resources/R_Modules/LoadRequiredCode.r | 16 -
.../sahm/pySAHM/Resources/R_Modules/PairsExplore.r | 435 -
.../pySAHM/Resources/R_Modules/PairsExplore2.r | 430 -
.../sahm/pySAHM/Resources/R_Modules/Pred.Surface.r | 54 -
.../sahm/pySAHM/Resources/R_Modules/PredictModel.r | 331 -
.../pySAHM/Resources/R_Modules/ResidualImage.r | 42 -
.../sahm/pySAHM/Resources/R_Modules/RunMaxEnt.jar | Bin 9304308 -> 0 bytes
.../pySAHM/Resources/R_Modules/TestTrainRocPlot.r | 372 -
.../pySAHM/Resources/R_Modules/TestTrainSplit.r | 188 -
.../Resources/R_Modules/Testing/CallPairsPlot.r | 114 -
.../pySAHM/Resources/R_Modules/Testing/Debugging.r | 173 -
.../pySAHM/Resources/R_Modules/Testing/Dickessel.r | 231 -
.../Resources/R_Modules/Testing/QuickDebug.r | 75 -
.../R_Modules/Testing/RunTestTrainSplit.r | 171 -
.../pySAHM/Resources/R_Modules/Testing/RunTests.r | 173 -
.../Resources/R_Modules/Testing/SyntheticData.r | 78 -
.../R_Modules/Testing/TestCountModelRuns.r | 186 -
.../Resources/R_Modules/Testing/TestFunction2.r | 23 -
.../R_Modules/Testing/TestModelRuns (2).r | 148 -
.../Resources/R_Modules/Testing/TestModelRuns.r | 174 -
.../R_Modules/Testing/TestingRandomForest.r | 17 -
.../pySAHM/Resources/R_Modules/Testing/unit.test.r | 49 -
.../sahm/pySAHM/Resources/R_Modules/check.libs.r | 16 -
contrib/sahm/pySAHM/Resources/R_Modules/make.auc.r | 136 -
.../sahm/pySAHM/Resources/R_Modules/modalDialog.R | 46 -
.../sahm/pySAHM/Resources/R_Modules/proc.tiff.r | 212 -
contrib/sahm/pySAHM/Resources/R_Modules/read.ma.r | 209 -
.../sahm/pySAHM/Resources/R_Modules/read.maNew.r | 224 -
.../pySAHM/Resources/R_Modules/tmp_ThrowsError.r | 1 -
contrib/sahm/pySAHM/__init__.py | 0
contrib/sahm/pySAHM/singlePARC.py | 71 -
contrib/sahm/pySAHM/singleRasterFormatConverter.py | 73 -
contrib/sahm/pySAHM/utilities.py | 261 -
contrib/sahm/utils.py | 481 -
contrib/sahm/widgets.py | 369 -
contrib/stem/__init__.py | 6 -
contrib/stem/code/STEM_Globals.R | 236 -
contrib/stem/code/STEM_Globals.R.bkup | 236 -
contrib/stem/code/STEM_ModelFitting.R | 201 -
contrib/stem/code/STEM_erd.srd.data.subsetting.R | 273 -
contrib/stem/code/STEM_st.matrix.cv.average.R | 95 -
contrib/stem/code/predict.eBird.ST.matrix.R | 200 -
contrib/stem/code/stem.library.A.R | 2088 -
contrib/stem/code/stem.library.B.R | 2124 -
contrib/stem/code/stem.library.ST.R | 2430 -
contrib/stem/current.vt | Bin 83005 -> 0 bytes
contrib/stem/init.py | 646 -
contrib/stem/mycurrent.vt | Bin 2882381 -> 0 bytes
contrib/stem/mycurrent2.vt | Bin 964975 -> 0 bytes
contrib/titan/__init__.py | 59 -
contrib/titan/base_module.py | 203 -
contrib/titan/class_tree.py | 268 -
contrib/titan/fix_classes.py | 51 -
contrib/titan/hasher.py | 36 -
contrib/titan/init.py | 1132 -
contrib/titan/inspectors.py | 232 -
contrib/titan/offscreen.py | 62 -
contrib/titan/tf_widget.py | 575 -
contrib/titan/vtk_parser.py | 528 -
contrib/titan/vtkcell.py | 1094 -
contrib/titan/vtkcell_rc.py | 793 -
contrib/titan/vtkhandler.py | 292 -
contrib/titan/vtkviewcell.py | 1032 -
contrib/trimesh2.py | 123 -
contrib/vtksnl/__init__.py | 53 -
contrib/vtksnl/base_module.py | 203 -
contrib/vtksnl/class_tree.py | 268 -
contrib/vtksnl/fix_classes.py | 51 -
contrib/vtksnl/hasher.py | 36 -
contrib/vtksnl/init.py | 1073 -
contrib/vtksnl/inspectors.py | 231 -
contrib/vtksnl/offscreen.py | 62 -
contrib/vtksnl/tf_widget.py | 575 -
contrib/vtksnl/vtk_parser.py | 514 -
contrib/vtksnl/vtkcell.py | 1094 -
contrib/vtksnl/vtkcell_rc.py | 793 -
contrib/vtksnl/vtkhandler.py | 291 -
contrib/vtksnl/vtkviewcell.py | 1032 -
data/1n25.pdb | 6334 -
data/carotid.vtk | 111734 ------------------
data/gktbhFA.vtk | Bin 864115 -> 0 bytes
data/gktbhL123.vtk | Bin 864137 -> 0 bytes
data/head.120.vtk | 91541 --------------
data/pdb.pdb | 3025 -
data/spx.vtk | 31678 -----
data/torus.vtk | 22046 ----
data/vslice_circ1.bp | 102 -
doc/dist/instructions.txt | 1 +
doc/usersguide/conf.py | 4 +-
doc/usersguide/controlflow.rst | 2 +
doc/usersguide/creating.rst | 8 +-
doc/usersguide/example_webservices.rst | 21 +-
.../figures/creating/module_configuration.png | Bin 14125 -> 0 bytes
.../figures/example_webservices/modules_list.png | Bin 51686 -> 13679 bytes
.../figures/example_webservices/pythonsource.png | Bin 83521 -> 0 bytes
.../example_webservices/version_tree_modules.png | Bin 30732 -> 0 bytes
.../figures/example_webservices/ws_preferences.png | Bin 188786 -> 0 bytes
.../figures/packages/after_enabled_package.png | Bin 76559 -> 0 bytes
.../figures/parameter_exploration/fig6_1.png | Bin 130189 -> 0 bytes
.../figures/parameter_exploration/fig6_2.png | Bin 53801 -> 0 bytes
.../figures/parameter_exploration/fig6_4.png | Bin 28751 -> 0 bytes
.../figures/parameter_exploration/fig6_5.png | Bin 28233 -> 0 bytes
.../figures/parameter_exploration/inspector.png | Bin 0 -> 21371 bytes
doc/usersguide/figures/querying/query4.png | Bin 8323 -> 0 bytes
.../spreadsheet/spreadsheet_cell_control.png | Bin 192558 -> 0 bytes
.../spreadsheet/spreadsheet_editing_mode.png | Bin 233535 -> 0 bytes
.../spreadsheet/spreadsheet_editing_mode_move.png | Bin 254908 -> 0 bytes
doc/usersguide/figures/version_tree/collapsed.png | Bin 109626 -> 0 bytes
.../figures/version_tree/creating_versions.png | Bin 153710 -> 0 bytes
doc/usersguide/figures/version_tree/expanded.png | Bin 117253 -> 0 bytes
doc/usersguide/parameter_exploration.rst | 30 +-
doc/usersguide/querying.rst | 8 -
doc/usersguide/vistrails_server.rst | 2 +-
doc/usersguide/vtl/gcd.vtl | 1 +
{examples => examples-internal}/XSLTSample.xsl | 0
{examples => examples-internal}/afront.xml | 0
{examples => examples-internal}/corie.xml | 0
{examples => examples-internal}/mummy.xml | 0
examples/gcd.vt | Bin 0 -> 12470 bytes
examples/gcd.xml | 1785 -
examples/primes.vt | Bin 0 -> 19976 bytes
examples/primes.xml | 2357 -
examples/scripting/combined_script.py | 11 +-
examples/scripting/vtk_book_3rd_p189_script.py | 11 +-
scripts/create_release_wiki_table.py | 4 +-
scripts/release_notes.py | 30 +-
scripts/update_db.py | 11 +-
scripts/update_hash.py | 7 +-
vistrails/core/application.py | 1 +
vistrails/core/collection/__init__.py | 2 +-
vistrails/core/collection/entity.py | 28 +-
vistrails/core/collection/mashup.py | 50 +-
vistrails/core/collection/parameter_exploration.py | 8 +-
vistrails/core/collection/search.py | 5 +-
vistrails/core/collection/thumbnail.py | 8 +-
vistrails/core/collection/vistrail.py | 16 +-
vistrails/core/collection/workflow.py | 8 +-
vistrails/core/collection/workflow_exec.py | 14 +-
vistrails/core/console_mode.py | 11 +-
vistrails/core/data_structures/graph.py | 51 +-
vistrails/core/mashup/controller.py | 40 +-
vistrails/core/mashup/mashup.py | 6 +-
vistrails/core/modules/basic_modules.py | 110 +-
vistrails/core/modules/package.py | 6 +-
vistrails/core/modules/paramexplore.py | 7 +-
vistrails/core/paramexplore/paramexplore.py | 16 +-
vistrails/core/system/__init__.py | 4 +-
vistrails/core/vistrail/controller.py | 73 +-
vistrails/db/services/io.py | 26 +-
vistrails/db/services/locator.py | 2 +-
vistrails/db/services/vistrail.py | 4 +
vistrails/db/specs/all.xml | 1 +
.../db/versions/v1_0_3/persistence/xml/auto_gen.py | 4 +
.../db/versions/v1_0_3/schemas/xml/vistrail.xsd | 1 +
vistrails/db/versions/v1_0_3/specs/all.xml | 1 +
vistrails/gui/application.py | 2 +
vistrails/gui/application_server.py | 210 +-
vistrails/gui/bundles/installbundle.py | 87 +-
vistrails/gui/bundles/linux_debian_install.py | 13 +-
vistrails/gui/collection/workspace.py | 209 +-
vistrails/gui/common_widgets.py | 4 +
vistrails/gui/graphics_view.py | 16 +-
vistrails/gui/mashups/mashup_app.py | 4 +-
vistrails/gui/modules/constant_configuration.py | 68 +-
vistrails/gui/modules/python_source_configure.py | 4 +-
vistrails/gui/modules/string_configure.py | 3 +-
.../gui/modules/stringformat_configuration.py | 86 +
vistrails/gui/paramexplore/param_view.py | 4 +
vistrails/gui/paramexplore/pe_inspector.py | 3 +-
vistrails/gui/paramexplore/pe_table.py | 2 +-
vistrails/gui/pipeline_view.py | 55 +-
vistrails/gui/preferences.py | 6 +
vistrails/gui/repository.py | 10 +-
vistrails/gui/requirements.py | 25 +-
.../gui/resources/images/vistrails_splash.png | Bin 160717 -> 162328 bytes
vistrails/gui/shell.py | 19 +
vistrails/gui/theme.py | 3 +
vistrails/gui/view_manager.py | 1 +
vistrails/gui/vistrail_view.py | 5 +-
vistrails/gui/vistrails_window.py | 6 +-
vistrails/index/__core.py | 143 -
vistrails/index/__init__.py | 35 -
vistrails/index/indexworkflow.py | 226 -
vistrails/index/spec_io.py | 137 -
vistrails/index/vistrailanalyzer.py | 116 -
vistrails/packages/CLTools/init.py | 20 +-
vistrails/packages/CLTools/wizard.py | 6 +-
vistrails/packages/HTTP/init.py | 2 +-
vistrails/packages/SUDSWebServices/init.py | 7 +-
vistrails/packages/controlflow/__init__.py | 2 +-
vistrails/packages/controlflow/init.py | 4 +
vistrails/packages/dialogs/__init__.py | 13 +-
vistrails/packages/dialogs/continue_prompt.py | 63 +
vistrails/packages/dialogs/init.py | 94 +-
vistrails/packages/matplotlib/bases.py | 121 +-
vistrails/packages/spreadsheet/basic_widgets.py | 22 +-
vistrails/packages/spreadsheet/spreadsheet_cell.py | 4 +-
.../spreadsheet/widgets/iebrowser/iecell.py | 2 +-
.../spreadsheet/widgets/imageviewer/imageviewer.py | 4 +-
.../spreadsheet/widgets/richtext/richtext.py | 29 +-
vistrails/packages/spreadsheet/widgets/svg/svg.py | 2 +-
.../spreadsheet/widgets/webview/webview.py | 2 +-
.../packages/tabledata/convert/convert_dates.py | 84 +-
vistrails/packages/tabledata/read/read_csv.py | 18 +-
vistrails/packages/tabledata/viewer.py | 2 +-
vistrails/packages/vtk/vtkcell.py | 2 +-
vistrails/packages/vtk/vtkviewcell.py | 2 +-
vistrails/run.py | 1 +
vistrails/tests/resources/spx_loop.vt | Bin 45577 -> 46018 bytes
vistrails/tests/utils.py | 5 +-
vistrails/vistrails_server.py | 48 +-
363 files changed, 1264 insertions(+), 359161 deletions(-)
diff --git a/RELEASE b/RELEASE
index fa4f501..b395268 100644
--- a/RELEASE
+++ b/RELEASE
@@ -1,6 +1,61 @@
RELEASE NOTES
-------------
-Release Name: v2.1.1 build 90975fc00211 from v2.1 branch
+Release Name: v2.1.4 build 269e4808eca3 from v2.1 branch
+
+Bug fixes:
+ - Pinch gesture was broken (2d5494ed1d10)
+ - Ticket 893: "Create Version" button on the spreadsheet does not work (d3db65418fad)
+ - New Parameter Exploration was created for each execution (c324acad38f9)
+ - Could not load saved Parameter Explorations (c324acad38f9)
+ - Ticket 762: Package.import_override.is_sys_pkg logic incorrect (bf5e20c923f7)
+ - Usersguide: Fixed parameter exploration vtl links (79c3021a50b3)
+ - Forces the use of PyQt4 (avoid PySide) (2460948327cc)
+ - Guess whether to use su/sudo with pip (18698fa909b3)
+
+From Release: v2.1.3 build 8262f078ed3b from v2.1 branch
+
+Bug fixes:
+ - Fixes scripting examples (8dd634391b71)
+ - Fixes Map and Filter modules outputting Variant (d597dcd6027f)
+ - Makes StringFormat handle {!r} or {:.2f} correctly (5f99a90fdc87)
+ - Fixes a test on newer pytz versions (2b4ecb3bc9bb)
+ - Displays exactly what we are going to install (214f98f478be)
+ - Fixes issue with missing PyQt4 (fbfada66f67e)
+ - Hide splashscreen when asking for file association (069c52f90130)
+
+From Release: v2.1.2 build 7d8a4ed2feeb from v2.1 branch
+
+Enhancements:
+ - Ticket 846: File Selection Dialog (78e8d01bd7ab)
+ - Ticket 824: Workflow execution output in console (8ea1231e736f)
+ - Adds PromptIsOkay module (WIP) (a1bad0cc2d46)
+ - Adds a YesNoDialog module (b267d2bed5eb)
+
+Bug fixes:
+ - Ticket 849: Autosave for existing vistrails not working (671eade8a9b8)
+ - Saving mashups to DB corrupts them (5be2ed41d33f)
+ - CLTools wizard does not show list type field (df8ef413aff4)
+ - Date error in workspace when using 8-bit characters (af83742a98ec)
+ - Ticket 850: Pipeline/history view scrollbars too sensitive (9e68064627c1)
+ - Ticket 686: Deleting a vistrail variable breaks workflows (1870f481103d)
+ - Ticket 830: Deleting a module does not delete vistrail variables connected to it (a197eba35396)
+ - Ticket 825: Vistrail Variables are not copied with modules (a197eba35396)
+ - Wrong view mode when switching between open vistrails (29bc0e1f47b7)
+ - Ticket 828: [Windows] Pinning a panel causes it to disappear (287e77ec7afd)
+ - Saving new vistrail caused view change (a95026c25968)
+ - Could not drop module in detached vistrail variables widget (63957fe80711)
+ - Vistrail Variables palette closed before it could be stickied (670f81d5eaff)
+ - Ticket 822: Exception if PyQt is installed but PyQt.QtOpenGL isn't (e4c1ded9d649)
+ - Ticket 783: Enabling packages automatically can make a different package fail (244084e837ec)
+ - Old-style imports did not work on vistrails server (eaded21310ee)
+ - Fixes adding a webservice through the context menu (d42e90689af2)
+ - Old mashuptrails were not deleted correctly in DB (5ada9ce79bcb)
+ - Mashups: Fixes alias copy bug (b5276f4c159e)
+ - SaveBundle did not copy mashups (ea12b6a1e2b3)
+ - Fixes date formatting in core.collection (1aaef5de72fb)
+ - Fixes major ImageViewerCell bug (d8ca797bf8b9)
+
+From Release: v2.1.1 build 90975fc00211 from v2.1 branch
Bug fixes:
- Ticket 816: Saved vistrail doesn't appear in 'my vistrails' (784414a617d2)
diff --git a/contrib/NumSciPy/Array.py b/contrib/NumSciPy/Array.py
deleted file mode 100644
index f9ef1a1..0000000
--- a/contrib/NumSciPy/Array.py
+++ /dev/null
@@ -1,250 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-
-import numpy
-
-class ArrayModule(object):
- my_namespace = 'numpy|array'
-
-class NDArray(Module, ArrayModule):
- """ Container class for the numpy.ndarray class """
- def __init__(self):
- Module.__init__(self)
- self.array = None
- self.names = {}
- self.general_name = None
- self.domain = ''
- self.range = ''
-
- def get_shape(self):
- return self.array.shape
-
- # Array Operation
- def reshape(self, shape):
- self.array.shape = shape
-
- # Array Access
- def get_reals(self):
- return self.array.real
-
- # Array Access
- def get_imaginary(self):
- return self.array.imag
-
- # Array Access
- def get_max(self):
- return self.array.max()
-
- # Array Access
- def get_mean(self, axis=None):
- return self.array.mean(axis=axis)
-
- # Array Access
- def get_min(self):
- return self.array.min()
-
- # Array Operation
- def cumulative_sum(self):
- return self.array.cumsum()
-
- # Array Access
- def get_arg_min(self):
- return self.array.argmin()
-
- # Array Access
- def get_arg_max(self):
- return self.array.argmax()
-
- # Array Access
- def get_diagonal(self):
- return self.array.diagonal()
-
- # Array Naming
- def get_name(self, row):
- if self.names.has_key(row):
- return self.names[row]
- else:
- return None
-
- # Array Naming
- def get_general_name(self):
- return self.general_name
-
- # Array Naming
- def set_name(self, name, index=False):
- self.general_name = name
- for i in range(self.array.shape[0]):
- if index:
- self.names[i] = name + " " + str(i+1)
- else:
- self.names[i] = name + " " + str(i)
-
- # Array Naming
- def set_row_name(self, name, row):
- self.names[row] = name
-
- # Array Naming
- def clear_names(self):
- self.general_name = None
- self.names = {}
-
- # Array Naming
- def get_domain_name(self):
- return self.domain
-
- # Array Naming
- def get_range_name(self):
- return self.range
-
- # Array Naming
- def set_domain_name(self, name):
- self.domain = name
-
- # Array Naming
- def set_range_name(self, name):
- self.range = name
-
- # Array Naming
- def clear_domain_name(self):
- self.domain = ''
-
- # Array Naming
- def clear_range_name(self):
- self.range = ''
-
- # Array Operation
- def sort_array(self, axis=-1, kind='quicksort', order=None):
- return self.array.argsort(axis, kind, order)
-
- # Array Access
- def get_array_as_type(self, t):
- return self.array.astype(t)
-
- # Array Operation
- def swap_bytes(self, view=False):
- return self.array.byteswap(view)
-
- # Array Access
- def get_conjugate(self):
- return self.array.conjugate().copy()
-
- # Array Operation
- def cumulative_product(self):
- return self.array.cumprod()
-
- # Array Convert
- def dump_to_file(self, fn):
- self.array.dump(fn)
-
- # Array Convert
- def dump_to_string(self):
- return self.array.dumps()
-
- # Array Operation
- def fill_array(self, val=0.):
- self.array.fill(val)
-
- # Array Access
- def get_flattened(self):
- return self.array.flatten()
-
- # Array Access
- def get_field(self, dtype, offset):
- return self.array.getfield(dtype, offset)
-
- # Array Access
- def get_item(self):
- return self.array.item()
-
- # Array Access
- def get_mem_size(self):
- return self.array.nbytes
-
- # Array Access
- def get_num_dims(self):
- return self.array.ndim
-
- # Array Access
- def get_nonzero_indices(self):
- return self.array.nonzero()
-
- # Array Operation
- def put(self, indices, values, mode):
- self.array.put(indices, values, mode)
-
- # Array Operation
- def ravel(self):
- return self.array.ravel()
-
- # Array Operation
- def resize(self, newshape, refcheck=True, order=False):
- return numpy.resize(self.array, newshape, refcheck=refcheck, order=order)
-
- # Array Operation
- def round(self, precision=0, out=None):
- return self.array.round(precision, out)
-
- # Array Operation
- def set_field(self, val, dtype, offset):
- self.array.set_field(val, dtype, offset)
-
- # Array Access
- def get_num_elements(self):
- return self.array.size
-
- # Array Operation
- def squeeze(self):
- return self.array.squeeze()
-
- # Array Operation
- def get_standard_deviation(self, axis=None, dtype=None, out=None):
- return self.array.std(axis, dtype, out)
-
- # Array Operation
- def get_sum(self):
- return self.array.sum()
-
- # Array Operation
- def swap_axes(self, axis1, axis2):
- return self.array.swapaxes(axis1, axis2)
-
- # Array Convert
- def tofile(self, file, sep, format="%s"):
- self.array.tofile(file, sep, format)
-
- # Array Convert
- def tolist(self):
- return self.array.tolist()
-
- # Array Convert
- def tostring(self, order='C'):
- return self.array.tostring(order)
-
- # Array Operation
- def get_trace(self, offset, axis1, axis2, dtype=None, out=None):
- return self.array.trace(offset, axis1, axis2, dtype, out)
-
- # Array Access
- def get_transpose(self):
- return self.array.transpose()
-
- # Array Operation
- def get_variance(self, axis=None, dtype=None, out=None):
- return self.array.var(axis, dtype, out)
-
- # Helper function for assignment
- def get_array(self):
- return self.array
-
- # Helper function for assignment
- def set_array(self, a):
- self.array = a
-
- # Array Access
- def get_row_range(self, start, to):
- return self.array[start:to+1,:]
-
- # Array Access
- def get_col_range(self, start, to):
- return self.array[:, start:to+1]
diff --git a/contrib/NumSciPy/ArrayAccess.py b/contrib/NumSciPy/ArrayAccess.py
deleted file mode 100644
index 70d9e29..0000000
--- a/contrib/NumSciPy/ArrayAccess.py
+++ /dev/null
@@ -1,342 +0,0 @@
-import core.modules
-from core.modules.vistrails_module import Module, ModuleError
-
-import numpy
-from Array import *
-
-class ArrayAccess(object):
- my_namespace = "numpy|array|access"
-
-class GetShape(Module, ArrayAccess):
- """ Get the size of each dimension of an N-dimensional array"""
- def compute(self):
- a = self.getInputFromPort("Array")
- sh = a.get_shape()
- dims = len(sh)
- for i in xrange(dims):
- pname = "dim" + str(i)
- self.setResult(pname, sh[i])
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Array Shape", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "dim0", (basic.Integer, 'Dim 0 Size'))
- reg.add_output_port(cls, "dim1", (basic.Integer, 'Dim 1 Size'))
- reg.add_output_port(cls, "dim2", (basic.Integer, 'Dim 2 Size'))
- reg.add_output_port(cls, "dim3", (basic.Integer, 'Dim 3 Size'), True)
- reg.add_output_port(cls, "dim4", (basic.Integer, 'Dim 4 Size'), True)
- reg.add_output_port(cls, "dim5", (basic.Integer, 'Dim 5 Size'), True)
- reg.add_output_port(cls, "dim6", (basic.Integer, 'Dim 6 Size'), True)
- reg.add_output_port(cls, "dim7", (basic.Integer, 'Dim 7 Size'), True)
-
-class GetReals(Module, ArrayAccess):
- """ Get the real component of a complex array """
- def compute(self):
- a = self.getInputFromPort("Array")
- b = a.get_reals()
- out = NDArray()
- out.set_array(b)
- self.setResult("Real Component", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Reals", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Real Component", (NDArray, 'Real Components'))
-
-
-class GetImaginaries(Module, ArrayAccess):
- """ Get the imaginary component of a complex array """
- def compute(self):
- a = self.getInputFromPort("Array")
- b = a.get_imaginary()
- out = NDArray()
- out.set_array(b)
- self.setResult("Im Component", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Imaginaries", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Im Component", (NDArray, 'Imaginary Components'))
-
-class GetMax(Module, ArrayAccess):
- """ Get the maximal value from an array """
- def compute(self):
- a = self.getInputFromPort("Array")
- self.setResult("Max", float(a.get_max()))
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Max", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Max", (basic.Float, 'Max Value'))
-
-class GetMean(Module, ArrayAccess):
- """ Get the mean value of an array """
- def compute(self):
- a = self.getInputFromPort("Array")
- axis = self.forceGetInputFromPort("Axis")
- out = NDArray()
- out.set_array(numpy.array(a.get_mean(axis)))
- self.setResult("Mean", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Mean", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Axis", (basic.Integer, 'Axis'), True)
- reg.add_output_port(cls, "Mean", (NDArray, 'Mean Value'))
-
-class GetMin(Module, ArrayAccess):
- """ Get the smallest value in an array """
- def compute(self):
- a = self.getInputFromPort("Array")
- self.setResult("Min", float(a.get_min()))
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Min", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Min", (basic.Float, 'Min Value'))
-
-class GetDiagonal(Module, ArrayAccess):
- """ Get an array representing the values on the diagonal of the input array """
- def compute(self):
- a = self.getInputFromPort("Array")
- out = NDArray()
- out.set_array(a.get_diagonal())
- self.setResult("Diagonal", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Diagonal", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Diagonal", (NDArray, 'Diagonal Elements'))
-
-class GetArrayAsType(Module, ArrayAccess):
- """ Cast the array to the given type """
- def compute(self):
- a = self.getInputFromPort("Array")
- t = self.getInputFromPort("Type")
- t.setValue("0")
- out = NDArray()
- out.set_array(a.get_array_as_type(type(t.value)))
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Cast Array", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Type", (basic.Constant, 'Cast To Type'))
- reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
-
-class GetConjugate(Module, ArrayAccess):
- """ Get the complex conjugate of the input array """
- def compute(self):
- a = self.getInputFromPort("Array")
- out = NDArray()
- out.set_array(a.get_conjugate())
- self.setResult("Conjugate", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Conjugate", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Conjugate", (NDArray, 'Complex Conjugate'))
-
-class GetFlattenedArray(Module, ArrayAccess):
- """ Get a flattened representation of the input array"""
- def compute(self):
- a = self.getInputFromPort("Array")
- out = NDArray()
- out.set_array(a.get_flattened())
- self.setResult("Flat Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Flattened Array", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Flat Array", (NDArray, 'Output Vector'))
-
-class GetField(Module, ArrayAccess):
- """ Get a field from an array given the output datatype and offset into the array"""
- def compute(self):
- a = self.getInputFromPort("Array")
- dt = self.getInputFromPort("DType")
- dt.setValue("0")
- o = self.getInputFromPort("Offset")
- out = NDArray()
- out.set_array(a.get_field(type(dt.value), o))
- self.setResult("Field", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Field", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "DType", (basic.Constant, 'Output Type'))
- reg.add_input_port(cls, "Offset", (basic.Integer, 'Offset'))
- reg.add_output_port(cls, "Field", (NDArray, 'Output Field'))
-
-class ToScalar(Module, ArrayAccess):
- """ Return an array of size 1 to a scalar """
- def compute(self):
- a = self.getInputFromPort("Array")
- self.setResult("Item", float(a.get_item()))
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="To Scalar", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Item", (basic.Float, 'Item'))
-
-class GetMemoryFootprint(Module, ArrayAccess):
- """ Return the amount of system memory consumed by the array """
- def compute(self):
- a = self.getInputFromPort("Array")
- self.setResult("Size", int(a.get_mem_size()))
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Memory Size", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'InputArray'))
- reg.add_output_port(cls, "Size", (basic.Integer, 'Memory Size'))
-
-class GetArrayRank(Module, ArrayAccess):
- """ Get the rank of the array """
- def compute(self):
- a = self.getInputFromPort("Array")
- self.setResult("Rank", int(a.get_num_dims()))
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Array Rank", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Rank", (basic.Integer, 'Array Rank'))
-
-class GetNonZeroEntries(Module, ArrayAccess):
- """ Get an array consisting of the indices to all non-zero entries of the input array."""
- def compute(self):
- a = self.getInputFromPort("Array")
- out = NDArray()
- out.set_array(a.get_nonzero_indices())
- self.setResult("Entries", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Non-Zero Entries", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Entreis", (NDArray, 'Output Array'))
-
-class GetArraySize(Module, ArrayAccess):
- """ Get the number of entries in an array """
- def compute(self):
- a = self.getInputFromPort("Array")
- self.setResult("Size", a.get_num_elements())
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Array Size", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Size", (basic.Integer, 'Number of Elements'))
-
-class GetTranspose(Module, ArrayAccess):
- """ Get the transpose of the array """
- def compute(self):
- a = self.getInputFromPort("Array")
- out = NDArray()
- out.set_array(a.get_transpose())
- self.setResult("Transpose", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Get Transpose", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Transpose", (NDArray, 'Transposed Array'))
-
-class GetRowRange(Module, ArrayAccess):
- """ Get a set of rows from the input array """
- def compute(self):
- a = self.getInputFromPort("Array")
- s = self.getInputFromPort("Start")
- e = self.getInputFromPort("End")
- out = NDArray()
- if self.forceGetInputFromPort("One Indexed"):
- s = s-1
- e = e-1
-
- out.set_array(a.get_row_range(s, e))
- new_index = 0
- for i in range(s,e+1):
- out.set_row_name(a.get_name(i), new_index)
- new_index += 1
-
- out.set_domain_name(a.get_domain_name())
- out.set_range_name(a.get_range_name())
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Start", (basic.Integer, 'Start Index'))
- reg.add_input_port(cls, "End", (basic.Integer, 'End Index'))
- reg.add_input_port(cls, "One Indexed", (basic.Boolean, 'One Indexed'), True)
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-
-class GetRows(Module, ArrayAccess):
- """ Get a set of rows from the input array defined by a list of indexes """
- def compute(self):
- l = self.forceGetInputFromPort("Index List")
- if l == None:
- l = self.forceGetInputListFromPort("Indexes")
-
- if l == None or len(l) == 0:
- raise ModuleError("No indexes provided")
-
- l.sort()
- inp = self.getInputFromPort("Array")
- in_ar = inp.get_array()
- out_ar = in_ar[l[0],::]
- for i in range(1,len(l)):
- out_ar = numpy.vstack((out_ar,in_ar[i,::]))
-
- out = NDArray()
- for i in range(out_ar.shape[0]):
- out.set_row_name(inp.get_row_name(l[i]), i)
-
- out.set_array(out_ar)
- out_order = NDArray()
- out_order.set_array(numpy.array(l))
- self.setResult("Output Array", out)
- self.setResult("Output Order", out_order)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Indexes", (basic.Integer, 'Index'))
- reg.add_input_port(cls, "Index List", (basic.List, 'Index List'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
- reg.add_output_port(cls, "Output Order", (NDArray, 'Output Ordering'))
-
-class GetColumnRange(Module, ArrayAccess):
- """ Get a set of columns from the input array """
- def compute(self):
- a = self.getInputFromPort("Array")
- s = self.getInputFromPort("Start")
- e = self.getInputFromPort("End")
- out = NDArray()
- out.set_array(a.get_col_range(s, e-1))
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Start", (basic.Integer, 'Start Index'))
- reg.add_input_port(cls, "End", (basic.Integer, 'End Index'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
diff --git a/contrib/NumSciPy/ArrayConvert.py b/contrib/NumSciPy/ArrayConvert.py
deleted file mode 100644
index 067c774..0000000
--- a/contrib/NumSciPy/ArrayConvert.py
+++ /dev/null
@@ -1,151 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from scipy import sparse
-from Array import *
-from Matrix import *
-
-class ArrayConvertModule(object):
- my_namespace = 'numpy|array|convert'
-
-class ArrayDumpToFile(ArrayConvertModule, Module):
- """ Pickle the input array and dump it to the specified file. This
- array can then be read in via pickle.load or numpy.load """
- def compute(self):
- a = self.getInputFromPort("Array")
- fn = self.getInputFromPort("Filename")
- a.dump_to_file(fn)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="ArrayToPickledFile", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
-
-class ArrayDumpToString(ArrayConvertModule, Module):
- """ Pickle the input array and dump it to a string. This array
- can then be read in via pickle.loads or numpy.loads """
- def compute(self):
- a = self.getInputFromPort("Array")
- self.setResult("Output String", a.dump_to_string())
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="ArrayToPickledString", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Output String", (basic.String, 'Output String'))
-
-class ArrayToFile(ArrayConvertModule, Module):
- """ Write the data to a file. If a separator char is given, the file
- will be written in ASCII with the given char acting as a delimiter. If
- no separator is given, the file is written in Binary. The array
- is always written in row-major format regardless of the order of the
- input array. """
- def compute(self):
- a = self.getInputFromPort("Array")
- fn = self.getInputFromPort("Filename")
- sep = ""
- if self.hasInputFromPort("Separator"):
- sep = self.getInputFromPort("Separator")
- a.tofile(fn, sep)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
- reg.add_input_port(cls, "Separator", (basic.String, 'Separator'), True)
-
-class ArrayToString(ArrayConvertModule, Module):
- """ Convert the array to a Python string. The output string will
- be represented in row-major form regardless of the ordering of the
- input array. """
- def compute(self):
- a = self.getInputFromPort("Array")
- self.setResult("Output String", a.tostring())
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Output String", (basic.String, 'Output String'))
-
-class ArrayToMatrix(ArrayConvertModule, Module):
- """ Convert the input Numpy Array to a Scipy Matrix. The input array
- must be no more than 2-dimensional """
- def compute(self):
- a = self.getInputFromPort("Array")
- try:
- mat = sparse.csc_matrix(a.get_array())
- out_mat = Matrix()
- out_mat.set_matrix(mat)
- self.setResult("Output Matrix", out_mat)
-
- except:
- raise ModuleError("Could not convert input array to matrix")
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Output Matrix", (Matrix, 'Output Matrix'))
-
-class ArrayToVTKImageData(ArrayConvertModule, Module):
- """ Convert the array to a vtImageData dataset. This works well for
- arrays up to (and including) rank 3. Behavior is undefined for array of
- rank > 3."""
- def compute(self):
- import vtk
-
- a = self.getInputFromPort("Array")
- sh = a.get_shape()
-
- if len(sh) < 2:
- sh = tuple([sh[0], 1, 0])
- if len(sh) < 3:
- sh = tuple([sh[0], sh[1], 0])
-
- (num_sigs, num_times, num_freqs) = sh
- num_pts = a.get_num_elements()
- vtk_set = core.modules.module_registry.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkStructuredPoints').module()
- vtk_set.vtkInstance = vtk.vtkImageData()
- vtk_set.vtkInstance.SetDimensions(sh[0], sh[1], sh[2]+1)
- vtk_set.vtkInstance.SetScalarTypeToFloat()
- scalars = vtk.vtkFloatArray()
-
- ar = a.get_array()
- for ar_x in xrange(sh[0]):
- for ar_y in xrange(sh[1]):
- if sh[2] == 0:
- val = ar[ar_x, ar_y]
- vtk_set.vtkInstance.SetScalarComponentFromFloat(ar_x, ar_y, 0, 0, val)
- else:
-
- for ar_z in xrange(sh[2]):
- val = ar[ar_x, ar_y, ar_z]
- vtk_set.vtkInstance.SetScalarComponentFromFloat(ar_x, ar_y, ar_z, 0, val)
-
- if self.hasInputFromPort("SpacingX"):
- x = self.getInputFromPort("SpacingX")
- else:
- x = 1.0
- if self.hasInputFromPort("SpacingY"):
- y = self.getInputFromPort("SpacingY")
- else:
- y = 1.0
- if self.hasInputFromPort("SpacingZ"):
- z = self.getInputFromPort("SpacingZ")
- else:
- z = 1.0
- vtk_set.vtkInstance.SetSpacing(x,y,z)
-
- self.setResult("vtkImageData", vtk_set)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array Volume'))
- reg.add_input_port(cls, "SpacingX", (basic.Float, 'X Spacing'))
- reg.add_input_port(cls, "SpacingY", (basic.Float, 'Y Spacing'))
- reg.add_input_port(cls, "SpacingZ", (basic.Float, 'Z Spacing'))
- reg.add_output_port(cls, "vtkImageData", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkImageData').module))
diff --git a/contrib/NumSciPy/ArrayIO.py b/contrib/NumSciPy/ArrayIO.py
deleted file mode 100644
index 554162e..0000000
--- a/contrib/NumSciPy/ArrayIO.py
+++ /dev/null
@@ -1,364 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-import numpy
-import scipy
-import scipy.io
-import pylab
-from Array import *
-from Matrix import *
-
-class ArrayIOModule(object):
- my_namespace = 'numpy|io'
-
-class NrrdHelper(object):
- def __init__(self):
- self.type = {}
- self.type['float32'] = 'f'
- self.type['float'] = 'f'
- self.type['float64'] = 'd'
- self.type['double'] = 'd'
- self.type['int'] = 'i'
- self.type['int16'] = 'i'
- self.type['long'] = 'l'
- self.type['int32'] = 'l'
- self.type['unsigned short'] = 's'
- self.type['unsigned char'] = 'c'
-
- self.nrrd_type = {}
- self.nrrd_type['float'] = 'float'
- self.nrrd_type['float32'] = 'float'
- self.nrrd_type['float64'] = 'double'
- self.nrrd_type['double'] = 'double'
- self.nrrd_type['int64'] = 'long'
- self.nrrd_type['long'] = 'long'
- self.nrrd_type['int32'] = 'int'
- self.nrrd_type['int16'] = 'short'
- self.nrrd_type['int8'] = 'uchar'
- self.nrrd_type['unsigned short'] = 'short'
-
- self.little_endian = True
-
- def num_bytes(self, dtype):
- if self.type.has_key(dtype):
- return self.type[dtype]
- else:
- print "Cannot find " + dtype + " in type library."
- print "Assuming float32 for dtype"
- return 'f'
-
- def get_nrrd_type(self, data):
- dt = data.dtype.name
- if self.nrrd_type.has_key(dt):
- return self.nrrd_type[dt]
- else:
- print "Cannot find " + dt + " in type library."
- print "Assuming float32 for dtype"
- return 'float'
-
- def read_raw(self, fn, sizes, dtype, little_end=True):
- try:
- fid = open(fn, 'rb')
- dt = self.num_bytes(dtype)
- ndim = len(sizes)
- num_el = 1
- for i in xrange(ndim):
- num_el *= sizes[i]
-
- if little_end:
- dt = '<'+dt
- else:
- dt = '>'+dt
-
- data = numpy.fromfile(fn, dt)
- fid.close()
- data.shape = sizes
- return data
- except:
- raise ModuleError("Could not read .raw file!")
-
- def write_raw(self, fn, data):
- try:
- fid = open(fn, 'wb')
- scipy.io.fwrite(fid, data.size, data)
- fid.close()
- except:
- raise ModuleError("Could not write .raw file!")
-
- def write_nhdr(self, fn, data):
- import os
- l = fn.split('/')
- name = l[len(l)-1]
- base = name.split('.')[0]
- rawname = base + '.raw'
- rawpath = fn.rstrip(name)
- rawpath += rawname
- self.write_raw(rawpath, data)
- cmd = 'unu make -h -t '
- cmd += self.get_nrrd_type(data) + ' '
- cmd += '-e raw -i ' + rawname + ' -s '
- sh = data.shape
- ndims = len(sh)
- for i in xrange(ndims):
- cmd += str(sh[i]) + ' '
-
- cmd += '-o ' + fn
- try:
- os.system(cmd)
- except:
- raise ModuleError("Could not write NHDR file. Please make sure the Teem and UNU utilities are on your path.")
-
- def read_nhdr(self, fn):
- import os.path
- try:
- fid = open(fn, 'r')
- for line in fid:
- if line.split(':')[0] == 'type':
- self.dtype = line.split(':')[1].strip()
- if line.split(':')[0] == 'dimension':
- self.ndim = int(line.split(':')[1].strip())
- if line.split(':')[0] == 'sizes':
- s = line.split(':')[1].strip().split(' ')
- self.sizes = []
- for l in s:
- self.sizes.append(int(l))
- if line.split(':')[0] == 'endian':
- if line.split(':')[1].strip() == 'little':
- self.little_endian = True
- else:
- self.little_endian = False
- if line.split(':')[0] == 'data file':
- self.fn = line.split(':')[1].strip()
- if line.split(':')[0] == 'encoding':
- self.encoding = line.split(':')[1].strip()
- fid.close()
- except:
- raise ModuleError("Could not read .nhdr file!")
-
- if self.encoding == 'raw':
- curpath = os.getcwd()
- npath = os.path.dirname(fn)
- os.chdir(npath)
- data = self.read_raw(self.fn, self.sizes, self.dtype, little_end=self.little_endian)
- os.chdir(curpath)
- return data
-
- raise ModuleError(".nhdr file contains file not in .raw format!")
-
-class ReadPNG(ArrayIOModule, Module):
- """ Load a .png type image into a Numpy Array. """
- def compute(self):
- fn = self.getInputFromPort("Filename")
- ar = pylab.imread(fn)
- out = NDArray()
- out.set_array(ar)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class WritePNG(ArrayIOModule, Module):
- """ Write a .png type image from a Numpy Array. """
- def compute(self):
- fn = self.getInputFromPort("Filename")
- ar = self.getInputFromPort("Image")
- minv = self.forceGetInputFromPort("Min")
- maxv = self.forceGetInputFromPort("Max")
- if minv == None:
- minv = 0
- if maxv == None:
- maxv = 255
- da_ar = ar.get_array().squeeze()
- im = scipy.misc.toimage(da_ar, cmin=minv, cmax=maxv).save(fn)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
- reg.add_input_port(cls, "Min", (basic.Integer, 'Min Value'))
- reg.add_input_port(cls, "Max", (basic.Integer, 'Max Value'))
- reg.add_input_port(cls, "Image", (NDArray, 'Image To Write'))
-
-class ReadRAW(ArrayIOModule, Module):
- """ Load a .raw file into a Numpy Array. The .raw files are
- assumed to be in the volvis format: http://www.volvis.org """
- def __init__(self):
- Module.__init__(self)
- self.helper = NrrdHelper()
-
- def compute(self):
- fn = self.getInputFromPort("Filename")
- sizes = self.getInputListFromPort("Sizes")
- dtype = self.getInputFromPort("DataType")
- ar = self.helper.read_raw(fn, sizes, dtype)
- out = NDArray()
- out.set_array(ar)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
- reg.add_input_port(cls, "Sizes", (basic.Integer, 'Dimension Sizes'))
- reg.add_input_port(cls, "DataType", (basic.String, 'Datatype'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class WriteRAW(ArrayIOModule, Module):
- """ Write a .raw file from a Numpy Array. """
- def __init__(self):
- Module.__init__(self)
- self.helper = NrrdHeler()
-
- def compute(self):
- fn = self.getInputFromPort("Filename")
- ar = self.getInputFromPort("Array").get_array()
- self.helper.write_raw(fn,ar)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
-
-class ReadNHDR(ArrayIOModule, Module):
- """ Load a .nhdr/.raw pair into a Numpy Array. """
- def __init__(self):
- Module.__init__(self)
- self.helper = NrrdHelper()
-
- def compute(self):
- fn = ''
- if self.hasInputFromPort("File"):
- fn = self.getInputFromPort("File").name
- else:
- fn = self.getInputFromPort("Filename")
- ar = self.helper.read_nhdr(fn)
- out = NDArray()
- out.set_array(ar)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
- reg.add_input_port(cls, "File", (basic.File, 'File'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class WriteNHDR(ArrayIOModule, Module):
- """ Write a .nhdr/.raw pair from a Numpy Array """
- def __init__(self):
- Module.__init__(self)
- self.helper = NrrdHelper()
-
- def compute(self):
- fn = self.getInputFromPort("Filename")
- ar = self.getInputFromPort("Array").get_array()
- self.helper.write_nhdr(fn,ar)
- self.setResult("Filename Out", fn)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Filename Out", (basic.String, 'Output Filename'))
-
-class ReadStatisticalSummary(ArrayIOModule, Module):
- """
- Documentation
- """
- def compute(self):
- fn = ''
- if self.hasInputFromPort("File"):
- fn = self.getInputFromPort("File").name
- else:
- fn = self.getInputFromPort("Filename")
-
- if self.forceGetInputFromPort("Allocate Aggregated Array"):
- alloc_array = True
- else:
- alloc_array = False
-
- fid = open(fn, 'r')
- dims = fid.readline().strip().split()
- n_pts = int(dims[0])
- n_bins = int(dims[1])
-
- min_ar = numpy.zeros(n_pts)
- lq_ar = numpy.zeros(n_pts)
- med_ar = numpy.zeros(n_pts)
- hq_ar = numpy.zeros(n_pts)
- max_ar = numpy.zeros(n_pts)
- mode_ar = numpy.zeros((n_pts, 4))
- hist_ar = numpy.zeros((n_pts, n_bins))
- if alloc_array:
- ag_ar = numpy.zeros((n_pts, 5+4+n_bins))
- for i in xrange(n_pts):
- l = fid.readline().strip().split()
- min_ar[i] = float(l[0])
- lq_ar[i] = float(l[1])
- med_ar[i] = float(l[2])
- hq_ar[i] = float(l[3])
- max_ar[i] = float(l[4])
- for j in xrange(4):
- mode_ar[i, j] = float(l[5+j])
-
- for b in xrange(n_bins):
- hist_ar[i, b] = float(l[9+b])
-
- if alloc_array:
- vals = numpy.array(l).astype('float')
- ag_ar[i,:] += vals
-
- fid.close()
-
- min_ar_out = NDArray()
- min_ar_out.set_array(min_ar)
- self.setResult("Min Array", min_ar_out)
-
- lq_ar_out = NDArray()
- lq_ar_out.set_array(lq_ar)
- self.setResult("Lower Quartile Array", lq_ar_out)
-
- med_ar_out = NDArray()
- med_ar_out.set_array(med_ar)
- self.setResult("Median Array", med_ar_out)
-
- hq_ar_out = NDArray()
- hq_ar_out.set_array(hq_ar)
- self.setResult("Upper Quartile Array", hq_ar_out)
-
- max_ar_out = NDArray()
- max_ar_out.set_array(max_ar)
- self.setResult("Max Array", max_ar_out)
-
- mode_ar_out = NDArray()
- mode_ar_out.set_array(mode_ar)
- self.setResult("Mode Array", mode_ar_out)
-
- hist_ar_out = NDArray()
- hist_ar_out.set_array(hist_ar)
- self.setResult("Histogram Array", hist_ar_out)
-
- if alloc_array:
- ag_ar_out = NDArray()
- ag_ar_out.set_array(ag_ar)
- self.setResult("Aggregated Array", ag_ar_out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
- reg.add_input_port(cls, "File", (basic.File, 'File'))
- reg.add_input_port(cls, "Allocate Aggregated Array", (basic.Boolean, 'Allocate Extra Space for Aggregated Array'), True)
- reg.add_output_port(cls, "Min Array", (NDArray, 'Minima Array'))
- reg.add_output_port(cls, "Lower Quartile Array", (NDArray, 'Lower Quartile Array'))
- reg.add_output_port(cls, "Median Array", (NDArray, 'Median Array'))
- reg.add_output_port(cls, "Upper Quartile Array", (NDArray, 'Upper Quartile Array'))
- reg.add_output_port(cls, "Max Array", (NDArray, 'Maxima Array'))
- reg.add_output_port(cls, "Mode Array", (NDArray, 'Mode Array'))
- reg.add_output_port(cls, "Histogram Array", (NDArray, 'Histogram Array'))
- reg.add_output_port(cls, "Aggregated Array", (NDArray, 'Aggregated Array'), True)
diff --git a/contrib/NumSciPy/ArrayInterpolate.py b/contrib/NumSciPy/ArrayInterpolate.py
deleted file mode 100644
index 3200c31..0000000
--- a/contrib/NumSciPy/ArrayInterpolate.py
+++ /dev/null
@@ -1,152 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-import scipy
-import scipy.interpolate
-import scipy.ndimage
-import vtk
-from Array import *
-from Matrix import *
-
-class ArrayInterpModule(object):
- my_namespace = 'scipy|interpolation'
-
-class RBFInterpolate(ArrayInterpModule, Module):
- """ Use radial basis function interpolation to project scalars from
- one mesh to another. The input, Source, describes the x,y,z coordinates and
- values of the points in the form: [[x,y,z,v]] The input, Destination,
- describes the x,y,z coordinates of the points to project onto in the form
- [[x,y,z]]. Additional (optional) inputs controll the basis function (basis),
- the smoothing factor (smoothing) and the tuning parameter (epsilon). Not
- all parameters are valid for all bases. The following defaults are applied:
-
- basis = inverse multiquadric
- smoothing = 0.0
- epsilon = 1.0
- """
-
- def compute(self):
- src = self.getInputFromPort("Source").get_array()
- if src.shape[1] != 4:
- raise ModuleError("Source array must be in the form [[x,y,z,v]]")
-
- dest = self.getInputFromPort("Destination").get_array()
- if dest.shape[1] != 3:
- raise ModuleError("Destination array must be in the form [[x,y,z]]")
-
- if self.hasInputFromPort("Basis"):
- self.basis = self.getInputFromPort("Basis")
- else:
- self.basis = 'inverse multiquadric'
-
- if self.hasInputFromPort("Smoothing"):
- self.smooth = self.getInputFromPort("Smoothing")
- else:
- self.smooth = 0.0
-
- if self.hasInputFromPort("Epsilon"):
- self.eps = self.getInputFromPort("Epsilon")
- else:
- self.eps = 1.0
-
- rbfi = scipy.interpolate.Rbf(src[:,0], src[:,1], src[:,2], src[:,3], function=self.basis, smooth=self.smooth, epsilon=self.eps)
-
- val_ar = rbfi(dest[:,0], dest[:,1], dest[:,2])
-
- out = NDArray()
- out.set_array(val_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Source", (NDArray, 'Source Array'))
- reg.add_input_port(cls, "Destination", (NDArray, 'Destination Array'))
- reg.add_input_port(cls, "Basis", (basic.String, 'Basis Function'), True)
- reg.add_input_port(cls, "Smoothing", (basic.Float, 'Smoothing Factor'), True)
- reg.add_input_port(cls, "Epsilon", (basic.Float, 'Basis Epsilon'), True)
- reg.add_output_port(cls, "Output", (NDArray, 'Output Scalars'))
-
-class BSplineInterpolate(ArrayInterpModule, Module):
- """
- Find the B-Spline representation of an N-dimensional curve.
- """
-
- def compute(self):
- in_ar = self.getInputFromPort("Input").get_array()
- num_samp = self.forceGetInputFromPort("Interpolant Support")
- if not num_samp:
- num_samp = in_ar.shape[0]
-
- smoothing = self.forceGetInputFromPort("Smoothing")
- if not smoothing:
- smoothing = 0.0
-
- degree = self.forceGetInputFromPort("Degree")
- if not degree:
- degree = 3
-
- (tckvec, u) = scipy.interpolate.splprep(in_ar, s=smoothing, k=degree, nest=-1)
- (x,y,z) = splev(numpy.linspace(0.,1.,num_samp), tckvec)
- out_ar = numpy.zeros((x.shape[0], 3))
- out_ar[:,0] = x
- out_ar[:,1] = y
- out_ar[:,2] = z
-
- out = NDArray()
- out.set_array(out_ar)
-
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, 'Source Array'))
- reg.add_input_port(cls, "Smoothing", (basic.Float, 'Smoothing Factor'), True)
- reg.add_input_port(cls, "Interpolant Support", (basic.Integer, 'Output Samples'), True)
- reg.add_input_port(cls, "Degree", (basic.Integer, 'Polynomial Degree'), True)
- reg.add_output_port(cls, "Output", (NDArray, 'Output Scalars'))
-
-class BSplineResample(ArrayInterpModule, Module):
- """
- Resample the input array using an order-n bspline
- """
- def compute(self):
- in_ar = self.getInputFromPort("Input").get_array()
- order = self.forceGetInputFromPort("Order")
- if order == None:
- order = 3
- planes = self.forceGetInputFromPort("Planes")
- ndim = in_ar.ndim
- gridshape = self.getInputFromPort("New Shape").values
-
- out_ar = None
- if planes:
- out_ar = []
- for i in range(in_ar.shape[0]):
- pl = in_ar[i].squeeze()
- arshape = pl.shape
- g = scipy.mgrid[tuple([slice(0, v1-1, complex(0,v2)) for (v1,v2) in zip(arshape, gridshape)])]
- coords = numpy.array(list(g))
- out_ar.append(scipy.ndimage.map_coordinates(pl, coords))
-
- out_ar = numpy.array(out_ar)
-
- else:
- arshape = in_ar.shape
- g = scipy.mgrid[tuple([slice(0, v1-1, complex(0,v2)) for (v1,v2) in zip(arshape, gridshape)])]
- coords = numpy.array(list(g))
- out_ar = scipy.ndimage.map_coordinates(in_ar, coords)
-
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, 'Source Array'))
- reg.add_input_port(cls, "Order", (basic.Integer, 'Bspline Order'), True)
- reg.add_input_port(cls, "New Shape", (basic.Tuple, 'New Array Shape'))
- reg.add_input_port(cls, "Planes", (basic.Boolean, 'Apply to each plane'), True)
- reg.add_output_port(cls, "Output", (NDArray, 'Output Scalars'))
diff --git a/contrib/NumSciPy/ArrayOperations.py b/contrib/NumSciPy/ArrayOperations.py
deleted file mode 100644
index d7cf0bc..0000000
--- a/contrib/NumSciPy/ArrayOperations.py
+++ /dev/null
@@ -1,632 +0,0 @@
-from core.modules.vistrails_module import Module, ModuleError
-from Array import *
-
-class ArrayOperationModule(object):
- my_namespace = 'numpy|array|operations'
-
-
-class ArrayReshape(ArrayOperationModule, Module):
- """ Reshape the input array. The dimension sizes are presented
- and used to reshape the array. Please note that the total number
- of elements in the array must remain the same before and after
- reshaping. """
- def compute(self):
- a = self.getInputFromPort("Array")
- dims = self.getInputFromPort("Dims")
- newdims = []
-
- for i in xrange(dims):
- pname = "dim" + str(i)
- newdims.append(self.getInputFromPort(pname))
-
- try:
- a.reshape(tuple(newdims))
- except:
- raise ModuleError("Could not assign new shape. Be sure the number of elements remains constant")
-
- self.setResult("Array Output", a.copy())
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="ReshapeArray", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Dims", (basic.Integer, 'New Dimensionality'))
- reg.add_input_port(cls, "dim0", (basic.Integer, 'Dimension Size'))
- reg.add_input_port(cls, "dim1", (basic.Integer, 'Dimension Size'))
- reg.add_input_port(cls, "dim2", (basic.Integer, 'Dimension Size'))
- reg.add_input_port(cls, "dim3", (basic.Integer, 'Dimension Size'), True)
- reg.add_input_port(cls, "dim4", (basic.Integer, 'Dimension Size'), True)
- reg.add_input_port(cls, "dim5", (basic.Integer, 'Dimension Size'), True)
- reg.add_input_port(cls, "dim6", (basic.Integer, 'Dimension Size'), True)
- reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
-
-class ArrayCumulativeSum(ArrayOperationModule, Module):
- """ Get the cumulative sum of a given array. This is returned as a
- flattened array of the same size as the input where each element
- of the array serves as the cumulative sum up until that point."""
- def compute(self):
- a = self.getInputFromPort("Array")
- b = a.cumulative_sum()
- out = NDArray()
- out.set_array(b)
- self.setResult("Array Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
-
-class ArrayScalarMultiply(ArrayOperationModule, Module):
- """ Multiply the input array with a given scalar """
- def compute(self):
- a = self.getInputFromPort("Array")
- b = self.getInputFromPort("Scalar")
- out = NDArray()
- out.set_array(a.get_array() * b)
- self.setResult("Array Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Scalar", (basic.Float, 'Input Scalar'))
- reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
-
-class ArraySort(ArrayOperationModule, Module):
- def __init__(self):
- Module.__init__(self)
- self.axis = -1
- self.kind = 'quicksort'
- self.order = None
-
- """ Sort the input array. By default, a flattened representation
- of the input array is used as input to a quicksort. Optional
- inputs are the axis in which to sort on and the type of sort to
- use.
-
- Sorting algorithms supported:
- quicksort - best average speed, unstable
- mergesort - needs additional working memory, stable
- heapsort - good worst-case performance, unstable
- """
- def compute(self):
- a = self.getInputFromPort("Array")
- if self.hasInputFromPort("Axis"):
- self.axis = self.getInputFromPort("Axis")
- if self.hasInputFromPort("Sort"):
- self.kind = self.getInputFromPort("Sort")
- if self.hasInputFromPort("Order"):
- self.order = self.getInputFromPort("Order")
-
- b = a.sort_array(axis=self.axis, kind=self.kind, order=self.order)
- out = NDArray()
- out.set_array(b.copy())
- self.setResult("Sorted Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Axis", (basic.Integer, 'Axis to sort'), True)
- reg.add_input_port(cls, "Sort", (basic.String, 'Sort Algorithm'), True)
- reg.add_input_port(cls, "Order", (basic.Integer, 'Order'),True)
- reg.add_output_port(cls, "Sorted Array", (NDArray, 'Sorted Array'))
-
-class ArrayCumulativeProduct(ArrayOperationModule, Module):
- """ Get the cumulative product of a given array. This is returned as
- a flattened array of the same size as the input where each element of
- the array serves as the cumulative product up until that point"""
- def compute(self):
- a = self.getInputFromPort("Array")
- b = a.cumulative_product()
- out = NDArray()
- out.set_array(b)
- self.setResult("Array Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
-
-class ArrayFill(ArrayOperationModule, Module):
- """ Fill the input array with the given value. If no value is given
- it is filled with 0.0"""
- def compute(self):
- a = self.getInputFromPort("Array")
- if self.hasInputFromPort("Value"):
- val = self.getInputFromPort("Value")
- else:
- val = 0.
-
- a.fill_array(val)
- self.setResult("Array Output", a)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Fill Array", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Value", (basic.Float, 'Value'))
- reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
-
-class ArrayResize(ArrayOperationModule, Module):
- """ Resize the input array. Unlike the ArrayReshape module,
- the number of elements of the array need not be conserved.
- If the shape is larger than the input array size, repeated
- copies of the input array will be copied to the resized version.
- If the shape is smaller, the input array will be cropped appropriately.
- """
- def compute(self):
- a = self.getInputFromPort("Array")
- dims = self.getInputFromPort("Dims")
- newdims = []
-
- for i in xrange(dims):
- pname = "dim" + str(i)
- newdims.append(self.getInputFromPort(pname))
-
- try:
- t = tuple(newdims)
- b = a.resize(t)
- out = NDArray()
- out.set_array(b.copy())
- except:
- raise ModuleError("Could not assign new shape.")
-
- self.setResult("Array Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Dims", (basic.Integer, 'Output Dimensionality'))
- reg.add_input_port(cls, "dim0", (basic.Integer, 'Dimension Size'))
- reg.add_input_port(cls, "dim1", (basic.Integer, 'Dimension Size'))
- reg.add_input_port(cls, "dim2", (basic.Integer, 'Dimension Size'))
- reg.add_input_port(cls, "dim3", (basic.Integer, 'Dimension Size'), True)
- reg.add_input_port(cls, "dim4", (basic.Integer, 'Dimension Size'), True)
- reg.add_input_port(cls, "dim5", (basic.Integer, 'Dimension Size'), True)
- reg.add_input_port(cls, "dim6", (basic.Integer, 'Dimension Size'), True)
- reg.add_input_port(cls, "dim7", (basic.Integer, 'Dimension Size'), True)
- reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
-
-class ArrayExtractRegion(ArrayOperationModule, Module):
- """ Extract a region from array as specified by the
- dimension and starting and ending indices """
- def compute(self):
- import operator
- a = self.getInputFromPort("Array")
- dims = self.getInputFromPort("Dims")
- a_dims = len(a.get_shape())
- if dims > a_dims:
- raise ModuleError("Output Dimensionality larger than Input Dimensionality")
-
- slices = []
- for i in xrange(dims):
- (start, stop) = self.getInputFromPort("dim"+str(i))
- slices.append(slice(start, stop))
-
- ar = operator.__getitem__(a.get_array(), tuple(slices))
- out = NDArray()
- out.set_array(ar)
- self.setResult("Array Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- l = [basic.Integer, basic.Integer]
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Dims", (basic.Integer, 'Output Dimensionality'))
- reg.add_input_port(cls, "dim0", l, True)
- reg.add_input_port(cls, "dim1", l, True)
- reg.add_input_port(cls, "dim2", l, True)
- reg.add_input_port(cls, "dim3", l, True)
- reg.add_input_port(cls, "dim4", l, True)
- reg.add_input_port(cls, "dim5", l, True)
- reg.add_input_port(cls, "dim6", l, True)
- reg.add_input_port(cls, "dim7", l, True)
- reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
-
-class ArrayRavel(ArrayOperationModule, Module):
- """ Get a 1D array containing the elements of the input array"""
- def compute(self):
- a = self.getInputFromPort("Array")
- b = NDArray()
- b.set_array(a.ravel().copy())
- self.setResult("Array Output", b)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
-
-class ArrayRound(ArrayOperationModule, Module):
- """ Round each element of the array to the given number of
- decimal places. This defaults to 0 resulting in a rounding
- to integers """
- def __init__(self):
- Module.__init__(self)
- self.decimals = 0
-
- def compute(self):
- a = self.getInputFromPort("Array")
- if self.hasInputFromPort("Decimals"):
- self.decimals = self.getInputFromPort("Decimals")
-
- out = NDArray()
- out.set_array(a.round(precision=self.decimals))
- self.setResult("Array Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Decimals", (basic.Integer, 'Precision'))
- reg.add_output_port(cls, "Array Output", (NDArray, 'Output Array'))
-
-class ArrayGetSigma(ArrayOperationModule, Module):
- """ Return the standard deviation of elements in the array """
- def __init__(self):
- Module.__init__(self)
- self.axis=None
-
- def compute(self):
- a = self.getInputFromPort("Array")
- if self.hasInputFromPort("Axis"):
- self.axis = self.getInputFromPort("Axis")
-
- out = NDArray()
- out.set_array(a.get_standard_deviation(self.axis))
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="ArrayStandardDeviation", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Axis", (basic.Integer, 'Axis'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArraySum(ArrayOperationModule, Module):
- """ Get the sum of all elements in the input array """
- def compute(self):
- a = self.getInputFromPort("Array")
- self.setResult("Array Sum", float(a.get_sum()))
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Array Sum", (basic.Float, 'Sum'))
-
-class ArrayElementMultiply(ArrayOperationModule, Module):
- """ Perform an element-wise multiply on the elements of two arrays """
- def compute(self):
- a1 = self.getInputFromPort("Array1")
- a2 = self.getInputFromPort("Array2")
- out = NDArray()
- out.set_array(a1.get_array() * a2.get_array())
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array1", (NDArray, 'Input Array 1'))
- reg.add_input_port(cls, "Array2", (NDArray, 'Input Array 2'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArraySetElement(ArrayOperationModule, Module):
- """ Set a set of array elements given arrays of values and indices
-
- Please note that this module creates a copy of the input to operate
- on to preserve the original array data. """
- def compute(self):
- a = self.getInputFromPort("Array")
- if self.hasInputFromPort("Scalar Value"):
- self.v = self.getInputFromPort("Scalar Value")
- else:
- self.v = self.getInputFromPort("Value Array")
-
- if self.hasInputFromPort("Single Index"):
- self.ind = self.getInputFromPort("Single Index")
- else:
- self.ind = self.getInputFromPort("Index Array")
-
- out_a = a.copy()
-
- out_a.put(self.ind, self.v)
- out = NDArray()
- out.set_array(out_a)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Scalar Value", (basic.Float, 'Value to Set'))
- reg.add_input_port(cls, "Value Array", (NDArray, 'Values to Set'))
- reg.add_input_port(cls, "Single Index", (basic.Integer, 'Index to Set'))
- reg.add_input_port(cls, "Index Array", (NDArray, 'Indexes to Set'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArrayVariance(ArrayOperationModule, Module):
- """ Calculate the variance of the elements of an array """
- def compute(self):
- a = self.getInputFromPort("Array")
- if self.hasInputFromPort("Axis"):
- self.setResult("Variance", float(a.get_variance(axis=self.getInputFromPort("Axis"))))
- else:
- self.setResult("Variance", float(a.get_variance()))
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Axis", (basic.Integer, 'Axis'))
- reg.add_output_port(cls, "Variance", (basic.Float, 'Variance'))
-
-class ArrayTrace(ArrayOperationModule, Module):
- """ Calculate the trace of the input array.
-
- The input array must have at least rank 2. The trace is taken
- on the diagonal given by the inputs Axis1 and Axis2 using the
- given Offset. If these values are not supplied, they default to:
-
- Axis1 = 0
- Axis2 = 1
- Offset = 0
- """
- def compute(self):
- a = self.getInputFromPort("Array")
- if self.hasInputFromPort("Axis1"):
- self.axis1 = self.getInputFromPort("Axis1")
- else:
- self.axis1 = 0
-
- if self.hasInputFromPort("Axis2"):
- self.axis2 = self.getInputFromPort("Axis2")
- else:
- self.axis2 = 1
-
- if self.hasInputFromPort("Offset"):
- self.offset = self.getInputFromPort("Offset")
- else:
- self.offset = 0
-
- self.setResult("Trace", float(a.get_trace(self.offset, self.axis1, self.axis2)))
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Axis1", (basic.Integer, 'Axis 1'))
- reg.add_input_port(cls, "Axis2", (basic.Integer, 'Axis 2'))
- reg.add_input_port(cls, "Offset", (basic.Integer, 'Offset'))
- reg.add_output_port(cls, "Trace", (basic.Float, 'Array Trace'))
-
-class ArraySwapAxes(ArrayOperationModule, Module):
- """ Create a new view of the input array with the
- given axes swapped.
- """
- def compute(self):
- a = self.getInputFromPort("Array")
- a1 = self.getInputFromPort("Axis1")
- a2 = self.getInputFromPort("Axis2")
- out = NDArray()
- out.set_array(a.swap_axes(a1, a2).copy())
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Axis1", (basic.Integer, 'Axis 1'))
- reg.add_input_port(cls, "Axis2", (basic.Integer, 'Axis 2'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArraySqueeze(ArrayOperationModule, Module):
- """ Eliminate all length-1 dimensions in the input array. """
- def compute(self):
- a = self.getInputFromPort("Array")
- out = NDArray()
- out.set_array(a.get_array().squeeze().copy())
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArrayAdd(ArrayOperationModule, Module):
- """ Add two arrays of the same size and shape """
- def compute(self):
- a1 = self.getInputFromPort("Array One").get_array()
- a2 = self.getInputFromPort("Array Two").get_array()
-
- if a1.shape != a2.shape:
- raise ModuleError("Cannot add arrays with different shapes")
-
- out = NDArray()
- out.set_array(a1 + a2)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array One", (NDArray, 'Input Array 1'))
- reg.add_input_port(cls, "Array Two", (NDArray, 'Input Array 2'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArrayScalarAdd(ArrayOperationModule, Module):
- """ Add two arrays of the same size and shape """
- def compute(self):
- a1 = self.getInputFromPort("Array One").get_array()
- s = self.getInputFromPort("Scalar")
-
- out = NDArray()
- out.set_array(a1 + s)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array One", (NDArray, 'Input Array 1'))
- reg.add_input_port(cls, "Scalar", (basic.Float, 'Scalar'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArrayLog10(ArrayOperationModule, Module):
- """ Take the base-10 log of each element in the input array """
- def compute(self):
- a = self.getInputFromPort("Array").get_array()
- out = NDArray()
- out.set_array(numpy.log10(a))
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArrayAtan2(ArrayOperationModule, Module):
- """ Calculate the oriented arc-tangent of a vector stored as two arrays.
- Reals: Real components of complex vectors
- Imaginaries: Imaginary components of complex vectors
- """
- def compute(self):
- r = self.getInputFromPort("Reals").get_array()
- i = self.getInputFromPort("Imaginaries").get_array()
- out = NDArray()
- out.set_array(numpy.arctan2(r,i))
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Reals", (NDArray, 'Real Components'))
- reg.add_input_port(cls, "Imaginaries", (NDArray, 'Imaginary Components'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArraySqrt(ArrayOperationModule, Module):
- """ Calculate the element-wise square root of the input array """
- def compute(self):
- a = self.getInputFromPort("Input Array").get_array()
- out = NDArray()
- out.set_array(numpy.sqrt(a))
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input Array", (NDArray, 'Input Array'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArrayThreshold(ArrayOperationModule, Module):
- """ Threshold the array keeping only the values above the scalar value, v. """
- def compute(self):
- in_ar = self.getInputFromPort("Input Array").get_array()
- v = self.getInputFromPort("Value")
- r = self.forceGetInputFromPort("Replacement")
- if r == None:
- r = 0.
- out = NDArray()
- out.set_array(numpy.where(in_ar > v, in_ar, r))
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Value", (basic.Float, 'Threshold Value'))
- reg.add_input_port(cls, "Replacement", (basic.Float, 'Replacement Value'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArrayWindow(ArrayOperationModule, Module):
- """ Threshold the array from both above and below, keeping only
- the values within the window. """
- def compute(self):
- in_ar = self.getInputFromPort("Input Array").get_array()
- lo = self.forceGetInputFromPort("Lower Bound")
- hi = self.forceGetInputFromPort("Upper Bound")
- r = self.forceGetInputFromPort("Replacement")
- if r == None:
- r = 0.
- if lo == None:
- lo = in_ar.min()
- if hi == None:
- hi = in_ar.max()
-
- out = NDArray()
- o = numpy.where(in_ar >= lo, in_ar, r)
- o = numpy.where(o <= hi, o, r)
- out.set_array(o)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Lower Bound", (basic.Float, 'Lower Threshold Value'))
- reg.add_input_port(cls, "Upper Bound", (basic.Float, 'Upper Threshold Value'))
- reg.add_input_port(cls, "Replacement", (basic.Float, 'Replacement Value'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArrayNormalize(ArrayOperationModule, Module):
- """ Normalize the input array """
- def compute(self):
- in_ar = self.getInputFromPort("Input Array").get_array()
- ar = numpy.zeros(in_ar.shape)
- if self.forceGetInputFromPort("Planes"):
- for i in range(in_ar.shape[0]):
- p = in_ar[i] - in_ar[i].min()
- ar[i] = p / p.max()
- else:
- ar = in_ar - in_ar.min()
- ar = ar/ar.max()
-
- out = NDArray()
- out.set_array(ar)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "Planes", (basic.Boolean, 'Plane-wise normalization'), True)
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ArrayName(ArrayOperationModule, Module):
- """ Assign a name or label to the entries of an array """
- def compute(self):
- in_ar = self.getInputFromPort("Input Array")
- gen_name = self.forceGetInputFromPort("Name")
- one_index = self.forceGetInputFromPort("One Indexed")
- if gen_name:
- in_ar.set_name(gen_name, index=one_index)
-
- name_list = self.forceGetInputListFromPort("Row Name")
- if name_list != None:
- for (i,n) in name_list:
- in_ar.set_row_name(n, i)
-
- dname = self.forceGetInputFromPort("Domain Name")
- if dname:
- in_ar.set_domain_name(dname)
-
- rname = self.forceGetInputFromPort("Range Name")
- if rname:
- in_ar.set_range_name(rname)
-
- self.setResult("Output Array", in_ar)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input Array", (NDArray, 'Input Array'))
- reg.add_input_port(cls, "One Indexed", (basic.Boolean, 'One Indexed'))
- reg.add_input_port(cls, "Name", (basic.String, 'Array Name'))
- reg.add_input_port(cls, "Row Name", [basic.Integer, basic.String], True)
- reg.add_input_port(cls, "Domain Name", (basic.String, 'Domain Label'))
- reg.add_input_port(cls, "Range Name", (basic.String, 'Range Label'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
diff --git a/contrib/NumSciPy/ArrayPlot.py b/contrib/NumSciPy/ArrayPlot.py
deleted file mode 100644
index ef6e1ae..0000000
--- a/contrib/NumSciPy/ArrayPlot.py
+++ /dev/null
@@ -1,638 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from core.modules.basic_modules import PythonSource
-from Array import *
-from Matrix import *
-
-import pylab
-import matplotlib
-import urllib
-import random
-
-class ArrayPlot(object):
- namespace = 'numpy|array|plotting'
- def get_label(self, ar, i):
- lab = ar.get_name(i)
- if lab == None:
- return 'Array ' + str(i)
- else:
- return lab
-
- def is_cacheable(self):
- return False
-
- def get_color(self, colors, i, randomcolor):
- if randomcolor:
- return (random.random(), random.random(), random.random())
-
- if self.color_dict == None:
- self.color_dict = {}
- for (k,r,g,b) in colors:
- self.color_dict[k] = (r,g,b)
-
- if self.color_dict.has_key(i):
- return self.color_dict[i]
- else:
- return None
-
- def get_marker(self, markers, i):
- if markers == None:
- return None
-
- if self.marker_dict == None:
- self.marker_dict = {}
- for (k,m) in markers:
- self.marker_dict[k] = m
-
- if self.marker_dict.has_key(i):
- return self.marker_dict[i]
- else:
- return None
-
- def get_alpha(self, alphas, i):
- return None
-
-class ArrayImage(ArrayPlot, Module):
- '''
- Display the 2D input Data Array as a color-mapped image.
- Independent control of the aspect ratio, colormap, presence of the
- colorbar and presented axis values are provided through the
- appropriate input ports: Aspect Ratio, Colormap, Colorbar,
- Extents. To change the colormap being used, it must be one of the
- pre-made maps provided by matplotlib.cm. Only 1 2D array can be
- viewed at a time.
- '''
- def compute(self):
- data = self.getInputFromPort("Data Array")
- da_ar = data.get_array().squeeze()
- if da_ar.ndim != 2:
- raise ModuleError("Input Data Array must have dimension = 2")
-
- aspect_ratio = self.forceGetInputFromPort("Aspect Ratio")
- colormap = self.forceGetInputFromPort("Colormap")
- colorbar = self.forceGetInputFromPort("Colorbar")
- extents = self.forceGetInputFromPort("Extents")
-
- # Quickly check the assigned colormap to make sure it's valid
- if colormap == None:
- colormap = "jet"
- if not hasattr(pylab, colormap):
- colormap = "jet"
-
- bg_color = self.forceGetInputFromPort("Background")
- array_x_t = self.forceGetInputFromPort("Use X Title")
- array_y_t = self.forceGetInputFromPort("Use Y Title")
-
- p_title = self.forceGetInputFromPort("Title")
- x_label = self.forceGetInputFromPort("X Title")
- y_label = self.forceGetInputFromPort("Y Title")
-
- s = urllib.unquote(str(self.forceGetInputFromPort("source", '')))
-
- s = 'from pylab import *\n' +\
- 'from numpy import *\n' +\
- 'import numpy\n'
-
- if bg_color == None:
- bg_color = 'w'
-
- if type(bg_color) == type(''):
- s += 'figure(facecolor=\'' + bg_color + '\')\n'
- else:
- s += 'figure(facecolor=' + str(bg_color) + ')\n'
-
- s += 'imshow(da_ar, interpolation=\'bicubic\''
- if aspect_ratio != None:
- s += ', aspect=' + str(aspect_ratio)
-
- if extents != None:
- s += ', extent=['+str(extents[0])+','+str(extents[1])+','+str(extents[2])+','+str(extents[3])+']'
- s += ')\n'
-
- s += colormap + '()\n'
-
- if colorbar:
- s += 'colorbar()\n'
-
- if array_x_t:
- s += 'xlabel(\'' + data.get_domain_name() + '\')\n'
- elif x_label:
- s += 'xlabel(\'' + x_label + '\')\n'
-
- if array_y_t:
- s += 'ylabel(\'' + data.get_range_name() + '\')\n'
- elif y_label:
- s += 'ylabel(\'' + y_label + '\')\n'
-
- if p_title:
- s += 'title(\'' + p_title + '\')\n'
-
- exec s
- self.setResult('source', s)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.namespace)
-
- @classmethod
- def register_ports(cls, reg, basic):
- reg.add_input_port(cls, "source", (basic.String, 'source'), True)
- reg.add_input_port(cls, "Data Array", (NDArray, 'Array to Plot'))
- reg.add_input_port(cls, "Aspect Ratio", (basic.Float, 'Aspect Ratio'))
- reg.add_input_port(cls, "Colormap", (basic.String, 'Colormap'))
- reg.add_input_port(cls, "Colorbar", (basic.Boolean, 'Show Colorbar'), True)
- reg.add_input_port(cls, "Extents", [basic.Float, basic.Float, basic.Float, basic.Float], True)
- reg.add_input_port(cls, "Background", [basic.Float, basic.Float, basic.Float], True)
- reg.add_input_port(cls, "Use X Title", (basic.Boolean, 'Apply X-axis Label'))
- reg.add_input_port(cls, "Use Y Title", (basic.Boolean, 'Apply Y-axis Label'))
- reg.add_input_port(cls, "Title", (basic.String, 'Figure Title'))
- reg.add_input_port(cls, "X Title", (basic.String, 'X-axis label'), True)
- reg.add_input_port(cls, "Y Title", (basic.String, 'Y-axis label'), True)
- reg.add_output_port(cls, "source", (basic.String, 'source'))
-
-class Histogram(ArrayPlot, Module):
- '''
- Plot a histogram of the data values. Multiple datasets can be
- presented by providing multiple connections to the Data Array
- port. These data are then differentiated by assigned colors and
- labels. By default, 10 bins are used to histogram the data.
- Additionally, recapturing the PDF of the data is possible by
- enabling the Normalize option.
- '''
- def compute(self):
- data = self.getInputListFromPort("Data Array")
- self.label_dict = None
- self.color_dict = None
- use_legend = self.forceGetInputFromPort("Legend")
- randomcolors = self.forceGetInputFromPort("Random Colors")
- colors = self.forceGetInputListFromPort("Colors")
- bg_color = self.forceGetInputFromPort("Background")
- array_x_t = self.forceGetInputFromPort("Use X Title")
- array_y_t = self.forceGetInputFromPort("Use Y Title")
- p_title = self.forceGetInputFromPort("Title")
- x_label = self.forceGetInputFromPort("X Title")
- nbins = self.forceGetInputFromPort("Bins")
- if nbins == None:
- nbins = 10
- normed = self.forceGetInputFromPort("Normalize")
- if normed == None:
- normed = False
-
- s = urllib.unquote(str(self.forceGetInputFromPort("source", '')))
- self.source = ''
-
- s = 'from pylab import *\n' +\
- 'from numpy import *\n' +\
- 'import numpy\n'
-
- if bg_color == None:
- bg_color = 'w'
-
- if type(bg_color) == type(''):
- s += 'figure(facecolor=\'' + bg_color + '\')\n'
- else:
- s += 'figure(facecolor=' + str(bg_color) + ')\n'
-
- data_list = []
- for i in data:
- data_list.append(i.get_array().squeeze())
-
- da_ar = None
- try:
- da_ar = numpy.array(data_list)
- except:
- raise ModuleException("Not all Data Array inputs are the same size!")
-
- for i in range(da_ar.shape[0]):
- lab = self.get_label(data[i], i)
- col = self.get_color(colors, i, randomcolors)
-
- s += 'hist(da_ar['+str(i)+',:], bins=' + str(nbins)
-
- if lab != None:
- s += ', label=\'' + lab + '\''
- if col != None:
- s += ', facecolor=' + str(col)
-
- s += ', normed='+str(normed)
- s += ')\n'
-
- if use_legend:
- s += 'legend()\n'
-
- if array_x_t:
- s += 'xlabel(\'' + data[0].get_domain_name() + '\')\n'
- elif x_label:
- s += 'xlabel(\'' + x_label + '\')\n'
-
- if array_y_t:
- s += 'ylabel(\'Histogram Value\')\n'
-
- if p_title:
- s += 'title(\'' + p_title + '\')\n'
-
- exec s
- self.setResult("source", s)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.namespace)
-
- @classmethod
- def register_ports(cls, reg, basic):
- reg.add_input_port(cls, "source", (basic.String, 'source'), True)
- reg.add_input_port(cls, "Data Array", (NDArray, 'Data Array to Plot'))
- reg.add_input_port(cls, "Legend", (basic.Boolean, 'Use Legend'), True)
- reg.add_input_port(cls, "Random Colors", (basic.Boolean, 'Assign Random Colors'), True)
- reg.add_input_port(cls, "Colors", [basic.Integer, basic.Float, basic.Float, basic.Float], True)
- reg.add_input_port(cls, "Background", [basic.Float, basic.Float, basic.Float], True)
- reg.add_input_port(cls, "Use X Title", (basic.Boolean, 'Apply X-axis Label'))
- reg.add_input_port(cls, "Use Y Title", (basic.Boolean, 'Apply Y-axis Label'))
- reg.add_input_port(cls, "Title", (basic.String, 'Figure Title'))
- reg.add_input_port(cls, "X Title", (basic.String, 'X-axis label'), True)
- reg.add_input_port(cls, "Bins", (basic.Integer, 'Number of Bins'))
- reg.add_input_port(cls, "Normalize", (basic.Boolean, 'Normalize to PDF'), True)
- reg.add_output_port(cls, "source", (basic.String, 'source'))
-
-class BarChart(ArrayPlot, Module):
- '''
- Create a bar chart of the input data. Different datasets can be
- used simultaneously by connecting to the Data input port multiple
- times. Each successive data connection will be rendered on top of
- the previous dataset. This creates a stacked bar chart. Error
- bars are drawn with the errors for each of the datasets connected
- to the Error Bars input port.
- '''
- def get_ticks(self, num):
- a = []
- for i in range(num):
- a.append('')
-
- for i in self.tick_dict.keys():
- a[i] = self.tick_dict[i]
-
- return a
-
- def compute(self):
- data = self.getInputListFromPort("Data")
- errs = self.forceGetInputListFromPort("Error Bars")
- if len(errs) == 0:
- errs = None
-
- self.label_dict = None
- self.color_dict = None
- use_legend = self.forceGetInputFromPort("Legend")
- randomcolors = self.forceGetInputFromPort("Random Colors")
- colors = self.forceGetInputListFromPort("Colors")
- bg_color = self.forceGetInputFromPort("Background")
- array_x_t = self.forceGetInputFromPort("Use X Title")
- array_y_t = self.forceGetInputFromPort("Use Y Title")
- ticks = self.forceGetInputListFromPort("Bar Labels")
- self.tick_dict = {}
- for (k,v) in ticks:
- self.tick_dict[k] = v
- p_title = self.forceGetInputFromPort("Title")
- x_label = self.forceGetInputFromPort("X Title")
- y_label = self.forceGetInputFromPort("Y Title")
-
- width = self.forceGetInputFromPort("Bar Width")
- if width == None:
- width = 0.5
-
- if errs != None:
- if len(data) != len(errs):
- raise ModuleError("Number of data does not match number of error bar data")
-
- s = urllib.unquote(str(self.forceGetInputFromPort("source", '')))
- self.source = ''
-
- s = 'from pylab import *\n' +\
- 'from numpy import *\n' +\
- 'import numpy\n'
-
- if bg_color == None:
- bg_color = 'w'
-
- if type(bg_color) == type(''):
- s += 'figure(facecolor=\'' + bg_color + '\')\n'
- else:
- s += 'figure(facecolor=' + str(bg_color) + ')\n'
-
- numpts = None
- ind = None
- prev = None
- ind = numpy.arange(data[0].get_array().flatten().shape[0])
- t = self.get_ticks(data[0].get_array().flatten().shape[0])
- ag_ar = numpy.zeros((len(data), data[0].get_array().flatten().shape[0]))
- for i in range(len(data)):
- da_ar = data[i].get_array().flatten()
- ag_ar[i,:] = da_ar
-
- er_ar = numpy.zeros((len(data), data[0].get_array().flatten().shape[0]))
- if errs != None:
- for i in range(len(data)):
- er_ar[i,:] = errs[i].get_array().flatten()
-
- for i in range(ag_ar.shape[0]):
- s += 'bar(ind, ag_ar[' + str(i) + ',:], width'
- lab = self.get_label(data[i], i)
- col = self.get_color(colors, i, randomcolors)
- if lab != None:
- s += ', label=\'' + lab + '\''
- if col != None:
- s += ', color=' + str(col)
-
- if errs != None:
- s += ', yerr=er_ar[' + str(i) + ',:]'
-
- if prev != None:
- s += ', bottom=ag_ar[' + str(i-1) + ',:]'
-
- s += ')\n'
- prev = ag_ar[i]
-
- if use_legend:
- s += 'legend()\n'
-
- if array_x_t:
- s += 'xlabel(\'' + data[0].get_domain_name() + '\')\n'
- elif x_label:
- s += 'xlabel(\'' + x_label + '\')\n'
-
- if array_y_t:
- s += 'ylabel(\'' + data[0].get_range_name() + '\')\n'
- elif y_label:
- s += 'ylabel(\'' + y_label + '\')\n'
-
- if p_title:
- s += 'title(\'' + p_title + '\')\n'
-
- s += 'xticks(ind + width/2., t)\n'
- exec s
- self.setResult("source", s)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.namespace)
-
- @classmethod
- def register_ports(cls, reg, basic):
- reg.add_input_port(cls, "source", (basic.String, 'source'), True)
- reg.add_input_port(cls, "Data", (NDArray, 'Data Array to Plot'))
- reg.add_input_port(cls, "Error Bars", (NDArray, 'Error Array to Plot'))
- reg.add_input_port(cls, "Legend", (basic.Boolean, 'Use Legend'), True)
- reg.add_input_port(cls, "Random Colors", (basic.Boolean, 'Assign Random Colors'), True)
- reg.add_input_port(cls, "Colors", [basic.Integer, basic.Float, basic.Float, basic.Float], True)
- reg.add_input_port(cls, "Background", [basic.Float, basic.Float, basic.Float], True)
- reg.add_input_port(cls, "Bar Labels", [basic.Integer, basic.String], True)
- reg.add_input_port(cls, "Use X Title", (basic.Boolean, 'Apply X-axis Label'))
- reg.add_input_port(cls, "Use Y Title", (basic.Boolean, 'Apply Y-axis Label'))
- reg.add_input_port(cls, "X Title", (basic.String, 'X-axis label'), True)
- reg.add_input_port(cls, "Y Title", (basic.String, 'Y-axis label'), True)
- reg.add_input_port(cls, "Title", (basic.String, 'Figure Title'))
- reg.add_input_port(cls, "Bar Width", (basic.Float, 'Bar Width'), True)
- reg.add_output_port(cls, "source", (basic.String, 'source'))
-
-class ScatterPlot(ArrayPlot, Module):
- '''
- Create a scatter plot from X and Y positions defined by the X
- Array and Y Array ports, respectively. Datasets can be added by
- connecting multiple arrays to the appropriate input ports.
- Symbols representing each dataset can be defined by using the
- Markers input assigning a valid pylab symbol to a dataset.
- '''
- def compute(self):
- xdata = self.getInputListFromPort("X Array")
- ydata = self.getInputListFromPort("Y Array")
- self.label_dict = None
- use_legend = self.forceGetInputFromPort("Legend")
- randomcolors = self.forceGetInputFromPort("Random Colors")
- colors = self.forceGetInputListFromPort("Colors")
- self.color_dict = None
- bg_color = self.forceGetInputFromPort("Background")
- markers = self.forceGetInputListFromPort("Markers")
- self.marker_dict = None
- ps = self.forceGetInputFromPort("Point Size")
- array_x_t = self.forceGetInputFromPort("Use X Title")
- array_y_t = self.forceGetInputFromPort("Use Y Title")
-
- p_title = self.forceGetInputFromPort("Title")
- x_label = self.forceGetInputFromPort("X Title")
- y_label = self.forceGetInputFromPort("Y Title")
-
- s = urllib.unquote(str(self.forceGetInputFromPort("source", '')))
- self.source = ''
-
- if len(xdata) != len(ydata):
- raise ModuleError("Cannot create scatter plot for different number of X and Y datasets.")
-
- s = 'from pylab import *\n' +\
- 'from numpy import *\n' +\
- 'import numpy\n'
-
- if bg_color == None:
- bg_color = 'w'
-
- if type(bg_color) == type(''):
- s += 'figure(facecolor=\'' + bg_color + '\')\n'
- else:
- s += 'figure(facecolor=' + str(bg_color) + ')\n'
-
- xdata_ar = numpy.zeros((len(xdata), xdata[0].get_array().flatten().shape[0]))
- ydata_ar = numpy.zeros((len(xdata), xdata[0].get_array().flatten().shape[0]))
-
- for i in range(len(xdata)):
- xd = xdata[i]
- yd = ydata[i]
- xdata_ar[i,:] = xd.get_array().flatten()
- ydata_ar[i,:] = yd.get_array().flatten()
-
- for i in range(len(xdata)):
- xar = xdata[i]
- yar = ydata[i]
-
- lab = self.get_label(xar, i)
- col = self.get_color(colors, i, randomcolors)
- mar = self.get_marker(markers, i)
-
- s += 'scatter(xdata_ar[' + str(i) +',:], ydata_ar[' + str(i) + ',:]'
-
- if lab != None:
- s += ', label=\'' + lab +'\''
- if col != None:
- s += ', color=' + str(col)
- if mar != None:
- s += ', marker=\'' + mar + '\''
- if ps != None:
- s += ', size=' + str(ps)
- s += ')\n'
-
- if use_legend:
- s += 'legend()\n'
-
- if array_x_t:
- s += 'xlabel(\'' + xar.get_domain_name() + '\')\n'
- elif x_label:
- s += 'xlabel(\'' + x_label + '\')\n'
-
- if array_y_t:
- s += 'ylabel(\'' + yar.get_domain_name() + '\')\n'
- elif y_label:
- s += 'ylabel(\'' + y_label + '\')\n'
-
- if p_title:
- s += 'title(\'' + p_title + '\')\n'
-
- print s
- exec s
- self.setResult("source", s)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.namespace)
-
- @classmethod
- def register_ports(cls, reg, basic):
- reg.add_input_port(cls, "source", (basic.String, 'source'), True)
- reg.add_input_port(cls, "X Array", (NDArray, 'X Array to Plot'))
- reg.add_input_port(cls, "Y Array", (NDArray, 'Y Array to Plot'))
- reg.add_input_port(cls, "Legend", (basic.Boolean, 'Use Legend'), True)
- reg.add_input_port(cls, "Random Colors", (basic.Boolean, 'Assign Random Colors'), True)
- reg.add_input_port(cls, "Colors", [basic.Integer, basic.Float, basic.Float, basic.Float], True)
- reg.add_input_port(cls, "Background", [basic.Float, basic.Float, basic.Float], True)
- reg.add_input_port(cls, "Markers", [basic.Integer, basic.String], True)
- reg.add_input_port(cls, "Use X Title", (basic.Boolean, 'Apply X-axis Label'))
- reg.add_input_port(cls, "Use Y Title", (basic.Boolean, 'Apply Y-axis Label'))
- reg.add_input_port(cls, "X Title", (basic.String, 'X-axis label'), True)
- reg.add_input_port(cls, "Y Title", (basic.String, 'Y-axis label'), True)
- reg.add_input_port(cls, "Title", (basic.String, 'Figure Title'))
- reg.add_input_port(cls, "Point Size", (basic.Float, 'Point Size'), True)
- reg.add_output_port(cls, "source", (basic.String, 'source'))
-
-class LinePlot(ArrayPlot, Module):
- '''
- Create a standard line plot from a 1 or 2-dimensional Input Array.
- If the Input Array is 2-dimensional, each row will be plotted as a
- new line.
- '''
- def compute(self):
- data = self.getInputFromPort("Input Array")
- indexes = self.forceGetInputFromPort("Indexes")
- self.label_dict = None
- use_legend = self.forceGetInputFromPort("Legend")
- randomcolors = self.forceGetInputFromPort("Random Colors")
- colors = self.forceGetInputListFromPort("Colors")
- self.color_dict = None
- markers = self.forceGetInputListFromPort("Markers")
- self.marker_dict = None
- x_label = self.forceGetInputFromPort("X Title")
- y_label = self.forceGetInputFromPort("Y Title")
- p_title = self.forceGetInputFromPort("Title")
- bg_color = self.forceGetInputFromPort("Background")
-
- array_x_t = self.forceGetInputFromPort("Use X Title")
- array_y_t = self.forceGetInputFromPort("Use Y Title")
-
- s = urllib.unquote(str(self.forceGetInputFromPort("source", '')))
- self.source = ''
- da_ar = data.get_array()
-
- if da_ar.ndim > 2:
- raise ModuleError("Cannot plot data with dimensions > 2")
-
- s = 'from pylab import *\n' +\
- 'from numpy import *\n' +\
- 'import numpy\n'
-
- if bg_color == None:
- bg_color = 'w'
-
- if type(bg_color) == type(''):
- s += 'figure(facecolor=\'' + bg_color + '\')\n'
- else:
- s += 'figure(facecolor=' + str(bg_color) + ')\n'
-
- if da_ar.ndim == 1:
- da_ar.shape = (1, da_ar.shape[0])
-
- xar = self.forceGetInputFromPort("X Values")
- sf = self.forceGetInputFromPort("Scaling Factor")
- if sf == None:
- sf = 1.
-
- if xar == None:
- start_i = None
- end_i = None
- if indexes == None:
- start_i = 0
- end_i = da_ar.shape[1]
- else:
- start_i = indexes[0]
- end_i = indexes[1]
-
- xar = numpy.arange(start_i, end_i)
- xar = xar * sf
- else:
- xar = xar.get_array()
-
- print da_ar.shape
- print xar.shape
- for i in range(da_ar.shape[0]):
- lab = self.get_label(data, i)
- col = self.get_color(colors, i, randomcolors)
- mar = self.get_marker(markers, i)
- if indexes == None:
- s += 'plot(xar, da_ar[' + str(i) + ',:]'
- else:
- s += 'plot(xar, da_ar[' + str(i) + ',' + str(indexes[0]) + ':' + str(indexes[1]) + ']'
-
- if lab != None:
- s += ', label=\'' + lab +'\''
- if col != None:
- s += ', color=' + str(col)
- if mar != None:
- s += ', marker=\'' + mar + '\''
- s += ')\n'
-
- if use_legend:
- s += 'legend()\n'
-
- if array_x_t:
- s += 'xlabel(\'' + data.get_domain_name() + '\')\n'
- elif x_label:
- s += 'xlabel(\'' + x_label + '\')\n'
-
- if array_y_t:
- s += 'ylabel(\'' + data.get_range_name() + '\')\n'
- elif y_label:
- s += 'ylabel(\'' + y_label + '\')\n'
-
- if p_title:
- s += 'title(\'' + p_title + '\')\n'
-
- exec s
- self.setResult("source", s)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.namespace)
-
- @classmethod
- def register_ports(cls, reg, basic):
- reg.add_input_port(cls, "source", (basic.String, 'source'), True)
- reg.add_input_port(cls, "Input Array", (NDArray, 'Array to Plot'))
- reg.add_input_port(cls, "X Values", (NDArray, 'Domain Values'))
- reg.add_input_port(cls, "Legend", (basic.Boolean, 'Use Legend'), True)
- reg.add_input_port(cls, "Random Colors", (basic.Boolean, 'Assign Random Colors'), True)
- reg.add_input_port(cls, "Colors", [basic.Integer, basic.Float, basic.Float, basic.Float], True)
- reg.add_input_port(cls, "Markers", [basic.Integer, basic.String], True)
- reg.add_input_port(cls, "Use X Title", (basic.Boolean, 'Apply X-axis Label'))
- reg.add_input_port(cls, "Use Y Title", (basic.Boolean, 'Apply Y-axis Label'))
- reg.add_input_port(cls, "X Title", (basic.String, 'X-axis label'), True)
- reg.add_input_port(cls, "Y Title", (basic.String, 'Y-axis label'), True)
- reg.add_input_port(cls, "Title", (basic.String, 'Figure Title'))
- reg.add_input_port(cls, "Background", [basic.Float, basic.Float, basic.Float], True)
- reg.add_input_port(cls, "Indexes", [basic.Integer, basic.Integer], True)
- reg.add_input_port(cls, "Scaling Factor", (basic.Float, 'Scaling Factor'), True)
- reg.add_output_port(cls, "source", (basic.String, 'source'))
diff --git a/contrib/NumSciPy/ArrayUtilities.py b/contrib/NumSciPy/ArrayUtilities.py
deleted file mode 100644
index 2f3ffa9..0000000
--- a/contrib/NumSciPy/ArrayUtilities.py
+++ /dev/null
@@ -1,254 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from scipy import sparse
-import vtk
-from Array import *
-from Matrix import *
-
-class ArrayUtilModule(object):
- my_namespace = 'numpy|array|utilities'
-
-class ArrayToVTKVectors(ArrayUtilModule, Module):
- def compute(self):
- v0 = self.forceGetInputFromPort("Array0")
- v1 = self.forceGetInputFromPort("Array1")
- v2 = self.forceGetInputFromPort("Array2")
- ds = self.getInputFromPort("VTK Data")
-
- v_name = self.forceGetInputFromPort("Vector Name")
- if v_name == None:
- v_name = 'vectors'
-
- vsize = 0
- if v0:
- vsize += 1
- v0 = v0.get_array().flatten()
- if v1:
- vsize += 1
- v1 = v1.get_array().flatten()
- if v2:
- vsize += 1
- v2 = v2.get_array().flatten()
-
- np = ds.vtkInstance.GetNumberOfPoints()
- pd = ds.vtkInstance.GetPointData()
- vtk_ar = vtk.vtkDoubleArray()
-# vtk_ar.SetNumberOfValues(np)
- vtk_ar.SetNumberOfComponents(3)
- for i in range(np):
- if vsize == 2:
- vtk_ar.InsertNextTuple3(v0[i], v1[i], 0.)
- elif vsize == 3:
- vtk_ar.InsertNextTuple3(v0[i], v1[i], v2[i])
-
- vtk_ar.SetName(v_name)
- ds.vtkInstance.GetPointData().AddArray(vtk_ar)
- ds.vtkInstance.GetPointData().SetVectors(vtk_ar)
-# ds.vtkInstance.GetPointData().SetActiveVectors(v_name)
- self.setResult("Output", ds)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
-
- @classmethod
- def register_ports(cls, reg, basic):
- reg.add_input_port(cls, "Array0", (NDArray, 'Scalar Array'))
- reg.add_input_port(cls, "Array1", (NDArray, 'Scalar Array'))
- reg.add_input_port(cls, "Array2", (NDArray, 'Scalar Array'))
- reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
- reg.add_input_port(cls, "Vector Name", (basic.String, 'Scalar Name'), True)
- reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
-
-class ArrayToTimeVaryingVTKVectors(ArrayUtilModule, Module):
- def update_progress(self, cur, total):
- t = float(cur) / float(total)
- self.logging.update_progress(self, t)
-
- def compute(self):
- v0 = self.forceGetInputFromPort("Array0")
- v1 = self.forceGetInputFromPort("Array1")
- v2 = self.forceGetInputFromPort("Array2")
- ds = self.getInputFromPort("VTK Data")
-
- v_name = self.forceGetInputFromPort("Vector Name")
- if v_name == None:
- v_name = 'vectors'
-
- vsize = 0
- if v0:
- vsize += 1
- if v1:
- vsize += 1
- if v2:
- vsize += 1
-
- num_times = ds.vtkInstance.GetNumberOfTimeSteps()
- for i in range(num_times):
- self.update_progress(i, num_times)
- np = ds.vtkInstance.GetTimeStep(i).GetNumberOfPoints()
- pd = ds.vtkInstance.GetTimeStep(i).GetPointData()
- vtk_ar = vtk.vtkDoubleArray()
-# vtk_ar.SetNumberOfValues(np)
- vtk_ar.SetNumberOfComponents(3)
- arx = v0.get_array().squeeze()
- arx = arx[i,::].squeeze().flatten()
- ary = v1.get_array().squeeze()
- ary = ary[i,::].squeeze().flatten()
- if vsize == 3:
- arz = v2.get_array().squeeze()
- arz = arz[i,::].squeeze().flatten()
- for j in range(np):
- if vsize == 2:
- vtk_ar.InsertNextTuple3(arx[j], ary[j], 0.)
- elif vsize == 3:
- vtk_ar.InsertNextTuple3(arz[j], ary[j], arz[j])
-
- vtk_ar.SetName(v_name)
- ds.vtkInstance.GetTimeStep(i).GetPointData().AddArray(vtk_ar)
- ds.vtkInstance.GetTimeStep(i).GetPointData().SetVectors(vtk_ar)
-# ds.vtkInstance.GetPointData().SetActiveVectors(v_name)
- self.setResult("Output", ds)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
-
- @classmethod
- def register_ports(cls, reg, basic):
- reg.add_input_port(cls, "Array0", (NDArray, 'Scalar Array'))
- reg.add_input_port(cls, "Array1", (NDArray, 'Scalar Array'))
- reg.add_input_port(cls, "Array2", (NDArray, 'Scalar Array'))
- reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
- reg.add_input_port(cls, "Vector Name", (basic.String, 'Scalar Name'), True)
- reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
-
-
-class ArrayToTimeVaryingVTKScalars(ArrayUtilModule, Module):
- def update_progress(self, cur, total):
- t = float(cur) / float(total)
- self.logging.update_progress(self, t)
-
- def compute(self):
- ds = self.getInputFromPort("VTK Data")
- ar = self.getInputFromPort("Scalars")
- v_name = self.forceGetInputFromPort("Array Name")
- if v_name == None:
- v_name = 'scalars'
- num_times = ds.vtkInstance.GetNumberOfTimeSteps()
- ar_ = ar.get_array()
- if ar_.shape[0] != num_times:
- raise ModuleError("Cannot process array with num timesteps = " +
- str(ar_.shape[0]) +
- " and vtkdata with " +
- str(num_times) + " timesteps")
-
- for i in range(num_times):
- self.update_progress(i, num_times)
- s_ar = ar_[i,::].squeeze().flatten()
- vtk_ar = vtk.vtkDoubleArray()
- vtk_ar.SetNumberOfValues(s_ar.size)
- vtk_ar.SetName(v_name)
- for j in range(s_ar.size):
- vtk_ar.InsertNextValue(s_ar[j])
-
- ds.vtkInstance.GetTimeStep(i).GetPointData().AddArray(vtk_ar)
- ds.vtkInstance.GetTimeStep(i).GetPointData().SetScalars(vtk_ar)
-
- self.setResult("Output", ds)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
-
- @classmethod
- def register_ports(cls, reg, basic):
- reg.add_input_port(cls, "Scalars", (NDArray, 'Scalar Array'))
- reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
- reg.add_input_port(cls, "Array Name", (basic.String, 'Scalar Name'), True)
- reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkTemporalDataSet').module))
-
-class ArrayToVTKScalars(ArrayUtilModule, Module):
- """ Take a scalar array and consider it as an array of scalars
- to assign to a VTK dataset. The number of elements in the
- scalar array must be equivalent to the number of points in
- the VTK dataset. Please note that this module adds a scalar
- array to the input dataset and can be considered a mutating filter
- because of this."""
-
- def compute(self):
- a = self.getInputFromPort("Array")
- ds = self.getInputFromPort("VTK Data")
- scalar_name = ''
- if self.hasInputFromPort("Scalar Name"):
- scalar_name = self.getInputFromPort("Scalar Name")
- else:
- scalar_name = 'scalars'
-
- s_ar = a.get_array().flatten()
- np = ds.vtkInstance.GetNumberOfPoints()
-# if s_ar.size != np:
-# raise ModuleError("Could not assign scalars to VTK dataset with different number of elements")
-
- pd = ds.vtkInstance.GetPointData()
- vtk_ar = vtk.vtkDoubleArray()
- vtk_ar.SetNumberOfValues(np)
- for i in xrange(np):
- vtk_ar.SetValue(i, s_ar[i])
-
- vtk_ar.SetName(scalar_name)
- ds.vtkInstance.GetPointData().AddArray(vtk_ar)
-# ds.vtkinstance.GetPointData().SetActiveScalars(scalar_name)
- ds.vtkInstance.GetPointData().SetScalars(vtk_ar)
- self.setResult("Output", ds)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
-
- @classmethod
- def register_ports(cls, reg, basic):
- reg.add_input_port(cls, "Array", (NDArray, 'Scalar Array'))
- reg.add_input_port(cls, "VTK Data", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
- reg.add_input_port(cls, "Scalar Name", (basic.String, 'Scalar Name'), True)
- reg.add_output_port(cls, "Output", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
-
-class VTKDataSetToPointArray(ArrayUtilModule, Module):
- """
- Extract points and scalar values from a vtkDataSet. The
- output will be of the form [[x,y,z,v]] with the v component
- optionally added if the IncludeScalars flag is set.
- """
- def compute(self):
- data = self.getInputFromPort("vtkDataSet").vtkInstance
- flag = self.forceGetInputFromPort("IncludeScalars")
-
- np = data.GetNumberOfPoints()
- ndim = 3
- if flag:
- ndim = 4
-
- out_ar = numpy.ones((np, ndim))
- for i in xrange(np):
- (out_ar[i,0], out_ar[i,1], out_ar[i,2]) = data.GetPoint(i)
- if flag:
- out_ar[i,3] = data.GetPointData().GetArray(0).GetTuple1(i)
-
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
-
- @classmethod
- def register_ports(cls, reg, basic):
- reg.add_input_port(cls, "vtkDataSet", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkDataSet').module))
- reg.add_input_port(cls, "IncludeScalars", (basic.Boolean, 'Include Scalars in Output'), True)
- reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
-
-
-
-
diff --git a/contrib/NumSciPy/DSP.py b/contrib/NumSciPy/DSP.py
deleted file mode 100644
index 15b4dcb..0000000
--- a/contrib/NumSciPy/DSP.py
+++ /dev/null
@@ -1,369 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from Matrix import *
-from Array import *
-import scipy
-import scipy.signal
-from scipy import fftpack
-import numpy
-
-class DSPModule(object):
- my_namespace = 'scipy|signals'
-
-class SignalGenerator(DSPModule, Module):
- my_namespace = 'scipy|signals|generator'
-
- def compute(self):
- samples = self.getInputFromPort("Samples")
- periods = self.getInputFromPort("Periods")
- freqs = self.getInputListFromPort("Frequencies")
-
- ar = numpy.linspace(0., float(periods) * 2. * scipy.pi, periods * samples)
- out_ar = numpy.zeros(periods * samples)
-
- for f in freqs:
- out_ar += scipy.sin(f * ar)
-
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Samples", (basic.Integer, "Sampling Rate"))
- reg.add_input_port(cls, "Periods", (basic.Integer, "Signal Length"))
- reg.add_input_port(cls, "Frequencies", (basic.Float, "Additive Frequency"))
- reg.add_output_port(cls, "Output", (NDArray, "Output Signal"))
-
-class FFT(DSPModule, Module):
- __doc__ = """ Calculate the discrete Fourier transform of the arbitrary
- sequence presented on the Signal port. This is done using
- SciPy's FFTPack module.\n\n"""
- __doc__ += """From fftpack.fft:\n\t"""
- __doc__ += fftpack.fft.__doc__
-
- my_namespace = 'scipy|signals|fourier'
-
- def compute(self):
- sig_array = self.getInputFromPort("Signals")
-
- # If there is no input on the samples port,
- # use the number of samples in an array row for
- # the number of fft points.
- if self.hasInputFromPort("Samples"):
- pts = self.getInputFromPort("Samples")
-
- else:
- try:
- pts = sig_array.get_shape()[1]
- except:
- pts = sig_array.get_shape()[0]
-
- sh = sig_array.get_shape()
- if len(sh) < 2:
- shp = (1, sh[0])
- sig_array.reshape(shp)
-
- (num_sigs, num_samps) = sig_array.get_shape()
- phasors = fftpack.fft(sig_array.get_row_range(0,0), pts)
- out_ar = phasors
-
- for i in xrange(1,num_sigs):
- phasors = fftpack.fft(sig_array.get_row_range(i,i), pts)
- out_ar = numpy.vstack([out_ar, phasors])
-
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("FFT Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Array'))
- reg.add_input_port(cls, "Samples", (basic.Integer, 'FFT Samples'))
- reg.add_output_port(cls, "FFT Output", (NDArray, 'FFT Output'))
-
-class FFTN(DSPModule, Module):
- __doc__ = """ Calculate the discrete Fourier transform of the arbitrary
- sequence presented on the Signal port. This is done using
- SciPy's FFTPack module.\n\n"""
- __doc__ += """From fftpack.fftn:\n\t"""
- __doc__ += fftpack.fftn.__doc__
-
- my_namespace = 'scipy|signals|fourier'
-
- def compute(self):
- sig_array = self.getInputFromPort("Signals")
- # If there is no input on the samples port,
- # use the number of samples in an array row for
- # the number of fft points.
- if self.hasInputFromPort("Samples"):
- pts = self.getInputFromPort("Samples")
-
- else:
- pts = sig_array.get_shape()[1]
-
- sh = (sig_array.get_shape()[0], pts)
-
- phasors = fftpack.fftn(sig_array.get_array(), shape=sh)
- out = NDArray()
- out.set_array(phasors)
- self.setResult("FFT Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Array'))
- reg.add_input_port(cls, "Samples", (basic.Integer, 'FFT Samples'))
- reg.add_output_port(cls, "FFT Output", (NDArray, 'FFT Output'))
-
-class ShortTimeFourierTransform(DSPModule, Module):
- """ Calculate the short time Fourier transform of the
- sequence presented on the Signal port. This is done using
- SciPy's FFTPack fft module in conjuction with an input window.
- If a window is not specified, a Hamming window of the specified
- size is used. """
- my_namespace = 'scipy|signals|fourier'
-
- def get_signal(self, sigs, window, offset, size):
- win = scipy.zeros(sigs.shape[0])
- win[offset:offset+size] = window
- part = sigs * win
- return part
-
- def compute(self):
- sigs = self.getInputFromPort("Signals")
- sr = self.getInputFromPort("SamplingRate")
-
- out_vol = None
-
- if self.hasInputFromPort("Window"):
- window = self.getInputFromPort("Window").get_array()
- win_size = window.shape[0]
- else:
- win_size = self.getInputFromPort("Window Size")
- window = scipy.signal.hamming(win_size)
-
- if self.hasInputFromPort("Stride"):
- stride = self.getInputFromPort("Stride")
- else:
- stride = int(win_size / 2)
-
- sh = sigs.get_shape()
- if len(sh) < 2:
- shp = (1, sh[0])
- sigs.reshape(shp)
- (num_sigs, num_samps) = sigs.get_shape()
-
- for i in xrange(num_sigs):
- offset = 0
- signal = sigs.get_array()[i]
- # We need to do the first window here so that we
- # can have something to call vstack on.
- sig = self.get_signal(signal, window, offset, win_size)
- im_array = fftpack.fft(sig)
- offset += stride
- while 1:
- try:
- sig = self.get_signal(signal, window, offset, win_size)
- phasors = fftpack.fft(sig)
- offset += stride
- im_array = numpy.vstack([im_array, phasors.ravel()])
- except:
- break
-
- # STFT of one signal is done. Clean up the output
- (slices, freqs) = im_array.shape
- ar = im_array[0:,0:sr*2]
- ar = ar[0:,::-1]
- if out_vol == None:
- out_vol = ar
- ovshape = out_vol.shape
- out_vol.shape = 1, ovshape[0], ovshape[1]
- else:
- arshape = ar.shape
- ar.shape = 1, arshape[0], arshape[1]
- out_vol = numpy.vstack([out_vol, ar])
-
- # All signals have been processed and are in the volume.
- out = NDArray()
- out.set_array(out_vol)
- self.setResult("FFT Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Signals", (NDArray, 'Signal Array'))
- reg.add_input_port(cls, "SamplingRate", (basic.Integer, 'Sampling Rate'))
- reg.add_input_port(cls, "Window", (NDArray, 'Windowing Function'))
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_input_port(cls, "Stride", (basic.Integer, 'Stride'))
- reg.add_output_port(cls, "FFT Output", (NDArray, 'FFT Output'))
-
-class SignalSmoothing(DSPModule, Module):
- """
- Documentation
- """
- def compute(self):
- window = self.getInputFromPort("Window").get_array()
- in_signal = self.getInputFromPort("Signal").get_array()
-
- to_conv = window/window.sum() # Make sure the window is normalized
- if in_signal.ndim > 1:
- out_ar = numpy.zeros(in_signal.shape)
- else:
- out_ar = numpy.zeros(1,in_signal.shape[0])
- in_signal.shape = (1, in_signal.shape[0])
-
- for row in xrange(in_signal.shape[0]):
- out_ar[row] = numpy.convolve(to_conv, in_signal[row], mode='same')
-
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Signal", (NDArray, "Input Signals"))
- reg.add_input_port(cls, "Window", (NDArray, "Smoothing Filter"))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Smoothed Signals'))
-
-# class SingleTrialPhaseLocking(DSPModule, Module):
-# """
-# Documentation
-# """
-# def get_time_indexes(self, t0, time_window):
-# if time_window % 2:
-# # odd number of samples: t0 +/- (window-1)/2
-# tw = (time_window - 1) / 2
-# else:
-# tw = time_window / 2
-# return (t0 - tw, t0 + tw)
-
-# def calc_pli(self, f_n_ar, f_m_ar):
-# phasors = numpy.concatenate((f_n_ar, f_m_ar))
-# norm_c = numpy.sqrt(phasors.real*phasors.real + phasors.imag*phasors.imag)
-# phasors /= norm_c
-# mean_phasor = phasors.mean()
-# pli = numpy.sqrt(mean_phasor.real*mean_phasor.real + mean_phasor.imag*mean_phasor.imag)
-# return pli
-
-# def compute(self):
-# phasors = self.getInputFromPort("Phasor Array").get_array()
-# time_window = self.getInputFromPort("Time Window")
-# time_step = self.forceGetInputFromPort("Time Step")
-# if time_step == None:
-# time_step = 1
-
-# ndims = phasors.ndim
-# if ndims == 2:
-# phasors.shape = (1, phasors.shape[0], phasors.shape[1])
-# elif ndims == 1:
-# phasors.shape = (1, phasors.shape[0], 1)
-# else:
-# raise ModuleError("Cannot Process Phasor set of dimension " + str(ndims))
-
-# num_freqs = phasors[0].shape[0]
-# num_times = phasors[0].shape[1]
-# num_times /= time_step
-# out_ar = numpy.zeros((phasors.shape[0], num_freqs, num_freqs, num_times))
-# for channel in xrange(phasors.shape[0]):
-# tfr = phasors[channel,:,:].squeeze()
-# for f_m in xrange(tfr.shape[0]):
-# f_m_row = tfr[f_m,:]
-# for f_n in xrange(f_m+1, tfr.shape[0], 1):
-# f_n_row = tfr[f_n,:]
-# t0 = 0
-# tn = 0
-# (start_i, end_i) = self.get_time_indexes(t0, time_window)
-# while t0 < f_m_row.shape[0]:
-# f_m_range = f_m_row[max(0,start_i):min(end_i,f_m_row.shape[0]-1)]
-# f_n_range = f_n_row[max(0,start_i):min(end_i,f_n_row.shape[0]-1)]
-# pli = self.calc_pli(f_m_range, f_n_range)
-# out_ar[channel, f_m, f_n, tn] = pli
-# out_ar[channel, f_n, f_m, tn] = pli
-# out_ar[channel, f_m, f_m, tn] = 1.0
-# tn += 1
-# t0 += time_step
-# start_i += time_step
-# end_i += time_step
-
-# out = NDArray()
-# out.set_array(out_ar)
-# self.setResult("Output Array", out)
-
-# @classmethod
-# def register(cls, reg, basic):
-# reg.add_module(cls, namespace=cls.my_namespace)
-# reg.add_input_port(cls, "Phasor Array", (NDArray, 'Phasor Array'))
-# reg.add_input_port(cls, "Time Step", (basic.Integer, 'Stride in the Time Domain'))
-# reg.add_input_port(cls, "Time Window", (basic.Integer, 'Samples per Timeslice'))
-# reg.add_output_port(cls, "Output Array", (NDArray, 'Result set'))
-
-# class CalculatePhaseLocking(DSPModule, Module):
-# """
-# documentation
-# """
-# def Phi(self, p):
-# return scipy.arctan2(p.real, p.imag)
-
-# def compute(self):
-# phasors = self.getInputFromPort("Phasor Array").get_array()
-# if phasors.ndim != 3:
-# raise ModuleError("Cannot handle phasor array with less than 3 dimensions")
-
-# (trials, times, frequencies) = phasors.shape
-# lowestF = self.getInputFromPort("Lowest Freq")
-# # highestF = self.getInputFromPort("Highest Freq")
-
-# Phi = self.Phi(phasors)
-
-# gamma_ar = numpy.zeros((times, frequencies, frequencies))
-
-# for t in range(times):
-# n = lowestF
-# for fn_i in range(frequencies):
-# n += fn_i
-# fn = fn_i + lowestF
-# m = lowestF
-# for fm_i in range(fn_i, frequencies, 1):
-# m += fm_i
-# fm = fm_i + lowestF
-# DeltaPhi = (float((n+m)/(2*m))Phi[:,t,fm_i] - float((n+m)/(2*n))Phi[:,t,fn_i]) % (2. * scipy.pi)
-# Gamma = exp(complex(0.,DeltaPhi))
-# Gamma = Gamma.sum()
-# Gamma = numpy.sqrt(Gamma * Gamma.conjugate())
-# gamma_ar[t, fn_i, fm_i] = Gamma
-# gamma_ar[t, fm_i, fn_i] = Gamma
-# m += 1
-# n += 1
-
-# out = NDArray()
-# out.set_array(gamma_ar)
-# self.setResults("Gamma", out)
-
-# @classmethod
-# def register(cls, reg, basic):
-# reg.add_module(cls, namespace=cls.my_namespace)
-# reg.add_input_port(cls, "Phasor Array", (NDArray, 'Phasor Array'))
-# reg.add_input_port(cls, "Lowest Freq", (basic.Integer, 'Lowest Frequency Phasor'))
-# reg.add_output_port(cls, "Gamma", (NDArray, 'Phase Locking Volume'))
-
-
-# class DifferentialPhaseLocking(DSPModule, Module):
-# """
-# documentation
-# """
-# def compute(self):
-# phasors = self.getInputFromPort("Phasor Array").get_array()
-# if phasors.ndim != 2:
-# raise ModuleError("Cannot handle phasor array with more than 2 dimensions")
-
-# mag = phasors.real*phasors.real + phasors.imag*phasors.imag
-# mag = numpy.sqrt(mag)
-# normalized = phasors / mag
-
-
diff --git a/contrib/NumSciPy/EnsembleOrdering.py b/contrib/NumSciPy/EnsembleOrdering.py
deleted file mode 100644
index 0b46b5a..0000000
--- a/contrib/NumSciPy/EnsembleOrdering.py
+++ /dev/null
@@ -1,297 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from Array import *
-import copy
-import scipy
-import numpy
-from scipy import fftpack
-import time
-
-class EnsembleModule(object):
- my_namespace = 'scipy|signals|ensembles'
-
-class ComputeDistance(EnsembleModule, Module):
- def compute(self):
- vol = self.getInputFromPort("Signals").get_array()
- num_im = vol.shape[0]
-
- out_ar = numpy.zeros((num_im, num_im))
- for i in range(num_im):
- im_i = vol[i].squeeze().flatten()
- for j in range(i+1, num_im, 1):
- im_j = vol[j].squeeze().flatten()
-
- d = (im_i - im_j)
- d = d * d
- d = numpy.sqrt(d.sum())
-
- out_ar[i,j] = d
- out_ar[j,i] = d
-
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Planes'))
- reg.add_output_port(cls, "Output", (NDArray, 'Output Distance Matrix'))
-
-class OrderByIndexes(EnsembleModule, Module):
- """ Order the inputs using an array containing the
- indexes they should appear in """
- def compute(self):
- vol = self.getInputFromPort("Signals")
- inds = self.getInputFromPort("Indexes")
-
- sh = vol.get_shape()
- vol = vol.get_array()
- inds = inds.get_array()
- out_ar = [vol[inds[0]]]
- for i in xrange(sh[0] - 1):
- i += 1
- try:
- out_ar = numpy.vstack((out_ar, [vol[inds[i]]]))
- except:
- pass
-
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Set'))
- reg.add_input_port(cls, "Indexes", (NDArray, 'Sorted Index Set'))
- reg.add_output_port(cls, "Output", (NDArray, 'Sorted Signal Set'))
-
-class OrderByCorrelation(EnsembleModule, Module):
- """ Order the inputs using the correlations between a given
- input index and all other slices in the volume """
- def append_slice(self, vol, sl):
- vol = numpy.vstack((vol, [sl]))
- return vol
-
- def append_cor(self, cor, sl_cor):
- cor.append(sl_cor)
- return cor
-
- def prepend_slice(self, vol, sl):
- vol = numpy.vstack(([sl], vol))
- return vol
-
- def prepend_cor(self, cor, sl_cor):
- cor.insert(0, sl_cor)
- return cor
-
- def find_max(self, a):
- f = a.max()
- sh = a.shape
- b = a.flatten()
- ind = b.argmax()
- row = int(ind/sh[1])
- col = ind - row * sh[1]
- return (row, col, f)
-
- def compute(self):
- ts = time.time()
- vol = self.getInputFromPort("Signals")
- ind = self.getInputFromPort("Key Slice")
- if self.hasInputFromPort("Normalize"):
- self.normalize = self.getInputFromPort("Normalize")
- else:
- self.normalize = False
-
- vol_ar = vol.get_array()
- if self.normalize:
- for i in range(vol_ar.shape[0]):
- sl = vol_ar[i]
- sl = sl - sl.min()
- sl = sl / sl.max()
- vol_ar[i] = sl
-
- pos = self.forceGetInputFromPort("Key Position")
-
- key_slice = vol_ar[ind]
- (r,c) = key_slice.shape
- key_fft = fftpack.fftn(key_slice)
- key_sq = key_slice * key_slice
- norm = key_sq.sum()
- norm = numpy.sqrt(norm)
-
- num_slices = vol.get_shape()[0]
- num_elements = key_slice.size
- cor = []
- for i in xrange(num_slices):
- cur_slice = vol_ar[i]
- cur_sq = cur_slice * cur_slice
- cur_norm = cur_sq.sum()
- cur_norm = numpy.sqrt(cur_norm)
-
- cur_fft = fftpack.fftn(cur_slice)
- cur_fft = cur_fft.conjugate()
-
- cur_max = cur_slice.max()
- prod_slice = key_fft * cur_fft
- prod_slice = prod_slice / (norm * cur_norm)
- cor_slice = fftpack.ifftn(prod_slice)
-
- (row,col,val) = self.find_max(cor_slice.real)
-
- cor.append((val,i,row,col))
-
- cor.sort(lambda x,y:cmp(y[0],x[0]))
- vol = [key_slice]
- key_slice_out = key_slice
- out_cor_ar = []
- if pos == None:
- app = True
- for i in range(len(cor)):
- sl_cor = cor[i]
- if sl_cor[1] == ind:
- continue
- sl = vol_ar[sl_cor[1]]
- if app:
- vol = self.append_slice(vol, sl)
- out_cor_ar = self.append_cor(out_cor_ar, cor[i][0])
- else:
- vol = self.prepend_slice(vol, sl)
- out_cor_ar = self.prepend_cor(out_cor_ar, cor[i][0])
-
- app = (app != True)
- else:
- for i in range(len(cor)):
- sl_cor = cor[i]
- sl = vol_ar[sl_cor[1]]
- vol = self.append_slice(vol, sl)
- out_cor_ar = self.append_cor(out_cor_ar, cor[i][0])
-
- elapsed = time.time() - ts
-# elapsed *= 1000000.
- print "took: ", elapsed
- out_vol = NDArray()
-
- out_vol.set_array(vol/vol.max())
- out_cor = NDArray()
- out_cor_ar = numpy.array(out_cor_ar)
- out_cor.set_array(out_cor_ar / out_cor_ar.max())
-
- out_key = NDArray()
- out_key.set_array(key_slice_out)
- self.setResult("Output Key Slice", out_key)
- self.setResult("Output Volume", out_vol)
- self.setResult("Output Correlation", out_cor)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Volume'))
- reg.add_input_port(cls, "Key Slice", (basic.Integer, 'Key Slice Index'))
- reg.add_input_port(cls, "Normalize", (basic.Boolean, 'Normalize Slice Power'))
- reg.add_input_port(cls, "Key Position", (basic.Integer, 'Key Slice Position'))
- reg.add_output_port(cls, "Output Volume", (NDArray, 'Sorted Signal Volume'))
- reg.add_output_port(cls, "Output Correlation", (NDArray, 'Sorted Correlation Array'))
- reg.add_output_port(cls, "Output Key Slice", (NDArray, 'Key Slice'))
-
-class OrderByProgressiveCorrelation(EnsembleModule, Module):
- def find_max(self, a):
- f = a.max()
- sh = a.shape
- b = a.flatten()
- ind = b.argmax()
- row = int(ind/sh[1])
- col = ind - row * sh[1]
- return (row, col, f)
-
- def correlate(self, plane, ref_im):
- (r,c) = ref_im.shape
- key_fft = fftpack.fftn(ref_im)
- key_sq = ref_im * ref_im
- norm = key_sq.sum()
- norm = numpy.sqrt(norm)
-
- cur_slice = plane
- cur_sq = cur_slice * cur_slice
- cur_norm = cur_sq.sum()
- cur_norm = numpy.sqrt(cur_norm)
-
- cur_fft = fftpack.fftn(cur_slice)
- cur_fft = cur_fft.conjugate()
-
- cur_max = cur_slice.max()
- prod_slice = key_fft * cur_fft
- prod_slice = prod_slice / (norm * cur_norm)
- cor_slice = fftpack.ifftn(prod_slice)
-
- (row,col,val) = self.find_max(cor_slice.real)
-
- return val
-
- def compute(self):
- vol = self.getInputFromPort("Signals").get_array()
- ind = self.getInputFromPort("Key Slice")
- normalize = self.forceGetInputFromPort("Normalize")
-
- if normalize:
- for i in range(vol.shape[0]):
- sl = vol[i]
- sl = sl - sl.min()
- sl = sl / sl.max()
- vol[i] = sl
-
- tmp_vol = copy.copy(vol)
-
- key_slice = vol[ind]
- vol_ind = numpy.arange(vol.shape[0]).tolist()
-
- out_ar = numpy.zeros(vol.shape)
- out_ar[0,:,:] = key_slice
- tmp_vol[ind,:,:] = 0.0
-
- tmp_size = 1
- cors_out = [self.correlate(key_slice,key_slice)]
- print "key cor = ", cors_out[0]
- while tmp_size < tmp_vol.shape[0]:
- ts = time.time()
- cors = []
- print "output size is currently: ", tmp_size,
- for i in range(tmp_vol.shape[0]):
- plane = tmp_vol[i]
- if plane.min() == 0. and plane.max() == 0.:
- continue
-
- cor = self.correlate(plane,out_ar[tmp_size-1,:,:])
- cors.append((cor,i))
-
- cors.sort(lambda x,y:cmp(y[0],x[0]))
- (max_cor,ind) = cors[0]
- print "\tcor = ", max_cor, ind
- cors_out.append(max_cor)
- out_ar[tmp_size,:,:] = vol[ind]
- tmp_vol[ind,:,:] = 0.
- tmp_size += 1
- elapsed = time.time() - ts
-# elapsed *= 1000000.
- print "\tCorrelation took: ", elapsed
-
- cor_ar = numpy.array(cors_out)
- cor_ar /= cor_ar.max()
- out = NDArray()
- out.set_array(out_ar)
- out_cor = NDArray()
- out_cor.set_array(cor_ar)
-
- self.setResult("Output Signals", out)
- self.setResult("Output Correlations", out_cor)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Signals", (NDArray, 'Input Time Frequency Planes'))
- reg.add_input_port(cls, "Key Slice", (basic.Integer, 'Key Slice'))
- reg.add_input_port(cls, "Normalize", (basic.Boolean, 'Normalize each plane'), True)
- reg.add_output_port(cls, "Output Signals", (NDArray, 'Output Time Frequency Planes'))
- reg.add_output_port(cls, "Output Correlations", (NDArray, 'Output Correlations'))
diff --git a/contrib/NumSciPy/Filters.py b/contrib/NumSciPy/Filters.py
deleted file mode 100644
index 11b588b..0000000
--- a/contrib/NumSciPy/Filters.py
+++ /dev/null
@@ -1,185 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from Array import *
-import scipy
-import scipy.signal
-from scipy import sparse, fftpack
-import numpy
-
-class WindowModule(object):
- my_namespace = 'scipy|signals|windows'
-
-class HanningWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- out = NDArray()
- out.set_array(scipy.signal.hanning(size))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class TriangularWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- out = NDArray()
- out.set_array(scipy.signal.triang(size))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class BlackmanWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- out = NDArray()
- out.set_array(scipy.signal.blackman(size))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class BlackmanHarrisWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- out = NDArray()
- out.set_array(scipy.signal.blackmanharris(size))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class ParzenWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- out = NDArray()
- out.set_array(scipy.signal.parzen(size))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class HammingWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- out = NDArray()
- out.set_array(scipy.signal.hamming(size))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class KaiserWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- beta = self.getInputFromPort("Beta")
- out = NDArray()
- out.set_array(scipy.signal.kaiser(size, beta))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_input_port(cls, "Beta", (basic.Float, 'Beta'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class BartlettHannWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- out = NDArray()
- out.set_array(scipy.signal.barthann(size))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class GaussianWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- sigma = self.getInputFromPort("Sigma")
- out = NDArray()
- out.set_array(scipy.signal.gaussian(size, sigma))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_input_port(cls, "Sigma", (basic.Float, 'Sigma'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class BoxcarWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- out = NDArray()
- out.set_array(scipy.signal.boxcar(size))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class BohmanWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- out = NDArray()
- out.set_array(scipy.signal.bohman(size))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class BartlettWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- out = NDArray()
- out.set_array(scipy.signal.bartlett(size))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
-class NuttallBlackmanHarrisWindow(WindowModule, Module):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- out = NDArray()
- out.set_array(scipy.signal.nuttall(size))
- self.setResult("Window", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(cls, "Window", (NDArray, 'Window Function'))
-
diff --git a/contrib/NumSciPy/Imaging.py b/contrib/NumSciPy/Imaging.py
deleted file mode 100644
index 2297e08..0000000
--- a/contrib/NumSciPy/Imaging.py
+++ /dev/null
@@ -1,193 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-import numpy
-import scipy
-import scipy.ndimage
-from Array import *
-from Matrix import *
-
-class ArrayImaging(object):
- my_namespace = 'numpy|imaging'
-
-class ExtractRGBAChannel(ArrayImaging, Module):
- """ Extract a single color channel from an array representing an
- RGBA type image. This will return a 2D array with the single channel
- specified as the scalar elements """
- def compute(self):
- im = self.getInputFromPort("Image").get_array()
- chan = self.getInputFromPort("Channel")
- ar = im[:,:,chan]
- out = NDArray()
- out.set_array(ar)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Image", (NDArray, 'Image Array'))
- reg.add_input_port(cls, "Channel", (basic.Integer, 'Channel'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class GaussianGradientMagnitude(ArrayImaging, Module):
- """ Calculate the Gradient Magnitude of an input NDArray using gaussian derivatives.
- The standard-deviation of the Gaussian filter are given for each axis as a sequence
- or as a single number, in which case the filter will be isotropic. """
- def compute(self):
- im = self.getInputFromPort("Image")
- sigma = self.getInputListFromPort("Sigmas")
- if len(sigma) <= 1:
- sigma = sigma[0]
- der = scipy.ndimage.gaussian_gradient_magnitude(im.get_array(), sigma)
- out = NDArray()
- out.set_array(der)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Image", (NDArray, 'Image Array'))
- reg.add_input_port(cls, "Sigmas", (basic.Float, 'Standard Deviations'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class JointHistogram(ArrayImaging, Module):
- """ Calculate the Joint Histogram of 2 inputs. The inputs can be of arbitrary dimension,
- but must be equivalently sized. """
- def compute(self):
- in_x = self.getInputFromPort("Array One").get_array()
- in_y = self.getInputFromPort("Array Two").get_array()
- size_x = self.getInputFromPort("Bins X")
- size_y = self.getInputFromPort("Bins Y")
-
- take_log = True
- if self.hasInputFromPort("Log10"):
- take_log = self.getInputFromPort("Log10")
-
- out_ar = numpy.zeros((size_x, size_y))
- min_x = in_x.min()
- max_x = in_x.max() - min_x
- min_y = in_y.min()
- max_y = in_y.max() - min_y
-
- in_x = in_x.flatten()
- in_y = in_y.flatten()
-
- for i in xrange(in_x.size):
- x_cor = int(((in_x[i] - min_x)/max_x) * (size_x - 1))
- y_cor = int(((in_y[i] - min_y)/max_y) * (size_y - 1))
-
- out_ar[x_cor,y_cor] += 1.0
-
- if take_log:
- out_ar = out_ar + 1.0
- out_ar = scipy.log(out_ar)
- out = NDArray()
- out_ar = out_ar.transpose()
- out_ar = out_ar[::-1]
- out.set_array(out_ar)
- self.setResult("Joint Histogram", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Array One", (NDArray, 'X Axis Input'))
- reg.add_input_port(cls, "Array Two", (NDArray, 'Y Axis Input'))
- reg.add_input_port(cls, "Log10", (basic.Boolean, 'Use Log of Histogram'), True)
- reg.add_input_port(cls, "Bins X", (basic.Integer, 'Number of X Bins'))
- reg.add_input_port(cls, "Bins Y", (basic.Integer, 'Number of Y Bins'))
- reg.add_output_port(cls, "Joint Histogram", (NDArray, 'Joint Histogram'))
-
-class GaussianSmooth(ArrayImaging, Module):
- """ Smooth the Input array with a multi-dimensional gaussian kernel.
- The standard-deviation of the Gaussian filter are given for each axis as a sequence
- or as a single number, in which case the filter will be isotropic. """
- def compute(self):
- im = self.getInputFromPort("Input Array")
- sigma = self.getInputListFromPort("Sigmas")
- if len(sigma) <= 1:
- sigma = sigma[0]
- der = scipy.ndimage.gaussian_filter(im.get_array(), sigma)
- out = NDArray()
- out.set_array(der)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input Array", (NDArray, 'Image Array'))
- reg.add_input_port(cls, "Sigmas", (basic.Float, 'Standard Deviations'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class MedianFilter(ArrayImaging, Module):
- """ Smooth the Input array with a multi-dimensional median filter. """
- def compute(self):
- im = self.getInputFromPort("Input Array")
- k_size = self.getInputFromPort("Size")
- der = scipy.ndimage.median_filter(im.get_array(), size=k_size)
- out = NDArray()
- out.set_array(der)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input Array", (NDArray, 'Image Array'))
- reg.add_input_port(cls, "Size", (basic.Integer, 'Kernel Size'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
-
-class ImageDifference(ArrayImaging, Module):
- """ Calculate the difference between two input images. """
- def compute(self):
- im = self.getInputFromPort("Input 1")
- im2 = self.getInputFromPort("Input 2")
-
- da_ar = im.get_array() - im2.get_array()
- da_ar = numpy.abs(da_ar)
-
- out = NDArray()
- out.set_array(da_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input 1", (NDArray, 'Image Array'))
- reg.add_input_port(cls, "Input 2", (NDArray, 'Image Array'))
- reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
-
-class ImageNormalize(ArrayImaging, Module):
- """ Move the range of the image to [0,1] """
- def compute(self):
- im = self.getInputFromPort("Input")
- im_max = im.get_array().max()
- im_ar = im.get_array() / im_max
-
- out = NDArray()
- out.set_array(im_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, 'Image Array'))
- reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
-
-class SobelGradientMagnitude(ArrayImaging, Module):
- """ Use n-dimensional sobel kernels to compute the gradient magnitude
- of an image """
- def compute(self):
- im = self.getInputFromPort("Input").get_array()
- mag = numpy.zeros(im.shape)
- for i in xrange(im.ndim):
- kern = scipy.ndimage.sobel(im, axis=i)
- mag += kern*kern
-
- out = NDArray()
- out.set_array(numpy.sqrt(mag))
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, 'Image Array'))
- reg.add_output_port(cls, "Output", (NDArray, 'Output Array'))
diff --git a/contrib/NumSciPy/Matrix.py b/contrib/NumSciPy/Matrix.py
deleted file mode 100644
index 013d687..0000000
--- a/contrib/NumSciPy/Matrix.py
+++ /dev/null
@@ -1,107 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-
-import scipy
-import numpy
-from scipy import sparse
-
-from Array import *
-
-class MatrixModule(object):
- my_namespace = 'scipy|matrix'
-
-class MatrixOp(object):
- my_namespace = 'scipy|matrix|operation'
-
-class Matrix(MatrixModule, Module):
- """ Container class for the scipy.sparse.csc_matrix class """
- def __init__(self):
- Module.__init__(self)
- self.matrix = None
-
- def get_shape(self):
- return self.matrix.shape
-
- def get_conjugate(self):
- return self.matrix.conjugate()
-
- def get_column(self, colId):
- return self.matrix.getcol(colId)
-
- def get_row(self, rowId):
- return self.matrix.getrow(rowId)
-
- def set_diagonal(self, vals):
- self.matrix.setdiag(vals)
-
- def toarray(self):
- return self.matrix.toarray()
-
- def transpose(self):
- return self.matrix.transpose()
-
- def get_num_elements(self):
- return self.matrix.getnnz()
-
- def get_max_elements(self):
- return self.matrix.nzmax
-
- def get_reals(self):
- return self.matrix._real()
-
- def get_imaginaries(self):
- return self.matrix._imag()
-
- def get_matrix(self):
- return self.matrix
-
- def set_matrix(self, mat):
- self.matrix = mat
-
-class MatrixMultiply(MatrixOp, Module):
- """ Multiply two matrices together """
- def compute(self):
- a = self.getInputFromPort("Matrix1")
- b = self.getInputFromPort("Matrix2")
- out = Matrix()
- out.set_matrix(a.get_matrix() * b.get_matrix())
-
- self.setResult("Matrix Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Matrix1", (Matrix, 'Input Matrix 1'))
- reg.add_input_port(cls, "Matrix2", (Matrix, 'Input Matrix 2'))
- reg.add_output_port(cls, "Matrix Output", (Matrix, 'Output Matrix'))
-
-class MatrixConjugate(MatrixOp, Module):
- """ Get the complex conjugate of the input matrix. """
- def compute(self):
- a = self.getInputFromPort("Matrix")
- b = a.get_conjugate().copy()
- out = Matrix()
- out.set_matrix(b)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Matrix", (Matrix, 'Input Matrix'))
- reg.add_output_port(cls, "Output", (Matrix, 'Output Matrix'))
-
-class MatrixToArray(MatrixOp, Module):
- """ Convert a SciPy matrix to a Numpy Array """
- def compute(self):
- m = self.getInputFromPort("Matrix")
- a = m.toarray()
- out = NDArray()
- out.set_array(a)
- self.setResult("Output Array", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Matrix", (Matrix, 'Input Matrix'))
- reg.add_output_port(cls, "Output Array", (NDArray, 'Output Array'))
diff --git a/contrib/NumSciPy/MatrixUtilities.py b/contrib/NumSciPy/MatrixUtilities.py
deleted file mode 100644
index 7729d9c..0000000
--- a/contrib/NumSciPy/MatrixUtilities.py
+++ /dev/null
@@ -1,93 +0,0 @@
-from core.modules.vistrails_module import Module, ModuleError
-from Matrix import *
-from Array import *
-import scipy
-from scipy import io, sparse
-
-
-class ArrayUtilityModule(object):
- my_namespace = 'scipy|matrix|utilities|Matlab'
-
-class MatlabReader(ArrayUtilityModule, Module):
- """ Read a Matlab .mat file into a SciPy matrix """
- # Gather inputs here
- def get_inputs(self):
- if self.hasInputFromPort("Filename"):
- self.fname = self.getInputFromPort("Filename")
- else:
- self.fname = self.getInputFromPort("File").name
-
- # Set required members externally. This is just a helper function!
- def set_member(self, name, val):
- setattr(self, name, val)
-
- # This is the work that the compute() method does
- def process_compute(self):
- m = io.loadmat(self.fname, None, 0)
- vals = m.values()
-
- for t in vals:
- if type(t) == numpy.ndarray:
- if t.dtype == 'object':
- continue
- mat = t
-
- return (mat,)
-
- # Take the returns from the processing and put them out on the outputs.
- def set_outputs(self, results):
- try:
- out = Matrix()
- out.set_matrix(sparse.csc_matrix(results[0]))
-
- self.setResult("Matrix Output", out)
- except:
- pass
-
- out_ar = NDArray()
- out_ar.set_array(numpy.array(results[0]))
- self.setResult("Array Output", out_ar)
-
- # The compute method for vistrails compatibility
- def compute(self):
- self.get_inputs()
- results = self.process_compute()
- self.set_outputs(results)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
- reg.add_input_port(cls, "File", (basic.File, 'File'))
- reg.add_output_port(cls, "Matrix Output", (Matrix, 'Matrix Output'))
- reg.add_output_port(cls, "Array Output", (NDArray, 'Array Output'))
-
-class MatlabWriter(ArrayUtilityModule, Module):
- """ Write a Matlab .mat file from a SciPy matrix """
- def compute(self):
- if self.hasInputFromPort("Filename"):
- fname = self.getInputFromPort("Filename")
- else:
- fname = self.getInputFromPort("File").name
-
- ar_list = self.getInputListFromPort("Arrays")
- mat_list = self.getInputListFromPort("Matrices")
- ar_dict = {}
- for i in xrange(len(ar_list)):
- ar_name = "array_" + str(i)
- ar_dict[ar_name] = ar_list[i].get_array()
-
- for i in xrange(len(mat_list)):
- mat_name = "matrix_" + str(i)
- ar_dict[mat_name] = mat_list[i].get_matrix()
-
- io.savemat(fname, ar_dict)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
- reg.add_input_port(cls, "File", (basic.File, 'File'))
- reg.add_input_port(cls, "Arrays", (NDArray, 'Arrays to Save'))
- reg.add_input_port(cls, "Matrices", (Matrix, 'Matrices to Save'))
-
diff --git a/contrib/NumSciPy/Stockwell.py b/contrib/NumSciPy/Stockwell.py
deleted file mode 100644
index 336c735..0000000
--- a/contrib/NumSciPy/Stockwell.py
+++ /dev/null
@@ -1,763 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from Matrix import *
-from Array import *
-from DSP import DSPModule
-import scipy
-import scipy.signal
-import scipy.fftpack
-import numpy
-import smt
-import st
-import time
-
-class StockwellModule(object):
- my_namespace = 'scipy|signals|stockwell'
-# my_namespace = 'scipy|signals'
-
-class IsotropicScaleVolumes(StockwellModule, Module):
- def compute(self):
- vol = self.getInputFromPort("Input").get_array()
- lof = self.getInputFromPort("Low Freq")
- hif = self.getInputFromPort("Hi Freq")
- max_vol = numpy.zeros(vol.shape)
- grav_vol = numpy.zeros(vol.shape)
-
- (slices,rows,cols) = vol.shape
- for z in range(slices):
- tr = time.time()
- for y in range(rows):
- ray = vol[z,y,:].squeeze()
- t = st.st(ray, lof, hif)
- for x in range(cols):
- scales = t[:,x].squeeze()
- scales = scales * scales.conjugate()
-
- max_vol[x,y,z] = float(scales.argmax())
-
- grav = 0.
- for i in range(scales.shape[0]):
- v = scales[i]
- f = lof + i
- grav += float(v) * float(f)
-
- grav_vol[x,y,z] = grav
-
- print "done z = ", z
- print "took: ", (time.time() - tr) * 1000.
-
- grav_vol = grav_vol - grav_vol.min()
- grav_vol = grav_vol / grav_vol.max()
- grav_vol = grav_vol * float(hif - lof)
- grav_vol = grav_vol + lof
- max_out = NDArray()
- max_out.set_array(max_vol)
- grav_out = NDArray()
- grav_out.set_array(grav_vol)
- self.setResult("Max Output", max_out)
- self.setResult("Grav Output", grav_out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, "Input Signals"))
- reg.add_input_port(cls, "Low Freq", (basic.Float, "Low Frequency"))
- reg.add_input_port(cls, "Hi Freq", (basic.Float, "High Frequency"))
- reg.add_output_port(cls, "Max Output", (NDArray, "Output Max TFR"))
- reg.add_output_port(cls, "Grav Output", (NDArray, "Output Grav TFR"))
-
-
-class ScaleVolumes(StockwellModule, Module):
- def compute(self):
- vol = self.getInputFromPort("Input").get_array()
- lof = self.getInputFromPort("Low Freq")
- hif = self.getInputFromPort("Hi Freq")
- sigma = self.forceGetInputFromPort("Sigma")
- max_vol = numpy.zeros(vol.shape)
- grav_vol = numpy.zeros(vol.shape)
-
- (slices,rows,cols) = vol.shape
- for z in range(slices):
- t = time.time()
- for y in range(rows):
- for x in range(cols):
- # grab our 3 rays
- xray = vol[z,y,:].squeeze()
- yray = vol[z,:,x].squeeze()
- zray = vol[:,y,x].squeeze()
-
- # Transform each ray
- xt = st.st(xray,lof,hif)
- yt = st.st(yray,lof,hif)
- zt = st.st(zray,lof,hif)
-
- # Grab the point at all valid scales
- xpt = xt[:,x]
- ypt = yt[:,y]
- zpt = zt[:,z]
-
- # Take the magnitude
- xpt = xpt * xpt.conjugate()
- ypt = ypt * ypt.conjugate()
- zpt = zpt * zpt.conjugate()
-
- scale_vec = xpt.real + ypt.real + zpt.real
- if sigma:
- scale_vec = scale_vec * scipy.signal.gaussian(scale_vec.shape[0], sigma)
-
- scale = scale_vec.argmax()
- max_vol[x,y,z] = scale
-
-# scale_vec =
-# scale_vec = scale_vec / scale_vec.sum()
-
-
- grav = 0
- for s in range(scale_vec.shape[0]):
- v = scale_vec[s]
- f = lof + s
- grav += float(f) * float(v)
-
-# grav = grav / float(scale_vec.shape[0])
-
- grav_vol[x,y,z] = grav
-
- print "done z = ", z
- print "took: ", (time.time() - t) * 1000.
-
- grav_vol = grav_vol - grav_vol.min()
- grav_vol = grav_vol / grav_vol.max()
- grav_vol = grav_vol * float(hif - lof)
- grav_vol = grav_vol + lof
- max_out = NDArray()
- max_out.set_array(max_vol)
- grav_out = NDArray()
- grav_out.set_array(grav_vol)
- self.setResult("Max Output", max_out)
- self.setResult("Grav Output", grav_out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, "Input Signals"))
- reg.add_input_port(cls, "Low Freq", (basic.Float, "Low Frequency"))
- reg.add_input_port(cls, "Hi Freq", (basic.Float, "High Frequency"))
- reg.add_input_port(cls, "Sigma", (basic.Float, "Sigma"))
- reg.add_output_port(cls, "Max Output", (NDArray, "Output Max TFR"))
- reg.add_output_port(cls, "Grav Output", (NDArray, "Output Grav TFR"))
-
-
-class MaximalScaleVolume(StockwellModule, Module):
- def compute(self):
- vol = self.getInputFromPort("Input").get_array()
- lof = self.getInputFromPort("Low Freq")
- hif = self.getInputFromPort("Hi Freq")
- sigma = self.forceGetInputFromPort("Sigma")
- out_vol = numpy.zeros(vol.shape)
-
- (slices,rows,cols) = vol.shape
- for z in range(slices):
- t = time.time()
- for y in range(rows):
- for x in range(cols):
- # grab our 3 rays
- xray = vol[z,y,:].squeeze()
- yray = vol[z,:,x].squeeze()
- zray = vol[:,y,x].squeeze()
-
- # Transform each ray
- xt = st.st(xray,lof,hif)
- yt = st.st(yray,lof,hif)
- zt = st.st(zray,lof,hif)
-
- # Grab the point at all valid scales
- xpt = xt[:,x]
- ypt = yt[:,y]
- zpt = zt[:,z]
-
- # Take the magnitude
- xpt = xpt * xpt.conjugate()
- ypt = ypt * ypt.conjugate()
- zpt = zpt * zpt.conjugate()
-
- scale_vec = xpt.real + ypt.real + zpt.real
- if sigma:
- scale_vec = scale_vec * scipy.signal.gaussian(scale_vec.shape[0], sigma)
-
- scale = scale_vec.argmax()
- out_vol[x,y,z] = scale
- print "done z = ", z
- print "took: ", (time.time() - t) * 1000.
-
- out = NDArray()
- out.set_array(out_vol)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, "Input Signals"))
- reg.add_input_port(cls, "Low Freq", (basic.Float, "Low Frequency"))
- reg.add_input_port(cls, "Hi Freq", (basic.Float, "High Frequency"))
- reg.add_input_port(cls, "Sigma", (basic.Float, "Sigma"))
- reg.add_output_port(cls, "Output", (NDArray, "Output TFR"))
-
-
-class StockwellTransform(StockwellModule, Module):
- def compute(self):
- t = time.time()
- signals = self.getInputFromPort("Signals").get_array()
- lof = self.getInputFromPort("Low Freq")
- hif = self.getInputFromPort("Hi Freq")
- if len(signals.shape) == 1:
- signals.shape = (1, signals.shape[0])
-
- outl = []
- for i in xrange(signals.shape[0]):
- sig_ar = signals[i]
- x = st.st(sig_ar, lof, hif)
- outl.append(x)
-
- out_ar = numpy.array(outl).squeeze()
- print "c time = ", (time.time() - t) * 1000.
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Signals", (NDArray, "Input Signals"))
- reg.add_input_port(cls, "Low Freq", (basic.Float, "Low Frequency"))
- reg.add_input_port(cls, "Hi Freq", (basic.Float, "High Frequency"))
- reg.add_output_port(cls, "Output", (NDArray, "Output TFR"))
-
-class PyStockwellTransform(StockwellModule, Module):
-
- def get_gaussian(self, length, freq, factor=1.0):
- g = numpy.arange(float(length))
- g = g*g
- g = scipy.exp(-2. * scipy.pi * scipy.pi * g / (float(freq)*float(freq)))
- return g
-# return numpy.roll(g, length/2)#.astype(complex)
-
- def compute(self):
- t = time.time()
- signal = self.getInputFromPort("Signal").get_array().squeeze()
- print "signal.shape = ", signal.shape
- f = scipy.fftpack.fft(signal)
- print "got f made"
- f = scipy.fftpack.hilbert(f)
- print "got hilbert done"
-# f2 = numpy.concatenate((f,f))
-
- lof = self.getInputFromPort("Low Freq")
- hif = self.getInputFromPort("Hi Freq")
-
- out_ar = numpy.zeros((hif-lof+1, signal.shape[0]))
-
- start = 0
- if lof == 0:
- out_ar[0,:] = signal.mean()
- start = 1
-
- for k in range(start, hif-lof, 1):
- g = self.get_gaussian(signal.shape[0], lof+k)
- o = scipy.fftpack.ifft(numpy.roll(f,lof+k) * g) / float(signal.size)
- out_ar[k,:] = o
-
- print "time = ", (time.time() - t) * 1000.
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Signal", (NDArray, "Input Signal"))
- reg.add_input_port(cls, "Low Freq", (basic.Integer, "Low Frequency"))
- reg.add_input_port(cls, "Hi Freq", (basic.Integer, "High Frequency"))
- reg.add_output_port(cls, "Output", (NDArray, "Output TFR"))
-
-class MultiTaperStockwellTransform(StockwellModule, Module):
- def compute(self):
- signals = self.getInputFromPort("Signals").get_array()
- sr = self.getInputFromPort("Sample Rate")
- lof = self.getInputFromPort("Low Freq")
- hif = self.getInputFromPort("Hi Freq")
-
- if len(signals.shape) == 1:
- signals.shape = (1, signals.shape[0])
-
- if self.hasInputFromPort("Bandwidth"):
- self.k = smt.calcK(self.getInputFromPort("Bandwidth"),signals.shape[1], sr)
- else:
- self.k = self.getInputFromPort("K")
-
- outl = []
- for i in xrange(signals.shape[0]):
- sig_ar = signals[i]
- x = smt.mtst(self.k, smt.calc_tapers(self.k, signals.shape[1]), sig_ar, lof, hif)
- outl.append(x)
-
- out_ar = numpy.array(outl).squeeze()
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Signals", (NDArray, 'Input Signal Array'))
- reg.add_input_port(cls, "Sample Rate", (basic.Integer, 'Sample Rate'))
- reg.add_input_port(cls, "K", (basic.Float, "K"))
- reg.add_input_port(cls, "Bandwidth", (basic.Float, "Bandwidth"))
- reg.add_input_port(cls, "Low Freq", (basic.Float, "Low Frequency"))
- reg.add_input_port(cls, "Hi Freq", (basic.Float, "High Frequency"))
- reg.add_output_port(cls, "Output", (NDArray, "Output TFR"))
-
-class FastStockwell3D(StockwellModule, Module):
- """
- Compute an approximation to the 3D Stockwell Transform.
- The output is a 4D array with dimensions as follows:
- output.shape = (voices, slices, rows, columns)
- """
- def compute(self):
- in_ar = self.getInputFromPort("Input").get_array()
- lo_f = self.getInputFromPort("Low Freq")
- hi_f = self.getInputFromPort("High Freq")
- num_f = hi_f - lo_f + 1
-
- (slices, rows, cols) = in_ar.shape
- out_ar = numpy.zeros((num_f, slices, rows, cols))
- for s in range(slices):
- for r in range(rows):
- sig = in_ar[s,r,:]
- t = st.st(sig,lo_f,hi_f)
- t = t.conjugate() * t
- t = t.real
- for f in range(t.shape[0]):
- out_ar[f,s,r,:] = t[f,:]
-
- print "done dim 1"
- for s in range(slices):
- for c in range(cols):
- sig = in_ar[s,:,c]
- t = st.st(sig,lo_f,hi_f)
- t = t.conjugate() * t
- t = t.real
- for f in range(t.shape[0]):
- out_ar[f,s,:,c] += t[f,:]
-
- print "done dim 2"
- for r in range(rows):
- for c in range(cols):
- sig = in_ar[:,r,c]
- t = st.st(sig,lo_f,hi_f)
- t = t.conjugate() * t
- t = t.real
- for f in range(t.shape[0]):
- out_ar[f,:,r,c] += t[f,:]
-
- print "done dim 3"
-# out_ar = out_ar * out_ar.conjugate()
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, 'Input Volume'))
- reg.add_input_port(cls, "Low Freq", (basic.Integer, 'Lowest Voice'))
- reg.add_input_port(cls, "High Freq", (basic.Integer, 'Highest Voice'))
- reg.add_output_port(cls, "Output", (NDArray, 'Output Voice Volume'))
-
-class ScaleSpaceHistogram(StockwellModule, Module):
- def compute(self):
- signal = self.getInputFromPort("Input").get_array()
- lof = self.getInputFromPort("Low Freq")
- hif = self.getInputFromPort("High Freq")
-
- num_pts = signal.size
- min_s = signal.min()
- max_s = signal.max()
- d = max_s - min_s
- print "Accumulating over " + str(num_pts) + " points"
- histo = numpy.zeros((512,hif-lof+1))
- print "Histo: ",histo.shape
- dist = numpy.zeros(512)
- for z in range(signal.shape[2]):
- for y in range(signal.shape[1]):
- for x in range(signal.shape[0]):
- sigx = signal[z,y,:]
- sigy = signal[z,:,x]
- tx = st.st(sigx, lof, hif)
- ty = st.st(sigy, lof, hif)
- sigz = signal[:,y,z]
- tz = st.st(sigz, lof, hif)
- tz = tz[:,x].squeeze()
- tz = tz * tz.conjugate()
- tx = tx[:,z].squeeze()
- ty = ty[:,y].squeeze()
- tx = tx * tx.conjugate()
- ty = ty * ty.conjugate()
-
- ar = tx.real + ty.real + tz.real
- ar = ar / ar.sum()
-# ar = ar.sum(axis=1)
-# print "ar: ", ar.shape
-# ar.shape = (ar.shape[0],1)
- scalar = signal[z,y,x]
- try:
- bin = int((scalar - min_s) / d * 511.)
-# dist[bin] += 1
-# print bin, scalar, ar
- sigma = self.forceGetInputFromPort("Sigma")
- if sigma:
- ar = scipy.signal.gaussian(ar.size, sigma) * ar
- histo[bin,:] += ar
- except:
- print "Cannot assign to bin: " + str(bin) +", scalar: " +str(scalar)
- print "location = ", x, y, z
- raise ModuleError("Cannot assign to bin: " + str(bin) +", scalar: " +str(scalar))
-
-# print "done with y = ", y
- print "done with z = ", z
-
- out = NDArray()
- out.set_array(histo)# / dist)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, 'Input Volume'))
- reg.add_input_port(cls, "Sigma", (basic.Float, 'Sigma'))
- reg.add_input_port(cls, "Low Freq", (basic.Integer, 'Lowest Voice'))
- reg.add_input_port(cls, "High Freq", (basic.Integer, 'Highest Voice'))
- reg.add_output_port(cls, "Output", (NDArray, 'Output Voice Volume'))
-
-class PyScaleSpaceHistogram(StockwellModule, Module):
- def get_gaussian(self, length, freq, factor=1.0):
- g = numpy.arange(float(length))
- g = g*g
- g = scipy.exp(-2. * scipy.pi * scipy.pi * g / (float(freq)*float(freq)))
- return g
-
- def stockwell(self, ray, lof, hif):
- ret = numpy.zeros((hif-lof,ray.shape[0]))
-# ray = scipy.fftpack.hilbert(ray)
-# ray = numpy.concatenate((ray,ray[::-1]))
- start = 0
- if lof == 0:
- ret[0,:] = ray.mean()
- start = 1
-
- for k in range(start, hif-lof, 1):
- g = self.get_gaussian(ray.shape[0], lof+k)
- o = scipy.fftpack.ifft(numpy.roll(ray,lof+k) * g) / float(ray.size)
- ret[k,:] = o
-
- return ret
-
- def compute(self):
- signal = self.getInputFromPort("Input").get_array().squeeze()
- print "signal.shape = ", signal.shape
- lof = self.getInputFromPort("Low Freq")
- hif = self.getInputFromPort("High Freq")
-
- num_scalar_bins = self.getInputFromPort("Scalar Bins")
-
- num_pts = signal.size
- min_s = signal.min()
- max_s = signal.max()
- d = max_s - min_s
- print "Accumulating over " + str(num_pts) + " points"
- histo = numpy.zeros((num_scalar_bins,hif-lof))
-
- f_sig = scipy.fftpack.fftn(signal)
-
- for z in range(signal.shape[0]):
- for y in range(signal.shape[1]):
- for x in range(signal.shape[2]):
- yray = f_sig[z,:,x].squeeze()
- ty = self.stockwell(yray, lof, hif)
- zray = f_sig[:,y,x].squeeze()
- tz = self.stockwell(zray, lof, hif)
- xray = f_sig[z,y,:].squeeze()
- tx = self.stockwell(xray, lof, hif)
-
- tx = tx[:,z].squeeze()
- ty = ty[:,y].squeeze()
- tz = tz[:,x].squeeze()
-
- tx = tx * tx.conjugate()
- ty = ty * ty.conjugate()
- tz = tz * tz.conjugate()
-
- ar = tx.real + ty.real + tz.real
- ar = ar / ar.sum()
-
-
- scalar = signal[z,y,x]
- try:
- bin = int((scalar - min_s) / d * float(num_scalar_bins-1.))
-# dist[bin] += 1
-# print bin, scalar, ar
- sigma = self.forceGetInputFromPort("Sigma")
- if sigma:
- ar = scipy.signal.gaussian(ar.size, sigma) * ar
- histo[bin,:] += ar
- except:
- print "Cannot assign to bin: " + str(bin) +", scalar: " +str(scalar)
- print "location = ", x, y, z
- raise ModuleError("Cannot assign to bin: " + str(bin) +", scalar: " +str(scalar))
-
-# print "done with y = ", y
- print "done with z = ", z
-
- out = NDArray()
- out.set_array(histo)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, 'Input Volume'))
- reg.add_input_port(cls, "Scalar Bins", (basic.Integer, 'Scalar Bins'))
- reg.add_input_port(cls, "Sigma", (basic.Float, 'Sigma'))
- reg.add_input_port(cls, "Low Freq", (basic.Integer, 'Lowest Voice'))
- reg.add_input_port(cls, "High Freq", (basic.Integer, 'Highest Voice'))
- reg.add_output_port(cls, "Output", (NDArray, 'Output Voice Volume'))
-
-class PointBasedStockwell(StockwellModule, Module):
- def compute(self):
- signal = self.getInputFromPort("Input").get_array()
- ptx = self.getInputFromPort("X")
- pty = self.getInputFromPort("Y")
- ptz = self.getInputFromPort("Z")
-
- lof = self.getInputFromPort("Low Freq")
- hif = self.getInputFromPort("High Freq")
-
- sigx = signal[ptz,pty,:]
- sigy = signal[ptz,:,ptx]
- sigz = signal[:,pty,ptx]
-
- tx = st.st(sigx, lof, hif)
- ty = st.st(sigy, lof, hif)
- tz = st.st(sigz, lof, hif)
-
- tx = tx * tx.conjugate()
- ty = ty * ty.conjugate()
- tz = tz * tz.conjugate()
-
- out_ar = tx.real + ty.real + tz.real
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, 'Input Volume'))
- reg.add_input_port(cls, "X", (basic.Integer, 'X'))
- reg.add_input_port(cls, "Y", (basic.Integer, 'Y'))
- reg.add_input_port(cls, "Z", (basic.Integer, 'Z'))
- reg.add_input_port(cls, "Low Freq", (basic.Integer, 'Lowest Voice'))
- reg.add_input_port(cls, "High Freq", (basic.Integer, 'Highest Voice'))
- reg.add_output_port(cls, "Output", (NDArray, 'Output Voice Volume'))
-
-class Stockwell2D(StockwellModule, Module):
- ''' Calculate the 3D Stockwell Transform '''
- def g_window(self, l, w):
- if w != 0.0:
- sigma = l / (2 * pi * w)
- else:
- print 'w is zero!'
- g = numpy.zeros(l)
- iarr = numpy.arange(float(l))
- ex = (iarr - l / 2) ** 2 / (2 * sigma ** 2)
- wl = numpy.where(numpy.ravel(ex < 25))[0]
- g = numpy.where(ex < 25., numpy.exp(-1.*ex), ex)
-# g = roll(g, -l / 2)
- return g.astype(complex)
-
- def get_gaussian(self, sx, sy, kx, ky, factor=1.0):
- wrow = factor * (float(sx) / float(kx))
- wcol = factor * (float(sy) / float(ky))
- sig_row = 1. / (2. * scipy.pi * wrow)
- sig_col = 1. / (2. * scipy.pi * wcol)
- print "sigmas = ", sig_row, sig_col
-
- grow = scipy.signal.gaussian(sx, sig_row)
- gcol = scipy.signal.gaussian(sy, sig_col)
-
- print "gaussians good?"
- grow.shape = sx,1
- gcol.shape = 1,sy
-
- print "gaussians reshaped"
- gwin = grow*gcol
- print "2d formed..."
- gwin = gwin.astype(complex)
- print "gaussian formed"
- return gwin
-
- def compute(self):
- in_ar = self.getInputFromPort("Input").get_array()
- lof = self.getInputFromPort("Low Freq")
- hif = self.getInputFromPort("High Freq")
- (nx,ny) = in_ar.shape
- nf = hif-lof
- kx_len = nf
- nyquist_x = nx/2 + 1
- ky_len = nf
- h = scipy.fftpack.fftn(in_ar)
- h = scipy.fftpack.fftshift(h)
- or_spe = h
-
- print "allocating output", nf,kx_len,ky_len
- # allocate output
- try:
- l = numpy.zeros((nf, nx, ny))
- except:
- raise ModuleError("Cannot allocate output array")
- print "Output Allocated - ", l.shape
-
- vf = 0
- for ky in range(lof, hif, 1):
- print "ky = ", ky
- for kx in range(lof, hif, 1):
- print "kx = ", kx
- if kx >= nyquist_x:
- kxwidth = nx - kx
- else:
- kxwidth = kx
-
- print "kxwidth = ", kxwidth
- gw = self.get_gaussian(nx,ny,kxwidth,ky)
-
- b = h * gw
- h = numpy.roll(h,-1,axis=0)
- voice = scipy.fftpack.ifftn(scipy.fftpack.ifftshift(b))
- print "voice shape = ", voice
- t = voice * voice.conjugate()
- print "t.min() = ", t.min()
- print "t.max() = ", t.max()
- l[vf,:,:] += t.real
- h = or_spe
- h = numpy.roll(h, -1, axis=1)
- vf += 1
-
- print l.shape
- out = NDArray()
- out.set_array(l)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input", (NDArray, 'Input Volume'))
- reg.add_input_port(cls, "Low Freq", (basic.Integer, 'Lowest Voice'))
- reg.add_input_port(cls, "High Freq", (basic.Integer, 'Highest Voice'))
- reg.add_output_port(cls, "Output", (NDArray, 'Output Voice Volume'))
-
-class FrequencyPhaseLocking(StockwellModule, Module):
- """
- Compute the phase-locking index with respect to a single frequency. The algorithm
- implemented is the realization of that outline in Sauseng et al. Cross-frequency phase
- synchronization: A brain mechanism of memory matching and attention: NeuroImage - 2008
-
- To summarize, the instantaneous phase of a signal at a given frequency and time is denoted
- \Phi(f, t) = arctan(F_{Real}(x(t)), F_{Imaginary}(x(t)))
-
- The generalized phase differences between two signal components with an m:n frequency relationship
- is:
-
- \frac{m+n}{2n}f_n = \frac{n+m}{2m}f_m
-
- \Delta \Phi(f_n,f_m,t) = (\frac{n+m}{2m} \Phi(f_m, t) - \frac{m+n}{2n}f_n \Phi(f_n, t)) % 2 \pi
-
- And the Phase Synchronization Index is defined as:
-
- \hat{\Gamma}_\Phi(f_n,f_m,t) = \|\langle e^{j \Delta \Phi(f_n,f_m,t)} \rangle\|, j = \sqrt{-1}
-
- """
- def make_delta_phi(self, phase_ar):
- (freqs,times) = phase_ar.shape
- dphi_ar = numpy.zeros((times, freqs, freqs))
- for t in range(times):
- for fn in range(freqs):
- f_n = float(fn) + float(self.lof)
- for fm in range(fn+1,freqs,1):
- f_m = float(fm) + float(self.lof)
- n = 1.
- m = f_n / f_m
- phi_m = phase_ar[fm,t]
- phi_n = phase_ar[fn,t]
- dphi = (((n+m)/2.*m) * phi_m) - (((n+m)/2.*n) * phi_n)
- dphi = dphi % (2. * numpy.pi)
- dphi_ar[t,fn,fm] = dphi
- dphi_ar[t,fm,fn] = dphi
-
- # dphi_ar.shape = (sig_len, freq_range, freq_range)
- return dphi_ar
-
- def compute(self):
- trial_ar = self.getInputFromPort("Single Trials").get_array()
- print "trial_ar.shape = ", trial_ar.shape
- self.lof = self.getInputFromPort("Low Freq")
- self.hif = self.getInputFromPort("High Freq")
- sensor_list = self.forceGetInputListFromPort("Sensors")
-
- if len(trial_ar.shape) != 3:
- raise ModuleError("Cannot process input with rank not 3")
-
- (trials, sensors, sig_len) = trial_ar.shape
- if sensor_list == None:
- sensor_list = numpy.arange(sensors)
- else:
- sensor_list = numpy.array(sensor_list)
-
- # Compute the TFR for a single sensor across all trials
- freq_range = self.hif - self.lof
- out_ar = numpy.zeros((sensor_list.shape[0], sig_len, freq_range+1, freq_range+1))
- print "sensor list = ", sensor_list
-
- # For each sensor to consider, extract the signal array
- for i in range(sensor_list.shape[0]):
- tmp_sig = trial_ar[:,sensor_list[i],:].squeeze()
- # For each trial, extract the signal
- for j in range(trials):
- sig = tmp_sig[j,:].squeeze()
- tfr = st.st(sig, self.lof, self.hif)
-
- # Compute the phase for the Time-freq plane
- p = numpy.arctan2(tfr.real, tfr.imag)
-
- # the ordering of p is: (freqs,times) = p.shape
- dphi_ar = numpy.array(0.-1.j*self.make_delta_phi(p.real))
- dphi_ar = numpy.exp(dphi_ar)
- out_ar[i,:,:,:] += dphi_ar
-
- print "Trial " + str(j) + " done processing..."
- print "out_ar done with all trials"
- out_ar[i,:,:,:] /= float(trials)
- out_ar[i,:,:,:] = out_ar[i,:,:,:] * out_ar[i,:,:,:].conjugate()
- out_ar[i,:,:,:] = out_ar[i,:,:,:].real
- print "min,max,mean = ", out_ar[i].min(), out_ar[i].max(), out_ar[i].mean()
- out = NDArray()
- out.set_array(out_ar)
- self.setResult("Output", out)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, namespace=cls.my_namespace)
- reg.add_input_port(cls, "Single Trials", (NDArray, "Input Single Trial Array"))
- reg.add_input_port(cls, "Low Freq", (basic.Integer, "Low Frequency"))
- reg.add_input_port(cls, "High Freq", (basic.Integer, "High Frequency"))
- reg.add_input_port(cls, "Sensors", (basic.Integer, "Sensors"))
- reg.add_output_port(cls, "Output", (NDArray, "Phase Locking Volume"))
diff --git a/contrib/NumSciPy/__init__.py b/contrib/NumSciPy/__init__.py
deleted file mode 100644
index 554b4b8..0000000
--- a/contrib/NumSciPy/__init__.py
+++ /dev/null
@@ -1,276 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-import scipy
-import scipy.interpolate
-
-# Numpy package imports
-import Array
-import ArrayAccess
-import ArrayOperations
-import ArrayUtilities
-import ArrayConvert
-import ArrayIO
-import Imaging
-
-# Scipy package imports
-import Matrix
-import MatrixUtilities
-import DSP
-import Filters
-import EnsembleOrdering
-
-# NumSciPy plotting
-import ArrayPlot
-
-version = '0.4.0'
-name = 'Num-SciPy'
-identifier = 'edu.utah.sci.vistrails.numpyscipy'
-
-def initialize(*args, **keywords):
- reg = core.modules.module_registry
- basic = core.modules.basic_modules
-
- clslst = []
-
- #########################################################################################
- # Numpy Registry
- reg.add_module(Array.NDArray, name="Numpy Array", namespace=Array.NDArray.my_namespace)
- reg.add_output_port(Array.NDArray, "self", (Array.NDArray, 'self'))
- reg.add_module(Matrix.Matrix, name="Scipy Matrix", namespace=Matrix.Matrix.my_namespace)
-
-
- #########################################################################################
- # Array Access registry
- accessclass = [ArrayAccess.GetShape,
- ArrayAccess.GetReals,
- ArrayAccess.GetImaginaries,
- ArrayAccess.GetMax,
- ArrayAccess.GetMean,
- ArrayAccess.GetMin,
- ArrayAccess.GetDiagonal,
- ArrayAccess.GetArrayAsType,
- ArrayAccess.GetConjugate,
- ArrayAccess.GetFlattenedArray,
- ArrayAccess.GetField,
- ArrayAccess.ToScalar,
- ArrayAccess.GetMemoryFootprint,
- ArrayAccess.GetArrayRank,
- ArrayAccess.GetNonZeroEntries,
- ArrayAccess.GetArraySize,
- ArrayAccess.GetTranspose,
- ArrayAccess.GetRowRange,
- ArrayAccess.GetColumnRange,
- ArrayAccess.GetRows]
-
- for cls in accessclass:
- cls.register(reg, basic)
-
-
- #########################################################################################
- # Array Operations registry
- opclasses = [ArrayOperations.ArrayReshape,
- ArrayOperations.ArrayCumulativeSum,
- ArrayOperations.ArraySort,
- ArrayOperations.ArrayCumulativeProduct,
- ArrayOperations.ArrayFill,
- ArrayOperations.ArrayResize,
- ArrayOperations.ArrayExtractRegion,
- ArrayOperations.ArrayRavel,
- ArrayOperations.ArrayRound,
- ArrayOperations.ArrayGetSigma,
- ArrayOperations.ArraySum,
- ArrayOperations.ArrayElementMultiply,
- ArrayOperations.ArraySetElement,
- ArrayOperations.ArrayVariance,
- ArrayOperations.ArrayTrace,
- ArrayOperations.ArraySwapAxes,
- ArrayOperations.ArraySqueeze,
- ArrayOperations.ArrayScalarMultiply,
- ArrayOperations.ArrayAdd,
- ArrayOperations.ArrayScalarAdd,
- ArrayOperations.ArrayLog10,
- ArrayOperations.ArrayAtan2,
- ArrayOperations.ArraySqrt,
- ArrayOperations.ArrayThreshold,
- ArrayOperations.ArrayWindow,
- ArrayOperations.ArrayNormalize,
- ArrayOperations.ArrayName]
-
- for cls in opclasses:
- cls.register(reg, basic)
-
-
- #########################################################################################
- # Array Convert registry
- convertclasses = [ArrayConvert.ArrayDumpToFile,
- ArrayConvert.ArrayDumpToString,
- ArrayConvert.ArrayToFile,
- ArrayConvert.ArrayToString,
- ArrayConvert.ArrayToMatrix,
- ArrayConvert.ArrayToVTKImageData]
-
- for cls in convertclasses:
- cls.register(reg, basic)
-
- #########################################################################################
- # Array IO registry
- ioclasses = [ArrayIO.ReadRAW,
- ArrayIO.ReadNHDR,
- ArrayIO.WriteRAW,
- ArrayIO.WriteNHDR,
- ArrayIO.ReadStatisticalSummary]
-
- try:
- import pylab
- ioclasses.append(ArrayIO.ReadPNG)
- ioclasses.append(ArrayIO.WritePNG)
- except:
- pass
-
- for cls in ioclasses:
- cls.register(reg, basic)
-
- #########################################################################################
- # Array Imaging registry
- ar_util = [ArrayUtilities.ArrayToVTKScalars,
- ArrayUtilities.ArrayToTimeVaryingVTKScalars,
- ArrayUtilities.ArrayToTimeVaryingVTKVectors,
- ArrayUtilities.ArrayToVTKVectors,
- ArrayUtilities.VTKDataSetToPointArray]
-
- clslst.extend(ar_util)
-
- for cls in ar_util:
- cls.register(reg, basic)
-
- #########################################################################################
- # Array Imaging registry
- imclasses = [Imaging.ExtractRGBAChannel,
- Imaging.GaussianGradientMagnitude,
- Imaging.JointHistogram,
- Imaging.GaussianSmooth,
- Imaging.MedianFilter,
- Imaging.ImageDifference,
- Imaging.ImageNormalize,
- Imaging.SobelGradientMagnitude]
-
- for cls in imclasses:
- cls.register(reg, basic)
-
- #########################################################################################
- # Scipy Registry
- matrixclasses = [Matrix.MatrixMultiply,
- Matrix.MatrixConjugate,
- Matrix.MatrixToArray]
-
- for cls in matrixclasses:
- cls.register(reg,basic)
-
- #########################################################################################
- # Scipy Matrix Utilities Registry
- matrixutils = [MatrixUtilities.MatlabReader,
- MatrixUtilities.MatlabWriter]
-
- for cls in matrixutils:
- cls.register(reg, basic)
-
- #########################################################################################
- # Scipy DSP Registry
- dspclasses = [DSP.FFT,
- DSP.FFTN,
- DSP.SignalSmoothing,
- DSP.ShortTimeFourierTransform,
- DSP.SignalGenerator]
-# DSP.FrequencyPhaseLocking,
-# DSP.SingleTrialPhaseLocking
-
- try:
- import smt
- import Stockwell
- dspclasses.append(Stockwell.StockwellTransform)
- dspclasses.append(Stockwell.MultiTaperStockwellTransform)
- dspclasses.append(Stockwell.FastStockwell3D)
- dspclasses.append(Stockwell.Stockwell2D)
- dspclasses.append(Stockwell.PyStockwellTransform)
- dspclasses.append(Stockwell.PointBasedStockwell)
- dspclasses.append(Stockwell.ScaleSpaceHistogram)
- dspclasses.append(Stockwell.PyScaleSpaceHistogram)
- dspclasses.append(Stockwell.MaximalScaleVolume)
- dspclasses.append(Stockwell.ScaleVolumes)
- dspclasses.append(Stockwell.IsotropicScaleVolumes)
- dspclasses.append(Stockwell.FrequencyPhaseLocking)
- except:
- pass
-
- for cls in dspclasses:
- cls.register(reg, basic)
-
- #########################################################################################
- # Scipy Interpolation Registry
- interpclasses = []
- try:
- import ArrayInterpolate
- interpclasses.append(ArrayInterpolate.RBFInterpolate)
- interpclasses.append(ArrayInterpolate.BSplineInterpolate)
- except:
- pass
-
- interpclasses.append(ArrayInterpolate.BSplineResample)
- for cls in interpclasses:
- cls.register(reg, basic)
-
- #########################################################################################
- # Scipy Windows Registry
- winclasses = [Filters.HanningWindow,
- Filters.TriangularWindow,
- Filters.BlackmanWindow,
- Filters.BlackmanHarrisWindow,
- Filters.ParzenWindow,
- Filters.HammingWindow,
- Filters.KaiserWindow,
- Filters.BartlettHannWindow,
- Filters.GaussianWindow,
- Filters.BoxcarWindow,
- Filters.BohmanWindow,
- Filters.BartlettWindow,
- Filters.NuttallBlackmanHarrisWindow]
-
- for cls in winclasses:
- cls.register(reg, basic)
-
- #########################################################################################
- # Scipy Signal Ensembles Registry
- ensembles = [EnsembleOrdering.OrderByIndexes,
- EnsembleOrdering.OrderByCorrelation,
- EnsembleOrdering.OrderByProgressiveCorrelation,
- EnsembleOrdering.ComputeDistance]
-
- for cls in ensembles:
- cls.register(reg, basic)
-
- #########################################################################################
- # NumSciPy Plotting Registry
- pl = [ArrayPlot.LinePlot,
- ArrayPlot.ScatterPlot,
- ArrayPlot.BarChart,
- ArrayPlot.Histogram,
- ArrayPlot.ArrayImage]
-
- for cls in pl:
- cls.register(reg, basic)
-
- clslst.extend(pl)
-
- #########################################################################################
- # Register all ports.
- for cls in clslst:
- cls.register_ports(reg, basic)
-
-def package_dependencies():
- import core.packagemanager
- manager = core.packagemanager.get_package_manager()
- if manager.has_package('edu.utah.sci.vistrails.vtk'):
- return ['edu.utah.sci.vistrails.vtk']
- else:
- return []
diff --git a/contrib/NumSciPy/smt.py b/contrib/NumSciPy/smt.py
deleted file mode 100644
index 590f313..0000000
--- a/contrib/NumSciPy/smt.py
+++ /dev/null
@@ -1,40 +0,0 @@
-import sys
-import numpy as npy
-from sine import sine_taper
-from st import st
-from math import sqrt
-
-def calcK(bw, N, srate):
- """Calculate K for a given bandwidth, length, and sampling rate.
- bw = 2p * fr, where fr = srate / N (frequency resolution).
- p specifies the half bandwidth in bins (fr units).
- K = 2p - 1"""
-
- K = int(bw * float(N) / srate + .5) - 1
- if K < 1: K = 1
- return K
-
-def calcbw(K, N, srate):
- """Calculate the bandwidth given K."""
-
- return float(K + 1) * srate / N
-
-# Precompute the tapers.
-
-def calc_tapers(K, N):
- return map(lambda k, N = N: sine_taper(k, N), npy.arange(K))
-
-# Multitaper Stockwell transform.
-
-def mtst(K, tapers, x, lo, hi):
- N = len(x)
- K2 = float(K * K)
- s = 0.
- n = 0.
- for k in range(K):
- X = st(tapers[k] * x, lo, hi)
- mu = 1. - k * k / K2
- s += mu * abs(X)**2
- n += mu
- s *= N / n
- return s
diff --git a/contrib/ParaView/PVBase.py b/contrib/ParaView/PVBase.py
deleted file mode 100644
index 315e4fc..0000000
--- a/contrib/ParaView/PVBase.py
+++ /dev/null
@@ -1,53 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-
-from paraview import servermanager
-import paraview.simple as pv
-
-def extract_pv_instances(paramList):
- newList = []
- for param in paramList:
- if hasattr(param, "pvInstance"):
- newList.append(param.pvInstance)
- else:
- newList.append(param)
- return newList
-
-class PVModule(Module):
- def __init__(self):
- Module.__init__(self)
- self.pvInstance = None
-
- def compute(self):
- if self.pvInstance:
- del self.pvInstance
- pv.SetActiveSource(None)
- if not self.pvInstance:
- if hasattr(self, "pvFunction"):
- self.pvInstance = self.pvFunction()
- else:
- self.pvInstance = getattr(pv, self.pvClass)()
-
- # We need to set input before other properties
- if self.inputPorts.has_key('Input'):
- inp = extract_pv_instances(self.forceGetInputListFromPort('Input'))[0]
- setattr(self.pvInstance, "Input", inp)
-
- for (function, connector_list) in self.inputPorts.iteritems():
- paramList = extract_pv_instances(self.forceGetInputListFromPort(function))
- if function != 'Input':
- if len(paramList) > 1:
- setattr(self.pvInstance, function, paramList)
- else:
- setattr(self.pvInstance, function, paramList[0])
-
- if hasattr(self.pvInstance, 'UpdatePipeline'):
- self.pvInstance.UpdatePipeline()
-
- self.setResult('Output', self)
-
-class _funcs_internals:
- "Internal class."
- rep_counter = 0
-
diff --git a/contrib/ParaView/__init__.py b/contrib/ParaView/__init__.py
deleted file mode 100644
index 06fc47d..0000000
--- a/contrib/ParaView/__init__.py
+++ /dev/null
@@ -1,22 +0,0 @@
-version = '0.0.1'
-name = 'ParaView'
-identifier = 'edu.utah.sci.eranders.ParaView'
-
-from configuration import configuration
-
-def package_dependencies():
- import core.packagemanager
- manager = core.packagemanager.get_package_manager()
- if manager.has_package('edu.utah.sci.vistrails.spreadsheet'):
- return ['edu.utah.sci.vistrails.spreadsheet']
- else:
- return []
-
-def package_requirements():
- import core.requirements
- if not core.requirements.python_module_exists('vtk'):
- raise core.requirements.MissingRequirement('vtk')
- if not core.requirements.python_module_exists('PyQt4'):
- print 'PyQt4 is not available. There will be no interaction',
- print 'between VTK and the spreadsheet.'
- import vtk
\ No newline at end of file
diff --git a/contrib/ParaView/configuration.py b/contrib/ParaView/configuration.py
deleted file mode 100644
index 963f4e2..0000000
--- a/contrib/ParaView/configuration.py
+++ /dev/null
@@ -1,7 +0,0 @@
-from core.configuration import ConfigurationObject
-
-configuration = ConfigurationObject(pvserver_bin=(None, str),
- mpiexec_bin=(None, str),
- start_server=False,
- num_proc=4,
- port=11111)
\ No newline at end of file
diff --git a/contrib/ParaView/contour.vt b/contrib/ParaView/contour.vt
deleted file mode 100644
index 31f0811..0000000
Binary files a/contrib/ParaView/contour.vt and /dev/null differ
diff --git a/contrib/ParaView/init.py b/contrib/ParaView/init.py
deleted file mode 100644
index d17d77d..0000000
--- a/contrib/ParaView/init.py
+++ /dev/null
@@ -1,185 +0,0 @@
-import paraview
-import paraview.simple
-import paraview.servermanager as sm
-import PVBase
-import core.modules
-import core.modules.module_registry
-from pvconfig import QPVConfigWindow
-from core.modules.vistrails_module import new_module, Module, ModuleError
-from core.modules.module_registry import (registry, add_module,
- has_input_port,
- add_input_port, add_output_port)
-from core.modules.source_configure import SourceConfigurationWidget
-from core.modules.python_source_configure import PythonEditor, PythonSourceConfigurationWidget
-from core.modules.basic_modules import PythonSource
-from configuration import configuration
-import urllib
-
-forbidden = ['AlltoN',
- 'Balance',
- 'CTHSurface',
- 'SelectionSourceBase']
-
-
-class ProgrammableFilterConfigurationWidget(SourceConfigurationWidget):
- def __init__(self, module, controller, parent=None):
- SourceConfigurationWidget.__init__(self, module, controller,
- PythonEditor, False, False, parent,
- portName='Script', encode=False)
-
-class PVServerPythonSourceConfigurationWidget(SourceConfigurationWidget):
- def __init__(self, module, controller, parent=None):
- SourceConfigurationWidget.__init__(self, module, controller,
- PythonEditor, True, False, parent,
- portName='Script', encode=False)
-
-class PVServerPythonSource(PVBase.PVModule):
-
- def compute(self):
- if self.pvInstance:
- del self.pvInstance
- paraview.simple.SetActiveSource(None)
- inputDefs = ''
- for k in self.inputPorts:
- if k=='Script':
- continue
- value = self.getInputFromPort(k)
- if type(value)==str:
- inputDefs += '%s = "%s"\n' % (k, value.replace('"', '\\"'))
- elif type(value)==int:
- inputDefs += '%s = %s\n' % (k, value)
- prefix = """
-import paraview.servermanager as sm
-import paraview.vtk.dataset_adapter as DA
-proc = sm.vtkProcessModule.GetProcessModule()
-nPartitions = proc.GetNumberOfLocalPartitions()
-partitionId = proc.GetPartitionId()
-result = ''
-"""
- source = self.forceGetInputFromPort('Script', '')
- suffix = """
-if len(result)>0:
- import vtk
- dataImporter = vtk.vtkImageImport()
- dataImporter.CopyImportVoidPointer(result, len(result))
- dataImporter.SetDataScalarTypeToUnsignedChar()
- dataImporter.SetNumberOfScalarComponents(1)
- dataImporter.SetDataExtent(0, len(result)-1, 0, 0, 0, 0)
- dataImporter.SetWholeExtent(0, len(result)-1, 0, 0, 0, 0)
- dataImporter.Update()
- self.GetOutputDataObject(0).DeepCopy(dataImporter.GetOutput())
-"""
- self.pvInstance = paraview.simple.ProgrammableFilter()
- self.pvInstance.OutputDataSetType = 'vtkImageData'
- self.pvInstance.Script = inputDefs + prefix + source + suffix
- self.pvInstance.UpdatePipeline()
-
- self.setResult('Output', self)
-
-
-class PVClientFetch(PythonSource):
-
- def compute(self):
- prefix = """
-import paraview.servermanager as sm
-import paraview.vtk.dataset_adapter as DA
-proc = sm.vtkProcessModule.GetProcessModule()
-nPartitions = proc.GetNumberOfPartitions(sm.ActiveConnection.ID)
-module = self.getInputFromPort('ServerModule')
-results = []
-for i in xrange(nPartitions):
- data = sm.Fetch(module.pvInstance, i)
- if data==None or data.GetPointData().GetNumberOfArrays()==0:
- continue
- narray = DA.numpy_support.vtk_to_numpy(data.GetPointData().GetArray(0))
- result = narray.tostring()
- results.append(result)
-"""
- s = urllib.unquote(str(self.forceGetInputFromPort('source', '')))
- self.run_code(prefix + s, use_input=True, use_output=True)
-
-
-def add_paraview_module(name, proxy, module_type, ns, hide=False, pvFunction=None):
-
- mod = new_module(module_type, name)
- mod.pvSpace = ns.lower()
- mod.pvClass = name
- if pvFunction != None:
- mod.pvFunction = pvFunction
- if name=='ProgrammableFilter':
- add_module(mod, name = name, namespace=ns, configureWidgetType=ProgrammableFilterConfigurationWidget)
- else:
- add_module(mod, name = name, namespace=ns)
-
- for prop in proxy.ListProperties():
- optional = False
- if hide and prop != "Input":
- optional = True
- p = proxy.GetProperty(prop)
- if isinstance(p, sm.ProxyProperty):
- add_input_port(mod, prop, PVBase.PVModule, optional)
- continue
- if isinstance(p, sm.EnumerationProperty):
- add_input_port(mod, prop, core.modules.basic_modules.String, optional)
- continue
- if isinstance(p, sm.VectorProperty):
- params = []
- typ = None
- if p.IsA("vtkSMDoubleVectorProperty"):
- typ = core.modules.basic_modules.Float
- elif p.IsA("vtkSMIntVectorProperty"):
- typ = core.modules.basic_modules.Integer
- elif p.IsA("vtkSMStringVectorProperty"):
- typ = core.modules.basic_modules.String
- elif p.IsA("vtkSMIdTypeVectorProperty"):
- typ = core.modules.basic_modules.Integer
- nel = len(p)
- if nel > 0:
- for i in range(nel):
- params.append(typ)
- else:
- params.append(typ)
- add_input_port(mod, prop, params, optional)
-
- add_output_port(mod, "Output", module_type)
-
-def initialize(*args, **keywords):
- reg = core.modules.module_registry
- basic = core.modules.basic_modules
- add_module(PVBase.PVModule, namespace='base')
- mod_dict = {}
-
- mlist = [("Sources", sm.sources), ("Filters", sm.filters),
- ("Animation", sm.animation), ("Writers", sm.writers)]
- for ns, m in mlist:
- dt = m.__dict__
- for key in dt.keys():
- if forbidden.__contains__(key):
- continue
- if key.__contains__('Base'):
- continue
- cl = dt[key]
- if not isinstance(cl, str):
- if paraview.simple._func_name_valid(key):
- add_paraview_module(key, m.__dict__[key](no_update=True), PVBase.PVModule, ns)
-
-
- add_paraview_module("GeometryRepresentation", sm.rendering.GeometryRepresentation(no_update=True), PVBase.PVModule, "Rendering", True, sm.rendering.GeometryRepresentation)
- add_paraview_module("PVLookupTable", sm.rendering.PVLookupTable(no_update=True), PVBase.PVModule, "Rendering", False, sm.rendering.PVLookupTable)
- add_paraview_module("ScalarBarWidgetRepresentation", sm.rendering.ScalarBarWidgetRepresentation(no_update=True), PVBase.PVModule, "Rendering", True, sm.rendering.ScalarBarWidgetRepresentation)
- add_module(PVServerPythonSource, name = "PVServerPythonSource", configureWidgetType=PVServerPythonSourceConfigurationWidget)
- add_input_port(PVServerPythonSource, "Script", (core.modules.basic_modules.String, ""), True)
- add_output_port(PVServerPythonSource, "self", PVServerPythonSource)
- add_module(PVClientFetch, name = "PVClientFetch", configureWidgetType=PythonSourceConfigurationWidget)
- add_input_port(PVClientFetch, "ServerModule", (PVServerPythonSource, ""))
- add_input_port(PVClientFetch, "source", (core.modules.basic_modules.String, ""))
-
- import pvcell
- pvcell.registerSelf()
-
- global pvConfigWindow
- pvConfigWindow = QPVConfigWindow(proc_num=configuration.num_proc,
- port=configuration.port)
- pvConfigWindow.show()
- if configuration.start_server == True:
- pvConfigWindow.togglePVServer()
\ No newline at end of file
diff --git a/contrib/ParaView/pv.vt b/contrib/ParaView/pv.vt
deleted file mode 100644
index 34d152b..0000000
Binary files a/contrib/ParaView/pv.vt and /dev/null differ
diff --git a/contrib/ParaView/pvcell.py b/contrib/ParaView/pvcell.py
deleted file mode 100644
index 3967630..0000000
--- a/contrib/ParaView/pvcell.py
+++ /dev/null
@@ -1,83 +0,0 @@
-from PyQt4 import QtCore
-from core.modules.module_registry import get_module_registry
-from packages.vtk.vtkcell import QVTKWidget
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-from packages.spreadsheet.spreadsheet_cell import QCellWidget
-from PVBase import PVModule
-import paraview.simple as pvsp
-import paraview.pvfilters
-import vtk
-
-class PVCell(SpreadsheetCell):
- def __init__(self):
- SpreadsheetCell.__init__(self)
- self.cellWidget = None
-
- def compute(self):
- """ compute() -> None
- Dispatch the vtkRenderer to the actual rendering widget
- """
- proxies = self.forceGetInputListFromPort('Proxy')
- self.cellWidget = self.displayAndWait(QParaViewWidget, (proxies,))
-
-class QParaViewWidget(QVTKWidget):
-
- def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
- QVTKWidget.__init__(self, parent, f)
- self.view = None
-
- def updateContents(self, inputPorts):
-
- if self.view==None:
- self.view = pvsp.CreateRenderView()
- renWin = self.view.GetRenderWindow()
- self.SetRenderWindow(renWin)
- iren = renWin.GetInteractor()
- print type(iren)
- iren.SetNonInteractiveRenderDelay(0)
- iren.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
-
- (representations, ) = inputPorts
- self.view.Representations = []
- for r in representations:
- self.view.Representations.append(r.pvInstance)
-
- self.view.ResetCamera()
- self.view.StillRender()
-
- QCellWidget.updateContents(self, inputPorts)
-
- def saveToPNG(self, filename):
- """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
-
- Save the current widget contents to an image file. If
- str==None, then it returns the vtkUnsignedCharArray containing
- the PNG image. Otherwise, the filename is returned.
-
- """
- image = self.view.CaptureWindow(1)
- image.UnRegister(None)
-
- writer = vtk.vtkPNGWriter()
- writer.SetInput(image)
- if filename!=None:
- writer.SetFileName(filename)
- else:
- writer.WriteToMemoryOn()
- writer.Write()
- if filename:
- return filename
- else:
- return writer.GetResult()
-
- def deleteLater(self):
- QCellWidget.deleteLater(self)
-
-
-
-def registerSelf():
- registry = get_module_registry()
- registry.add_module(PVCell)
- registry.add_input_port(PVCell, "Location", CellLocation)
- registry.add_input_port(PVCell, "Proxy", PVModule)
- registry.add_output_port(PVCell, "self", PVCell)
diff --git a/contrib/ParaView/pvconfig.py b/contrib/ParaView/pvconfig.py
deleted file mode 100644
index 2da11b7..0000000
--- a/contrib/ParaView/pvconfig.py
+++ /dev/null
@@ -1,89 +0,0 @@
-from PyQt4 import QtCore, QtGui
-import sys
-import paraview.simple as pv
-from configuration import configuration
-
-class QPVConfigWindow(QtGui.QWidget):
-
- def __init__(self, proc_num=4, port=11111, parent=None):
- QtGui.QWidget.__init__(self, parent)
- self.setWindowTitle('ParaView Local Server')
- vbox = QtGui.QVBoxLayout()
- self.setLayout(vbox)
-
- hbox = QtGui.QHBoxLayout()
- vbox.addLayout(hbox)
-
- hbox.addWidget(QtGui.QLabel('# Procs'))
- self.procSpin = QtGui.QSpinBox()
- self.procSpin.setRange(1, 1024*1024)
- self.procSpin.setValue(proc_num)
- hbox.addWidget(self.procSpin)
-
- hbox.addWidget(QtGui.QLabel('Port'))
- self.portSpin = QtGui.QSpinBox()
- self.portSpin.setRange(0, 64*1024)
- self.portSpin.setValue(port)
- hbox.addWidget(self.portSpin)
-
- hbox.addStretch()
-
- self.cmdOut = QtGui.QTextEdit()
- self.cmdOut.setReadOnly(True)
- vbox.addWidget(self.cmdOut)
-
- self.runButton = QtGui.QPushButton('Start')
- vbox.addWidget(self.runButton)
-
- self.pvProcess = QtCore.QProcess()
- self.pvProcess.setProcessChannelMode(QtCore.QProcess.MergedChannels)
- self.connect(self.pvProcess, QtCore.SIGNAL('readyReadStandardOutput()'), self.updateLogs)
- self.connect(self.pvProcess, QtCore.SIGNAL('error()'), self.updateError)
- self.connect(self.pvProcess, QtCore.SIGNAL('finished(int,QProcess::ExitStatus)'), self.pvServerFinished)
-
- self.connect(self.runButton, QtCore.SIGNAL('clicked()'), self.togglePVServer)
-
- def buildArguments(self):
- #defaults
- mpiexec_bin = '/usr/bin/mpiexec'
- pvserver_bin = '/usr/local/bin/pvserver'
-
- if configuration.check('mpiexec_bin'):
- mpiexec_bin = configuration.mpiexec_bin
- if configuration.check("pvserver_bin"):
- pvserver_bin = configuration.pvserver_bin
-
- return (mpiexec_bin, ['-n', str(self.procSpin.value()), pvserver_bin, '--server-port=%s' % self.portSpin.value()])
-
- def sizeHint(self):
- return QtCore.QSize(384, 512)
-
- def togglePVServer(self):
- if self.pvProcess.state()==QtCore.QProcess.NotRunning:
- self.runButton.setEnabled(False)
- self.cmdOut.append('Starting...\n')
- self.pvProcess.start(*self.buildArguments())
- self.pvProcess.waitForStarted()
- if self.pvProcess.state()==QtCore.QProcess.Running:
- self.runButton.setText('Stop')
- pv.Connect('localhost', self.portSpin.value())
- self.runButton.setEnabled(True)
- else:
- self.pvProcess.terminate()
- self.pvProcess.waitForFinished()
-
- def updateLogs(self):
- self.cmdOut.append(QtCore.QString(self.pvProcess.readAllStandardOutput()))
-
- def updateError(self, error):
- self.cmdOut.append('ERROR %s\n' % error)
-
- def pvServerFinished(self, exitCode, exitStatus):
- self.cmdOut.append('Exited\n')
- self.runButton.setText('Start')
-
-if __name__=='__main__':
- app = QtGui.QApplication(sys.argv)
- window = QPVConfigWindow()
- window.show()
- app.exec_()
diff --git a/contrib/SCIRun/__init__.py b/contrib/SCIRun/__init__.py
deleted file mode 100644
index 27cd2cb..0000000
--- a/contrib/SCIRun/__init__.py
+++ /dev/null
@@ -1,9001 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-# This file was generated using vistrail_converter.py
-
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from core.modules.basic_modules import Constant
-import sr_py
-import os
-import time
-
-
-version = "0.9.1"
-identifier = "edu.utah.sci.vistrails.scirun"
-name = "SCIRun"
-
-class Time(Constant):
- def compute(self):
- pass
-
-class Converters(Constant):
- def compute(self):
- pass
-
-class Texture(Constant):
- def compute(self):
- pass
-
-class Visualization(Constant):
- def compute(self):
- pass
-
-class MiscField(Constant):
- def compute(self):
- pass
-
-class DataArrayMath(Constant):
- def compute(self):
- pass
-
-class Math(Constant):
- def compute(self):
- pass
-
-class ChangeMesh(Constant):
- def compute(self):
- pass
-
-class ChangeFieldData(Constant):
- def compute(self):
- pass
-
-class Geometry(Constant):
- def compute(self):
- pass
-
-class NewField(Constant):
- def compute(self):
- pass
-
-class ColorMap(Constant):
- def compute(self):
- pass
-
-class Field(Constant):
- def compute(self):
- pass
-
-class Nrrd(Constant):
- def compute(self):
- pass
-
-class Matrix(Constant):
- def compute(self):
- pass
-
-class ColorMap2(Constant):
- def compute(self):
- pass
-
-class Path(Constant):
- def compute(self):
- pass
-
-class String(Constant):
- def compute(self):
- pass
-
-class Bundle(Constant):
- def compute(self):
- pass
-
-class DataIO(Constant):
- def compute(self):
- pass
-
-class WriteBundle(DataIO) :
- def compute(self) :
- p = sr_py.WriteBundleAlg()
- if self.hasInputFromPort('p_filetype') :
- p.set_p_filetype(self.getInputFromPort('p_filetype'))
- if self.hasInputFromPort('p_confirm') :
- p.set_p_confirm(self.getInputFromPort('p_confirm'))
- if self.hasInputFromPort('p_confirm_once') :
- p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(bundle, Filename)
-
-class WritePath(DataIO) :
- def compute(self) :
- p = sr_py.WritePathAlg()
- if self.hasInputFromPort('p_filetype') :
- p.set_p_filetype(self.getInputFromPort('p_filetype'))
- if self.hasInputFromPort('p_confirm') :
- p.set_p_confirm(self.getInputFromPort('p_confirm'))
- if self.hasInputFromPort('p_confirm_once') :
- p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
- Input_Data = 0
- if self.hasInputFromPort('Input Data') :
- Input_Data = self.getInputFromPort('Input Data')
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Input_Data, Filename)
-
-class WriteColorMap2D(DataIO) :
- def compute(self) :
- p = sr_py.WriteColorMap2DAlg()
- if self.hasInputFromPort('p_filetype') :
- p.set_p_filetype(self.getInputFromPort('p_filetype'))
- if self.hasInputFromPort('p_confirm') :
- p.set_p_confirm(self.getInputFromPort('p_confirm'))
- if self.hasInputFromPort('p_confirm_once') :
- p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
- if self.hasInputFromPort('p_exporttype') :
- p.set_p_exporttype(self.getInputFromPort('p_exporttype'))
- Input_Data = 0
- if self.hasInputFromPort('Input Data') :
- Input_Data = self.getInputFromPort('Input Data')
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Input_Data, Filename)
-
-class ReadHDF5File(DataIO) :
- def compute(self) :
- p = sr_py.ReadHDF5FileAlg()
- if self.hasInputFromPort('p_have_HDF5') :
- p.set_p_have_HDF5(self.getInputFromPort('p_have_HDF5'))
- if self.hasInputFromPort('p_power_app') :
- p.set_p_power_app(self.getInputFromPort('p_power_app'))
- if self.hasInputFromPort('p_datasets') :
- p.set_p_datasets(self.getInputFromPort('p_datasets'))
- if self.hasInputFromPort('p_dumpname') :
- p.set_p_dumpname(self.getInputFromPort('p_dumpname'))
- if self.hasInputFromPort('p_ports') :
- p.set_p_ports(self.getInputFromPort('p_ports'))
- if self.hasInputFromPort('p_ndims') :
- p.set_p_ndims(self.getInputFromPort('p_ndims'))
- if self.hasInputFromPort('p_mergeData') :
- p.set_p_mergeData(self.getInputFromPort('p_mergeData'))
- if self.hasInputFromPort('p_assumeSVT') :
- p.set_p_assumeSVT(self.getInputFromPort('p_assumeSVT'))
- if self.hasInputFromPort('p_animate') :
- p.set_p_animate(self.getInputFromPort('p_animate'))
- if self.hasInputFromPort('p_animate_tab') :
- p.set_p_animate_tab(self.getInputFromPort('p_animate_tab'))
- if self.hasInputFromPort('p_basic_tab') :
- p.set_p_basic_tab(self.getInputFromPort('p_basic_tab'))
- if self.hasInputFromPort('p_extended_tab') :
- p.set_p_extended_tab(self.getInputFromPort('p_extended_tab'))
- if self.hasInputFromPort('p_playmode_tab') :
- p.set_p_playmode_tab(self.getInputFromPort('p_playmode_tab'))
- if self.hasInputFromPort('p_selectable_min') :
- p.set_p_selectable_min(self.getInputFromPort('p_selectable_min'))
- if self.hasInputFromPort('p_selectable_max') :
- p.set_p_selectable_max(self.getInputFromPort('p_selectable_max'))
- if self.hasInputFromPort('p_selectable_inc') :
- p.set_p_selectable_inc(self.getInputFromPort('p_selectable_inc'))
- if self.hasInputFromPort('p_range_min') :
- p.set_p_range_min(self.getInputFromPort('p_range_min'))
- if self.hasInputFromPort('p_range_max') :
- p.set_p_range_max(self.getInputFromPort('p_range_max'))
- if self.hasInputFromPort('p_playmode') :
- p.set_p_playmode(self.getInputFromPort('p_playmode'))
- if self.hasInputFromPort('p_current') :
- p.set_p_current(self.getInputFromPort('p_current'))
- if self.hasInputFromPort('p_execmode') :
- p.set_p_execmode(self.getInputFromPort('p_execmode'))
- if self.hasInputFromPort('p_delay') :
- p.set_p_delay(self.getInputFromPort('p_delay'))
- if self.hasInputFromPort('p_inc_amount') :
- p.set_p_inc_amount(self.getInputFromPort('p_inc_amount'))
- if self.hasInputFromPort('p_update_type') :
- p.set_p_update_type(self.getInputFromPort('p_update_type'))
- if self.hasInputFromPort('p_have_group') :
- p.set_p_have_group(self.getInputFromPort('p_have_group'))
- if self.hasInputFromPort('p_have_attributes') :
- p.set_p_have_attributes(self.getInputFromPort('p_have_attributes'))
- if self.hasInputFromPort('p_have_datasets') :
- p.set_p_have_datasets(self.getInputFromPort('p_have_datasets'))
- if self.hasInputFromPort('p_continuous') :
- p.set_p_continuous(self.getInputFromPort('p_continuous'))
- if self.hasInputFromPort('p_selectionString') :
- p.set_p_selectionString(self.getInputFromPort('p_selectionString'))
- if self.hasInputFromPort('p_regexp') :
- p.set_p_regexp(self.getInputFromPort('p_regexp'))
- if self.hasInputFromPort('p_allow_selection') :
- p.set_p_allow_selection(self.getInputFromPort('p_allow_selection'))
- if self.hasInputFromPort('p_read_error') :
- p.set_p_read_error(self.getInputFromPort('p_read_error'))
- if self.hasInputFromPort('p_max_dims') :
- p.set_p_max_dims(self.getInputFromPort('p_max_dims'))
- if self.hasInputFromPort('p_0_dim') :
- p.set_p_0_dim(self.getInputFromPort('p_0_dim'))
- if self.hasInputFromPort('p_0_start') :
- p.set_p_0_start(self.getInputFromPort('p_0_start'))
- if self.hasInputFromPort('p_0_start2') :
- p.set_p_0_start2(self.getInputFromPort('p_0_start2'))
- if self.hasInputFromPort('p_0_count') :
- p.set_p_0_count(self.getInputFromPort('p_0_count'))
- if self.hasInputFromPort('p_0_count2') :
- p.set_p_0_count2(self.getInputFromPort('p_0_count2'))
- if self.hasInputFromPort('p_0_stride') :
- p.set_p_0_stride(self.getInputFromPort('p_0_stride'))
- if self.hasInputFromPort('p_0_stride2') :
- p.set_p_0_stride2(self.getInputFromPort('p_0_stride2'))
- if self.hasInputFromPort('p_1_dim') :
- p.set_p_1_dim(self.getInputFromPort('p_1_dim'))
- if self.hasInputFromPort('p_1_start') :
- p.set_p_1_start(self.getInputFromPort('p_1_start'))
- if self.hasInputFromPort('p_1_start2') :
- p.set_p_1_start2(self.getInputFromPort('p_1_start2'))
- if self.hasInputFromPort('p_1_count') :
- p.set_p_1_count(self.getInputFromPort('p_1_count'))
- if self.hasInputFromPort('p_1_count2') :
- p.set_p_1_count2(self.getInputFromPort('p_1_count2'))
- if self.hasInputFromPort('p_1_stride') :
- p.set_p_1_stride(self.getInputFromPort('p_1_stride'))
- if self.hasInputFromPort('p_1_stride2') :
- p.set_p_1_stride2(self.getInputFromPort('p_1_stride2'))
- if self.hasInputFromPort('p_2_dim') :
- p.set_p_2_dim(self.getInputFromPort('p_2_dim'))
- if self.hasInputFromPort('p_2_start') :
- p.set_p_2_start(self.getInputFromPort('p_2_start'))
- if self.hasInputFromPort('p_2_start2') :
- p.set_p_2_start2(self.getInputFromPort('p_2_start2'))
- if self.hasInputFromPort('p_2_count') :
- p.set_p_2_count(self.getInputFromPort('p_2_count'))
- if self.hasInputFromPort('p_2_count2') :
- p.set_p_2_count2(self.getInputFromPort('p_2_count2'))
- if self.hasInputFromPort('p_2_stride') :
- p.set_p_2_stride(self.getInputFromPort('p_2_stride'))
- if self.hasInputFromPort('p_2_stride2') :
- p.set_p_2_stride2(self.getInputFromPort('p_2_stride2'))
- if self.hasInputFromPort('p_3_dim') :
- p.set_p_3_dim(self.getInputFromPort('p_3_dim'))
- if self.hasInputFromPort('p_3_start') :
- p.set_p_3_start(self.getInputFromPort('p_3_start'))
- if self.hasInputFromPort('p_3_start2') :
- p.set_p_3_start2(self.getInputFromPort('p_3_start2'))
- if self.hasInputFromPort('p_3_count') :
- p.set_p_3_count(self.getInputFromPort('p_3_count'))
- if self.hasInputFromPort('p_3_count2') :
- p.set_p_3_count2(self.getInputFromPort('p_3_count2'))
- if self.hasInputFromPort('p_3_stride') :
- p.set_p_3_stride(self.getInputFromPort('p_3_stride'))
- if self.hasInputFromPort('p_3_stride2') :
- p.set_p_3_stride2(self.getInputFromPort('p_3_stride2'))
- if self.hasInputFromPort('p_4_dim') :
- p.set_p_4_dim(self.getInputFromPort('p_4_dim'))
- if self.hasInputFromPort('p_4_start') :
- p.set_p_4_start(self.getInputFromPort('p_4_start'))
- if self.hasInputFromPort('p_4_start2') :
- p.set_p_4_start2(self.getInputFromPort('p_4_start2'))
- if self.hasInputFromPort('p_4_count') :
- p.set_p_4_count(self.getInputFromPort('p_4_count'))
- if self.hasInputFromPort('p_4_count2') :
- p.set_p_4_count2(self.getInputFromPort('p_4_count2'))
- if self.hasInputFromPort('p_4_stride') :
- p.set_p_4_stride(self.getInputFromPort('p_4_stride'))
- if self.hasInputFromPort('p_4_stride2') :
- p.set_p_4_stride2(self.getInputFromPort('p_4_stride2'))
- if self.hasInputFromPort('p_5_dim') :
- p.set_p_5_dim(self.getInputFromPort('p_5_dim'))
- if self.hasInputFromPort('p_5_start') :
- p.set_p_5_start(self.getInputFromPort('p_5_start'))
- if self.hasInputFromPort('p_5_start2') :
- p.set_p_5_start2(self.getInputFromPort('p_5_start2'))
- if self.hasInputFromPort('p_5_count') :
- p.set_p_5_count(self.getInputFromPort('p_5_count'))
- if self.hasInputFromPort('p_5_count2') :
- p.set_p_5_count2(self.getInputFromPort('p_5_count2'))
- if self.hasInputFromPort('p_5_stride') :
- p.set_p_5_stride(self.getInputFromPort('p_5_stride'))
- if self.hasInputFromPort('p_5_stride2') :
- p.set_p_5_stride2(self.getInputFromPort('p_5_stride2'))
- Full_filename = ''
- if self.hasInputFromPort('Full filename') :
- Full_filename = self.getInputFromPort('Full filename')
- Current_Index = 0
- if self.hasInputFromPort('Current Index') :
- Current_Index = self.getInputFromPort('Current Index')
- results = p.execute(Full_filename, Current_Index)
- self.setResult('Output 0 Nrrd', results[0])
- self.setResult('Output 1 Nrrd', results[1])
- self.setResult('Output 2 Nrrd', results[2])
- self.setResult('Output 3 Nrrd', results[3])
- self.setResult('Output 4 Nrrd', results[4])
- self.setResult('Output 5 Nrrd', results[5])
- self.setResult('Output 6 Nrrd', results[6])
- self.setResult('Output 7 Nrrd', results[7])
- self.setResult('Selected Index', results[8])
-
-class ReadField(DataIO) :
- def compute(self) :
- p = sr_py.ReadFieldAlg()
- if self.hasInputFromPort('p_from_env') :
- p.set_p_from_env(self.getInputFromPort('p_from_env'))
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Filename)
- self.setResult('Output Data', results[0])
- self.setResult('Filename', results[1])
-
-class WriteColorMap(DataIO) :
- def compute(self) :
- p = sr_py.WriteColorMapAlg()
- if self.hasInputFromPort('p_filetype') :
- p.set_p_filetype(self.getInputFromPort('p_filetype'))
- if self.hasInputFromPort('p_confirm') :
- p.set_p_confirm(self.getInputFromPort('p_confirm'))
- if self.hasInputFromPort('p_confirm_once') :
- p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
- if self.hasInputFromPort('p_exporttype') :
- p.set_p_exporttype(self.getInputFromPort('p_exporttype'))
- Input_Data = 0
- if self.hasInputFromPort('Input Data') :
- Input_Data = self.getInputFromPort('Input Data')
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Input_Data, Filename)
-
-class ReadColorMap2D(DataIO) :
- def compute(self) :
- p = sr_py.ReadColorMap2DAlg()
- if self.hasInputFromPort('p_from_env') :
- p.set_p_from_env(self.getInputFromPort('p_from_env'))
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Filename)
- self.setResult('Output Data', results[0])
- self.setResult('Filename', results[1])
-
-class ReadString(DataIO) :
- def compute(self) :
- p = sr_py.ReadStringAlg()
- if self.hasInputFromPort('p_from_env') :
- p.set_p_from_env(self.getInputFromPort('p_from_env'))
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Filename)
- self.setResult('Output Data', results[0])
- self.setResult('Filename', results[1])
-
-class ReadColorMap(DataIO) :
- def compute(self) :
- p = sr_py.ReadColorMapAlg()
- if self.hasInputFromPort('p_from_env') :
- p.set_p_from_env(self.getInputFromPort('p_from_env'))
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Filename)
- self.setResult('Output Data', results[0])
- self.setResult('Filename', results[1])
-
-class ReadMatrix(DataIO) :
- def compute(self) :
- p = sr_py.ReadMatrixAlg()
- if self.hasInputFromPort('p_from_env') :
- p.set_p_from_env(self.getInputFromPort('p_from_env'))
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Filename)
- self.setResult('Output Data', results[0])
- self.setResult('Filename', results[1])
-
-class WriteString(DataIO) :
- def compute(self) :
- p = sr_py.WriteStringAlg()
- if self.hasInputFromPort('p_filetype') :
- p.set_p_filetype(self.getInputFromPort('p_filetype'))
- if self.hasInputFromPort('p_confirm') :
- p.set_p_confirm(self.getInputFromPort('p_confirm'))
- if self.hasInputFromPort('p_confirm_once') :
- p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
- String = ''
- if self.hasInputFromPort('String') :
- String = self.getInputFromPort('String')
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(String, Filename)
-
-class ReadPath(DataIO) :
- def compute(self) :
- p = sr_py.ReadPathAlg()
- if self.hasInputFromPort('p_from_env') :
- p.set_p_from_env(self.getInputFromPort('p_from_env'))
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Filename)
- self.setResult('Output Data', results[0])
- self.setResult('Filename', results[1])
-
-class WriteField(DataIO) :
- def compute(self) :
- p = sr_py.WriteFieldAlg()
- if self.hasInputFromPort('p_filetype') :
- p.set_p_filetype(self.getInputFromPort('p_filetype'))
- if self.hasInputFromPort('p_confirm') :
- p.set_p_confirm(self.getInputFromPort('p_confirm'))
- if self.hasInputFromPort('p_confirm_once') :
- p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
- if self.hasInputFromPort('p_exporttype') :
- p.set_p_exporttype(self.getInputFromPort('p_exporttype'))
- if self.hasInputFromPort('p_increment') :
- p.set_p_increment(self.getInputFromPort('p_increment'))
- if self.hasInputFromPort('p_current') :
- p.set_p_current(self.getInputFromPort('p_current'))
- Input_Data = 0
- if self.hasInputFromPort('Input Data') :
- Input_Data = self.getInputFromPort('Input Data')
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Input_Data, Filename)
-
-class ReadBundle(DataIO) :
- def compute(self) :
- p = sr_py.ReadBundleAlg()
- if self.hasInputFromPort('p_from_env') :
- p.set_p_from_env(self.getInputFromPort('p_from_env'))
- if self.hasInputFromPort('p_types') :
- p.set_p_types(self.getInputFromPort('p_types'))
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Filename)
- self.setResult('bundle', results[0])
- self.setResult('Filename', results[1])
-
-class StreamMatrixFromDisk(DataIO) :
- def compute(self) :
- p = sr_py.StreamMatrixFromDiskAlg()
- if self.hasInputFromPort('p_row_or_col') :
- p.set_p_row_or_col(self.getInputFromPort('p_row_or_col'))
- if self.hasInputFromPort('p_slider_min') :
- p.set_p_slider_min(self.getInputFromPort('p_slider_min'))
- if self.hasInputFromPort('p_slider_max') :
- p.set_p_slider_max(self.getInputFromPort('p_slider_max'))
- if self.hasInputFromPort('p_range_min') :
- p.set_p_range_min(self.getInputFromPort('p_range_min'))
- if self.hasInputFromPort('p_range_max') :
- p.set_p_range_max(self.getInputFromPort('p_range_max'))
- if self.hasInputFromPort('p_playmode') :
- p.set_p_playmode(self.getInputFromPort('p_playmode'))
- if self.hasInputFromPort('p_current') :
- p.set_p_current(self.getInputFromPort('p_current'))
- if self.hasInputFromPort('p_execmode') :
- p.set_p_execmode(self.getInputFromPort('p_execmode'))
- if self.hasInputFromPort('p_delay') :
- p.set_p_delay(self.getInputFromPort('p_delay'))
- if self.hasInputFromPort('p_inc_amount') :
- p.set_p_inc_amount(self.getInputFromPort('p_inc_amount'))
- if self.hasInputFromPort('p_send_amount') :
- p.set_p_send_amount(self.getInputFromPort('p_send_amount'))
- Indices = 0
- if self.hasInputFromPort('Indices') :
- Indices = self.getInputFromPort('Indices')
- Weights = 0
- if self.hasInputFromPort('Weights') :
- Weights = self.getInputFromPort('Weights')
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Indices, Weights, Filename)
- self.setResult('DataVector', results[0])
- self.setResult('Index', results[1])
- self.setResult('Scaled Index', results[2])
- self.setResult('Filename', results[3])
-
-class WriteMatrix(DataIO) :
- def compute(self) :
- p = sr_py.WriteMatrixAlg()
- if self.hasInputFromPort('p_filetype') :
- p.set_p_filetype(self.getInputFromPort('p_filetype'))
- if self.hasInputFromPort('p_confirm') :
- p.set_p_confirm(self.getInputFromPort('p_confirm'))
- if self.hasInputFromPort('p_confirm_once') :
- p.set_p_confirm_once(self.getInputFromPort('p_confirm_once'))
- if self.hasInputFromPort('p_exporttype') :
- p.set_p_exporttype(self.getInputFromPort('p_exporttype'))
- if self.hasInputFromPort('p_split') :
- p.set_p_split(self.getInputFromPort('p_split'))
- Input_Data = 0
- if self.hasInputFromPort('Input Data') :
- Input_Data = self.getInputFromPort('Input Data')
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Input_Data, Filename)
-
-class ReadNrrd(DataIO) :
- def compute(self) :
- p = sr_py.ReadNrrdAlg()
- if self.hasInputFromPort('p_from_env') :
- p.set_p_from_env(self.getInputFromPort('p_from_env'))
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Filename)
- self.setResult('Output Data', results[0])
- self.setResult('Filename', results[1])
-
-class JoinFields(NewField) :
- def compute(self) :
- p = sr_py.JoinFieldsAlg()
- if self.hasInputFromPort('p_tolerance') :
- p.set_p_tolerance(self.getInputFromPort('p_tolerance'))
- if self.hasInputFromPort('p_force_nodemerge') :
- p.set_p_force_nodemerge(self.getInputFromPort('p_force_nodemerge'))
- if self.hasInputFromPort('p_force_pointcloud') :
- p.set_p_force_pointcloud(self.getInputFromPort('p_force_pointcloud'))
- if self.hasInputFromPort('p_matchval') :
- p.set_p_matchval(self.getInputFromPort('p_matchval'))
- if self.hasInputFromPort('p_meshonly') :
- p.set_p_meshonly(self.getInputFromPort('p_meshonly'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('Output Field', results)
-
-class RefineMeshByIsovalue(NewField) :
- def compute(self) :
- p = sr_py.RefineMeshByIsovalueAlg()
- if self.hasInputFromPort('p_isoval') :
- p.set_p_isoval(self.getInputFromPort('p_isoval'))
- if self.hasInputFromPort('p_lte') :
- p.set_p_lte(self.getInputFromPort('p_lte'))
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- Optional_Isovalue = 0
- if self.hasInputFromPort('Optional Isovalue') :
- Optional_Isovalue = self.getInputFromPort('Optional Isovalue')
- results = p.execute(Input, Optional_Isovalue)
- self.setResult('Refined', results[0])
- self.setResult('Mapping', results[1])
-
-class FairMesh(NewField) :
- def compute(self) :
- p = sr_py.FairMeshAlg()
- if self.hasInputFromPort('p_iterations') :
- p.set_p_iterations(self.getInputFromPort('p_iterations'))
- if self.hasInputFromPort('p_method') :
- p.set_p_method(self.getInputFromPort('p_method'))
- Input_Mesh = 0
- if self.hasInputFromPort('Input Mesh') :
- Input_Mesh = self.getInputFromPort('Input Mesh')
- results = p.execute(Input_Mesh)
- self.setResult('Faired Mesh', results)
-
-class CreateStructHex(NewField) :
- def compute(self) :
- p = sr_py.CreateStructHexAlg()
- if self.hasInputFromPort('p_sizex') :
- p.set_p_sizex(self.getInputFromPort('p_sizex'))
- if self.hasInputFromPort('p_sizey') :
- p.set_p_sizey(self.getInputFromPort('p_sizey'))
- if self.hasInputFromPort('p_sizez') :
- p.set_p_sizez(self.getInputFromPort('p_sizez'))
- if self.hasInputFromPort('p_padpercent') :
- p.set_p_padpercent(self.getInputFromPort('p_padpercent'))
- if self.hasInputFromPort('p_data_at') :
- p.set_p_data_at(self.getInputFromPort('p_data_at'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Sample Field', results)
-
-class ClipLatVolByIndicesOrWidget(NewField) :
- def compute(self) :
- p = sr_py.ClipLatVolByIndicesOrWidgetAlg()
- if self.hasInputFromPort('p_use_text_bbox') :
- p.set_p_use_text_bbox(self.getInputFromPort('p_use_text_bbox'))
- if self.hasInputFromPort('p_text_min_x') :
- p.set_p_text_min_x(self.getInputFromPort('p_text_min_x'))
- if self.hasInputFromPort('p_text_min_y') :
- p.set_p_text_min_y(self.getInputFromPort('p_text_min_y'))
- if self.hasInputFromPort('p_text_min_z') :
- p.set_p_text_min_z(self.getInputFromPort('p_text_min_z'))
- if self.hasInputFromPort('p_text_max_x') :
- p.set_p_text_max_x(self.getInputFromPort('p_text_max_x'))
- if self.hasInputFromPort('p_text_max_y') :
- p.set_p_text_max_y(self.getInputFromPort('p_text_max_y'))
- if self.hasInputFromPort('p_text_max_z') :
- p.set_p_text_max_z(self.getInputFromPort('p_text_max_z'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Selection Widget', results[0])
- self.setResult('Output Field', results[1])
- self.setResult('MaskVector', results[2])
-
-class GetFieldBoundary(NewField) :
- def compute(self) :
- p = sr_py.GetFieldBoundaryAlg()
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('BoundaryField', results[0])
- self.setResult('Mapping', results[1])
-
-class ConvertMatricesToMesh(NewField) :
- def compute(self) :
- p = sr_py.ConvertMatricesToMeshAlg()
- if self.hasInputFromPort('p_fieldname') :
- p.set_p_fieldname(self.getInputFromPort('p_fieldname'))
- if self.hasInputFromPort('p_meshname') :
- p.set_p_meshname(self.getInputFromPort('p_meshname'))
- if self.hasInputFromPort('p_fieldbasetype') :
- p.set_p_fieldbasetype(self.getInputFromPort('p_fieldbasetype'))
- if self.hasInputFromPort('p_datatype') :
- p.set_p_datatype(self.getInputFromPort('p_datatype'))
- Mesh_Elements = 0
- if self.hasInputFromPort('Mesh Elements') :
- Mesh_Elements = self.getInputFromPort('Mesh Elements')
- Mesh_Positions = 0
- if self.hasInputFromPort('Mesh Positions') :
- Mesh_Positions = self.getInputFromPort('Mesh Positions')
- Mesh_Normals = 0
- if self.hasInputFromPort('Mesh Normals') :
- Mesh_Normals = self.getInputFromPort('Mesh Normals')
- results = p.execute(Mesh_Elements, Mesh_Positions, Mesh_Normals)
- self.setResult('Output Field', results)
-
-class ClipFieldToFieldOrWidget(NewField) :
- def compute(self) :
- p = sr_py.ClipFieldToFieldOrWidgetAlg()
- if self.hasInputFromPort('p_clip_location') :
- p.set_p_clip_location(self.getInputFromPort('p_clip_location'))
- if self.hasInputFromPort('p_clipmode') :
- p.set_p_clipmode(self.getInputFromPort('p_clipmode'))
- if self.hasInputFromPort('p_autoexecute') :
- p.set_p_autoexecute(self.getInputFromPort('p_autoexecute'))
- if self.hasInputFromPort('p_autoinvert') :
- p.set_p_autoinvert(self.getInputFromPort('p_autoinvert'))
- if self.hasInputFromPort('p_execmode') :
- p.set_p_execmode(self.getInputFromPort('p_execmode'))
- if self.hasInputFromPort('p_center_x') :
- p.set_p_center_x(self.getInputFromPort('p_center_x'))
- if self.hasInputFromPort('p_center_y') :
- p.set_p_center_y(self.getInputFromPort('p_center_y'))
- if self.hasInputFromPort('p_center_z') :
- p.set_p_center_z(self.getInputFromPort('p_center_z'))
- if self.hasInputFromPort('p_right_x') :
- p.set_p_right_x(self.getInputFromPort('p_right_x'))
- if self.hasInputFromPort('p_right_y') :
- p.set_p_right_y(self.getInputFromPort('p_right_y'))
- if self.hasInputFromPort('p_right_z') :
- p.set_p_right_z(self.getInputFromPort('p_right_z'))
- if self.hasInputFromPort('p_down_x') :
- p.set_p_down_x(self.getInputFromPort('p_down_x'))
- if self.hasInputFromPort('p_down_y') :
- p.set_p_down_y(self.getInputFromPort('p_down_y'))
- if self.hasInputFromPort('p_down_z') :
- p.set_p_down_z(self.getInputFromPort('p_down_z'))
- if self.hasInputFromPort('p_in_x') :
- p.set_p_in_x(self.getInputFromPort('p_in_x'))
- if self.hasInputFromPort('p_in_y') :
- p.set_p_in_y(self.getInputFromPort('p_in_y'))
- if self.hasInputFromPort('p_in_z') :
- p.set_p_in_z(self.getInputFromPort('p_in_z'))
- if self.hasInputFromPort('p_scale') :
- p.set_p_scale(self.getInputFromPort('p_scale'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- Clip_Field = 0
- if self.hasInputFromPort('Clip Field') :
- Clip_Field = self.getInputFromPort('Clip Field')
- results = p.execute(Input_Field, Clip_Field)
- self.setResult('Selection Widget', results[0])
- self.setResult('Output Field', results[1])
-
-class RefineMeshByIsovalue2(NewField) :
- def compute(self) :
- p = sr_py.RefineMeshByIsovalue2Alg()
- if self.hasInputFromPort('p_isoval') :
- p.set_p_isoval(self.getInputFromPort('p_isoval'))
- if self.hasInputFromPort('p_lte') :
- p.set_p_lte(self.getInputFromPort('p_lte'))
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- Optional_Isovalue = 0
- if self.hasInputFromPort('Optional Isovalue') :
- Optional_Isovalue = self.getInputFromPort('Optional Isovalue')
- results = p.execute(Input, Optional_Isovalue)
- self.setResult('Refined', results[0])
- self.setResult('Mapping', results[1])
-
-class CreateLatVol(NewField) :
- def compute(self) :
- p = sr_py.CreateLatVolAlg()
- if self.hasInputFromPort('p_sizex') :
- p.set_p_sizex(self.getInputFromPort('p_sizex'))
- if self.hasInputFromPort('p_sizey') :
- p.set_p_sizey(self.getInputFromPort('p_sizey'))
- if self.hasInputFromPort('p_sizez') :
- p.set_p_sizez(self.getInputFromPort('p_sizez'))
- if self.hasInputFromPort('p_padpercent') :
- p.set_p_padpercent(self.getInputFromPort('p_padpercent'))
- if self.hasInputFromPort('p_data_at') :
- p.set_p_data_at(self.getInputFromPort('p_data_at'))
- if self.hasInputFromPort('p_element_size') :
- p.set_p_element_size(self.getInputFromPort('p_element_size'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- LatVol_Size = 0
- if self.hasInputFromPort('LatVol Size') :
- LatVol_Size = self.getInputFromPort('LatVol Size')
- results = p.execute(Input_Field, LatVol_Size)
- self.setResult('Output Sample Field', results)
-
-class InterfaceWithCamal(NewField) :
- def compute(self) :
- p = sr_py.InterfaceWithCamalAlg()
- TriSurf = 0
- if self.hasInputFromPort('TriSurf') :
- TriSurf = self.getInputFromPort('TriSurf')
- results = p.execute(TriSurf)
- self.setResult('TetVol', results)
-
-class ClipVolumeByIsovalue(NewField) :
- def compute(self) :
- p = sr_py.ClipVolumeByIsovalueAlg()
- if self.hasInputFromPort('p_isoval_min') :
- p.set_p_isoval_min(self.getInputFromPort('p_isoval_min'))
- if self.hasInputFromPort('p_isoval_max') :
- p.set_p_isoval_max(self.getInputFromPort('p_isoval_max'))
- if self.hasInputFromPort('p_isoval') :
- p.set_p_isoval(self.getInputFromPort('p_isoval'))
- if self.hasInputFromPort('p_lte') :
- p.set_p_lte(self.getInputFromPort('p_lte'))
- if self.hasInputFromPort('p_update_type') :
- p.set_p_update_type(self.getInputFromPort('p_update_type'))
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- Optional_Isovalue = 0
- if self.hasInputFromPort('Optional Isovalue') :
- Optional_Isovalue = self.getInputFromPort('Optional Isovalue')
- results = p.execute(Input, Optional_Isovalue)
- self.setResult('Clipped', results[0])
- self.setResult('Mapping', results[1])
-
-class RefineMesh(NewField) :
- def compute(self) :
- p = sr_py.RefineMeshAlg()
- if self.hasInputFromPort('p_select') :
- p.set_p_select(self.getInputFromPort('p_select'))
- if self.hasInputFromPort('p_method') :
- p.set_p_method(self.getInputFromPort('p_method'))
- if self.hasInputFromPort('p_isoval') :
- p.set_p_isoval(self.getInputFromPort('p_isoval'))
- Mesh = 0
- if self.hasInputFromPort('Mesh') :
- Mesh = self.getInputFromPort('Mesh')
- Isovalue = 0
- if self.hasInputFromPort('Isovalue') :
- Isovalue = self.getInputFromPort('Isovalue')
- results = p.execute(Mesh, Isovalue)
- self.setResult('RefinedMesh', results[0])
- self.setResult('Mapping', results[1])
-
-class MergeFields(NewField) :
- def compute(self) :
- p = sr_py.MergeFieldsAlg()
- Container_Mesh = 0
- if self.hasInputFromPort('Container Mesh') :
- Container_Mesh = self.getInputFromPort('Container Mesh')
- Insert_Field = 0
- if self.hasInputFromPort('Insert Field') :
- Insert_Field = self.getInputFromPort('Insert Field')
- results = p.execute(Container_Mesh, Insert_Field)
- self.setResult('Combined Field', results[0])
- self.setResult('Extended Insert Field', results[1])
- self.setResult('Combined To Extended Mapping', results[2])
-
-class GetCentroidsFromMesh(NewField) :
- def compute(self) :
- p = sr_py.GetCentroidsFromMeshAlg()
- TetVolField = 0
- if self.hasInputFromPort('TetVolField') :
- TetVolField = self.getInputFromPort('TetVolField')
- results = p.execute(TetVolField)
- self.setResult('PointCloudField', results)
-
-class ExtractIsosurfaceByFunction(NewField) :
- def compute(self) :
- p = sr_py.ExtractIsosurfaceByFunctionAlg()
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- if self.hasInputFromPort('p_zero_checks') :
- p.set_p_zero_checks(self.getInputFromPort('p_zero_checks'))
- if self.hasInputFromPort('p_slice_value_min') :
- p.set_p_slice_value_min(self.getInputFromPort('p_slice_value_min'))
- if self.hasInputFromPort('p_slice_value_max') :
- p.set_p_slice_value_max(self.getInputFromPort('p_slice_value_max'))
- if self.hasInputFromPort('p_slice_value') :
- p.set_p_slice_value(self.getInputFromPort('p_slice_value'))
- if self.hasInputFromPort('p_slice_value_typed') :
- p.set_p_slice_value_typed(self.getInputFromPort('p_slice_value_typed'))
- if self.hasInputFromPort('p_slice_value_quantity') :
- p.set_p_slice_value_quantity(self.getInputFromPort('p_slice_value_quantity'))
- if self.hasInputFromPort('p_quantity_range') :
- p.set_p_quantity_range(self.getInputFromPort('p_quantity_range'))
- if self.hasInputFromPort('p_quantity_clusive') :
- p.set_p_quantity_clusive(self.getInputFromPort('p_quantity_clusive'))
- if self.hasInputFromPort('p_quantity_min') :
- p.set_p_quantity_min(self.getInputFromPort('p_quantity_min'))
- if self.hasInputFromPort('p_quantity_max') :
- p.set_p_quantity_max(self.getInputFromPort('p_quantity_max'))
- if self.hasInputFromPort('p_quantity_list') :
- p.set_p_quantity_list(self.getInputFromPort('p_quantity_list'))
- if self.hasInputFromPort('p_slice_value_list') :
- p.set_p_slice_value_list(self.getInputFromPort('p_slice_value_list'))
- if self.hasInputFromPort('p_matrix_list') :
- p.set_p_matrix_list(self.getInputFromPort('p_matrix_list'))
- if self.hasInputFromPort('p_algorithm') :
- p.set_p_algorithm(self.getInputFromPort('p_algorithm'))
- if self.hasInputFromPort('p_active_slice_value_selection_tab') :
- p.set_p_active_slice_value_selection_tab(self.getInputFromPort('p_active_slice_value_selection_tab'))
- if self.hasInputFromPort('p_active_tab') :
- p.set_p_active_tab(self.getInputFromPort('p_active_tab'))
- if self.hasInputFromPort('p_update_type') :
- p.set_p_update_type(self.getInputFromPort('p_update_type'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- Optional_Slice_values = 0
- if self.hasInputFromPort('Optional Slice values') :
- Optional_Slice_values = self.getInputFromPort('Optional Slice values')
- results = p.execute(Input_Field, Optional_Slice_values)
- self.setResult('Output Field', results)
-
-class MergeTriSurfs(NewField) :
- def compute(self) :
- p = sr_py.MergeTriSurfsAlg()
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Field', results)
-
-class InterfaceWithTetGen(NewField) :
- def compute(self) :
- p = sr_py.InterfaceWithTetGenAlg()
- if self.hasInputFromPort('p_switch') :
- p.set_p_switch(self.getInputFromPort('p_switch'))
- Main = 0
- if self.hasInputFromPort('Main') :
- Main = self.getInputFromPort('Main')
- Points = 0
- if self.hasInputFromPort('Points') :
- Points = self.getInputFromPort('Points')
- Region_Attribs = 0
- if self.hasInputFromPort('Region Attribs') :
- Region_Attribs = self.getInputFromPort('Region Attribs')
- Regions = 0
- if self.hasInputFromPort('Regions') :
- Regions = self.getInputFromPort('Regions')
- results = p.execute(Main, Points, Region_Attribs, Regions)
- self.setResult('TetVol', results)
-
-class CreateImage(NewField) :
- def compute(self) :
- p = sr_py.CreateImageAlg()
- if self.hasInputFromPort('p_sizex') :
- p.set_p_sizex(self.getInputFromPort('p_sizex'))
- if self.hasInputFromPort('p_sizey') :
- p.set_p_sizey(self.getInputFromPort('p_sizey'))
- if self.hasInputFromPort('p_sizez') :
- p.set_p_sizez(self.getInputFromPort('p_sizez'))
- if self.hasInputFromPort('p_z_value') :
- p.set_p_z_value(self.getInputFromPort('p_z_value'))
- if self.hasInputFromPort('p_auto_size') :
- p.set_p_auto_size(self.getInputFromPort('p_auto_size'))
- if self.hasInputFromPort('p_axis') :
- p.set_p_axis(self.getInputFromPort('p_axis'))
- if self.hasInputFromPort('p_padpercent') :
- p.set_p_padpercent(self.getInputFromPort('p_padpercent'))
- if self.hasInputFromPort('p_pos') :
- p.set_p_pos(self.getInputFromPort('p_pos'))
- if self.hasInputFromPort('p_data_at') :
- p.set_p_data_at(self.getInputFromPort('p_data_at'))
- if self.hasInputFromPort('p_update_type') :
- p.set_p_update_type(self.getInputFromPort('p_update_type'))
- if self.hasInputFromPort('p_corigin_x') :
- p.set_p_corigin_x(self.getInputFromPort('p_corigin_x'))
- if self.hasInputFromPort('p_corigin_y') :
- p.set_p_corigin_y(self.getInputFromPort('p_corigin_y'))
- if self.hasInputFromPort('p_corigin_z') :
- p.set_p_corigin_z(self.getInputFromPort('p_corigin_z'))
- if self.hasInputFromPort('p_cnormal_x') :
- p.set_p_cnormal_x(self.getInputFromPort('p_cnormal_x'))
- if self.hasInputFromPort('p_cnormal_y') :
- p.set_p_cnormal_y(self.getInputFromPort('p_cnormal_y'))
- if self.hasInputFromPort('p_cnormal_z') :
- p.set_p_cnormal_z(self.getInputFromPort('p_cnormal_z'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Sample Field', results)
-
-class InsertHexVolSheetAlongSurface(NewField) :
- def compute(self) :
- p = sr_py.InsertHexVolSheetAlongSurfaceAlg()
- if self.hasInputFromPort('p_side') :
- p.set_p_side(self.getInputFromPort('p_side'))
- if self.hasInputFromPort('p_addlayer') :
- p.set_p_addlayer(self.getInputFromPort('p_addlayer'))
- HexField = 0
- if self.hasInputFromPort('HexField') :
- HexField = self.getInputFromPort('HexField')
- TriField = 0
- if self.hasInputFromPort('TriField') :
- TriField = self.getInputFromPort('TriField')
- results = p.execute(HexField, TriField)
- self.setResult('Side1Field', results[0])
- self.setResult('Side2Field', results[1])
-
-class GenerateSinglePointProbeFromField(NewField) :
- def compute(self) :
- p = sr_py.GenerateSinglePointProbeFromFieldAlg()
- if self.hasInputFromPort('p_main_frame') :
- p.set_p_main_frame(self.getInputFromPort('p_main_frame'))
- if self.hasInputFromPort('p_locx') :
- p.set_p_locx(self.getInputFromPort('p_locx'))
- if self.hasInputFromPort('p_locy') :
- p.set_p_locy(self.getInputFromPort('p_locy'))
- if self.hasInputFromPort('p_locz') :
- p.set_p_locz(self.getInputFromPort('p_locz'))
- if self.hasInputFromPort('p_value') :
- p.set_p_value(self.getInputFromPort('p_value'))
- if self.hasInputFromPort('p_node') :
- p.set_p_node(self.getInputFromPort('p_node'))
- if self.hasInputFromPort('p_edge') :
- p.set_p_edge(self.getInputFromPort('p_edge'))
- if self.hasInputFromPort('p_face') :
- p.set_p_face(self.getInputFromPort('p_face'))
- if self.hasInputFromPort('p_cell') :
- p.set_p_cell(self.getInputFromPort('p_cell'))
- if self.hasInputFromPort('p_show_value') :
- p.set_p_show_value(self.getInputFromPort('p_show_value'))
- if self.hasInputFromPort('p_show_node') :
- p.set_p_show_node(self.getInputFromPort('p_show_node'))
- if self.hasInputFromPort('p_show_edge') :
- p.set_p_show_edge(self.getInputFromPort('p_show_edge'))
- if self.hasInputFromPort('p_show_face') :
- p.set_p_show_face(self.getInputFromPort('p_show_face'))
- if self.hasInputFromPort('p_show_cell') :
- p.set_p_show_cell(self.getInputFromPort('p_show_cell'))
- if self.hasInputFromPort('p_probe_scale') :
- p.set_p_probe_scale(self.getInputFromPort('p_probe_scale'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('GenerateSinglePointProbeFromField Widget', results[0])
- self.setResult('GenerateSinglePointProbeFromField Point', results[1])
- self.setResult('Element Index', results[2])
-
-class InterfaceWithCubit(NewField) :
- def compute(self) :
- p = sr_py.InterfaceWithCubitAlg()
- if self.hasInputFromPort('p_cubitdir') :
- p.set_p_cubitdir(self.getInputFromPort('p_cubitdir'))
- if self.hasInputFromPort('p_ncdump') :
- p.set_p_ncdump(self.getInputFromPort('p_ncdump'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- PointCloudField = 0
- if self.hasInputFromPort('PointCloudField') :
- PointCloudField = self.getInputFromPort('PointCloudField')
- results = p.execute(Field, PointCloudField)
- self.setResult('Field', results)
-
-class ClipFieldByFunction(NewField) :
- def compute(self) :
- p = sr_py.ClipFieldByFunctionAlg()
- if self.hasInputFromPort('p_mode') :
- p.set_p_mode(self.getInputFromPort('p_mode'))
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- Function = ''
- if self.hasInputFromPort('Function') :
- Function = self.getInputFromPort('Function')
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- results = p.execute(Function, Input)
- self.setResult('Clipped', results[0])
- self.setResult('Mapping', results[1])
- self.setResult('MaskVector', results[2])
-
-class GetDomainBoundary(NewField) :
- def compute(self) :
- p = sr_py.GetDomainBoundaryAlg()
- if self.hasInputFromPort('p_userange') :
- p.set_p_userange(self.getInputFromPort('p_userange'))
- if self.hasInputFromPort('p_minrange') :
- p.set_p_minrange(self.getInputFromPort('p_minrange'))
- if self.hasInputFromPort('p_maxrange') :
- p.set_p_maxrange(self.getInputFromPort('p_maxrange'))
- if self.hasInputFromPort('p_usevalue') :
- p.set_p_usevalue(self.getInputFromPort('p_usevalue'))
- if self.hasInputFromPort('p_value') :
- p.set_p_value(self.getInputFromPort('p_value'))
- if self.hasInputFromPort('p_includeouterboundary') :
- p.set_p_includeouterboundary(self.getInputFromPort('p_includeouterboundary'))
- if self.hasInputFromPort('p_innerboundaryonly') :
- p.set_p_innerboundaryonly(self.getInputFromPort('p_innerboundaryonly'))
- if self.hasInputFromPort('p_noinnerboundary') :
- p.set_p_noinnerboundary(self.getInputFromPort('p_noinnerboundary'))
- if self.hasInputFromPort('p_disconnect') :
- p.set_p_disconnect(self.getInputFromPort('p_disconnect'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- MinValueValue = 0
- if self.hasInputFromPort('MinValueValue') :
- MinValueValue = self.getInputFromPort('MinValueValue')
- MaxValue = 0
- if self.hasInputFromPort('MaxValue') :
- MaxValue = self.getInputFromPort('MaxValue')
- results = p.execute(Field, MinValueValue, MaxValue)
- self.setResult('Field', results)
-
-class CollectFields(NewField) :
- def compute(self) :
- p = sr_py.CollectFieldsAlg()
- if self.hasInputFromPort('p_buffersize') :
- p.set_p_buffersize(self.getInputFromPort('p_buffersize'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- BufferSize = 0
- if self.hasInputFromPort('BufferSize') :
- BufferSize = self.getInputFromPort('BufferSize')
- results = p.execute(Field, BufferSize)
- self.setResult('Fields', results)
-
-class GeneratePointSamplesFromField(NewField) :
- def compute(self) :
- p = sr_py.GeneratePointSamplesFromFieldAlg()
- if self.hasInputFromPort('p_num_seeds') :
- p.set_p_num_seeds(self.getInputFromPort('p_num_seeds'))
- if self.hasInputFromPort('p_probe_scale') :
- p.set_p_probe_scale(self.getInputFromPort('p_probe_scale'))
- if self.hasInputFromPort('p_send') :
- p.set_p_send(self.getInputFromPort('p_send'))
- if self.hasInputFromPort('p_widget') :
- p.set_p_widget(self.getInputFromPort('p_widget'))
- if self.hasInputFromPort('p_red') :
- p.set_p_red(self.getInputFromPort('p_red'))
- if self.hasInputFromPort('p_green') :
- p.set_p_green(self.getInputFromPort('p_green'))
- if self.hasInputFromPort('p_blue') :
- p.set_p_blue(self.getInputFromPort('p_blue'))
- if self.hasInputFromPort('p_auto_execute') :
- p.set_p_auto_execute(self.getInputFromPort('p_auto_execute'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('GeneratePointSamplesFromField Widget', results[0])
- self.setResult('GeneratePointSamplesFromField Point', results[1])
-
-class GeneratePointSamplesFromFieldOrWidget(NewField) :
- def compute(self) :
- p = sr_py.GeneratePointSamplesFromFieldOrWidgetAlg()
- if self.hasInputFromPort('p_wtype') :
- p.set_p_wtype(self.getInputFromPort('p_wtype'))
- if self.hasInputFromPort('p_endpoints') :
- p.set_p_endpoints(self.getInputFromPort('p_endpoints'))
- if self.hasInputFromPort('p_maxseeds') :
- p.set_p_maxseeds(self.getInputFromPort('p_maxseeds'))
- if self.hasInputFromPort('p_numseeds') :
- p.set_p_numseeds(self.getInputFromPort('p_numseeds'))
- if self.hasInputFromPort('p_rngseed') :
- p.set_p_rngseed(self.getInputFromPort('p_rngseed'))
- if self.hasInputFromPort('p_rnginc') :
- p.set_p_rnginc(self.getInputFromPort('p_rnginc'))
- if self.hasInputFromPort('p_clamp') :
- p.set_p_clamp(self.getInputFromPort('p_clamp'))
- if self.hasInputFromPort('p_autoexecute') :
- p.set_p_autoexecute(self.getInputFromPort('p_autoexecute'))
- if self.hasInputFromPort('p_dist') :
- p.set_p_dist(self.getInputFromPort('p_dist'))
- if self.hasInputFromPort('p_whichtab') :
- p.set_p_whichtab(self.getInputFromPort('p_whichtab'))
- Field_to_Sample = 0
- if self.hasInputFromPort('Field to Sample') :
- Field_to_Sample = self.getInputFromPort('Field to Sample')
- results = p.execute(Field_to_Sample)
- self.setResult('Samples', results[0])
- self.setResult('Sampling Widget', results[1])
-
-class DecimateTriSurf(NewField) :
- def compute(self) :
- p = sr_py.DecimateTriSurfAlg()
- TriSurf = 0
- if self.hasInputFromPort('TriSurf') :
- TriSurf = self.getInputFromPort('TriSurf')
- results = p.execute(TriSurf)
- self.setResult('Decimated', results)
-
-class GetSliceFromStructuredFieldByIndices(NewField) :
- def compute(self) :
- p = sr_py.GetSliceFromStructuredFieldByIndicesAlg()
- if self.hasInputFromPort('p_axis') :
- p.set_p_axis(self.getInputFromPort('p_axis'))
- if self.hasInputFromPort('p_dims') :
- p.set_p_dims(self.getInputFromPort('p_dims'))
- if self.hasInputFromPort('p_dim_i') :
- p.set_p_dim_i(self.getInputFromPort('p_dim_i'))
- if self.hasInputFromPort('p_dim_j') :
- p.set_p_dim_j(self.getInputFromPort('p_dim_j'))
- if self.hasInputFromPort('p_dim_k') :
- p.set_p_dim_k(self.getInputFromPort('p_dim_k'))
- if self.hasInputFromPort('p_index_i') :
- p.set_p_index_i(self.getInputFromPort('p_index_i'))
- if self.hasInputFromPort('p_index_j') :
- p.set_p_index_j(self.getInputFromPort('p_index_j'))
- if self.hasInputFromPort('p_index_k') :
- p.set_p_index_k(self.getInputFromPort('p_index_k'))
- if self.hasInputFromPort('p_update_type') :
- p.set_p_update_type(self.getInputFromPort('p_update_type'))
- if self.hasInputFromPort('p_continuous') :
- p.set_p_continuous(self.getInputFromPort('p_continuous'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- Input_Matrix = 0
- if self.hasInputFromPort('Input Matrix') :
- Input_Matrix = self.getInputFromPort('Input Matrix')
- results = p.execute(Input_Field, Input_Matrix)
- self.setResult('Output Field', results[0])
- self.setResult('Output Matrix', results[1])
-
-class RemoveHexVolSheet(NewField) :
- def compute(self) :
- p = sr_py.RemoveHexVolSheetAlg()
- if self.hasInputFromPort('p_edge_list') :
- p.set_p_edge_list(self.getInputFromPort('p_edge_list'))
- HexField = 0
- if self.hasInputFromPort('HexField') :
- HexField = self.getInputFromPort('HexField')
- results = p.execute(HexField)
- self.setResult('NewHexField', results[0])
- self.setResult('ExtractedHexes', results[1])
-
-class SubsampleStructuredFieldByIndices(NewField) :
- def compute(self) :
- p = sr_py.SubsampleStructuredFieldByIndicesAlg()
- if self.hasInputFromPort('p_power_app') :
- p.set_p_power_app(self.getInputFromPort('p_power_app'))
- if self.hasInputFromPort('p_wrap') :
- p.set_p_wrap(self.getInputFromPort('p_wrap'))
- if self.hasInputFromPort('p_dims') :
- p.set_p_dims(self.getInputFromPort('p_dims'))
- if self.hasInputFromPort('p_dim_i') :
- p.set_p_dim_i(self.getInputFromPort('p_dim_i'))
- if self.hasInputFromPort('p_dim_j') :
- p.set_p_dim_j(self.getInputFromPort('p_dim_j'))
- if self.hasInputFromPort('p_dim_k') :
- p.set_p_dim_k(self.getInputFromPort('p_dim_k'))
- if self.hasInputFromPort('p_start_i') :
- p.set_p_start_i(self.getInputFromPort('p_start_i'))
- if self.hasInputFromPort('p_start_j') :
- p.set_p_start_j(self.getInputFromPort('p_start_j'))
- if self.hasInputFromPort('p_start_k') :
- p.set_p_start_k(self.getInputFromPort('p_start_k'))
- if self.hasInputFromPort('p_stop_i') :
- p.set_p_stop_i(self.getInputFromPort('p_stop_i'))
- if self.hasInputFromPort('p_stop_j') :
- p.set_p_stop_j(self.getInputFromPort('p_stop_j'))
- if self.hasInputFromPort('p_stop_k') :
- p.set_p_stop_k(self.getInputFromPort('p_stop_k'))
- if self.hasInputFromPort('p_stride_i') :
- p.set_p_stride_i(self.getInputFromPort('p_stride_i'))
- if self.hasInputFromPort('p_stride_j') :
- p.set_p_stride_j(self.getInputFromPort('p_stride_j'))
- if self.hasInputFromPort('p_stride_k') :
- p.set_p_stride_k(self.getInputFromPort('p_stride_k'))
- if self.hasInputFromPort('p_wrap_i') :
- p.set_p_wrap_i(self.getInputFromPort('p_wrap_i'))
- if self.hasInputFromPort('p_wrap_j') :
- p.set_p_wrap_j(self.getInputFromPort('p_wrap_j'))
- if self.hasInputFromPort('p_wrap_k') :
- p.set_p_wrap_k(self.getInputFromPort('p_wrap_k'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- Input_Matrix = 0
- if self.hasInputFromPort('Input Matrix') :
- Input_Matrix = self.getInputFromPort('Input Matrix')
- results = p.execute(Input_Field, Input_Matrix)
- self.setResult('Output Field', results[0])
- self.setResult('Output Matrix', results[1])
-
-class GetAllSegmentationBoundaries(NewField) :
- def compute(self) :
- p = sr_py.GetAllSegmentationBoundariesAlg()
- Segmentations = 0
- if self.hasInputFromPort('Segmentations') :
- Segmentations = self.getInputFromPort('Segmentations')
- results = p.execute(Segmentations)
- self.setResult('Boundaries', results)
-
-class ClipFieldWithSeed(NewField) :
- def compute(self) :
- p = sr_py.ClipFieldWithSeedAlg()
- if self.hasInputFromPort('p_mode') :
- p.set_p_mode(self.getInputFromPort('p_mode'))
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- Function = ''
- if self.hasInputFromPort('Function') :
- Function = self.getInputFromPort('Function')
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- Seeds = 0
- if self.hasInputFromPort('Seeds') :
- Seeds = self.getInputFromPort('Seeds')
- results = p.execute(Function, Input, Seeds)
- self.setResult('Clipped', results[0])
- self.setResult('Mapping', results[1])
- self.setResult('MaskVector', results[2])
-
-class SplitNodesByDomain(NewField) :
- def compute(self) :
- p = sr_py.SplitNodesByDomainAlg()
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('SplitField', results)
-
-class ApplyMappingMatrix(ChangeFieldData) :
- def compute(self) :
- p = sr_py.ApplyMappingMatrixAlg()
- Source = 0
- if self.hasInputFromPort('Source') :
- Source = self.getInputFromPort('Source')
- Destination = 0
- if self.hasInputFromPort('Destination') :
- Destination = self.getInputFromPort('Destination')
- Mapping = 0
- if self.hasInputFromPort('Mapping') :
- Mapping = self.getInputFromPort('Mapping')
- results = p.execute(Source, Destination, Mapping)
- self.setResult('Output', results)
-
-class MaskLatVolWithTriSurf(ChangeFieldData) :
- def compute(self) :
- p = sr_py.MaskLatVolWithTriSurfAlg()
- LatVolField = 0
- if self.hasInputFromPort('LatVolField') :
- LatVolField = self.getInputFromPort('LatVolField')
- TriSurfField = 0
- if self.hasInputFromPort('TriSurfField') :
- TriSurfField = self.getInputFromPort('TriSurfField')
- results = p.execute(LatVolField, TriSurfField)
- self.setResult('LatVol Mask', results)
-
-class ConvertFieldBasis(ChangeFieldData) :
- def compute(self) :
- p = sr_py.ConvertFieldBasisAlg()
- if self.hasInputFromPort('p_output_basis') :
- p.set_p_output_basis(self.getInputFromPort('p_output_basis'))
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- results = p.execute(Input)
- self.setResult('Output', results[0])
- self.setResult('Mapping', results[1])
-
-class ReportMeshQualityMeasures(ChangeFieldData) :
- def compute(self) :
- p = sr_py.ReportMeshQualityMeasuresAlg()
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- results = p.execute(Input)
- self.setResult('Checked', results)
-
-class SelectAndSetFieldData(ChangeFieldData) :
- def compute(self) :
- p = sr_py.SelectAndSetFieldDataAlg()
- if self.hasInputFromPort('p_selection1') :
- p.set_p_selection1(self.getInputFromPort('p_selection1'))
- if self.hasInputFromPort('p_function1') :
- p.set_p_function1(self.getInputFromPort('p_function1'))
- if self.hasInputFromPort('p_selection2') :
- p.set_p_selection2(self.getInputFromPort('p_selection2'))
- if self.hasInputFromPort('p_function2') :
- p.set_p_function2(self.getInputFromPort('p_function2'))
- if self.hasInputFromPort('p_selection3') :
- p.set_p_selection3(self.getInputFromPort('p_selection3'))
- if self.hasInputFromPort('p_function3') :
- p.set_p_function3(self.getInputFromPort('p_function3'))
- if self.hasInputFromPort('p_selection4') :
- p.set_p_selection4(self.getInputFromPort('p_selection4'))
- if self.hasInputFromPort('p_function4') :
- p.set_p_function4(self.getInputFromPort('p_function4'))
- if self.hasInputFromPort('p_functiondef') :
- p.set_p_functiondef(self.getInputFromPort('p_functiondef'))
- if self.hasInputFromPort('p_format') :
- p.set_p_format(self.getInputFromPort('p_format'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- Array = 0
- if self.hasInputFromPort('Array') :
- Array = self.getInputFromPort('Array')
- results = p.execute(Field, Array)
- self.setResult('Field', results)
-
-class CalculateFieldData3(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateFieldData3Alg()
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- if self.hasInputFromPort('p_format') :
- p.set_p_format(self.getInputFromPort('p_format'))
- Field1 = 0
- if self.hasInputFromPort('Field1') :
- Field1 = self.getInputFromPort('Field1')
- Field2 = 0
- if self.hasInputFromPort('Field2') :
- Field2 = self.getInputFromPort('Field2')
- Field3 = 0
- if self.hasInputFromPort('Field3') :
- Field3 = self.getInputFromPort('Field3')
- Function = ''
- if self.hasInputFromPort('Function') :
- Function = self.getInputFromPort('Function')
- Array = 0
- if self.hasInputFromPort('Array') :
- Array = self.getInputFromPort('Array')
- results = p.execute(Field1, Field2, Field3, Function, Array)
- self.setResult('Field', results)
-
-class SetFieldData(ChangeFieldData) :
- def compute(self) :
- p = sr_py.SetFieldDataAlg()
- if self.hasInputFromPort('p_keepscalartype') :
- p.set_p_keepscalartype(self.getInputFromPort('p_keepscalartype'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- Matrix_Data = 0
- if self.hasInputFromPort('Matrix Data') :
- Matrix_Data = self.getInputFromPort('Matrix Data')
- Nrrd_Data = 0
- if self.hasInputFromPort('Nrrd Data') :
- Nrrd_Data = self.getInputFromPort('Nrrd Data')
- results = p.execute(Field, Matrix_Data, Nrrd_Data)
- self.setResult('Field', results)
-
-class SwapFieldDataWithMatrixEntries(ChangeFieldData) :
- def compute(self) :
- p = sr_py.SwapFieldDataWithMatrixEntriesAlg()
- if self.hasInputFromPort('p_preserve_scalar_type') :
- p.set_p_preserve_scalar_type(self.getInputFromPort('p_preserve_scalar_type'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- Input_Matrix = 0
- if self.hasInputFromPort('Input Matrix') :
- Input_Matrix = self.getInputFromPort('Input Matrix')
- results = p.execute(Input_Field, Input_Matrix)
- self.setResult('Output Field', results[0])
- self.setResult('Output Matrix', results[1])
-
-class ConvertLatVolDataFromElemToNode(ChangeFieldData) :
- def compute(self) :
- p = sr_py.ConvertLatVolDataFromElemToNodeAlg()
- Elem_Field = 0
- if self.hasInputFromPort('Elem Field') :
- Elem_Field = self.getInputFromPort('Elem Field')
- results = p.execute(Elem_Field)
- self.setResult('Node Field', results)
-
-class CalculateNodeNormals(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateNodeNormalsAlg()
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- Input_Point = 0
- if self.hasInputFromPort('Input Point') :
- Input_Point = self.getInputFromPort('Input Point')
- results = p.execute(Input_Field, Input_Point)
- self.setResult('Output Field', results)
-
-class CalculateVectorMagnitudes(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateVectorMagnitudesAlg()
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output CalculateVectorMagnitudes', results)
-
-class ConvertIndicesToFieldData(ChangeFieldData) :
- def compute(self) :
- p = sr_py.ConvertIndicesToFieldDataAlg()
- if self.hasInputFromPort('p_outputtype') :
- p.set_p_outputtype(self.getInputFromPort('p_outputtype'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- Data = 0
- if self.hasInputFromPort('Data') :
- Data = self.getInputFromPort('Data')
- results = p.execute(Field, Data)
- self.setResult('Field', results)
-
-class CalculateDistanceToFieldBoundary(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateDistanceToFieldBoundaryAlg()
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('DistanceField', results)
-
-class MapFieldDataFromSourceToDestination(ChangeFieldData) :
- def compute(self) :
- p = sr_py.MapFieldDataFromSourceToDestinationAlg()
- if self.hasInputFromPort('p_interpolation_basis') :
- p.set_p_interpolation_basis(self.getInputFromPort('p_interpolation_basis'))
- if self.hasInputFromPort('p_map_source_to_single_dest') :
- p.set_p_map_source_to_single_dest(self.getInputFromPort('p_map_source_to_single_dest'))
- if self.hasInputFromPort('p_exhaustive_search') :
- p.set_p_exhaustive_search(self.getInputFromPort('p_exhaustive_search'))
- if self.hasInputFromPort('p_exhaustive_search_max_dist') :
- p.set_p_exhaustive_search_max_dist(self.getInputFromPort('p_exhaustive_search_max_dist'))
- if self.hasInputFromPort('p_np') :
- p.set_p_np(self.getInputFromPort('p_np'))
- Source = 0
- if self.hasInputFromPort('Source') :
- Source = self.getInputFromPort('Source')
- Destination = 0
- if self.hasInputFromPort('Destination') :
- Destination = self.getInputFromPort('Destination')
- results = p.execute(Source, Destination)
- self.setResult('Remapped Destination', results)
-
-class SelectAndSetFieldData3(ChangeFieldData) :
- def compute(self) :
- p = sr_py.SelectAndSetFieldData3Alg()
- if self.hasInputFromPort('p_selection1') :
- p.set_p_selection1(self.getInputFromPort('p_selection1'))
- if self.hasInputFromPort('p_function1') :
- p.set_p_function1(self.getInputFromPort('p_function1'))
- if self.hasInputFromPort('p_selection2') :
- p.set_p_selection2(self.getInputFromPort('p_selection2'))
- if self.hasInputFromPort('p_function2') :
- p.set_p_function2(self.getInputFromPort('p_function2'))
- if self.hasInputFromPort('p_selection3') :
- p.set_p_selection3(self.getInputFromPort('p_selection3'))
- if self.hasInputFromPort('p_function3') :
- p.set_p_function3(self.getInputFromPort('p_function3'))
- if self.hasInputFromPort('p_selection4') :
- p.set_p_selection4(self.getInputFromPort('p_selection4'))
- if self.hasInputFromPort('p_function4') :
- p.set_p_function4(self.getInputFromPort('p_function4'))
- if self.hasInputFromPort('p_functiondef') :
- p.set_p_functiondef(self.getInputFromPort('p_functiondef'))
- if self.hasInputFromPort('p_format') :
- p.set_p_format(self.getInputFromPort('p_format'))
- Field1 = 0
- if self.hasInputFromPort('Field1') :
- Field1 = self.getInputFromPort('Field1')
- Field2 = 0
- if self.hasInputFromPort('Field2') :
- Field2 = self.getInputFromPort('Field2')
- Field3 = 0
- if self.hasInputFromPort('Field3') :
- Field3 = self.getInputFromPort('Field3')
- Array = 0
- if self.hasInputFromPort('Array') :
- Array = self.getInputFromPort('Array')
- results = p.execute(Field1, Field2, Field3, Array)
- self.setResult('Field', results)
-
-class CreateFieldData(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CreateFieldDataAlg()
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- if self.hasInputFromPort('p_format') :
- p.set_p_format(self.getInputFromPort('p_format'))
- if self.hasInputFromPort('p_basis') :
- p.set_p_basis(self.getInputFromPort('p_basis'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- Function = ''
- if self.hasInputFromPort('Function') :
- Function = self.getInputFromPort('Function')
- DataArray = 0
- if self.hasInputFromPort('DataArray') :
- DataArray = self.getInputFromPort('DataArray')
- results = p.execute(Field, Function, DataArray)
- self.setResult('Field', results)
-
-class ConvertLatVolDataFromNodeToElem(ChangeFieldData) :
- def compute(self) :
- p = sr_py.ConvertLatVolDataFromNodeToElemAlg()
- Node_Field = 0
- if self.hasInputFromPort('Node Field') :
- Node_Field = self.getInputFromPort('Node Field')
- results = p.execute(Node_Field)
- self.setResult('Elem Field', results)
-
-class CalculateFieldDataCompiled(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateFieldDataCompiledAlg()
- if self.hasInputFromPort('p_outputdatatype') :
- p.set_p_outputdatatype(self.getInputFromPort('p_outputdatatype'))
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- if self.hasInputFromPort('p_cache') :
- p.set_p_cache(self.getInputFromPort('p_cache'))
- Function = ''
- if self.hasInputFromPort('Function') :
- Function = self.getInputFromPort('Function')
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Function, Input_Field)
- self.setResult('Output Field', results)
-
-class MapFieldDataFromElemToNode(ChangeFieldData) :
- def compute(self) :
- p = sr_py.MapFieldDataFromElemToNodeAlg()
- if self.hasInputFromPort('p_method') :
- p.set_p_method(self.getInputFromPort('p_method'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('Field', results)
-
-class ApplyFilterToFieldData(ChangeFieldData) :
- def compute(self) :
- p = sr_py.ApplyFilterToFieldDataAlg()
- if self.hasInputFromPort('p_method') :
- p.set_p_method(self.getInputFromPort('p_method'))
- if self.hasInputFromPort('p_ed_method') :
- p.set_p_ed_method(self.getInputFromPort('p_ed_method'))
- if self.hasInputFromPort('p_ed_iterations') :
- p.set_p_ed_iterations(self.getInputFromPort('p_ed_iterations'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('Field', results)
-
-class GetFieldData(ChangeFieldData) :
- def compute(self) :
- p = sr_py.GetFieldDataAlg()
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('Data', results)
-
-class CalculateFieldData2(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateFieldData2Alg()
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- if self.hasInputFromPort('p_format') :
- p.set_p_format(self.getInputFromPort('p_format'))
- Field1 = 0
- if self.hasInputFromPort('Field1') :
- Field1 = self.getInputFromPort('Field1')
- Field2 = 0
- if self.hasInputFromPort('Field2') :
- Field2 = self.getInputFromPort('Field2')
- Function = ''
- if self.hasInputFromPort('Function') :
- Function = self.getInputFromPort('Function')
- Array = 0
- if self.hasInputFromPort('Array') :
- Array = self.getInputFromPort('Array')
- results = p.execute(Field1, Field2, Function, Array)
- self.setResult('Field', results)
-
-class CalculateLatVolGradientsAtNodes(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateLatVolGradientsAtNodesAlg()
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Gradient', results)
-
-class CalculateGradients(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateGradientsAlg()
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output CalculateGradients', results)
-
-class CalculateSignedDistanceToField(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateSignedDistanceToFieldAlg()
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- ObjectField = 0
- if self.hasInputFromPort('ObjectField') :
- ObjectField = self.getInputFromPort('ObjectField')
- results = p.execute(Field, ObjectField)
- self.setResult('SignedDistanceField', results)
-
-class CalculateInsideWhichField(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateInsideWhichFieldAlg()
- if self.hasInputFromPort('p_outputbasis') :
- p.set_p_outputbasis(self.getInputFromPort('p_outputbasis'))
- if self.hasInputFromPort('p_outputtype') :
- p.set_p_outputtype(self.getInputFromPort('p_outputtype'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- Object = 0
- if self.hasInputFromPort('Object') :
- Object = self.getInputFromPort('Object')
- results = p.execute(Field, Object)
- self.setResult('Field', results)
-
-class MapFieldDataFromNodeToElem(ChangeFieldData) :
- def compute(self) :
- p = sr_py.MapFieldDataFromNodeToElemAlg()
- if self.hasInputFromPort('p_method') :
- p.set_p_method(self.getInputFromPort('p_method'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('Field', results)
-
-class ConvertFieldDataType(ChangeFieldData) :
- def compute(self) :
- p = sr_py.ConvertFieldDataTypeAlg()
- if self.hasInputFromPort('p_outputdatatype') :
- p.set_p_outputdatatype(self.getInputFromPort('p_outputdatatype'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Field', results)
-
-class CalculateIsInsideField(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateIsInsideFieldAlg()
- if self.hasInputFromPort('p_outputtype') :
- p.set_p_outputtype(self.getInputFromPort('p_outputtype'))
- if self.hasInputFromPort('p_outval') :
- p.set_p_outval(self.getInputFromPort('p_outval'))
- if self.hasInputFromPort('p_inval') :
- p.set_p_inval(self.getInputFromPort('p_inval'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- ObjectField = 0
- if self.hasInputFromPort('ObjectField') :
- ObjectField = self.getInputFromPort('ObjectField')
- results = p.execute(Field, ObjectField)
- self.setResult('Field', results)
-
-class CalculateFieldData(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateFieldDataAlg()
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- if self.hasInputFromPort('p_format') :
- p.set_p_format(self.getInputFromPort('p_format'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- Function = ''
- if self.hasInputFromPort('Function') :
- Function = self.getInputFromPort('Function')
- Array = 0
- if self.hasInputFromPort('Array') :
- Array = self.getInputFromPort('Array')
- results = p.execute(Field, Function, Array)
- self.setResult('Field', results)
-
-class CalculateDistanceToField(ChangeFieldData) :
- def compute(self) :
- p = sr_py.CalculateDistanceToFieldAlg()
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- ObjectField = 0
- if self.hasInputFromPort('ObjectField') :
- ObjectField = self.getInputFromPort('ObjectField')
- results = p.execute(Field, ObjectField)
- self.setResult('DistanceField', results)
-
-class TransformPlanarMesh(ChangeMesh) :
- def compute(self) :
- p = sr_py.TransformPlanarMeshAlg()
- if self.hasInputFromPort('p_axis') :
- p.set_p_axis(self.getInputFromPort('p_axis'))
- if self.hasInputFromPort('p_invert') :
- p.set_p_invert(self.getInputFromPort('p_invert'))
- if self.hasInputFromPort('p_trans_x') :
- p.set_p_trans_x(self.getInputFromPort('p_trans_x'))
- if self.hasInputFromPort('p_trans_y') :
- p.set_p_trans_y(self.getInputFromPort('p_trans_y'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- Index_Matrix = 0
- if self.hasInputFromPort('Index Matrix') :
- Index_Matrix = self.getInputFromPort('Index Matrix')
- results = p.execute(Input_Field, Index_Matrix)
- self.setResult('Transformed Field', results)
-
-class ConvertMeshToUnstructuredMesh(ChangeMesh) :
- def compute(self) :
- p = sr_py.ConvertMeshToUnstructuredMeshAlg()
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Field', results)
-
-class ConvertQuadSurfToTriSurf(ChangeMesh) :
- def compute(self) :
- p = sr_py.ConvertQuadSurfToTriSurfAlg()
- QuadSurf = 0
- if self.hasInputFromPort('QuadSurf') :
- QuadSurf = self.getInputFromPort('QuadSurf')
- results = p.execute(QuadSurf)
- self.setResult('TriSurf', results)
-
-class TransformMeshWithFunction(ChangeMesh) :
- def compute(self) :
- p = sr_py.TransformMeshWithFunctionAlg()
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Field', results)
-
-class ConvertHexVolToTetVol(ChangeMesh) :
- def compute(self) :
- p = sr_py.ConvertHexVolToTetVolAlg()
- HexVol = 0
- if self.hasInputFromPort('HexVol') :
- HexVol = self.getInputFromPort('HexVol')
- results = p.execute(HexVol)
- self.setResult('TetVol', results)
-
-class ConvertMeshCoordinateSystem(ChangeMesh) :
- def compute(self) :
- p = sr_py.ConvertMeshCoordinateSystemAlg()
- if self.hasInputFromPort('p_oldsystem') :
- p.set_p_oldsystem(self.getInputFromPort('p_oldsystem'))
- if self.hasInputFromPort('p_newsystem') :
- p.set_p_newsystem(self.getInputFromPort('p_newsystem'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Field', results)
-
-class ConvertMeshToPointCloud(ChangeMesh) :
- def compute(self) :
- p = sr_py.ConvertMeshToPointCloudAlg()
- if self.hasInputFromPort('p_datalocation') :
- p.set_p_datalocation(self.getInputFromPort('p_datalocation'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('Field', results)
-
-class TransformMeshWithTransform(ChangeMesh) :
- def compute(self) :
- p = sr_py.TransformMeshWithTransformAlg()
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- Transform_Matrix = 0
- if self.hasInputFromPort('Transform Matrix') :
- Transform_Matrix = self.getInputFromPort('Transform Matrix')
- results = p.execute(Input_Field, Transform_Matrix)
- self.setResult('Transformed Field', results)
-
-class ConvertRegularMeshToStructuredMesh(ChangeMesh) :
- def compute(self) :
- p = sr_py.ConvertRegularMeshToStructuredMeshAlg()
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Field', results)
-
-class CalculateMeshNodes(ChangeMesh) :
- def compute(self) :
- p = sr_py.CalculateMeshNodesAlg()
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- Function = ''
- if self.hasInputFromPort('Function') :
- Function = self.getInputFromPort('Function')
- Array = 0
- if self.hasInputFromPort('Array') :
- Array = self.getInputFromPort('Array')
- results = p.execute(Field, Function, Array)
- self.setResult('Field', results)
-
-class SmoothMesh(ChangeMesh) :
- def compute(self) :
- p = sr_py.SmoothMeshAlg()
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- IsoValue = 0
- if self.hasInputFromPort('IsoValue') :
- IsoValue = self.getInputFromPort('IsoValue')
- results = p.execute(Input, IsoValue)
- self.setResult('Smoothed', results)
-
-class EditMeshBoundingBox(ChangeMesh) :
- def compute(self) :
- p = sr_py.EditMeshBoundingBoxAlg()
- if self.hasInputFromPort('p_outputcenterx') :
- p.set_p_outputcenterx(self.getInputFromPort('p_outputcenterx'))
- if self.hasInputFromPort('p_outputcentery') :
- p.set_p_outputcentery(self.getInputFromPort('p_outputcentery'))
- if self.hasInputFromPort('p_outputcenterz') :
- p.set_p_outputcenterz(self.getInputFromPort('p_outputcenterz'))
- if self.hasInputFromPort('p_outputsizex') :
- p.set_p_outputsizex(self.getInputFromPort('p_outputsizex'))
- if self.hasInputFromPort('p_outputsizey') :
- p.set_p_outputsizey(self.getInputFromPort('p_outputsizey'))
- if self.hasInputFromPort('p_outputsizez') :
- p.set_p_outputsizez(self.getInputFromPort('p_outputsizez'))
- if self.hasInputFromPort('p_useoutputcenter') :
- p.set_p_useoutputcenter(self.getInputFromPort('p_useoutputcenter'))
- if self.hasInputFromPort('p_useoutputsize') :
- p.set_p_useoutputsize(self.getInputFromPort('p_useoutputsize'))
- if self.hasInputFromPort('p_box_scale') :
- p.set_p_box_scale(self.getInputFromPort('p_box_scale'))
- if self.hasInputFromPort('p_box_mode') :
- p.set_p_box_mode(self.getInputFromPort('p_box_mode'))
- if self.hasInputFromPort('p_box_real_scale') :
- p.set_p_box_real_scale(self.getInputFromPort('p_box_real_scale'))
- if self.hasInputFromPort('p_box_center_x') :
- p.set_p_box_center_x(self.getInputFromPort('p_box_center_x'))
- if self.hasInputFromPort('p_box_center_y') :
- p.set_p_box_center_y(self.getInputFromPort('p_box_center_y'))
- if self.hasInputFromPort('p_box_center_z') :
- p.set_p_box_center_z(self.getInputFromPort('p_box_center_z'))
- if self.hasInputFromPort('p_box_right_x') :
- p.set_p_box_right_x(self.getInputFromPort('p_box_right_x'))
- if self.hasInputFromPort('p_box_right_y') :
- p.set_p_box_right_y(self.getInputFromPort('p_box_right_y'))
- if self.hasInputFromPort('p_box_right_z') :
- p.set_p_box_right_z(self.getInputFromPort('p_box_right_z'))
- if self.hasInputFromPort('p_box_down_x') :
- p.set_p_box_down_x(self.getInputFromPort('p_box_down_x'))
- if self.hasInputFromPort('p_box_down_y') :
- p.set_p_box_down_y(self.getInputFromPort('p_box_down_y'))
- if self.hasInputFromPort('p_box_down_z') :
- p.set_p_box_down_z(self.getInputFromPort('p_box_down_z'))
- if self.hasInputFromPort('p_box_in_x') :
- p.set_p_box_in_x(self.getInputFromPort('p_box_in_x'))
- if self.hasInputFromPort('p_box_in_y') :
- p.set_p_box_in_y(self.getInputFromPort('p_box_in_y'))
- if self.hasInputFromPort('p_box_in_z') :
- p.set_p_box_in_z(self.getInputFromPort('p_box_in_z'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Field', results[0])
- self.setResult('Transformation Widget', results[1])
- self.setResult('Transformation Matrix', results[2])
-
-class SwapNodeLocationsWithMatrixEntries(ChangeMesh) :
- def compute(self) :
- p = sr_py.SwapNodeLocationsWithMatrixEntriesAlg()
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- Input_Matrix = 0
- if self.hasInputFromPort('Input Matrix') :
- Input_Matrix = self.getInputFromPort('Input Matrix')
- results = p.execute(Input_Field, Input_Matrix)
- self.setResult('Output Field', results[0])
- self.setResult('Output Matrix', results[1])
-
-class MapFieldDataToNodeCoordinate(ChangeMesh) :
- def compute(self) :
- p = sr_py.MapFieldDataToNodeCoordinateAlg()
- if self.hasInputFromPort('p_coord') :
- p.set_p_coord(self.getInputFromPort('p_coord'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Field', results)
-
-class ScaleFieldMeshAndData(ChangeMesh) :
- def compute(self) :
- p = sr_py.ScaleFieldMeshAndDataAlg()
- if self.hasInputFromPort('p_datascale') :
- p.set_p_datascale(self.getInputFromPort('p_datascale'))
- if self.hasInputFromPort('p_geomscale') :
- p.set_p_geomscale(self.getInputFromPort('p_geomscale'))
- if self.hasInputFromPort('p_usegeomcenter') :
- p.set_p_usegeomcenter(self.getInputFromPort('p_usegeomcenter'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- GeomScaleFactor = 0
- if self.hasInputFromPort('GeomScaleFactor') :
- GeomScaleFactor = self.getInputFromPort('GeomScaleFactor')
- DataScaleFactor = 0
- if self.hasInputFromPort('DataScaleFactor') :
- DataScaleFactor = self.getInputFromPort('DataScaleFactor')
- results = p.execute(Field, GeomScaleFactor, DataScaleFactor)
- self.setResult('Field', results)
-
-class ReportColumnMatrixMisfit(Math) :
- def compute(self) :
- p = sr_py.ReportColumnMatrixMisfitAlg()
- if self.hasInputFromPort('p_have_ui') :
- p.set_p_have_ui(self.getInputFromPort('p_have_ui'))
- if self.hasInputFromPort('p_methodTCL') :
- p.set_p_methodTCL(self.getInputFromPort('p_methodTCL'))
- if self.hasInputFromPort('p_pTCL') :
- p.set_p_pTCL(self.getInputFromPort('p_pTCL'))
- Vec1 = 0
- if self.hasInputFromPort('Vec1') :
- Vec1 = self.getInputFromPort('Vec1')
- Vec2 = 0
- if self.hasInputFromPort('Vec2') :
- Vec2 = self.getInputFromPort('Vec2')
- results = p.execute(Vec1, Vec2)
- self.setResult('Error Out', results)
-
-class EvaluateLinAlgGeneral(Math) :
- def compute(self) :
- p = sr_py.EvaluateLinAlgGeneralAlg()
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- i1 = 0
- if self.hasInputFromPort('i1') :
- i1 = self.getInputFromPort('i1')
- i2 = 0
- if self.hasInputFromPort('i2') :
- i2 = self.getInputFromPort('i2')
- i3 = 0
- if self.hasInputFromPort('i3') :
- i3 = self.getInputFromPort('i3')
- i4 = 0
- if self.hasInputFromPort('i4') :
- i4 = self.getInputFromPort('i4')
- i5 = 0
- if self.hasInputFromPort('i5') :
- i5 = self.getInputFromPort('i5')
- results = p.execute(i1, i2, i3, i4, i5)
- self.setResult('o1', results[0])
- self.setResult('o2', results[1])
- self.setResult('o3', results[2])
- self.setResult('o4', results[3])
- self.setResult('o5', results[4])
-
-class AppendMatrix(Math) :
- def compute(self) :
- p = sr_py.AppendMatrixAlg()
- if self.hasInputFromPort('p_row_or_column') :
- p.set_p_row_or_column(self.getInputFromPort('p_row_or_column'))
- BaseMatrix = 0
- if self.hasInputFromPort('BaseMatrix') :
- BaseMatrix = self.getInputFromPort('BaseMatrix')
- AppendMatrix = 0
- if self.hasInputFromPort('AppendMatrix') :
- AppendMatrix = self.getInputFromPort('AppendMatrix')
- results = p.execute(BaseMatrix, AppendMatrix)
- self.setResult('Matrix', results)
-
-class EvaluateLinAlgBinary(Math) :
- def compute(self) :
- p = sr_py.EvaluateLinAlgBinaryAlg()
- if self.hasInputFromPort('p_op') :
- p.set_p_op(self.getInputFromPort('p_op'))
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- A = 0
- if self.hasInputFromPort('A') :
- A = self.getInputFromPort('A')
- B = 0
- if self.hasInputFromPort('B') :
- B = self.getInputFromPort('B')
- results = p.execute(A, B)
- self.setResult('Output', results)
-
-class ConvertMaskVectorToMappingMatrix(Math) :
- def compute(self) :
- p = sr_py.ConvertMaskVectorToMappingMatrixAlg()
- MaskVector = 0
- if self.hasInputFromPort('MaskVector') :
- MaskVector = self.getInputFromPort('MaskVector')
- results = p.execute(MaskVector)
- self.setResult('MappingMatrix', results)
-
-class SolveLinearSystem(Math) :
- def compute(self) :
- p = sr_py.SolveLinearSystemAlg()
- if self.hasInputFromPort('p_target_error') :
- p.set_p_target_error(self.getInputFromPort('p_target_error'))
- if self.hasInputFromPort('p_flops') :
- p.set_p_flops(self.getInputFromPort('p_flops'))
- if self.hasInputFromPort('p_floprate') :
- p.set_p_floprate(self.getInputFromPort('p_floprate'))
- if self.hasInputFromPort('p_memrefs') :
- p.set_p_memrefs(self.getInputFromPort('p_memrefs'))
- if self.hasInputFromPort('p_memrate') :
- p.set_p_memrate(self.getInputFromPort('p_memrate'))
- if self.hasInputFromPort('p_orig_error') :
- p.set_p_orig_error(self.getInputFromPort('p_orig_error'))
- if self.hasInputFromPort('p_current_error') :
- p.set_p_current_error(self.getInputFromPort('p_current_error'))
- if self.hasInputFromPort('p_method') :
- p.set_p_method(self.getInputFromPort('p_method'))
- if self.hasInputFromPort('p_precond') :
- p.set_p_precond(self.getInputFromPort('p_precond'))
- if self.hasInputFromPort('p_iteration') :
- p.set_p_iteration(self.getInputFromPort('p_iteration'))
- if self.hasInputFromPort('p_maxiter') :
- p.set_p_maxiter(self.getInputFromPort('p_maxiter'))
- if self.hasInputFromPort('p_use_previous_soln') :
- p.set_p_use_previous_soln(self.getInputFromPort('p_use_previous_soln'))
- if self.hasInputFromPort('p_emit_partial') :
- p.set_p_emit_partial(self.getInputFromPort('p_emit_partial'))
- if self.hasInputFromPort('p_emit_iter') :
- p.set_p_emit_iter(self.getInputFromPort('p_emit_iter'))
- if self.hasInputFromPort('p_status') :
- p.set_p_status(self.getInputFromPort('p_status'))
- if self.hasInputFromPort('p_np') :
- p.set_p_np(self.getInputFromPort('p_np'))
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- RHS = 0
- if self.hasInputFromPort('RHS') :
- RHS = self.getInputFromPort('RHS')
- results = p.execute(Matrix, RHS)
- self.setResult('Solution', results)
-
-class ReportMatrixColumnMeasure(Math) :
- def compute(self) :
- p = sr_py.ReportMatrixColumnMeasureAlg()
- if self.hasInputFromPort('p_method') :
- p.set_p_method(self.getInputFromPort('p_method'))
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(Matrix)
- self.setResult('Vector', results)
-
-class SortMatrix(Math) :
- def compute(self) :
- p = sr_py.SortMatrixAlg()
- if self.hasInputFromPort('p_row_or_col') :
- p.set_p_row_or_col(self.getInputFromPort('p_row_or_col'))
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(Matrix)
- self.setResult('Matrix', results)
-
-class CreateGeometricTransform(Math) :
- def compute(self) :
- p = sr_py.CreateGeometricTransformAlg()
- if self.hasInputFromPort('p_rotate_x') :
- p.set_p_rotate_x(self.getInputFromPort('p_rotate_x'))
- if self.hasInputFromPort('p_rotate_y') :
- p.set_p_rotate_y(self.getInputFromPort('p_rotate_y'))
- if self.hasInputFromPort('p_rotate_z') :
- p.set_p_rotate_z(self.getInputFromPort('p_rotate_z'))
- if self.hasInputFromPort('p_rotate_theta') :
- p.set_p_rotate_theta(self.getInputFromPort('p_rotate_theta'))
- if self.hasInputFromPort('p_translate_x') :
- p.set_p_translate_x(self.getInputFromPort('p_translate_x'))
- if self.hasInputFromPort('p_translate_y') :
- p.set_p_translate_y(self.getInputFromPort('p_translate_y'))
- if self.hasInputFromPort('p_translate_z') :
- p.set_p_translate_z(self.getInputFromPort('p_translate_z'))
- if self.hasInputFromPort('p_scale_uniform') :
- p.set_p_scale_uniform(self.getInputFromPort('p_scale_uniform'))
- if self.hasInputFromPort('p_scale_x') :
- p.set_p_scale_x(self.getInputFromPort('p_scale_x'))
- if self.hasInputFromPort('p_scale_y') :
- p.set_p_scale_y(self.getInputFromPort('p_scale_y'))
- if self.hasInputFromPort('p_scale_z') :
- p.set_p_scale_z(self.getInputFromPort('p_scale_z'))
- if self.hasInputFromPort('p_shear_plane_a') :
- p.set_p_shear_plane_a(self.getInputFromPort('p_shear_plane_a'))
- if self.hasInputFromPort('p_shear_plane_b') :
- p.set_p_shear_plane_b(self.getInputFromPort('p_shear_plane_b'))
- if self.hasInputFromPort('p_shear_plane_c') :
- p.set_p_shear_plane_c(self.getInputFromPort('p_shear_plane_c'))
- if self.hasInputFromPort('p_widget_resizable') :
- p.set_p_widget_resizable(self.getInputFromPort('p_widget_resizable'))
- if self.hasInputFromPort('p_permute_x') :
- p.set_p_permute_x(self.getInputFromPort('p_permute_x'))
- if self.hasInputFromPort('p_permute_y') :
- p.set_p_permute_y(self.getInputFromPort('p_permute_y'))
- if self.hasInputFromPort('p_permute_z') :
- p.set_p_permute_z(self.getInputFromPort('p_permute_z'))
- if self.hasInputFromPort('p_pre_transform') :
- p.set_p_pre_transform(self.getInputFromPort('p_pre_transform'))
- if self.hasInputFromPort('p_which_transform') :
- p.set_p_which_transform(self.getInputFromPort('p_which_transform'))
- if self.hasInputFromPort('p_widget_scale') :
- p.set_p_widget_scale(self.getInputFromPort('p_widget_scale'))
- if self.hasInputFromPort('p_ignoring_widget_changes') :
- p.set_p_ignoring_widget_changes(self.getInputFromPort('p_ignoring_widget_changes'))
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(Matrix)
- self.setResult('Matrix', results[0])
- self.setResult('Geometry', results[1])
-
-class ChooseMatrix(Math) :
- def compute(self) :
- p = sr_py.ChooseMatrixAlg()
- if self.hasInputFromPort('p_use_first_valid') :
- p.set_p_use_first_valid(self.getInputFromPort('p_use_first_valid'))
- if self.hasInputFromPort('p_port_valid_index') :
- p.set_p_port_valid_index(self.getInputFromPort('p_port_valid_index'))
- if self.hasInputFromPort('p_port_selected_index') :
- p.set_p_port_selected_index(self.getInputFromPort('p_port_selected_index'))
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(Matrix)
- self.setResult('Matrix', results)
-
-class ConvertMappingMatrixToMaskVector(Math) :
- def compute(self) :
- p = sr_py.ConvertMappingMatrixToMaskVectorAlg()
- MappingMatrix = 0
- if self.hasInputFromPort('MappingMatrix') :
- MappingMatrix = self.getInputFromPort('MappingMatrix')
- results = p.execute(MappingMatrix)
- self.setResult('MaskVector', results)
-
-class ResizeMatrix(Math) :
- def compute(self) :
- p = sr_py.ResizeMatrixAlg()
- if self.hasInputFromPort('p_dim_m') :
- p.set_p_dim_m(self.getInputFromPort('p_dim_m'))
- if self.hasInputFromPort('p_dim_n') :
- p.set_p_dim_n(self.getInputFromPort('p_dim_n'))
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- M = 0
- if self.hasInputFromPort('M') :
- M = self.getInputFromPort('M')
- N = 0
- if self.hasInputFromPort('N') :
- N = self.getInputFromPort('N')
- results = p.execute(Matrix, M, N)
- self.setResult('Matrix', results)
-
-class CollectMatrices(Math) :
- def compute(self) :
- p = sr_py.CollectMatricesAlg()
- if self.hasInputFromPort('p_append') :
- p.set_p_append(self.getInputFromPort('p_append'))
- if self.hasInputFromPort('p_row') :
- p.set_p_row(self.getInputFromPort('p_row'))
- if self.hasInputFromPort('p_front') :
- p.set_p_front(self.getInputFromPort('p_front'))
- Optional_BaseMatrix = 0
- if self.hasInputFromPort('Optional BaseMatrix') :
- Optional_BaseMatrix = self.getInputFromPort('Optional BaseMatrix')
- SubMatrix = 0
- if self.hasInputFromPort('SubMatrix') :
- SubMatrix = self.getInputFromPort('SubMatrix')
- results = p.execute(Optional_BaseMatrix, SubMatrix)
- self.setResult('CompositeMatrix', results)
-
-class GetColumnOrRowFromMatrix(Math) :
- def compute(self) :
- p = sr_py.GetColumnOrRowFromMatrixAlg()
- if self.hasInputFromPort('p_row_or_col') :
- p.set_p_row_or_col(self.getInputFromPort('p_row_or_col'))
- if self.hasInputFromPort('p_selectable_min') :
- p.set_p_selectable_min(self.getInputFromPort('p_selectable_min'))
- if self.hasInputFromPort('p_selectable_max') :
- p.set_p_selectable_max(self.getInputFromPort('p_selectable_max'))
- if self.hasInputFromPort('p_selectable_inc') :
- p.set_p_selectable_inc(self.getInputFromPort('p_selectable_inc'))
- if self.hasInputFromPort('p_selectable_units') :
- p.set_p_selectable_units(self.getInputFromPort('p_selectable_units'))
- if self.hasInputFromPort('p_range_min') :
- p.set_p_range_min(self.getInputFromPort('p_range_min'))
- if self.hasInputFromPort('p_range_max') :
- p.set_p_range_max(self.getInputFromPort('p_range_max'))
- if self.hasInputFromPort('p_playmode') :
- p.set_p_playmode(self.getInputFromPort('p_playmode'))
- if self.hasInputFromPort('p_current') :
- p.set_p_current(self.getInputFromPort('p_current'))
- if self.hasInputFromPort('p_execmode') :
- p.set_p_execmode(self.getInputFromPort('p_execmode'))
- if self.hasInputFromPort('p_delay') :
- p.set_p_delay(self.getInputFromPort('p_delay'))
- if self.hasInputFromPort('p_inc_amount') :
- p.set_p_inc_amount(self.getInputFromPort('p_inc_amount'))
- if self.hasInputFromPort('p_send_amount') :
- p.set_p_send_amount(self.getInputFromPort('p_send_amount'))
- if self.hasInputFromPort('p_data_series_done') :
- p.set_p_data_series_done(self.getInputFromPort('p_data_series_done'))
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- Weight_Vector = 0
- if self.hasInputFromPort('Weight Vector') :
- Weight_Vector = self.getInputFromPort('Weight Vector')
- Current_Index = 0
- if self.hasInputFromPort('Current Index') :
- Current_Index = self.getInputFromPort('Current Index')
- results = p.execute(Matrix, Weight_Vector, Current_Index)
- self.setResult('Vector', results[0])
- self.setResult('Selected Index', results[1])
-
-class BuildNoiseColumnMatrix(Math) :
- def compute(self) :
- p = sr_py.BuildNoiseColumnMatrixAlg()
- if self.hasInputFromPort('p_snr') :
- p.set_p_snr(self.getInputFromPort('p_snr'))
- Signal = 0
- if self.hasInputFromPort('Signal') :
- Signal = self.getInputFromPort('Signal')
- results = p.execute(Signal)
- self.setResult('Noise', results)
-
-class EvaluateLinAlgUnary(Math) :
- def compute(self) :
- p = sr_py.EvaluateLinAlgUnaryAlg()
- if self.hasInputFromPort('p_op') :
- p.set_p_op(self.getInputFromPort('p_op'))
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- results = p.execute(Input)
- self.setResult('Output', results)
-
-class GetSubmatrix(Math) :
- def compute(self) :
- p = sr_py.GetSubmatrixAlg()
- if self.hasInputFromPort('p_mincol') :
- p.set_p_mincol(self.getInputFromPort('p_mincol'))
- if self.hasInputFromPort('p_maxcol') :
- p.set_p_maxcol(self.getInputFromPort('p_maxcol'))
- if self.hasInputFromPort('p_minrow') :
- p.set_p_minrow(self.getInputFromPort('p_minrow'))
- if self.hasInputFromPort('p_maxrow') :
- p.set_p_maxrow(self.getInputFromPort('p_maxrow'))
- if self.hasInputFromPort('p_nrow') :
- p.set_p_nrow(self.getInputFromPort('p_nrow'))
- if self.hasInputFromPort('p_ncol') :
- p.set_p_ncol(self.getInputFromPort('p_ncol'))
- Input_Matrix = 0
- if self.hasInputFromPort('Input Matrix') :
- Input_Matrix = self.getInputFromPort('Input Matrix')
- Optional_Range_Bounds = 0
- if self.hasInputFromPort('Optional Range Bounds') :
- Optional_Range_Bounds = self.getInputFromPort('Optional Range Bounds')
- results = p.execute(Input_Matrix, Optional_Range_Bounds)
- self.setResult('Output Matrix', results)
-
-class ReorderMatrixByReverseCuthillMcKee(Math) :
- def compute(self) :
- p = sr_py.ReorderMatrixByReverseCuthillMcKeeAlg()
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(Matrix)
- self.setResult('Matrix', results[0])
- self.setResult('Mapping', results[1])
- self.setResult('InverseMapping', results[2])
-
-class CreateMatrix(Math) :
- def compute(self) :
- p = sr_py.CreateMatrixAlg()
- if self.hasInputFromPort('p_rows') :
- p.set_p_rows(self.getInputFromPort('p_rows'))
- if self.hasInputFromPort('p_cols') :
- p.set_p_cols(self.getInputFromPort('p_cols'))
- if self.hasInputFromPort('p_data') :
- p.set_p_data(self.getInputFromPort('p_data'))
- if self.hasInputFromPort('p_clabel') :
- p.set_p_clabel(self.getInputFromPort('p_clabel'))
- if self.hasInputFromPort('p_rlabel') :
- p.set_p_rlabel(self.getInputFromPort('p_rlabel'))
- results = p.execute()
- self.setResult('matrix', results)
-
-class SolveMinNormLeastSqSystem(Math) :
- def compute(self) :
- p = sr_py.SolveMinNormLeastSqSystemAlg()
- BasisVec1 = 0
- if self.hasInputFromPort('BasisVec1') :
- BasisVec1 = self.getInputFromPort('BasisVec1')
- BasisVec2 = 0
- if self.hasInputFromPort('BasisVec2') :
- BasisVec2 = self.getInputFromPort('BasisVec2')
- BasisVec3 = 0
- if self.hasInputFromPort('BasisVec3') :
- BasisVec3 = self.getInputFromPort('BasisVec3')
- TargetVec = 0
- if self.hasInputFromPort('TargetVec') :
- TargetVec = self.getInputFromPort('TargetVec')
- results = p.execute(BasisVec1, BasisVec2, BasisVec3, TargetVec)
- self.setResult('WeightVec(Col)', results[0])
- self.setResult('ResultVec(Col)', results[1])
-
-class ConvertMatrixType(Math) :
- def compute(self) :
- p = sr_py.ConvertMatrixTypeAlg()
- if self.hasInputFromPort('p_oldtype') :
- p.set_p_oldtype(self.getInputFromPort('p_oldtype'))
- if self.hasInputFromPort('p_newtype') :
- p.set_p_newtype(self.getInputFromPort('p_newtype'))
- if self.hasInputFromPort('p_nrow') :
- p.set_p_nrow(self.getInputFromPort('p_nrow'))
- if self.hasInputFromPort('p_ncol') :
- p.set_p_ncol(self.getInputFromPort('p_ncol'))
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- results = p.execute(Input)
- self.setResult('Output', results)
-
-class ReportMatrixRowMeasure(Math) :
- def compute(self) :
- p = sr_py.ReportMatrixRowMeasureAlg()
- if self.hasInputFromPort('p_method') :
- p.set_p_method(self.getInputFromPort('p_method'))
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(Matrix)
- self.setResult('Vector', results)
-
-class ReorderMatrixByCuthillMcKee(Math) :
- def compute(self) :
- p = sr_py.ReorderMatrixByCuthillMcKeeAlg()
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(Matrix)
- self.setResult('Matrix', results[0])
- self.setResult('Mapping', results[1])
- self.setResult('InverseMapping', results[2])
-
-class ReportMatrixInfo(Math) :
- def compute(self) :
- p = sr_py.ReportMatrixInfoAlg()
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- results = p.execute(Input)
- self.setResult('NumRows', results[0])
- self.setResult('NumCols', results[1])
- self.setResult('NumElements', results[2])
-
-class RemoveZerosFromMatrix(Math) :
- def compute(self) :
- p = sr_py.RemoveZerosFromMatrixAlg()
- if self.hasInputFromPort('p_row_or_col') :
- p.set_p_row_or_col(self.getInputFromPort('p_row_or_col'))
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(Matrix)
- self.setResult('Matrix', results)
-
-class RemoveZeroRowsAndColumns(Math) :
- def compute(self) :
- p = sr_py.RemoveZeroRowsAndColumnsAlg()
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(Matrix)
- self.setResult('ReducedMatrix', results[0])
- self.setResult('LeftMapping', results[1])
- self.setResult('RightMapping', results[2])
-
-class CreateDataArray(DataArrayMath) :
- def compute(self) :
- p = sr_py.CreateDataArrayAlg()
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- if self.hasInputFromPort('p_format') :
- p.set_p_format(self.getInputFromPort('p_format'))
- Size = 0
- if self.hasInputFromPort('Size') :
- Size = self.getInputFromPort('Size')
- Function = ''
- if self.hasInputFromPort('Function') :
- Function = self.getInputFromPort('Function')
- Array = 0
- if self.hasInputFromPort('Array') :
- Array = self.getInputFromPort('Array')
- results = p.execute(Size, Function, Array)
- self.setResult('DataArray', results)
-
-class CreateDataArrayFromIndices(DataArrayMath) :
- def compute(self) :
- p = sr_py.CreateDataArrayFromIndicesAlg()
- Indices = 0
- if self.hasInputFromPort('Indices') :
- Indices = self.getInputFromPort('Indices')
- Template = 0
- if self.hasInputFromPort('Template') :
- Template = self.getInputFromPort('Template')
- results = p.execute(Indices, Template)
- self.setResult('DataArray', results)
-
-class ReportDataArrayInfo(DataArrayMath) :
- def compute(self) :
- p = sr_py.ReportDataArrayInfoAlg()
- DataArray = 0
- if self.hasInputFromPort('DataArray') :
- DataArray = self.getInputFromPort('DataArray')
- results = p.execute(DataArray)
- self.setResult('NumElements', results)
-
-class CreateVectorArray(DataArrayMath) :
- def compute(self) :
- p = sr_py.CreateVectorArrayAlg()
- X = 0
- if self.hasInputFromPort('X') :
- X = self.getInputFromPort('X')
- Y = 0
- if self.hasInputFromPort('Y') :
- Y = self.getInputFromPort('Y')
- Z = 0
- if self.hasInputFromPort('Z') :
- Z = self.getInputFromPort('Z')
- results = p.execute(X, Y, Z)
- self.setResult('Vector', results)
-
-class ReplicateDataArray(DataArrayMath) :
- def compute(self) :
- p = sr_py.ReplicateDataArrayAlg()
- if self.hasInputFromPort('p_size') :
- p.set_p_size(self.getInputFromPort('p_size'))
- DataArray = 0
- if self.hasInputFromPort('DataArray') :
- DataArray = self.getInputFromPort('DataArray')
- Size = 0
- if self.hasInputFromPort('Size') :
- Size = self.getInputFromPort('Size')
- results = p.execute(DataArray, Size)
- self.setResult('DataArray', results)
-
-class SplitVectorArrayInXYZ(DataArrayMath) :
- def compute(self) :
- p = sr_py.SplitVectorArrayInXYZAlg()
- VectorArray = 0
- if self.hasInputFromPort('VectorArray') :
- VectorArray = self.getInputFromPort('VectorArray')
- results = p.execute(VectorArray)
- self.setResult('X', results[0])
- self.setResult('Y', results[1])
- self.setResult('Z', results[2])
-
-class DecomposeTensorArrayIntoEigenVectors(DataArrayMath) :
- def compute(self) :
- p = sr_py.DecomposeTensorArrayIntoEigenVectorsAlg()
- TensorArray = 0
- if self.hasInputFromPort('TensorArray') :
- TensorArray = self.getInputFromPort('TensorArray')
- results = p.execute(TensorArray)
- self.setResult('EigenVector1', results[0])
- self.setResult('EigenVector2', results[1])
- self.setResult('EigenVector3', results[2])
- self.setResult('EigenValue1', results[3])
- self.setResult('EigenValue2', results[4])
- self.setResult('EigenValue3', results[5])
-
-class CalculateDataArray(DataArrayMath) :
- def compute(self) :
- p = sr_py.CalculateDataArrayAlg()
- if self.hasInputFromPort('p_function') :
- p.set_p_function(self.getInputFromPort('p_function'))
- if self.hasInputFromPort('p_format') :
- p.set_p_format(self.getInputFromPort('p_format'))
- DataArray = 0
- if self.hasInputFromPort('DataArray') :
- DataArray = self.getInputFromPort('DataArray')
- Function = ''
- if self.hasInputFromPort('Function') :
- Function = self.getInputFromPort('Function')
- Array = 0
- if self.hasInputFromPort('Array') :
- Array = self.getInputFromPort('Array')
- results = p.execute(DataArray, Function, Array)
- self.setResult('DataArray', results)
-
-class ReportDataArrayMeasure(DataArrayMath) :
- def compute(self) :
- p = sr_py.ReportDataArrayMeasureAlg()
- if self.hasInputFromPort('p_measure') :
- p.set_p_measure(self.getInputFromPort('p_measure'))
- Array = 0
- if self.hasInputFromPort('Array') :
- Array = self.getInputFromPort('Array')
- results = p.execute(Array)
- self.setResult('Measure', results)
-
-class AppendDataArrays(DataArrayMath) :
- def compute(self) :
- p = sr_py.AppendDataArraysAlg()
- Array = 0
- if self.hasInputFromPort('Array') :
- Array = self.getInputFromPort('Array')
- results = p.execute(Array)
- self.setResult('Array', results)
-
-class CreateTensorArray(DataArrayMath) :
- def compute(self) :
- p = sr_py.CreateTensorArrayAlg()
- EigenVector1 = 0
- if self.hasInputFromPort('EigenVector1') :
- EigenVector1 = self.getInputFromPort('EigenVector1')
- EigenVector2 = 0
- if self.hasInputFromPort('EigenVector2') :
- EigenVector2 = self.getInputFromPort('EigenVector2')
- EigenValue1 = 0
- if self.hasInputFromPort('EigenValue1') :
- EigenValue1 = self.getInputFromPort('EigenValue1')
- EigenValue2 = 0
- if self.hasInputFromPort('EigenValue2') :
- EigenValue2 = self.getInputFromPort('EigenValue2')
- EigenValue3 = 0
- if self.hasInputFromPort('EigenValue3') :
- EigenValue3 = self.getInputFromPort('EigenValue3')
- results = p.execute(EigenVector1, EigenVector2, EigenValue1, EigenValue2, EigenValue3)
- self.setResult('TensorArray', results)
-
-class PrintMatrixIntoString(String) :
- def compute(self) :
- p = sr_py.PrintMatrixIntoStringAlg()
- if self.hasInputFromPort('p_formatstring') :
- p.set_p_formatstring(self.getInputFromPort('p_formatstring'))
- Format = ''
- if self.hasInputFromPort('Format') :
- Format = self.getInputFromPort('Format')
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- results = p.execute(Format, Input)
- self.setResult('Output', results)
-
-class GetFileName(String) :
- def compute(self) :
- p = sr_py.GetFileNameAlg()
- if self.hasInputFromPort('p_filename_base') :
- p.set_p_filename_base(self.getInputFromPort('p_filename_base'))
- if self.hasInputFromPort('p_delay') :
- p.set_p_delay(self.getInputFromPort('p_delay'))
- if self.hasInputFromPort('p_pinned') :
- p.set_p_pinned(self.getInputFromPort('p_pinned'))
- results = p.execute()
- self.setResult('Full Filename', results)
-
-class SplitFileName(String) :
- def compute(self) :
- p = sr_py.SplitFileNameAlg()
- Filename = ''
- if self.hasInputFromPort('Filename') :
- Filename = self.getInputFromPort('Filename')
- results = p.execute(Filename)
- self.setResult('Pathname', results[0])
- self.setResult('Filename Base', results[1])
- self.setResult('Extension', results[2])
- self.setResult('Filename', results[3])
-
-class PrintStringIntoString(String) :
- def compute(self) :
- p = sr_py.PrintStringIntoStringAlg()
- if self.hasInputFromPort('p_formatstring') :
- p.set_p_formatstring(self.getInputFromPort('p_formatstring'))
- Format = ''
- if self.hasInputFromPort('Format') :
- Format = self.getInputFromPort('Format')
- Input = ''
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- results = p.execute(Format, Input)
- self.setResult('Output', results)
-
-class CreateString(String) :
- def compute(self) :
- p = sr_py.CreateStringAlg()
- if self.hasInputFromPort('p_inputstring') :
- p.set_p_inputstring(self.getInputFromPort('p_inputstring'))
- results = p.execute()
- self.setResult('Output', results)
-
-class ReportStringInfo(String) :
- def compute(self) :
- p = sr_py.ReportStringInfoAlg()
- if self.hasInputFromPort('p_inputstring') :
- p.set_p_inputstring(self.getInputFromPort('p_inputstring'))
- Input = ''
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- results = p.execute(Input)
-
-class JoinStrings(String) :
- def compute(self) :
- p = sr_py.JoinStringsAlg()
- input = ''
- if self.hasInputFromPort('input') :
- input = self.getInputFromPort('input')
- results = p.execute(input)
- self.setResult('Output', results)
-
-class GetNetworkFileName(String) :
- def compute(self) :
- p = sr_py.GetNetworkFileNameAlg()
- results = p.execute()
- self.setResult('String', results)
-
-class SetFieldProperty(MiscField) :
- def compute(self) :
- p = sr_py.SetFieldPropertyAlg()
- if self.hasInputFromPort('p_num_entries') :
- p.set_p_num_entries(self.getInputFromPort('p_num_entries'))
- if self.hasInputFromPort('p_property') :
- p.set_p_property(self.getInputFromPort('p_property'))
- if self.hasInputFromPort('p_type') :
- p.set_p_type(self.getInputFromPort('p_type'))
- if self.hasInputFromPort('p_value') :
- p.set_p_value(self.getInputFromPort('p_value'))
- if self.hasInputFromPort('p_readonly') :
- p.set_p_readonly(self.getInputFromPort('p_readonly'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('Field', results)
-
-class ReportScalarFieldStats(MiscField) :
- def compute(self) :
- p = sr_py.ReportScalarFieldStatsAlg()
- if self.hasInputFromPort('p_min') :
- p.set_p_min(self.getInputFromPort('p_min'))
- if self.hasInputFromPort('p_max') :
- p.set_p_max(self.getInputFromPort('p_max'))
- if self.hasInputFromPort('p_mean') :
- p.set_p_mean(self.getInputFromPort('p_mean'))
- if self.hasInputFromPort('p_median') :
- p.set_p_median(self.getInputFromPort('p_median'))
- if self.hasInputFromPort('p_sigma') :
- p.set_p_sigma(self.getInputFromPort('p_sigma'))
- if self.hasInputFromPort('p_is_fixed') :
- p.set_p_is_fixed(self.getInputFromPort('p_is_fixed'))
- if self.hasInputFromPort('p_nbuckets') :
- p.set_p_nbuckets(self.getInputFromPort('p_nbuckets'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
-
-class SelectFieldROIWithBoxWidget(MiscField) :
- def compute(self) :
- p = sr_py.SelectFieldROIWithBoxWidgetAlg()
- if self.hasInputFromPort('p_stampvalue') :
- p.set_p_stampvalue(self.getInputFromPort('p_stampvalue'))
- if self.hasInputFromPort('p_runmode') :
- p.set_p_runmode(self.getInputFromPort('p_runmode'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Selection Widget', results[0])
- self.setResult('Output Field', results[1])
-
-class BuildMatrixOfSurfaceNormals(MiscField) :
- def compute(self) :
- p = sr_py.BuildMatrixOfSurfaceNormalsAlg()
- Surface_Field = 0
- if self.hasInputFromPort('Surface Field') :
- Surface_Field = self.getInputFromPort('Surface Field')
- results = p.execute(Surface_Field)
- self.setResult('Nodal Surface Normals', results)
-
-class ReportFieldInfo(MiscField) :
- def compute(self) :
- p = sr_py.ReportFieldInfoAlg()
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('NumNodes', results[0])
- self.setResult('NumElements', results[1])
- self.setResult('NumData', results[2])
- self.setResult('DataMin', results[3])
- self.setResult('DataMax', results[4])
- self.setResult('FieldSize', results[5])
- self.setResult('FieldCenter', results[6])
- self.setResult('Dimensions', results[7])
-
-class ReportFieldGeometryMeasures(MiscField) :
- def compute(self) :
- p = sr_py.ReportFieldGeometryMeasuresAlg()
- if self.hasInputFromPort('p_simplexString') :
- p.set_p_simplexString(self.getInputFromPort('p_simplexString'))
- if self.hasInputFromPort('p_xFlag') :
- p.set_p_xFlag(self.getInputFromPort('p_xFlag'))
- if self.hasInputFromPort('p_yFlag') :
- p.set_p_yFlag(self.getInputFromPort('p_yFlag'))
- if self.hasInputFromPort('p_zFlag') :
- p.set_p_zFlag(self.getInputFromPort('p_zFlag'))
- if self.hasInputFromPort('p_idxFlag') :
- p.set_p_idxFlag(self.getInputFromPort('p_idxFlag'))
- if self.hasInputFromPort('p_sizeFlag') :
- p.set_p_sizeFlag(self.getInputFromPort('p_sizeFlag'))
- if self.hasInputFromPort('p_normalsFlag') :
- p.set_p_normalsFlag(self.getInputFromPort('p_normalsFlag'))
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Measures Matrix', results)
-
-class SetFieldOrMeshStringProperty(MiscField) :
- def compute(self) :
- p = sr_py.SetFieldOrMeshStringPropertyAlg()
- if self.hasInputFromPort('p_prop') :
- p.set_p_prop(self.getInputFromPort('p_prop'))
- if self.hasInputFromPort('p_val') :
- p.set_p_val(self.getInputFromPort('p_val'))
- if self.hasInputFromPort('p_meshprop') :
- p.set_p_meshprop(self.getInputFromPort('p_meshprop'))
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- results = p.execute(Input)
- self.setResult('Output', results)
-
-class ManageFieldSeries(MiscField) :
- def compute(self) :
- p = sr_py.ManageFieldSeriesAlg()
- if self.hasInputFromPort('p_num_ports') :
- p.set_p_num_ports(self.getInputFromPort('p_num_ports'))
- Input = 0
- if self.hasInputFromPort('Input') :
- Input = self.getInputFromPort('Input')
- results = p.execute(Input)
- self.setResult('Output 0', results[0])
- self.setResult('Output 1', results[1])
- self.setResult('Output 2', results[2])
- self.setResult('Output 3', results[3])
-
-class ReportSearchGridInfo(MiscField) :
- def compute(self) :
- p = sr_py.ReportSearchGridInfoAlg()
- Input_Field = 0
- if self.hasInputFromPort('Input Field') :
- Input_Field = self.getInputFromPort('Input Field')
- results = p.execute(Input_Field)
- self.setResult('Output Sample Field', results)
-
-class ChooseField(MiscField) :
- def compute(self) :
- p = sr_py.ChooseFieldAlg()
- if self.hasInputFromPort('p_use_first_valid') :
- p.set_p_use_first_valid(self.getInputFromPort('p_use_first_valid'))
- if self.hasInputFromPort('p_port_valid_index') :
- p.set_p_port_valid_index(self.getInputFromPort('p_port_valid_index'))
- if self.hasInputFromPort('p_port_selected_index') :
- p.set_p_port_selected_index(self.getInputFromPort('p_port_selected_index'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('Field', results)
-
-class BuildPointCloudToLatVolMappingMatrix(MiscField) :
- def compute(self) :
- p = sr_py.BuildPointCloudToLatVolMappingMatrixAlg()
- if self.hasInputFromPort('p_epsilon') :
- p.set_p_epsilon(self.getInputFromPort('p_epsilon'))
- PointCloudField = 0
- if self.hasInputFromPort('PointCloudField') :
- PointCloudField = self.getInputFromPort('PointCloudField')
- LatVolField = 0
- if self.hasInputFromPort('LatVolField') :
- LatVolField = self.getInputFromPort('LatVolField')
- results = p.execute(PointCloudField, LatVolField)
- self.setResult('MappingMatrix', results)
-
-class BuildMappingMatrix(MiscField) :
- def compute(self) :
- p = sr_py.BuildMappingMatrixAlg()
- if self.hasInputFromPort('p_interpolation_basis') :
- p.set_p_interpolation_basis(self.getInputFromPort('p_interpolation_basis'))
- if self.hasInputFromPort('p_map_source_to_single_dest') :
- p.set_p_map_source_to_single_dest(self.getInputFromPort('p_map_source_to_single_dest'))
- if self.hasInputFromPort('p_exhaustive_search') :
- p.set_p_exhaustive_search(self.getInputFromPort('p_exhaustive_search'))
- if self.hasInputFromPort('p_exhaustive_search_max_dist') :
- p.set_p_exhaustive_search_max_dist(self.getInputFromPort('p_exhaustive_search_max_dist'))
- if self.hasInputFromPort('p_np') :
- p.set_p_np(self.getInputFromPort('p_np'))
- Source = 0
- if self.hasInputFromPort('Source') :
- Source = self.getInputFromPort('Source')
- Destination = 0
- if self.hasInputFromPort('Destination') :
- Destination = self.getInputFromPort('Destination')
- results = p.execute(Source, Destination)
- self.setResult('Mapping', results)
-
-class CoregisterPointClouds(MiscField) :
- def compute(self) :
- p = sr_py.CoregisterPointCloudsAlg()
- if self.hasInputFromPort('p_allowScale') :
- p.set_p_allowScale(self.getInputFromPort('p_allowScale'))
- if self.hasInputFromPort('p_allowRotate') :
- p.set_p_allowRotate(self.getInputFromPort('p_allowRotate'))
- if self.hasInputFromPort('p_allowTranslate') :
- p.set_p_allowTranslate(self.getInputFromPort('p_allowTranslate'))
- if self.hasInputFromPort('p_seed') :
- p.set_p_seed(self.getInputFromPort('p_seed'))
- if self.hasInputFromPort('p_iters') :
- p.set_p_iters(self.getInputFromPort('p_iters'))
- if self.hasInputFromPort('p_misfitTol') :
- p.set_p_misfitTol(self.getInputFromPort('p_misfitTol'))
- if self.hasInputFromPort('p_method') :
- p.set_p_method(self.getInputFromPort('p_method'))
- Fixed_PointCloudField = 0
- if self.hasInputFromPort('Fixed PointCloudField') :
- Fixed_PointCloudField = self.getInputFromPort('Fixed PointCloudField')
- Mobile_PointCloudField = 0
- if self.hasInputFromPort('Mobile PointCloudField') :
- Mobile_PointCloudField = self.getInputFromPort('Mobile PointCloudField')
- DistanceField_From_Fixed = 0
- if self.hasInputFromPort('DistanceField From Fixed') :
- DistanceField_From_Fixed = self.getInputFromPort('DistanceField From Fixed')
- results = p.execute(Fixed_PointCloudField, Mobile_PointCloudField, DistanceField_From_Fixed)
- self.setResult('Transform', results)
-
-class CollectPointClouds(MiscField) :
- def compute(self) :
- p = sr_py.CollectPointCloudsAlg()
- if self.hasInputFromPort('p_num_fields') :
- p.set_p_num_fields(self.getInputFromPort('p_num_fields'))
- Point_Cloud = 0
- if self.hasInputFromPort('Point Cloud') :
- Point_Cloud = self.getInputFromPort('Point Cloud')
- results = p.execute(Point_Cloud)
- self.setResult('Curve', results)
-
-class GetColorMapsFromBundle(Bundle) :
- def compute(self) :
- p = sr_py.GetColorMapsFromBundleAlg()
- if self.hasInputFromPort('p_colormap1_name') :
- p.set_p_colormap1_name(self.getInputFromPort('p_colormap1_name'))
- if self.hasInputFromPort('p_colormap2_name') :
- p.set_p_colormap2_name(self.getInputFromPort('p_colormap2_name'))
- if self.hasInputFromPort('p_colormap3_name') :
- p.set_p_colormap3_name(self.getInputFromPort('p_colormap3_name'))
- if self.hasInputFromPort('p_colormap4_name') :
- p.set_p_colormap4_name(self.getInputFromPort('p_colormap4_name'))
- if self.hasInputFromPort('p_colormap5_name') :
- p.set_p_colormap5_name(self.getInputFromPort('p_colormap5_name'))
- if self.hasInputFromPort('p_colormap6_name') :
- p.set_p_colormap6_name(self.getInputFromPort('p_colormap6_name'))
- if self.hasInputFromPort('p_colormap_selection') :
- p.set_p_colormap_selection(self.getInputFromPort('p_colormap_selection'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- results = p.execute(bundle)
- self.setResult('bundle', results[0])
- self.setResult('colormap1', results[1])
- self.setResult('colormap2', results[2])
- self.setResult('colormap3', results[3])
- self.setResult('colormap4', results[4])
- self.setResult('colormap5', results[5])
- self.setResult('colormap6', results[6])
-
-class InsertFieldsIntoBundle(Bundle) :
- def compute(self) :
- p = sr_py.InsertFieldsIntoBundleAlg()
- if self.hasInputFromPort('p_field1_name') :
- p.set_p_field1_name(self.getInputFromPort('p_field1_name'))
- if self.hasInputFromPort('p_field2_name') :
- p.set_p_field2_name(self.getInputFromPort('p_field2_name'))
- if self.hasInputFromPort('p_field3_name') :
- p.set_p_field3_name(self.getInputFromPort('p_field3_name'))
- if self.hasInputFromPort('p_field4_name') :
- p.set_p_field4_name(self.getInputFromPort('p_field4_name'))
- if self.hasInputFromPort('p_field5_name') :
- p.set_p_field5_name(self.getInputFromPort('p_field5_name'))
- if self.hasInputFromPort('p_field6_name') :
- p.set_p_field6_name(self.getInputFromPort('p_field6_name'))
- if self.hasInputFromPort('p_replace1') :
- p.set_p_replace1(self.getInputFromPort('p_replace1'))
- if self.hasInputFromPort('p_replace2') :
- p.set_p_replace2(self.getInputFromPort('p_replace2'))
- if self.hasInputFromPort('p_replace3') :
- p.set_p_replace3(self.getInputFromPort('p_replace3'))
- if self.hasInputFromPort('p_replace4') :
- p.set_p_replace4(self.getInputFromPort('p_replace4'))
- if self.hasInputFromPort('p_replace5') :
- p.set_p_replace5(self.getInputFromPort('p_replace5'))
- if self.hasInputFromPort('p_replace6') :
- p.set_p_replace6(self.getInputFromPort('p_replace6'))
- if self.hasInputFromPort('p_bundlename') :
- p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- field1 = 0
- if self.hasInputFromPort('field1') :
- field1 = self.getInputFromPort('field1')
- field2 = 0
- if self.hasInputFromPort('field2') :
- field2 = self.getInputFromPort('field2')
- field3 = 0
- if self.hasInputFromPort('field3') :
- field3 = self.getInputFromPort('field3')
- field4 = 0
- if self.hasInputFromPort('field4') :
- field4 = self.getInputFromPort('field4')
- field5 = 0
- if self.hasInputFromPort('field5') :
- field5 = self.getInputFromPort('field5')
- field6 = 0
- if self.hasInputFromPort('field6') :
- field6 = self.getInputFromPort('field6')
- results = p.execute(bundle, field1, field2, field3, field4, field5, field6)
- self.setResult('bundle', results)
-
-class GetFieldsFromBundle(Bundle) :
- def compute(self) :
- p = sr_py.GetFieldsFromBundleAlg()
- if self.hasInputFromPort('p_field1_name') :
- p.set_p_field1_name(self.getInputFromPort('p_field1_name'))
- if self.hasInputFromPort('p_field2_name') :
- p.set_p_field2_name(self.getInputFromPort('p_field2_name'))
- if self.hasInputFromPort('p_field3_name') :
- p.set_p_field3_name(self.getInputFromPort('p_field3_name'))
- if self.hasInputFromPort('p_field4_name') :
- p.set_p_field4_name(self.getInputFromPort('p_field4_name'))
- if self.hasInputFromPort('p_field5_name') :
- p.set_p_field5_name(self.getInputFromPort('p_field5_name'))
- if self.hasInputFromPort('p_field6_name') :
- p.set_p_field6_name(self.getInputFromPort('p_field6_name'))
- if self.hasInputFromPort('p_field_selection') :
- p.set_p_field_selection(self.getInputFromPort('p_field_selection'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- results = p.execute(bundle)
- self.setResult('bundle', results[0])
- self.setResult('field1', results[1])
- self.setResult('field2', results[2])
- self.setResult('field3', results[3])
- self.setResult('field4', results[4])
- self.setResult('field5', results[5])
- self.setResult('field6', results[6])
-
-class InsertColorMap2sIntoBundle(Bundle) :
- def compute(self) :
- p = sr_py.InsertColorMap2sIntoBundleAlg()
- if self.hasInputFromPort('p_colormap21_name') :
- p.set_p_colormap21_name(self.getInputFromPort('p_colormap21_name'))
- if self.hasInputFromPort('p_colormap22_name') :
- p.set_p_colormap22_name(self.getInputFromPort('p_colormap22_name'))
- if self.hasInputFromPort('p_colormap23_name') :
- p.set_p_colormap23_name(self.getInputFromPort('p_colormap23_name'))
- if self.hasInputFromPort('p_colormap24_name') :
- p.set_p_colormap24_name(self.getInputFromPort('p_colormap24_name'))
- if self.hasInputFromPort('p_colormap25_name') :
- p.set_p_colormap25_name(self.getInputFromPort('p_colormap25_name'))
- if self.hasInputFromPort('p_colormap26_name') :
- p.set_p_colormap26_name(self.getInputFromPort('p_colormap26_name'))
- if self.hasInputFromPort('p_replace1') :
- p.set_p_replace1(self.getInputFromPort('p_replace1'))
- if self.hasInputFromPort('p_replace2') :
- p.set_p_replace2(self.getInputFromPort('p_replace2'))
- if self.hasInputFromPort('p_replace3') :
- p.set_p_replace3(self.getInputFromPort('p_replace3'))
- if self.hasInputFromPort('p_replace4') :
- p.set_p_replace4(self.getInputFromPort('p_replace4'))
- if self.hasInputFromPort('p_replace5') :
- p.set_p_replace5(self.getInputFromPort('p_replace5'))
- if self.hasInputFromPort('p_replace6') :
- p.set_p_replace6(self.getInputFromPort('p_replace6'))
- if self.hasInputFromPort('p_bundlename') :
- p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- colormap21 = 0
- if self.hasInputFromPort('colormap21') :
- colormap21 = self.getInputFromPort('colormap21')
- colormap22 = 0
- if self.hasInputFromPort('colormap22') :
- colormap22 = self.getInputFromPort('colormap22')
- colormap23 = 0
- if self.hasInputFromPort('colormap23') :
- colormap23 = self.getInputFromPort('colormap23')
- colormap24 = 0
- if self.hasInputFromPort('colormap24') :
- colormap24 = self.getInputFromPort('colormap24')
- colormap25 = 0
- if self.hasInputFromPort('colormap25') :
- colormap25 = self.getInputFromPort('colormap25')
- colormap26 = 0
- if self.hasInputFromPort('colormap26') :
- colormap26 = self.getInputFromPort('colormap26')
- results = p.execute(bundle, colormap21, colormap22, colormap23, colormap24, colormap25, colormap26)
- self.setResult('bundle', results)
-
-class GetBundlesFromBundle(Bundle) :
- def compute(self) :
- p = sr_py.GetBundlesFromBundleAlg()
- if self.hasInputFromPort('p_bundle1_name') :
- p.set_p_bundle1_name(self.getInputFromPort('p_bundle1_name'))
- if self.hasInputFromPort('p_bundle2_name') :
- p.set_p_bundle2_name(self.getInputFromPort('p_bundle2_name'))
- if self.hasInputFromPort('p_bundle3_name') :
- p.set_p_bundle3_name(self.getInputFromPort('p_bundle3_name'))
- if self.hasInputFromPort('p_bundle4_name') :
- p.set_p_bundle4_name(self.getInputFromPort('p_bundle4_name'))
- if self.hasInputFromPort('p_bundle5_name') :
- p.set_p_bundle5_name(self.getInputFromPort('p_bundle5_name'))
- if self.hasInputFromPort('p_bundle6_name') :
- p.set_p_bundle6_name(self.getInputFromPort('p_bundle6_name'))
- if self.hasInputFromPort('p_bundle_selection') :
- p.set_p_bundle_selection(self.getInputFromPort('p_bundle_selection'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- results = p.execute(bundle)
- self.setResult('bundle', results[0])
- self.setResult('bundle1', results[1])
- self.setResult('bundle2', results[2])
- self.setResult('bundle3', results[3])
- self.setResult('bundle4', results[4])
- self.setResult('bundle5', results[5])
- self.setResult('bundle6', results[6])
-
-class GetPathsFromBundle(Bundle) :
- def compute(self) :
- p = sr_py.GetPathsFromBundleAlg()
- if self.hasInputFromPort('p_path1_name') :
- p.set_p_path1_name(self.getInputFromPort('p_path1_name'))
- if self.hasInputFromPort('p_path2_name') :
- p.set_p_path2_name(self.getInputFromPort('p_path2_name'))
- if self.hasInputFromPort('p_path3_name') :
- p.set_p_path3_name(self.getInputFromPort('p_path3_name'))
- if self.hasInputFromPort('p_path4_name') :
- p.set_p_path4_name(self.getInputFromPort('p_path4_name'))
- if self.hasInputFromPort('p_path5_name') :
- p.set_p_path5_name(self.getInputFromPort('p_path5_name'))
- if self.hasInputFromPort('p_path6_name') :
- p.set_p_path6_name(self.getInputFromPort('p_path6_name'))
- if self.hasInputFromPort('p_path_selection') :
- p.set_p_path_selection(self.getInputFromPort('p_path_selection'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- results = p.execute(bundle)
- self.setResult('bundle', results[0])
- self.setResult('path1', results[1])
- self.setResult('path2', results[2])
- self.setResult('path3', results[3])
- self.setResult('path4', results[4])
- self.setResult('path5', results[5])
- self.setResult('path6', results[6])
-
-class InsertStringsIntoBundle(Bundle) :
- def compute(self) :
- p = sr_py.InsertStringsIntoBundleAlg()
- if self.hasInputFromPort('p_string1_name') :
- p.set_p_string1_name(self.getInputFromPort('p_string1_name'))
- if self.hasInputFromPort('p_string2_name') :
- p.set_p_string2_name(self.getInputFromPort('p_string2_name'))
- if self.hasInputFromPort('p_string3_name') :
- p.set_p_string3_name(self.getInputFromPort('p_string3_name'))
- if self.hasInputFromPort('p_string4_name') :
- p.set_p_string4_name(self.getInputFromPort('p_string4_name'))
- if self.hasInputFromPort('p_string5_name') :
- p.set_p_string5_name(self.getInputFromPort('p_string5_name'))
- if self.hasInputFromPort('p_string6_name') :
- p.set_p_string6_name(self.getInputFromPort('p_string6_name'))
- if self.hasInputFromPort('p_replace1') :
- p.set_p_replace1(self.getInputFromPort('p_replace1'))
- if self.hasInputFromPort('p_replace2') :
- p.set_p_replace2(self.getInputFromPort('p_replace2'))
- if self.hasInputFromPort('p_replace3') :
- p.set_p_replace3(self.getInputFromPort('p_replace3'))
- if self.hasInputFromPort('p_replace4') :
- p.set_p_replace4(self.getInputFromPort('p_replace4'))
- if self.hasInputFromPort('p_replace5') :
- p.set_p_replace5(self.getInputFromPort('p_replace5'))
- if self.hasInputFromPort('p_replace6') :
- p.set_p_replace6(self.getInputFromPort('p_replace6'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- string1 = ''
- if self.hasInputFromPort('string1') :
- string1 = self.getInputFromPort('string1')
- string2 = ''
- if self.hasInputFromPort('string2') :
- string2 = self.getInputFromPort('string2')
- string3 = ''
- if self.hasInputFromPort('string3') :
- string3 = self.getInputFromPort('string3')
- string4 = ''
- if self.hasInputFromPort('string4') :
- string4 = self.getInputFromPort('string4')
- string5 = ''
- if self.hasInputFromPort('string5') :
- string5 = self.getInputFromPort('string5')
- string6 = ''
- if self.hasInputFromPort('string6') :
- string6 = self.getInputFromPort('string6')
- results = p.execute(bundle, string1, string2, string3, string4, string5, string6)
- self.setResult('bundle', results)
-
-class GetNrrdsFromBundle(Bundle) :
- def compute(self) :
- p = sr_py.GetNrrdsFromBundleAlg()
- if self.hasInputFromPort('p_nrrd1_name') :
- p.set_p_nrrd1_name(self.getInputFromPort('p_nrrd1_name'))
- if self.hasInputFromPort('p_nrrd2_name') :
- p.set_p_nrrd2_name(self.getInputFromPort('p_nrrd2_name'))
- if self.hasInputFromPort('p_nrrd3_name') :
- p.set_p_nrrd3_name(self.getInputFromPort('p_nrrd3_name'))
- if self.hasInputFromPort('p_nrrd4_name') :
- p.set_p_nrrd4_name(self.getInputFromPort('p_nrrd4_name'))
- if self.hasInputFromPort('p_nrrd5_name') :
- p.set_p_nrrd5_name(self.getInputFromPort('p_nrrd5_name'))
- if self.hasInputFromPort('p_nrrd6_name') :
- p.set_p_nrrd6_name(self.getInputFromPort('p_nrrd6_name'))
- if self.hasInputFromPort('p_transposenrrd1') :
- p.set_p_transposenrrd1(self.getInputFromPort('p_transposenrrd1'))
- if self.hasInputFromPort('p_transposenrrd2') :
- p.set_p_transposenrrd2(self.getInputFromPort('p_transposenrrd2'))
- if self.hasInputFromPort('p_transposenrrd3') :
- p.set_p_transposenrrd3(self.getInputFromPort('p_transposenrrd3'))
- if self.hasInputFromPort('p_transposenrrd4') :
- p.set_p_transposenrrd4(self.getInputFromPort('p_transposenrrd4'))
- if self.hasInputFromPort('p_transposenrrd5') :
- p.set_p_transposenrrd5(self.getInputFromPort('p_transposenrrd5'))
- if self.hasInputFromPort('p_transposenrrd6') :
- p.set_p_transposenrrd6(self.getInputFromPort('p_transposenrrd6'))
- if self.hasInputFromPort('p_nrrd_selection') :
- p.set_p_nrrd_selection(self.getInputFromPort('p_nrrd_selection'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- results = p.execute(bundle)
- self.setResult('bundle', results[0])
- self.setResult('nrrd1', results[1])
- self.setResult('nrrd2', results[2])
- self.setResult('nrrd3', results[3])
- self.setResult('nrrd4', results[4])
- self.setResult('nrrd5', results[5])
- self.setResult('nrrd6', results[6])
-
-class GetMatricesFromBundle(Bundle) :
- def compute(self) :
- p = sr_py.GetMatricesFromBundleAlg()
- if self.hasInputFromPort('p_matrix1_name') :
- p.set_p_matrix1_name(self.getInputFromPort('p_matrix1_name'))
- if self.hasInputFromPort('p_matrix2_name') :
- p.set_p_matrix2_name(self.getInputFromPort('p_matrix2_name'))
- if self.hasInputFromPort('p_matrix3_name') :
- p.set_p_matrix3_name(self.getInputFromPort('p_matrix3_name'))
- if self.hasInputFromPort('p_matrix4_name') :
- p.set_p_matrix4_name(self.getInputFromPort('p_matrix4_name'))
- if self.hasInputFromPort('p_matrix5_name') :
- p.set_p_matrix5_name(self.getInputFromPort('p_matrix5_name'))
- if self.hasInputFromPort('p_matrix6_name') :
- p.set_p_matrix6_name(self.getInputFromPort('p_matrix6_name'))
- if self.hasInputFromPort('p_transposenrrd1') :
- p.set_p_transposenrrd1(self.getInputFromPort('p_transposenrrd1'))
- if self.hasInputFromPort('p_transposenrrd2') :
- p.set_p_transposenrrd2(self.getInputFromPort('p_transposenrrd2'))
- if self.hasInputFromPort('p_transposenrrd3') :
- p.set_p_transposenrrd3(self.getInputFromPort('p_transposenrrd3'))
- if self.hasInputFromPort('p_transposenrrd4') :
- p.set_p_transposenrrd4(self.getInputFromPort('p_transposenrrd4'))
- if self.hasInputFromPort('p_transposenrrd5') :
- p.set_p_transposenrrd5(self.getInputFromPort('p_transposenrrd5'))
- if self.hasInputFromPort('p_transposenrrd6') :
- p.set_p_transposenrrd6(self.getInputFromPort('p_transposenrrd6'))
- if self.hasInputFromPort('p_matrix_selection') :
- p.set_p_matrix_selection(self.getInputFromPort('p_matrix_selection'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- results = p.execute(bundle)
- self.setResult('bundle', results[0])
- self.setResult('matrix1', results[1])
- self.setResult('matrix2', results[2])
- self.setResult('matrix3', results[3])
- self.setResult('matrix4', results[4])
- self.setResult('matrix5', results[5])
- self.setResult('matrix6', results[6])
-
-class JoinBundles(Bundle) :
- def compute(self) :
- p = sr_py.JoinBundlesAlg()
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- results = p.execute(bundle)
- self.setResult('bundle', results)
-
-class ReportBundleInfo(Bundle) :
- def compute(self) :
- p = sr_py.ReportBundleInfoAlg()
- if self.hasInputFromPort('p_tclinfostring') :
- p.set_p_tclinfostring(self.getInputFromPort('p_tclinfostring'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- results = p.execute(bundle)
-
-class InsertPathsIntoBundle(Bundle) :
- def compute(self) :
- p = sr_py.InsertPathsIntoBundleAlg()
- if self.hasInputFromPort('p_path1_name') :
- p.set_p_path1_name(self.getInputFromPort('p_path1_name'))
- if self.hasInputFromPort('p_path2_name') :
- p.set_p_path2_name(self.getInputFromPort('p_path2_name'))
- if self.hasInputFromPort('p_path3_name') :
- p.set_p_path3_name(self.getInputFromPort('p_path3_name'))
- if self.hasInputFromPort('p_path4_name') :
- p.set_p_path4_name(self.getInputFromPort('p_path4_name'))
- if self.hasInputFromPort('p_path5_name') :
- p.set_p_path5_name(self.getInputFromPort('p_path5_name'))
- if self.hasInputFromPort('p_path6_name') :
- p.set_p_path6_name(self.getInputFromPort('p_path6_name'))
- if self.hasInputFromPort('p_replace1') :
- p.set_p_replace1(self.getInputFromPort('p_replace1'))
- if self.hasInputFromPort('p_replace2') :
- p.set_p_replace2(self.getInputFromPort('p_replace2'))
- if self.hasInputFromPort('p_replace3') :
- p.set_p_replace3(self.getInputFromPort('p_replace3'))
- if self.hasInputFromPort('p_replace4') :
- p.set_p_replace4(self.getInputFromPort('p_replace4'))
- if self.hasInputFromPort('p_replace5') :
- p.set_p_replace5(self.getInputFromPort('p_replace5'))
- if self.hasInputFromPort('p_replace6') :
- p.set_p_replace6(self.getInputFromPort('p_replace6'))
- if self.hasInputFromPort('p_bundlename') :
- p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- path1 = 0
- if self.hasInputFromPort('path1') :
- path1 = self.getInputFromPort('path1')
- path2 = 0
- if self.hasInputFromPort('path2') :
- path2 = self.getInputFromPort('path2')
- path3 = 0
- if self.hasInputFromPort('path3') :
- path3 = self.getInputFromPort('path3')
- path4 = 0
- if self.hasInputFromPort('path4') :
- path4 = self.getInputFromPort('path4')
- path5 = 0
- if self.hasInputFromPort('path5') :
- path5 = self.getInputFromPort('path5')
- path6 = 0
- if self.hasInputFromPort('path6') :
- path6 = self.getInputFromPort('path6')
- results = p.execute(bundle, path1, path2, path3, path4, path5, path6)
- self.setResult('bundle', results)
-
-class GetColorMap2sFromBundle(Bundle) :
- def compute(self) :
- p = sr_py.GetColorMap2sFromBundleAlg()
- if self.hasInputFromPort('p_colormap21_name') :
- p.set_p_colormap21_name(self.getInputFromPort('p_colormap21_name'))
- if self.hasInputFromPort('p_colormap22_name') :
- p.set_p_colormap22_name(self.getInputFromPort('p_colormap22_name'))
- if self.hasInputFromPort('p_colormap23_name') :
- p.set_p_colormap23_name(self.getInputFromPort('p_colormap23_name'))
- if self.hasInputFromPort('p_colormap24_name') :
- p.set_p_colormap24_name(self.getInputFromPort('p_colormap24_name'))
- if self.hasInputFromPort('p_colormap25_name') :
- p.set_p_colormap25_name(self.getInputFromPort('p_colormap25_name'))
- if self.hasInputFromPort('p_colormap26_name') :
- p.set_p_colormap26_name(self.getInputFromPort('p_colormap26_name'))
- if self.hasInputFromPort('p_colormap2_selection') :
- p.set_p_colormap2_selection(self.getInputFromPort('p_colormap2_selection'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- results = p.execute(bundle)
- self.setResult('bundle', results[0])
- self.setResult('colormap21', results[1])
- self.setResult('colormap22', results[2])
- self.setResult('colormap23', results[3])
- self.setResult('colormap24', results[4])
- self.setResult('colormap25', results[5])
- self.setResult('colormap26', results[6])
-
-class InsertMatricesIntoBundle(Bundle) :
- def compute(self) :
- p = sr_py.InsertMatricesIntoBundleAlg()
- if self.hasInputFromPort('p_matrix1_name') :
- p.set_p_matrix1_name(self.getInputFromPort('p_matrix1_name'))
- if self.hasInputFromPort('p_matrix2_name') :
- p.set_p_matrix2_name(self.getInputFromPort('p_matrix2_name'))
- if self.hasInputFromPort('p_matrix3_name') :
- p.set_p_matrix3_name(self.getInputFromPort('p_matrix3_name'))
- if self.hasInputFromPort('p_matrix4_name') :
- p.set_p_matrix4_name(self.getInputFromPort('p_matrix4_name'))
- if self.hasInputFromPort('p_matrix5_name') :
- p.set_p_matrix5_name(self.getInputFromPort('p_matrix5_name'))
- if self.hasInputFromPort('p_matrix6_name') :
- p.set_p_matrix6_name(self.getInputFromPort('p_matrix6_name'))
- if self.hasInputFromPort('p_replace1') :
- p.set_p_replace1(self.getInputFromPort('p_replace1'))
- if self.hasInputFromPort('p_replace2') :
- p.set_p_replace2(self.getInputFromPort('p_replace2'))
- if self.hasInputFromPort('p_replace3') :
- p.set_p_replace3(self.getInputFromPort('p_replace3'))
- if self.hasInputFromPort('p_replace4') :
- p.set_p_replace4(self.getInputFromPort('p_replace4'))
- if self.hasInputFromPort('p_replace5') :
- p.set_p_replace5(self.getInputFromPort('p_replace5'))
- if self.hasInputFromPort('p_replace6') :
- p.set_p_replace6(self.getInputFromPort('p_replace6'))
- if self.hasInputFromPort('p_bundlename') :
- p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- matrix1 = 0
- if self.hasInputFromPort('matrix1') :
- matrix1 = self.getInputFromPort('matrix1')
- matrix2 = 0
- if self.hasInputFromPort('matrix2') :
- matrix2 = self.getInputFromPort('matrix2')
- matrix3 = 0
- if self.hasInputFromPort('matrix3') :
- matrix3 = self.getInputFromPort('matrix3')
- matrix4 = 0
- if self.hasInputFromPort('matrix4') :
- matrix4 = self.getInputFromPort('matrix4')
- matrix5 = 0
- if self.hasInputFromPort('matrix5') :
- matrix5 = self.getInputFromPort('matrix5')
- matrix6 = 0
- if self.hasInputFromPort('matrix6') :
- matrix6 = self.getInputFromPort('matrix6')
- results = p.execute(bundle, matrix1, matrix2, matrix3, matrix4, matrix5, matrix6)
- self.setResult('bundle', results)
-
-class InsertNrrdsIntoBundle(Bundle) :
- def compute(self) :
- p = sr_py.InsertNrrdsIntoBundleAlg()
- if self.hasInputFromPort('p_nrrd1_name') :
- p.set_p_nrrd1_name(self.getInputFromPort('p_nrrd1_name'))
- if self.hasInputFromPort('p_nrrd2_name') :
- p.set_p_nrrd2_name(self.getInputFromPort('p_nrrd2_name'))
- if self.hasInputFromPort('p_nrrd3_name') :
- p.set_p_nrrd3_name(self.getInputFromPort('p_nrrd3_name'))
- if self.hasInputFromPort('p_nrrd4_name') :
- p.set_p_nrrd4_name(self.getInputFromPort('p_nrrd4_name'))
- if self.hasInputFromPort('p_nrrd5_name') :
- p.set_p_nrrd5_name(self.getInputFromPort('p_nrrd5_name'))
- if self.hasInputFromPort('p_nrrd6_name') :
- p.set_p_nrrd6_name(self.getInputFromPort('p_nrrd6_name'))
- if self.hasInputFromPort('p_replace1') :
- p.set_p_replace1(self.getInputFromPort('p_replace1'))
- if self.hasInputFromPort('p_replace2') :
- p.set_p_replace2(self.getInputFromPort('p_replace2'))
- if self.hasInputFromPort('p_replace3') :
- p.set_p_replace3(self.getInputFromPort('p_replace3'))
- if self.hasInputFromPort('p_replace4') :
- p.set_p_replace4(self.getInputFromPort('p_replace4'))
- if self.hasInputFromPort('p_replace5') :
- p.set_p_replace5(self.getInputFromPort('p_replace5'))
- if self.hasInputFromPort('p_replace6') :
- p.set_p_replace6(self.getInputFromPort('p_replace6'))
- if self.hasInputFromPort('p_bundlename') :
- p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- nrrd1 = 0
- if self.hasInputFromPort('nrrd1') :
- nrrd1 = self.getInputFromPort('nrrd1')
- nrrd2 = 0
- if self.hasInputFromPort('nrrd2') :
- nrrd2 = self.getInputFromPort('nrrd2')
- nrrd3 = 0
- if self.hasInputFromPort('nrrd3') :
- nrrd3 = self.getInputFromPort('nrrd3')
- nrrd4 = 0
- if self.hasInputFromPort('nrrd4') :
- nrrd4 = self.getInputFromPort('nrrd4')
- nrrd5 = 0
- if self.hasInputFromPort('nrrd5') :
- nrrd5 = self.getInputFromPort('nrrd5')
- nrrd6 = 0
- if self.hasInputFromPort('nrrd6') :
- nrrd6 = self.getInputFromPort('nrrd6')
- results = p.execute(bundle, nrrd1, nrrd2, nrrd3, nrrd4, nrrd5, nrrd6)
- self.setResult('bundle', results)
-
-class InsertBundlesIntoBundle(Bundle) :
- def compute(self) :
- p = sr_py.InsertBundlesIntoBundleAlg()
- if self.hasInputFromPort('p_bundle1_name') :
- p.set_p_bundle1_name(self.getInputFromPort('p_bundle1_name'))
- if self.hasInputFromPort('p_bundle2_name') :
- p.set_p_bundle2_name(self.getInputFromPort('p_bundle2_name'))
- if self.hasInputFromPort('p_bundle3_name') :
- p.set_p_bundle3_name(self.getInputFromPort('p_bundle3_name'))
- if self.hasInputFromPort('p_bundle4_name') :
- p.set_p_bundle4_name(self.getInputFromPort('p_bundle4_name'))
- if self.hasInputFromPort('p_bundle5_name') :
- p.set_p_bundle5_name(self.getInputFromPort('p_bundle5_name'))
- if self.hasInputFromPort('p_bundle6_name') :
- p.set_p_bundle6_name(self.getInputFromPort('p_bundle6_name'))
- if self.hasInputFromPort('p_replace1') :
- p.set_p_replace1(self.getInputFromPort('p_replace1'))
- if self.hasInputFromPort('p_replace2') :
- p.set_p_replace2(self.getInputFromPort('p_replace2'))
- if self.hasInputFromPort('p_replace3') :
- p.set_p_replace3(self.getInputFromPort('p_replace3'))
- if self.hasInputFromPort('p_replace4') :
- p.set_p_replace4(self.getInputFromPort('p_replace4'))
- if self.hasInputFromPort('p_replace5') :
- p.set_p_replace5(self.getInputFromPort('p_replace5'))
- if self.hasInputFromPort('p_replace6') :
- p.set_p_replace6(self.getInputFromPort('p_replace6'))
- if self.hasInputFromPort('p_bundlename') :
- p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- bundle1 = 0
- if self.hasInputFromPort('bundle1') :
- bundle1 = self.getInputFromPort('bundle1')
- bundle2 = 0
- if self.hasInputFromPort('bundle2') :
- bundle2 = self.getInputFromPort('bundle2')
- bundle3 = 0
- if self.hasInputFromPort('bundle3') :
- bundle3 = self.getInputFromPort('bundle3')
- bundle4 = 0
- if self.hasInputFromPort('bundle4') :
- bundle4 = self.getInputFromPort('bundle4')
- bundle5 = 0
- if self.hasInputFromPort('bundle5') :
- bundle5 = self.getInputFromPort('bundle5')
- bundle6 = 0
- if self.hasInputFromPort('bundle6') :
- bundle6 = self.getInputFromPort('bundle6')
- results = p.execute(bundle, bundle1, bundle2, bundle3, bundle4, bundle5, bundle6)
- self.setResult('bundle', results)
-
-class GetStringsFromBundle(Bundle) :
- def compute(self) :
- p = sr_py.GetStringsFromBundleAlg()
- if self.hasInputFromPort('p_string1_name') :
- p.set_p_string1_name(self.getInputFromPort('p_string1_name'))
- if self.hasInputFromPort('p_string2_name') :
- p.set_p_string2_name(self.getInputFromPort('p_string2_name'))
- if self.hasInputFromPort('p_string3_name') :
- p.set_p_string3_name(self.getInputFromPort('p_string3_name'))
- if self.hasInputFromPort('p_string4_name') :
- p.set_p_string4_name(self.getInputFromPort('p_string4_name'))
- if self.hasInputFromPort('p_string5_name') :
- p.set_p_string5_name(self.getInputFromPort('p_string5_name'))
- if self.hasInputFromPort('p_string6_name') :
- p.set_p_string6_name(self.getInputFromPort('p_string6_name'))
- if self.hasInputFromPort('p_string_selection') :
- p.set_p_string_selection(self.getInputFromPort('p_string_selection'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- results = p.execute(bundle)
- self.setResult('bundle', results[0])
- self.setResult('string1', results[1])
- self.setResult('string2', results[2])
- self.setResult('string3', results[3])
- self.setResult('string4', results[4])
- self.setResult('string5', results[5])
- self.setResult('string6', results[6])
-
-class InsertColorMapsIntoBundle(Bundle) :
- def compute(self) :
- p = sr_py.InsertColorMapsIntoBundleAlg()
- if self.hasInputFromPort('p_colormap1_name') :
- p.set_p_colormap1_name(self.getInputFromPort('p_colormap1_name'))
- if self.hasInputFromPort('p_colormap2_name') :
- p.set_p_colormap2_name(self.getInputFromPort('p_colormap2_name'))
- if self.hasInputFromPort('p_colormap3_name') :
- p.set_p_colormap3_name(self.getInputFromPort('p_colormap3_name'))
- if self.hasInputFromPort('p_colormap4_name') :
- p.set_p_colormap4_name(self.getInputFromPort('p_colormap4_name'))
- if self.hasInputFromPort('p_colormap5_name') :
- p.set_p_colormap5_name(self.getInputFromPort('p_colormap5_name'))
- if self.hasInputFromPort('p_colormap6_name') :
- p.set_p_colormap6_name(self.getInputFromPort('p_colormap6_name'))
- if self.hasInputFromPort('p_replace1') :
- p.set_p_replace1(self.getInputFromPort('p_replace1'))
- if self.hasInputFromPort('p_replace2') :
- p.set_p_replace2(self.getInputFromPort('p_replace2'))
- if self.hasInputFromPort('p_replace3') :
- p.set_p_replace3(self.getInputFromPort('p_replace3'))
- if self.hasInputFromPort('p_replace4') :
- p.set_p_replace4(self.getInputFromPort('p_replace4'))
- if self.hasInputFromPort('p_replace5') :
- p.set_p_replace5(self.getInputFromPort('p_replace5'))
- if self.hasInputFromPort('p_replace6') :
- p.set_p_replace6(self.getInputFromPort('p_replace6'))
- if self.hasInputFromPort('p_bundlename') :
- p.set_p_bundlename(self.getInputFromPort('p_bundlename'))
- bundle = 0
- if self.hasInputFromPort('bundle') :
- bundle = self.getInputFromPort('bundle')
- colormap1 = 0
- if self.hasInputFromPort('colormap1') :
- colormap1 = self.getInputFromPort('colormap1')
- colormap2 = 0
- if self.hasInputFromPort('colormap2') :
- colormap2 = self.getInputFromPort('colormap2')
- colormap3 = 0
- if self.hasInputFromPort('colormap3') :
- colormap3 = self.getInputFromPort('colormap3')
- colormap4 = 0
- if self.hasInputFromPort('colormap4') :
- colormap4 = self.getInputFromPort('colormap4')
- colormap5 = 0
- if self.hasInputFromPort('colormap5') :
- colormap5 = self.getInputFromPort('colormap5')
- colormap6 = 0
- if self.hasInputFromPort('colormap6') :
- colormap6 = self.getInputFromPort('colormap6')
- results = p.execute(bundle, colormap1, colormap2, colormap3, colormap4, colormap5, colormap6)
- self.setResult('bundle', results)
-
-class CreateParameterBundle(Bundle) :
- def compute(self) :
- p = sr_py.CreateParameterBundleAlg()
- if self.hasInputFromPort('p_data') :
- p.set_p_data(self.getInputFromPort('p_data'))
- if self.hasInputFromPort('p_new_field_count') :
- p.set_p_new_field_count(self.getInputFromPort('p_new_field_count'))
- if self.hasInputFromPort('p_update_all') :
- p.set_p_update_all(self.getInputFromPort('p_update_all'))
- results = p.execute()
- self.setResult('ParameterList', results)
-
-class InsertEnvironmentIntoBundle(Bundle) :
- def compute(self) :
- p = sr_py.InsertEnvironmentIntoBundleAlg()
- results = p.execute()
- self.setResult('Environment', results)
-
-class ShowColorMap(Visualization) :
- def compute(self) :
- p = sr_py.ShowColorMapAlg()
- if self.hasInputFromPort('p_length') :
- p.set_p_length(self.getInputFromPort('p_length'))
- if self.hasInputFromPort('p_side') :
- p.set_p_side(self.getInputFromPort('p_side'))
- if self.hasInputFromPort('p_numlabels') :
- p.set_p_numlabels(self.getInputFromPort('p_numlabels'))
- if self.hasInputFromPort('p_scale') :
- p.set_p_scale(self.getInputFromPort('p_scale'))
- if self.hasInputFromPort('p_numsigdigits') :
- p.set_p_numsigdigits(self.getInputFromPort('p_numsigdigits'))
- if self.hasInputFromPort('p_units') :
- p.set_p_units(self.getInputFromPort('p_units'))
- if self.hasInputFromPort('p_color_r') :
- p.set_p_color_r(self.getInputFromPort('p_color_r'))
- if self.hasInputFromPort('p_color_g') :
- p.set_p_color_g(self.getInputFromPort('p_color_g'))
- if self.hasInputFromPort('p_color_b') :
- p.set_p_color_b(self.getInputFromPort('p_color_b'))
- if self.hasInputFromPort('p_text_fontsize') :
- p.set_p_text_fontsize(self.getInputFromPort('p_text_fontsize'))
- if self.hasInputFromPort('p_extra_padding') :
- p.set_p_extra_padding(self.getInputFromPort('p_extra_padding'))
- ColorMap = 0
- if self.hasInputFromPort('ColorMap') :
- ColorMap = self.getInputFromPort('ColorMap')
- results = p.execute(ColorMap)
- self.setResult('Geometry', results)
-
-class CreateAndEditColorMap2D(Visualization) :
- def compute(self) :
- p = sr_py.CreateAndEditColorMap2DAlg()
- if self.hasInputFromPort('p_histo') :
- p.set_p_histo(self.getInputFromPort('p_histo'))
- if self.hasInputFromPort('p_selected_widget') :
- p.set_p_selected_widget(self.getInputFromPort('p_selected_widget'))
- if self.hasInputFromPort('p_selected_object') :
- p.set_p_selected_object(self.getInputFromPort('p_selected_object'))
- if self.hasInputFromPort('p_num_entries') :
- p.set_p_num_entries(self.getInputFromPort('p_num_entries'))
- if self.hasInputFromPort('p_marker') :
- p.set_p_marker(self.getInputFromPort('p_marker'))
- if self.hasInputFromPort('p_cm2view_targ') :
- p.set_p_cm2view_targ(self.getInputFromPort('p_cm2view_targ'))
- if self.hasInputFromPort('p_id') :
- p.set_p_id(self.getInputFromPort('p_id'))
- Input_Colormap = 0
- if self.hasInputFromPort('Input Colormap') :
- Input_Colormap = self.getInputFromPort('Input Colormap')
- Histogram = 0
- if self.hasInputFromPort('Histogram') :
- Histogram = self.getInputFromPort('Histogram')
- results = p.execute(Input_Colormap, Histogram)
- self.setResult('Output Colormap', results)
-
-class ShowField(Visualization) :
- def compute(self) :
- p = sr_py.ShowFieldAlg()
- if self.hasInputFromPort('p_nodes_on') :
- p.set_p_nodes_on(self.getInputFromPort('p_nodes_on'))
- if self.hasInputFromPort('p_nodes_transparency') :
- p.set_p_nodes_transparency(self.getInputFromPort('p_nodes_transparency'))
- if self.hasInputFromPort('p_nodes_color_type') :
- p.set_p_nodes_color_type(self.getInputFromPort('p_nodes_color_type'))
- if self.hasInputFromPort('p_nodes_display_type') :
- p.set_p_nodes_display_type(self.getInputFromPort('p_nodes_display_type'))
- if self.hasInputFromPort('p_edges_on') :
- p.set_p_edges_on(self.getInputFromPort('p_edges_on'))
- if self.hasInputFromPort('p_edges_transparency') :
- p.set_p_edges_transparency(self.getInputFromPort('p_edges_transparency'))
- if self.hasInputFromPort('p_edges_color_type') :
- p.set_p_edges_color_type(self.getInputFromPort('p_edges_color_type'))
- if self.hasInputFromPort('p_edges_display_type') :
- p.set_p_edges_display_type(self.getInputFromPort('p_edges_display_type'))
- if self.hasInputFromPort('p_faces_on') :
- p.set_p_faces_on(self.getInputFromPort('p_faces_on'))
- if self.hasInputFromPort('p_faces_transparency') :
- p.set_p_faces_transparency(self.getInputFromPort('p_faces_transparency'))
- if self.hasInputFromPort('p_faces_color_type') :
- p.set_p_faces_color_type(self.getInputFromPort('p_faces_color_type'))
- if self.hasInputFromPort('p_faces_normals') :
- p.set_p_faces_normals(self.getInputFromPort('p_faces_normals'))
- if self.hasInputFromPort('p_faces_usetexture') :
- p.set_p_faces_usetexture(self.getInputFromPort('p_faces_usetexture'))
- if self.hasInputFromPort('p_text_on') :
- p.set_p_text_on(self.getInputFromPort('p_text_on'))
- if self.hasInputFromPort('p_text_color_type') :
- p.set_p_text_color_type(self.getInputFromPort('p_text_color_type'))
- if self.hasInputFromPort('p_text_color_r') :
- p.set_p_text_color_r(self.getInputFromPort('p_text_color_r'))
- if self.hasInputFromPort('p_text_color_g') :
- p.set_p_text_color_g(self.getInputFromPort('p_text_color_g'))
- if self.hasInputFromPort('p_text_color_b') :
- p.set_p_text_color_b(self.getInputFromPort('p_text_color_b'))
- if self.hasInputFromPort('p_text_backface_cull') :
- p.set_p_text_backface_cull(self.getInputFromPort('p_text_backface_cull'))
- if self.hasInputFromPort('p_text_always_visible') :
- p.set_p_text_always_visible(self.getInputFromPort('p_text_always_visible'))
- if self.hasInputFromPort('p_text_fontsize') :
- p.set_p_text_fontsize(self.getInputFromPort('p_text_fontsize'))
- if self.hasInputFromPort('p_text_precision') :
- p.set_p_text_precision(self.getInputFromPort('p_text_precision'))
- if self.hasInputFromPort('p_text_render_locations') :
- p.set_p_text_render_locations(self.getInputFromPort('p_text_render_locations'))
- if self.hasInputFromPort('p_text_show_data') :
- p.set_p_text_show_data(self.getInputFromPort('p_text_show_data'))
- if self.hasInputFromPort('p_text_show_nodes') :
- p.set_p_text_show_nodes(self.getInputFromPort('p_text_show_nodes'))
- if self.hasInputFromPort('p_text_show_edges') :
- p.set_p_text_show_edges(self.getInputFromPort('p_text_show_edges'))
- if self.hasInputFromPort('p_text_show_faces') :
- p.set_p_text_show_faces(self.getInputFromPort('p_text_show_faces'))
- if self.hasInputFromPort('p_text_show_cells') :
- p.set_p_text_show_cells(self.getInputFromPort('p_text_show_cells'))
- if self.hasInputFromPort('p_def_color_r') :
- p.set_p_def_color_r(self.getInputFromPort('p_def_color_r'))
- if self.hasInputFromPort('p_def_color_g') :
- p.set_p_def_color_g(self.getInputFromPort('p_def_color_g'))
- if self.hasInputFromPort('p_def_color_b') :
- p.set_p_def_color_b(self.getInputFromPort('p_def_color_b'))
- if self.hasInputFromPort('p_def_color_a') :
- p.set_p_def_color_a(self.getInputFromPort('p_def_color_a'))
- if self.hasInputFromPort('p_nodes_scale') :
- p.set_p_nodes_scale(self.getInputFromPort('p_nodes_scale'))
- if self.hasInputFromPort('p_nodes_scaleNV') :
- p.set_p_nodes_scaleNV(self.getInputFromPort('p_nodes_scaleNV'))
- if self.hasInputFromPort('p_edges_scale') :
- p.set_p_edges_scale(self.getInputFromPort('p_edges_scale'))
- if self.hasInputFromPort('p_edges_scaleNV') :
- p.set_p_edges_scaleNV(self.getInputFromPort('p_edges_scaleNV'))
- if self.hasInputFromPort('p_active_tab') :
- p.set_p_active_tab(self.getInputFromPort('p_active_tab'))
- if self.hasInputFromPort('p_interactive_mode') :
- p.set_p_interactive_mode(self.getInputFromPort('p_interactive_mode'))
- if self.hasInputFromPort('p_show_progress') :
- p.set_p_show_progress(self.getInputFromPort('p_show_progress'))
- if self.hasInputFromPort('p_field_name') :
- p.set_p_field_name(self.getInputFromPort('p_field_name'))
- if self.hasInputFromPort('p_field_name_override') :
- p.set_p_field_name_override(self.getInputFromPort('p_field_name_override'))
- if self.hasInputFromPort('p_nodes_resolution') :
- p.set_p_nodes_resolution(self.getInputFromPort('p_nodes_resolution'))
- if self.hasInputFromPort('p_edges_resolution') :
- p.set_p_edges_resolution(self.getInputFromPort('p_edges_resolution'))
- if self.hasInputFromPort('p_approx_div') :
- p.set_p_approx_div(self.getInputFromPort('p_approx_div'))
- if self.hasInputFromPort('p_use_default_size') :
- p.set_p_use_default_size(self.getInputFromPort('p_use_default_size'))
- Mesh = 0
- if self.hasInputFromPort('Mesh') :
- Mesh = self.getInputFromPort('Mesh')
- ColorMap = 0
- if self.hasInputFromPort('ColorMap') :
- ColorMap = self.getInputFromPort('ColorMap')
- results = p.execute(Mesh, ColorMap)
- self.setResult('Scene Graph', results)
-
-class ExtractIsosurface(Visualization) :
- def compute(self) :
- p = sr_py.ExtractIsosurfaceAlg()
- if self.hasInputFromPort('p_isoval_min') :
- p.set_p_isoval_min(self.getInputFromPort('p_isoval_min'))
- if self.hasInputFromPort('p_isoval_max') :
- p.set_p_isoval_max(self.getInputFromPort('p_isoval_max'))
- if self.hasInputFromPort('p_isoval') :
- p.set_p_isoval(self.getInputFromPort('p_isoval'))
- if self.hasInputFromPort('p_isoval_typed') :
- p.set_p_isoval_typed(self.getInputFromPort('p_isoval_typed'))
- if self.hasInputFromPort('p_isoval_quantity') :
- p.set_p_isoval_quantity(self.getInputFromPort('p_isoval_quantity'))
- if self.hasInputFromPort('p_quantity_range') :
- p.set_p_quantity_range(self.getInputFromPort('p_quantity_range'))
- if self.hasInputFromPort('p_quantity_clusive') :
- p.set_p_quantity_clusive(self.getInputFromPort('p_quantity_clusive'))
- if self.hasInputFromPort('p_quantity_min') :
- p.set_p_quantity_min(self.getInputFromPort('p_quantity_min'))
- if self.hasInputFromPort('p_quantity_max') :
- p.set_p_quantity_max(self.getInputFromPort('p_quantity_max'))
- if self.hasInputFromPort('p_quantity_list') :
- p.set_p_quantity_list(self.getInputFromPort('p_quantity_list'))
- if self.hasInputFromPort('p_isoval_list') :
- p.set_p_isoval_list(self.getInputFromPort('p_isoval_list'))
- if self.hasInputFromPort('p_matrix_list') :
- p.set_p_matrix_list(self.getInputFromPort('p_matrix_list'))
- if self.hasInputFromPort('p_algorithm') :
- p.set_p_algorithm(self.getInputFromPort('p_algorithm'))
- if self.hasInputFromPort('p_build_trisurf') :
- p.set_p_build_trisurf(self.getInputFromPort('p_build_trisurf'))
- if self.hasInputFromPort('p_build_geom') :
- p.set_p_build_geom(self.getInputFromPort('p_build_geom'))
- if self.hasInputFromPort('p_transparency') :
- p.set_p_transparency(self.getInputFromPort('p_transparency'))
- if self.hasInputFromPort('p_np') :
- p.set_p_np(self.getInputFromPort('p_np'))
- if self.hasInputFromPort('p_active_isoval_selection_tab') :
- p.set_p_active_isoval_selection_tab(self.getInputFromPort('p_active_isoval_selection_tab'))
- if self.hasInputFromPort('p_active_tab') :
- p.set_p_active_tab(self.getInputFromPort('p_active_tab'))
- if self.hasInputFromPort('p_update_type') :
- p.set_p_update_type(self.getInputFromPort('p_update_type'))
- if self.hasInputFromPort('p_color_r') :
- p.set_p_color_r(self.getInputFromPort('p_color_r'))
- if self.hasInputFromPort('p_color_g') :
- p.set_p_color_g(self.getInputFromPort('p_color_g'))
- if self.hasInputFromPort('p_color_b') :
- p.set_p_color_b(self.getInputFromPort('p_color_b'))
- if self.hasInputFromPort('p_color_a') :
- p.set_p_color_a(self.getInputFromPort('p_color_a'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- Optional_Color_Map = 0
- if self.hasInputFromPort('Optional Color Map') :
- Optional_Color_Map = self.getInputFromPort('Optional Color Map')
- Optional_Isovalues = 0
- if self.hasInputFromPort('Optional Isovalues') :
- Optional_Isovalues = self.getInputFromPort('Optional Isovalues')
- results = p.execute(Field, Optional_Color_Map, Optional_Isovalues)
- self.setResult('Surface', results[0])
- self.setResult('Geometry', results[1])
- self.setResult('Mapping', results[2])
-
-class CreateViewerAxes(Visualization) :
- def compute(self) :
- p = sr_py.CreateViewerAxesAlg()
- if self.hasInputFromPort('p_precision') :
- p.set_p_precision(self.getInputFromPort('p_precision'))
- if self.hasInputFromPort('p_squash') :
- p.set_p_squash(self.getInputFromPort('p_squash'))
- if self.hasInputFromPort('p_valuerez') :
- p.set_p_valuerez(self.getInputFromPort('p_valuerez'))
- if self.hasInputFromPort('p_labelrez') :
- p.set_p_labelrez(self.getInputFromPort('p_labelrez'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_absolute') :
- p.set_p_Plane_01_0_Axis_absolute(self.getInputFromPort('p_Plane_01_0_Axis_absolute'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_divisions') :
- p.set_p_Plane_01_0_Axis_divisions(self.getInputFromPort('p_Plane_01_0_Axis_divisions'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_offset') :
- p.set_p_Plane_01_0_Axis_offset(self.getInputFromPort('p_Plane_01_0_Axis_offset'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_range_first') :
- p.set_p_Plane_01_0_Axis_range_first(self.getInputFromPort('p_Plane_01_0_Axis_range_first'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_range_second') :
- p.set_p_Plane_01_0_Axis_range_second(self.getInputFromPort('p_Plane_01_0_Axis_range_second'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_min_absolute') :
- p.set_p_Plane_01_0_Axis_min_absolute(self.getInputFromPort('p_Plane_01_0_Axis_min_absolute'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_max_absolute') :
- p.set_p_Plane_01_0_Axis_max_absolute(self.getInputFromPort('p_Plane_01_0_Axis_max_absolute'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_minplane') :
- p.set_p_Plane_01_0_Axis_minplane(self.getInputFromPort('p_Plane_01_0_Axis_minplane'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_maxplane') :
- p.set_p_Plane_01_0_Axis_maxplane(self.getInputFromPort('p_Plane_01_0_Axis_maxplane'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_lines') :
- p.set_p_Plane_01_0_Axis_lines(self.getInputFromPort('p_Plane_01_0_Axis_lines'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_minticks') :
- p.set_p_Plane_01_0_Axis_minticks(self.getInputFromPort('p_Plane_01_0_Axis_minticks'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_maxticks') :
- p.set_p_Plane_01_0_Axis_maxticks(self.getInputFromPort('p_Plane_01_0_Axis_maxticks'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_minlabel') :
- p.set_p_Plane_01_0_Axis_minlabel(self.getInputFromPort('p_Plane_01_0_Axis_minlabel'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_maxlabel') :
- p.set_p_Plane_01_0_Axis_maxlabel(self.getInputFromPort('p_Plane_01_0_Axis_maxlabel'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_minvalue') :
- p.set_p_Plane_01_0_Axis_minvalue(self.getInputFromPort('p_Plane_01_0_Axis_minvalue'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_maxvalue') :
- p.set_p_Plane_01_0_Axis_maxvalue(self.getInputFromPort('p_Plane_01_0_Axis_maxvalue'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_width') :
- p.set_p_Plane_01_0_Axis_width(self.getInputFromPort('p_Plane_01_0_Axis_width'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_tickangle') :
- p.set_p_Plane_01_0_Axis_tickangle(self.getInputFromPort('p_Plane_01_0_Axis_tickangle'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_ticktilt') :
- p.set_p_Plane_01_0_Axis_ticktilt(self.getInputFromPort('p_Plane_01_0_Axis_ticktilt'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_ticksize') :
- p.set_p_Plane_01_0_Axis_ticksize(self.getInputFromPort('p_Plane_01_0_Axis_ticksize'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_labelangle') :
- p.set_p_Plane_01_0_Axis_labelangle(self.getInputFromPort('p_Plane_01_0_Axis_labelangle'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_labelheight') :
- p.set_p_Plane_01_0_Axis_labelheight(self.getInputFromPort('p_Plane_01_0_Axis_labelheight'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_valuesize') :
- p.set_p_Plane_01_0_Axis_valuesize(self.getInputFromPort('p_Plane_01_0_Axis_valuesize'))
- if self.hasInputFromPort('p_Plane_01_0_Axis_valuesquash') :
- p.set_p_Plane_01_0_Axis_valuesquash(self.getInputFromPort('p_Plane_01_0_Axis_valuesquash'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_absolute') :
- p.set_p_Plane_01_1_Axis_absolute(self.getInputFromPort('p_Plane_01_1_Axis_absolute'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_divisions') :
- p.set_p_Plane_01_1_Axis_divisions(self.getInputFromPort('p_Plane_01_1_Axis_divisions'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_offset') :
- p.set_p_Plane_01_1_Axis_offset(self.getInputFromPort('p_Plane_01_1_Axis_offset'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_range_first') :
- p.set_p_Plane_01_1_Axis_range_first(self.getInputFromPort('p_Plane_01_1_Axis_range_first'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_range_second') :
- p.set_p_Plane_01_1_Axis_range_second(self.getInputFromPort('p_Plane_01_1_Axis_range_second'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_min_absolute') :
- p.set_p_Plane_01_1_Axis_min_absolute(self.getInputFromPort('p_Plane_01_1_Axis_min_absolute'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_max_absolute') :
- p.set_p_Plane_01_1_Axis_max_absolute(self.getInputFromPort('p_Plane_01_1_Axis_max_absolute'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_minplane') :
- p.set_p_Plane_01_1_Axis_minplane(self.getInputFromPort('p_Plane_01_1_Axis_minplane'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_maxplane') :
- p.set_p_Plane_01_1_Axis_maxplane(self.getInputFromPort('p_Plane_01_1_Axis_maxplane'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_lines') :
- p.set_p_Plane_01_1_Axis_lines(self.getInputFromPort('p_Plane_01_1_Axis_lines'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_minticks') :
- p.set_p_Plane_01_1_Axis_minticks(self.getInputFromPort('p_Plane_01_1_Axis_minticks'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_maxticks') :
- p.set_p_Plane_01_1_Axis_maxticks(self.getInputFromPort('p_Plane_01_1_Axis_maxticks'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_minlabel') :
- p.set_p_Plane_01_1_Axis_minlabel(self.getInputFromPort('p_Plane_01_1_Axis_minlabel'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_maxlabel') :
- p.set_p_Plane_01_1_Axis_maxlabel(self.getInputFromPort('p_Plane_01_1_Axis_maxlabel'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_minvalue') :
- p.set_p_Plane_01_1_Axis_minvalue(self.getInputFromPort('p_Plane_01_1_Axis_minvalue'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_maxvalue') :
- p.set_p_Plane_01_1_Axis_maxvalue(self.getInputFromPort('p_Plane_01_1_Axis_maxvalue'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_width') :
- p.set_p_Plane_01_1_Axis_width(self.getInputFromPort('p_Plane_01_1_Axis_width'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_tickangle') :
- p.set_p_Plane_01_1_Axis_tickangle(self.getInputFromPort('p_Plane_01_1_Axis_tickangle'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_ticktilt') :
- p.set_p_Plane_01_1_Axis_ticktilt(self.getInputFromPort('p_Plane_01_1_Axis_ticktilt'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_ticksize') :
- p.set_p_Plane_01_1_Axis_ticksize(self.getInputFromPort('p_Plane_01_1_Axis_ticksize'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_labelangle') :
- p.set_p_Plane_01_1_Axis_labelangle(self.getInputFromPort('p_Plane_01_1_Axis_labelangle'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_labelheight') :
- p.set_p_Plane_01_1_Axis_labelheight(self.getInputFromPort('p_Plane_01_1_Axis_labelheight'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_valuesize') :
- p.set_p_Plane_01_1_Axis_valuesize(self.getInputFromPort('p_Plane_01_1_Axis_valuesize'))
- if self.hasInputFromPort('p_Plane_01_1_Axis_valuesquash') :
- p.set_p_Plane_01_1_Axis_valuesquash(self.getInputFromPort('p_Plane_01_1_Axis_valuesquash'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_absolute') :
- p.set_p_Plane_02_0_Axis_absolute(self.getInputFromPort('p_Plane_02_0_Axis_absolute'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_divisions') :
- p.set_p_Plane_02_0_Axis_divisions(self.getInputFromPort('p_Plane_02_0_Axis_divisions'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_offset') :
- p.set_p_Plane_02_0_Axis_offset(self.getInputFromPort('p_Plane_02_0_Axis_offset'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_range_first') :
- p.set_p_Plane_02_0_Axis_range_first(self.getInputFromPort('p_Plane_02_0_Axis_range_first'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_range_second') :
- p.set_p_Plane_02_0_Axis_range_second(self.getInputFromPort('p_Plane_02_0_Axis_range_second'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_min_absolute') :
- p.set_p_Plane_02_0_Axis_min_absolute(self.getInputFromPort('p_Plane_02_0_Axis_min_absolute'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_max_absolute') :
- p.set_p_Plane_02_0_Axis_max_absolute(self.getInputFromPort('p_Plane_02_0_Axis_max_absolute'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_minplane') :
- p.set_p_Plane_02_0_Axis_minplane(self.getInputFromPort('p_Plane_02_0_Axis_minplane'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_maxplane') :
- p.set_p_Plane_02_0_Axis_maxplane(self.getInputFromPort('p_Plane_02_0_Axis_maxplane'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_lines') :
- p.set_p_Plane_02_0_Axis_lines(self.getInputFromPort('p_Plane_02_0_Axis_lines'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_minticks') :
- p.set_p_Plane_02_0_Axis_minticks(self.getInputFromPort('p_Plane_02_0_Axis_minticks'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_maxticks') :
- p.set_p_Plane_02_0_Axis_maxticks(self.getInputFromPort('p_Plane_02_0_Axis_maxticks'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_minlabel') :
- p.set_p_Plane_02_0_Axis_minlabel(self.getInputFromPort('p_Plane_02_0_Axis_minlabel'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_maxlabel') :
- p.set_p_Plane_02_0_Axis_maxlabel(self.getInputFromPort('p_Plane_02_0_Axis_maxlabel'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_minvalue') :
- p.set_p_Plane_02_0_Axis_minvalue(self.getInputFromPort('p_Plane_02_0_Axis_minvalue'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_maxvalue') :
- p.set_p_Plane_02_0_Axis_maxvalue(self.getInputFromPort('p_Plane_02_0_Axis_maxvalue'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_width') :
- p.set_p_Plane_02_0_Axis_width(self.getInputFromPort('p_Plane_02_0_Axis_width'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_tickangle') :
- p.set_p_Plane_02_0_Axis_tickangle(self.getInputFromPort('p_Plane_02_0_Axis_tickangle'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_ticktilt') :
- p.set_p_Plane_02_0_Axis_ticktilt(self.getInputFromPort('p_Plane_02_0_Axis_ticktilt'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_ticksize') :
- p.set_p_Plane_02_0_Axis_ticksize(self.getInputFromPort('p_Plane_02_0_Axis_ticksize'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_labelangle') :
- p.set_p_Plane_02_0_Axis_labelangle(self.getInputFromPort('p_Plane_02_0_Axis_labelangle'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_labelheight') :
- p.set_p_Plane_02_0_Axis_labelheight(self.getInputFromPort('p_Plane_02_0_Axis_labelheight'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_valuesize') :
- p.set_p_Plane_02_0_Axis_valuesize(self.getInputFromPort('p_Plane_02_0_Axis_valuesize'))
- if self.hasInputFromPort('p_Plane_02_0_Axis_valuesquash') :
- p.set_p_Plane_02_0_Axis_valuesquash(self.getInputFromPort('p_Plane_02_0_Axis_valuesquash'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_absolute') :
- p.set_p_Plane_02_2_Axis_absolute(self.getInputFromPort('p_Plane_02_2_Axis_absolute'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_divisions') :
- p.set_p_Plane_02_2_Axis_divisions(self.getInputFromPort('p_Plane_02_2_Axis_divisions'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_offset') :
- p.set_p_Plane_02_2_Axis_offset(self.getInputFromPort('p_Plane_02_2_Axis_offset'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_range_first') :
- p.set_p_Plane_02_2_Axis_range_first(self.getInputFromPort('p_Plane_02_2_Axis_range_first'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_range_second') :
- p.set_p_Plane_02_2_Axis_range_second(self.getInputFromPort('p_Plane_02_2_Axis_range_second'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_min_absolute') :
- p.set_p_Plane_02_2_Axis_min_absolute(self.getInputFromPort('p_Plane_02_2_Axis_min_absolute'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_max_absolute') :
- p.set_p_Plane_02_2_Axis_max_absolute(self.getInputFromPort('p_Plane_02_2_Axis_max_absolute'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_minplane') :
- p.set_p_Plane_02_2_Axis_minplane(self.getInputFromPort('p_Plane_02_2_Axis_minplane'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_maxplane') :
- p.set_p_Plane_02_2_Axis_maxplane(self.getInputFromPort('p_Plane_02_2_Axis_maxplane'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_lines') :
- p.set_p_Plane_02_2_Axis_lines(self.getInputFromPort('p_Plane_02_2_Axis_lines'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_minticks') :
- p.set_p_Plane_02_2_Axis_minticks(self.getInputFromPort('p_Plane_02_2_Axis_minticks'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_maxticks') :
- p.set_p_Plane_02_2_Axis_maxticks(self.getInputFromPort('p_Plane_02_2_Axis_maxticks'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_minlabel') :
- p.set_p_Plane_02_2_Axis_minlabel(self.getInputFromPort('p_Plane_02_2_Axis_minlabel'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_maxlabel') :
- p.set_p_Plane_02_2_Axis_maxlabel(self.getInputFromPort('p_Plane_02_2_Axis_maxlabel'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_minvalue') :
- p.set_p_Plane_02_2_Axis_minvalue(self.getInputFromPort('p_Plane_02_2_Axis_minvalue'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_maxvalue') :
- p.set_p_Plane_02_2_Axis_maxvalue(self.getInputFromPort('p_Plane_02_2_Axis_maxvalue'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_width') :
- p.set_p_Plane_02_2_Axis_width(self.getInputFromPort('p_Plane_02_2_Axis_width'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_tickangle') :
- p.set_p_Plane_02_2_Axis_tickangle(self.getInputFromPort('p_Plane_02_2_Axis_tickangle'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_ticktilt') :
- p.set_p_Plane_02_2_Axis_ticktilt(self.getInputFromPort('p_Plane_02_2_Axis_ticktilt'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_ticksize') :
- p.set_p_Plane_02_2_Axis_ticksize(self.getInputFromPort('p_Plane_02_2_Axis_ticksize'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_labelangle') :
- p.set_p_Plane_02_2_Axis_labelangle(self.getInputFromPort('p_Plane_02_2_Axis_labelangle'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_labelheight') :
- p.set_p_Plane_02_2_Axis_labelheight(self.getInputFromPort('p_Plane_02_2_Axis_labelheight'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_valuesize') :
- p.set_p_Plane_02_2_Axis_valuesize(self.getInputFromPort('p_Plane_02_2_Axis_valuesize'))
- if self.hasInputFromPort('p_Plane_02_2_Axis_valuesquash') :
- p.set_p_Plane_02_2_Axis_valuesquash(self.getInputFromPort('p_Plane_02_2_Axis_valuesquash'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_absolute') :
- p.set_p_Plane_12_1_Axis_absolute(self.getInputFromPort('p_Plane_12_1_Axis_absolute'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_divisions') :
- p.set_p_Plane_12_1_Axis_divisions(self.getInputFromPort('p_Plane_12_1_Axis_divisions'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_offset') :
- p.set_p_Plane_12_1_Axis_offset(self.getInputFromPort('p_Plane_12_1_Axis_offset'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_range_first') :
- p.set_p_Plane_12_1_Axis_range_first(self.getInputFromPort('p_Plane_12_1_Axis_range_first'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_range_second') :
- p.set_p_Plane_12_1_Axis_range_second(self.getInputFromPort('p_Plane_12_1_Axis_range_second'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_min_absolute') :
- p.set_p_Plane_12_1_Axis_min_absolute(self.getInputFromPort('p_Plane_12_1_Axis_min_absolute'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_max_absolute') :
- p.set_p_Plane_12_1_Axis_max_absolute(self.getInputFromPort('p_Plane_12_1_Axis_max_absolute'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_minplane') :
- p.set_p_Plane_12_1_Axis_minplane(self.getInputFromPort('p_Plane_12_1_Axis_minplane'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_maxplane') :
- p.set_p_Plane_12_1_Axis_maxplane(self.getInputFromPort('p_Plane_12_1_Axis_maxplane'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_lines') :
- p.set_p_Plane_12_1_Axis_lines(self.getInputFromPort('p_Plane_12_1_Axis_lines'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_minticks') :
- p.set_p_Plane_12_1_Axis_minticks(self.getInputFromPort('p_Plane_12_1_Axis_minticks'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_maxticks') :
- p.set_p_Plane_12_1_Axis_maxticks(self.getInputFromPort('p_Plane_12_1_Axis_maxticks'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_minlabel') :
- p.set_p_Plane_12_1_Axis_minlabel(self.getInputFromPort('p_Plane_12_1_Axis_minlabel'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_maxlabel') :
- p.set_p_Plane_12_1_Axis_maxlabel(self.getInputFromPort('p_Plane_12_1_Axis_maxlabel'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_minvalue') :
- p.set_p_Plane_12_1_Axis_minvalue(self.getInputFromPort('p_Plane_12_1_Axis_minvalue'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_maxvalue') :
- p.set_p_Plane_12_1_Axis_maxvalue(self.getInputFromPort('p_Plane_12_1_Axis_maxvalue'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_width') :
- p.set_p_Plane_12_1_Axis_width(self.getInputFromPort('p_Plane_12_1_Axis_width'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_tickangle') :
- p.set_p_Plane_12_1_Axis_tickangle(self.getInputFromPort('p_Plane_12_1_Axis_tickangle'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_ticktilt') :
- p.set_p_Plane_12_1_Axis_ticktilt(self.getInputFromPort('p_Plane_12_1_Axis_ticktilt'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_ticksize') :
- p.set_p_Plane_12_1_Axis_ticksize(self.getInputFromPort('p_Plane_12_1_Axis_ticksize'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_labelangle') :
- p.set_p_Plane_12_1_Axis_labelangle(self.getInputFromPort('p_Plane_12_1_Axis_labelangle'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_labelheight') :
- p.set_p_Plane_12_1_Axis_labelheight(self.getInputFromPort('p_Plane_12_1_Axis_labelheight'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_valuesize') :
- p.set_p_Plane_12_1_Axis_valuesize(self.getInputFromPort('p_Plane_12_1_Axis_valuesize'))
- if self.hasInputFromPort('p_Plane_12_1_Axis_valuesquash') :
- p.set_p_Plane_12_1_Axis_valuesquash(self.getInputFromPort('p_Plane_12_1_Axis_valuesquash'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_absolute') :
- p.set_p_Plane_12_2_Axis_absolute(self.getInputFromPort('p_Plane_12_2_Axis_absolute'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_divisions') :
- p.set_p_Plane_12_2_Axis_divisions(self.getInputFromPort('p_Plane_12_2_Axis_divisions'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_offset') :
- p.set_p_Plane_12_2_Axis_offset(self.getInputFromPort('p_Plane_12_2_Axis_offset'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_range_first') :
- p.set_p_Plane_12_2_Axis_range_first(self.getInputFromPort('p_Plane_12_2_Axis_range_first'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_range_second') :
- p.set_p_Plane_12_2_Axis_range_second(self.getInputFromPort('p_Plane_12_2_Axis_range_second'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_min_absolute') :
- p.set_p_Plane_12_2_Axis_min_absolute(self.getInputFromPort('p_Plane_12_2_Axis_min_absolute'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_max_absolute') :
- p.set_p_Plane_12_2_Axis_max_absolute(self.getInputFromPort('p_Plane_12_2_Axis_max_absolute'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_minplane') :
- p.set_p_Plane_12_2_Axis_minplane(self.getInputFromPort('p_Plane_12_2_Axis_minplane'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_maxplane') :
- p.set_p_Plane_12_2_Axis_maxplane(self.getInputFromPort('p_Plane_12_2_Axis_maxplane'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_lines') :
- p.set_p_Plane_12_2_Axis_lines(self.getInputFromPort('p_Plane_12_2_Axis_lines'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_minticks') :
- p.set_p_Plane_12_2_Axis_minticks(self.getInputFromPort('p_Plane_12_2_Axis_minticks'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_maxticks') :
- p.set_p_Plane_12_2_Axis_maxticks(self.getInputFromPort('p_Plane_12_2_Axis_maxticks'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_minlabel') :
- p.set_p_Plane_12_2_Axis_minlabel(self.getInputFromPort('p_Plane_12_2_Axis_minlabel'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_maxlabel') :
- p.set_p_Plane_12_2_Axis_maxlabel(self.getInputFromPort('p_Plane_12_2_Axis_maxlabel'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_minvalue') :
- p.set_p_Plane_12_2_Axis_minvalue(self.getInputFromPort('p_Plane_12_2_Axis_minvalue'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_maxvalue') :
- p.set_p_Plane_12_2_Axis_maxvalue(self.getInputFromPort('p_Plane_12_2_Axis_maxvalue'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_width') :
- p.set_p_Plane_12_2_Axis_width(self.getInputFromPort('p_Plane_12_2_Axis_width'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_tickangle') :
- p.set_p_Plane_12_2_Axis_tickangle(self.getInputFromPort('p_Plane_12_2_Axis_tickangle'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_ticktilt') :
- p.set_p_Plane_12_2_Axis_ticktilt(self.getInputFromPort('p_Plane_12_2_Axis_ticktilt'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_ticksize') :
- p.set_p_Plane_12_2_Axis_ticksize(self.getInputFromPort('p_Plane_12_2_Axis_ticksize'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_labelangle') :
- p.set_p_Plane_12_2_Axis_labelangle(self.getInputFromPort('p_Plane_12_2_Axis_labelangle'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_labelheight') :
- p.set_p_Plane_12_2_Axis_labelheight(self.getInputFromPort('p_Plane_12_2_Axis_labelheight'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_valuesize') :
- p.set_p_Plane_12_2_Axis_valuesize(self.getInputFromPort('p_Plane_12_2_Axis_valuesize'))
- if self.hasInputFromPort('p_Plane_12_2_Axis_valuesquash') :
- p.set_p_Plane_12_2_Axis_valuesquash(self.getInputFromPort('p_Plane_12_2_Axis_valuesquash'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('Axes', results)
-
-class RescaleColorMap(Visualization) :
- def compute(self) :
- p = sr_py.RescaleColorMapAlg()
- if self.hasInputFromPort('p_main_frame') :
- p.set_p_main_frame(self.getInputFromPort('p_main_frame'))
- if self.hasInputFromPort('p_isFixed') :
- p.set_p_isFixed(self.getInputFromPort('p_isFixed'))
- if self.hasInputFromPort('p_min') :
- p.set_p_min(self.getInputFromPort('p_min'))
- if self.hasInputFromPort('p_max') :
- p.set_p_max(self.getInputFromPort('p_max'))
- if self.hasInputFromPort('p_makeSymmetric') :
- p.set_p_makeSymmetric(self.getInputFromPort('p_makeSymmetric'))
- ColorMap = 0
- if self.hasInputFromPort('ColorMap') :
- ColorMap = self.getInputFromPort('ColorMap')
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(ColorMap, Field)
- self.setResult('ColorMap', results)
-
-class ConvertNrrdsToTexture(Visualization) :
- def compute(self) :
- p = sr_py.ConvertNrrdsToTextureAlg()
- if self.hasInputFromPort('p_vmin') :
- p.set_p_vmin(self.getInputFromPort('p_vmin'))
- if self.hasInputFromPort('p_vmax') :
- p.set_p_vmax(self.getInputFromPort('p_vmax'))
- if self.hasInputFromPort('p_gmin') :
- p.set_p_gmin(self.getInputFromPort('p_gmin'))
- if self.hasInputFromPort('p_gmax') :
- p.set_p_gmax(self.getInputFromPort('p_gmax'))
- if self.hasInputFromPort('p_mmin') :
- p.set_p_mmin(self.getInputFromPort('p_mmin'))
- if self.hasInputFromPort('p_mmax') :
- p.set_p_mmax(self.getInputFromPort('p_mmax'))
- if self.hasInputFromPort('p_is_fixed') :
- p.set_p_is_fixed(self.getInputFromPort('p_is_fixed'))
- if self.hasInputFromPort('p_card_mem') :
- p.set_p_card_mem(self.getInputFromPort('p_card_mem'))
- if self.hasInputFromPort('p_card_mem_auto') :
- p.set_p_card_mem_auto(self.getInputFromPort('p_card_mem_auto'))
- if self.hasInputFromPort('p_is_uchar') :
- p.set_p_is_uchar(self.getInputFromPort('p_is_uchar'))
- if self.hasInputFromPort('p_histogram') :
- p.set_p_histogram(self.getInputFromPort('p_histogram'))
- if self.hasInputFromPort('p_gamma') :
- p.set_p_gamma(self.getInputFromPort('p_gamma'))
- Value_Nrrd = 0
- if self.hasInputFromPort('Value Nrrd') :
- Value_Nrrd = self.getInputFromPort('Value Nrrd')
- Gradient_Magnitude_Nrrd = 0
- if self.hasInputFromPort('Gradient Magnitude Nrrd') :
- Gradient_Magnitude_Nrrd = self.getInputFromPort('Gradient Magnitude Nrrd')
- results = p.execute(Value_Nrrd, Gradient_Magnitude_Nrrd)
- self.setResult('Texture', results[0])
- self.setResult('JointHistoGram', results[1])
-
-class ChooseColorMap(Visualization) :
- def compute(self) :
- p = sr_py.ChooseColorMapAlg()
- if self.hasInputFromPort('p_use_first_valid') :
- p.set_p_use_first_valid(self.getInputFromPort('p_use_first_valid'))
- if self.hasInputFromPort('p_port_valid_index') :
- p.set_p_port_valid_index(self.getInputFromPort('p_port_valid_index'))
- if self.hasInputFromPort('p_port_selected_index') :
- p.set_p_port_selected_index(self.getInputFromPort('p_port_selected_index'))
- ColorMap = 0
- if self.hasInputFromPort('ColorMap') :
- ColorMap = self.getInputFromPort('ColorMap')
- results = p.execute(ColorMap)
- self.setResult('ColorMap', results)
-
-class CreateLightForViewer(Visualization) :
- def compute(self) :
- p = sr_py.CreateLightForViewerAlg()
- if self.hasInputFromPort('p_control_pos_saved') :
- p.set_p_control_pos_saved(self.getInputFromPort('p_control_pos_saved'))
- if self.hasInputFromPort('p_control_x') :
- p.set_p_control_x(self.getInputFromPort('p_control_x'))
- if self.hasInputFromPort('p_control_y') :
- p.set_p_control_y(self.getInputFromPort('p_control_y'))
- if self.hasInputFromPort('p_control_z') :
- p.set_p_control_z(self.getInputFromPort('p_control_z'))
- if self.hasInputFromPort('p_at_x') :
- p.set_p_at_x(self.getInputFromPort('p_at_x'))
- if self.hasInputFromPort('p_at_y') :
- p.set_p_at_y(self.getInputFromPort('p_at_y'))
- if self.hasInputFromPort('p_at_z') :
- p.set_p_at_z(self.getInputFromPort('p_at_z'))
- if self.hasInputFromPort('p_type') :
- p.set_p_type(self.getInputFromPort('p_type'))
- if self.hasInputFromPort('p_on') :
- p.set_p_on(self.getInputFromPort('p_on'))
- results = p.execute()
- self.setResult('Geometry', results)
-
-class ShowTextureVolume(Visualization) :
- def compute(self) :
- p = sr_py.ShowTextureVolumeAlg()
- if self.hasInputFromPort('p_sampling_rate_hi') :
- p.set_p_sampling_rate_hi(self.getInputFromPort('p_sampling_rate_hi'))
- if self.hasInputFromPort('p_sampling_rate_lo') :
- p.set_p_sampling_rate_lo(self.getInputFromPort('p_sampling_rate_lo'))
- if self.hasInputFromPort('p_gradient_min') :
- p.set_p_gradient_min(self.getInputFromPort('p_gradient_min'))
- if self.hasInputFromPort('p_gradient_max') :
- p.set_p_gradient_max(self.getInputFromPort('p_gradient_max'))
- if self.hasInputFromPort('p_adaptive') :
- p.set_p_adaptive(self.getInputFromPort('p_adaptive'))
- if self.hasInputFromPort('p_cmap_size') :
- p.set_p_cmap_size(self.getInputFromPort('p_cmap_size'))
- if self.hasInputFromPort('p_sw_raster') :
- p.set_p_sw_raster(self.getInputFromPort('p_sw_raster'))
- if self.hasInputFromPort('p_render_style') :
- p.set_p_render_style(self.getInputFromPort('p_render_style'))
- if self.hasInputFromPort('p_alpha_scale') :
- p.set_p_alpha_scale(self.getInputFromPort('p_alpha_scale'))
- if self.hasInputFromPort('p_interp_mode') :
- p.set_p_interp_mode(self.getInputFromPort('p_interp_mode'))
- if self.hasInputFromPort('p_shading') :
- p.set_p_shading(self.getInputFromPort('p_shading'))
- if self.hasInputFromPort('p_ambient') :
- p.set_p_ambient(self.getInputFromPort('p_ambient'))
- if self.hasInputFromPort('p_diffuse') :
- p.set_p_diffuse(self.getInputFromPort('p_diffuse'))
- if self.hasInputFromPort('p_specular') :
- p.set_p_specular(self.getInputFromPort('p_specular'))
- if self.hasInputFromPort('p_shine') :
- p.set_p_shine(self.getInputFromPort('p_shine'))
- if self.hasInputFromPort('p_light') :
- p.set_p_light(self.getInputFromPort('p_light'))
- if self.hasInputFromPort('p_blend_res') :
- p.set_p_blend_res(self.getInputFromPort('p_blend_res'))
- if self.hasInputFromPort('p_multi_level') :
- p.set_p_multi_level(self.getInputFromPort('p_multi_level'))
- if self.hasInputFromPort('p_use_stencil') :
- p.set_p_use_stencil(self.getInputFromPort('p_use_stencil'))
- if self.hasInputFromPort('p_invert_opacity') :
- p.set_p_invert_opacity(self.getInputFromPort('p_invert_opacity'))
- if self.hasInputFromPort('p_num_clipping_planes') :
- p.set_p_num_clipping_planes(self.getInputFromPort('p_num_clipping_planes'))
- if self.hasInputFromPort('p_show_clipping_widgets') :
- p.set_p_show_clipping_widgets(self.getInputFromPort('p_show_clipping_widgets'))
- if self.hasInputFromPort('p_level_on') :
- p.set_p_level_on(self.getInputFromPort('p_level_on'))
- if self.hasInputFromPort('p_level_vals') :
- p.set_p_level_vals(self.getInputFromPort('p_level_vals'))
- if self.hasInputFromPort('p_id') :
- p.set_p_id(self.getInputFromPort('p_id'))
- Texture = 0
- if self.hasInputFromPort('Texture') :
- Texture = self.getInputFromPort('Texture')
- ColorMap = 0
- if self.hasInputFromPort('ColorMap') :
- ColorMap = self.getInputFromPort('ColorMap')
- ColorMap2 = 0
- if self.hasInputFromPort('ColorMap2') :
- ColorMap2 = self.getInputFromPort('ColorMap2')
- results = p.execute(Texture, ColorMap, ColorMap2)
- self.setResult('Geometry', results[0])
- self.setResult('ColorMap', results[1])
-
-class ShowFieldGlyphs(Visualization) :
- def compute(self) :
- p = sr_py.ShowFieldGlyphsAlg()
- if self.hasInputFromPort('p_scalars_has_data') :
- p.set_p_scalars_has_data(self.getInputFromPort('p_scalars_has_data'))
- if self.hasInputFromPort('p_scalars_on') :
- p.set_p_scalars_on(self.getInputFromPort('p_scalars_on'))
- if self.hasInputFromPort('p_scalars_display_type') :
- p.set_p_scalars_display_type(self.getInputFromPort('p_scalars_display_type'))
- if self.hasInputFromPort('p_scalars_transparency') :
- p.set_p_scalars_transparency(self.getInputFromPort('p_scalars_transparency'))
- if self.hasInputFromPort('p_scalars_normalize') :
- p.set_p_scalars_normalize(self.getInputFromPort('p_scalars_normalize'))
- if self.hasInputFromPort('p_scalars_color_type') :
- p.set_p_scalars_color_type(self.getInputFromPort('p_scalars_color_type'))
- if self.hasInputFromPort('p_scalars_resolution') :
- p.set_p_scalars_resolution(self.getInputFromPort('p_scalars_resolution'))
- if self.hasInputFromPort('p_vectors_has_data') :
- p.set_p_vectors_has_data(self.getInputFromPort('p_vectors_has_data'))
- if self.hasInputFromPort('p_vectors_on') :
- p.set_p_vectors_on(self.getInputFromPort('p_vectors_on'))
- if self.hasInputFromPort('p_vectors_display_type') :
- p.set_p_vectors_display_type(self.getInputFromPort('p_vectors_display_type'))
- if self.hasInputFromPort('p_vectors_transparency') :
- p.set_p_vectors_transparency(self.getInputFromPort('p_vectors_transparency'))
- if self.hasInputFromPort('p_vectors_normalize') :
- p.set_p_vectors_normalize(self.getInputFromPort('p_vectors_normalize'))
- if self.hasInputFromPort('p_vectors_bidirectional') :
- p.set_p_vectors_bidirectional(self.getInputFromPort('p_vectors_bidirectional'))
- if self.hasInputFromPort('p_vectors_color_type') :
- p.set_p_vectors_color_type(self.getInputFromPort('p_vectors_color_type'))
- if self.hasInputFromPort('p_vectors_resolution') :
- p.set_p_vectors_resolution(self.getInputFromPort('p_vectors_resolution'))
- if self.hasInputFromPort('p_tensors_has_data') :
- p.set_p_tensors_has_data(self.getInputFromPort('p_tensors_has_data'))
- if self.hasInputFromPort('p_tensors_on') :
- p.set_p_tensors_on(self.getInputFromPort('p_tensors_on'))
- if self.hasInputFromPort('p_tensors_display_type') :
- p.set_p_tensors_display_type(self.getInputFromPort('p_tensors_display_type'))
- if self.hasInputFromPort('p_tensors_transparency') :
- p.set_p_tensors_transparency(self.getInputFromPort('p_tensors_transparency'))
- if self.hasInputFromPort('p_tensors_normalize') :
- p.set_p_tensors_normalize(self.getInputFromPort('p_tensors_normalize'))
- if self.hasInputFromPort('p_tensors_color_type') :
- p.set_p_tensors_color_type(self.getInputFromPort('p_tensors_color_type'))
- if self.hasInputFromPort('p_tensors_resolution') :
- p.set_p_tensors_resolution(self.getInputFromPort('p_tensors_resolution'))
- if self.hasInputFromPort('p_tensors_emphasis') :
- p.set_p_tensors_emphasis(self.getInputFromPort('p_tensors_emphasis'))
- if self.hasInputFromPort('p_secondary_has_data') :
- p.set_p_secondary_has_data(self.getInputFromPort('p_secondary_has_data'))
- if self.hasInputFromPort('p_secondary_on') :
- p.set_p_secondary_on(self.getInputFromPort('p_secondary_on'))
- if self.hasInputFromPort('p_secondary_display_type') :
- p.set_p_secondary_display_type(self.getInputFromPort('p_secondary_display_type'))
- if self.hasInputFromPort('p_secondary_color_type') :
- p.set_p_secondary_color_type(self.getInputFromPort('p_secondary_color_type'))
- if self.hasInputFromPort('p_secondary_alpha') :
- p.set_p_secondary_alpha(self.getInputFromPort('p_secondary_alpha'))
- if self.hasInputFromPort('p_secondary_value') :
- p.set_p_secondary_value(self.getInputFromPort('p_secondary_value'))
- if self.hasInputFromPort('p_tertiary_has_data') :
- p.set_p_tertiary_has_data(self.getInputFromPort('p_tertiary_has_data'))
- if self.hasInputFromPort('p_tertiary_on') :
- p.set_p_tertiary_on(self.getInputFromPort('p_tertiary_on'))
- if self.hasInputFromPort('p_tertiary_display_type') :
- p.set_p_tertiary_display_type(self.getInputFromPort('p_tertiary_display_type'))
- if self.hasInputFromPort('p_tertiary_color_type') :
- p.set_p_tertiary_color_type(self.getInputFromPort('p_tertiary_color_type'))
- if self.hasInputFromPort('p_tertiary_alpha') :
- p.set_p_tertiary_alpha(self.getInputFromPort('p_tertiary_alpha'))
- if self.hasInputFromPort('p_tertiary_value') :
- p.set_p_tertiary_value(self.getInputFromPort('p_tertiary_value'))
- if self.hasInputFromPort('p_text_on') :
- p.set_p_text_on(self.getInputFromPort('p_text_on'))
- if self.hasInputFromPort('p_text_color_type') :
- p.set_p_text_color_type(self.getInputFromPort('p_text_color_type'))
- if self.hasInputFromPort('p_text_color_r') :
- p.set_p_text_color_r(self.getInputFromPort('p_text_color_r'))
- if self.hasInputFromPort('p_text_color_g') :
- p.set_p_text_color_g(self.getInputFromPort('p_text_color_g'))
- if self.hasInputFromPort('p_text_color_b') :
- p.set_p_text_color_b(self.getInputFromPort('p_text_color_b'))
- if self.hasInputFromPort('p_text_backface_cull') :
- p.set_p_text_backface_cull(self.getInputFromPort('p_text_backface_cull'))
- if self.hasInputFromPort('p_text_always_visible') :
- p.set_p_text_always_visible(self.getInputFromPort('p_text_always_visible'))
- if self.hasInputFromPort('p_text_fontsize') :
- p.set_p_text_fontsize(self.getInputFromPort('p_text_fontsize'))
- if self.hasInputFromPort('p_text_precision') :
- p.set_p_text_precision(self.getInputFromPort('p_text_precision'))
- if self.hasInputFromPort('p_text_render_locations') :
- p.set_p_text_render_locations(self.getInputFromPort('p_text_render_locations'))
- if self.hasInputFromPort('p_text_show_data') :
- p.set_p_text_show_data(self.getInputFromPort('p_text_show_data'))
- if self.hasInputFromPort('p_text_show_nodes') :
- p.set_p_text_show_nodes(self.getInputFromPort('p_text_show_nodes'))
- if self.hasInputFromPort('p_text_show_edges') :
- p.set_p_text_show_edges(self.getInputFromPort('p_text_show_edges'))
- if self.hasInputFromPort('p_text_show_faces') :
- p.set_p_text_show_faces(self.getInputFromPort('p_text_show_faces'))
- if self.hasInputFromPort('p_text_show_cells') :
- p.set_p_text_show_cells(self.getInputFromPort('p_text_show_cells'))
- if self.hasInputFromPort('p_def_color_r') :
- p.set_p_def_color_r(self.getInputFromPort('p_def_color_r'))
- if self.hasInputFromPort('p_def_color_g') :
- p.set_p_def_color_g(self.getInputFromPort('p_def_color_g'))
- if self.hasInputFromPort('p_def_color_b') :
- p.set_p_def_color_b(self.getInputFromPort('p_def_color_b'))
- if self.hasInputFromPort('p_def_color_a') :
- p.set_p_def_color_a(self.getInputFromPort('p_def_color_a'))
- if self.hasInputFromPort('p_active_tab') :
- p.set_p_active_tab(self.getInputFromPort('p_active_tab'))
- if self.hasInputFromPort('p_interactive_mode') :
- p.set_p_interactive_mode(self.getInputFromPort('p_interactive_mode'))
- if self.hasInputFromPort('p_show_progress') :
- p.set_p_show_progress(self.getInputFromPort('p_show_progress'))
- if self.hasInputFromPort('p_field_name') :
- p.set_p_field_name(self.getInputFromPort('p_field_name'))
- if self.hasInputFromPort('p_field_name_override') :
- p.set_p_field_name_override(self.getInputFromPort('p_field_name_override'))
- if self.hasInputFromPort('p_approx_div') :
- p.set_p_approx_div(self.getInputFromPort('p_approx_div'))
- if self.hasInputFromPort('p_use_default_size') :
- p.set_p_use_default_size(self.getInputFromPort('p_use_default_size'))
- Primary_Data = 0
- if self.hasInputFromPort('Primary Data') :
- Primary_Data = self.getInputFromPort('Primary Data')
- Primary_ColorMap = 0
- if self.hasInputFromPort('Primary ColorMap') :
- Primary_ColorMap = self.getInputFromPort('Primary ColorMap')
- Secondary_Data = 0
- if self.hasInputFromPort('Secondary Data') :
- Secondary_Data = self.getInputFromPort('Secondary Data')
- Secondary_ColorMap = 0
- if self.hasInputFromPort('Secondary ColorMap') :
- Secondary_ColorMap = self.getInputFromPort('Secondary ColorMap')
- Tertiary_Data = 0
- if self.hasInputFromPort('Tertiary Data') :
- Tertiary_Data = self.getInputFromPort('Tertiary Data')
- Tertiary_ColorMap = 0
- if self.hasInputFromPort('Tertiary ColorMap') :
- Tertiary_ColorMap = self.getInputFromPort('Tertiary ColorMap')
- results = p.execute(Primary_Data, Primary_ColorMap, Secondary_Data, Secondary_ColorMap, Tertiary_Data, Tertiary_ColorMap)
- self.setResult('Scene Graph', results)
-
-class GenerateStreamLines(Visualization) :
- def compute(self) :
- p = sr_py.GenerateStreamLinesAlg()
- if self.hasInputFromPort('p_stepsize') :
- p.set_p_stepsize(self.getInputFromPort('p_stepsize'))
- if self.hasInputFromPort('p_tolerance') :
- p.set_p_tolerance(self.getInputFromPort('p_tolerance'))
- if self.hasInputFromPort('p_maxsteps') :
- p.set_p_maxsteps(self.getInputFromPort('p_maxsteps'))
- if self.hasInputFromPort('p_direction') :
- p.set_p_direction(self.getInputFromPort('p_direction'))
- if self.hasInputFromPort('p_value') :
- p.set_p_value(self.getInputFromPort('p_value'))
- if self.hasInputFromPort('p_remove_colinear_pts') :
- p.set_p_remove_colinear_pts(self.getInputFromPort('p_remove_colinear_pts'))
- if self.hasInputFromPort('p_method') :
- p.set_p_method(self.getInputFromPort('p_method'))
- if self.hasInputFromPort('p_nthreads') :
- p.set_p_nthreads(self.getInputFromPort('p_nthreads'))
- if self.hasInputFromPort('p_auto_parameterize') :
- p.set_p_auto_parameterize(self.getInputFromPort('p_auto_parameterize'))
- Vector_Field = 0
- if self.hasInputFromPort('Vector Field') :
- Vector_Field = self.getInputFromPort('Vector Field')
- Seed_Points = 0
- if self.hasInputFromPort('Seed Points') :
- Seed_Points = self.getInputFromPort('Seed Points')
- results = p.execute(Vector_Field, Seed_Points)
- self.setResult('Streamlines', results)
-
-class GenerateStreamLinesWithPlacementHeuristic(Visualization) :
- def compute(self) :
- p = sr_py.GenerateStreamLinesWithPlacementHeuristicAlg()
- if self.hasInputFromPort('p_numsl') :
- p.set_p_numsl(self.getInputFromPort('p_numsl'))
- if self.hasInputFromPort('p_numpts') :
- p.set_p_numpts(self.getInputFromPort('p_numpts'))
- if self.hasInputFromPort('p_minper') :
- p.set_p_minper(self.getInputFromPort('p_minper'))
- if self.hasInputFromPort('p_maxper') :
- p.set_p_maxper(self.getInputFromPort('p_maxper'))
- if self.hasInputFromPort('p_ming') :
- p.set_p_ming(self.getInputFromPort('p_ming'))
- if self.hasInputFromPort('p_maxg') :
- p.set_p_maxg(self.getInputFromPort('p_maxg'))
- if self.hasInputFromPort('p_numsamples') :
- p.set_p_numsamples(self.getInputFromPort('p_numsamples'))
- if self.hasInputFromPort('p_method') :
- p.set_p_method(self.getInputFromPort('p_method'))
- if self.hasInputFromPort('p_stepsize') :
- p.set_p_stepsize(self.getInputFromPort('p_stepsize'))
- if self.hasInputFromPort('p_stepout') :
- p.set_p_stepout(self.getInputFromPort('p_stepout'))
- if self.hasInputFromPort('p_maxsteps') :
- p.set_p_maxsteps(self.getInputFromPort('p_maxsteps'))
- if self.hasInputFromPort('p_minmag') :
- p.set_p_minmag(self.getInputFromPort('p_minmag'))
- if self.hasInputFromPort('p_direction') :
- p.set_p_direction(self.getInputFromPort('p_direction'))
- Source = 0
- if self.hasInputFromPort('Source') :
- Source = self.getInputFromPort('Source')
- Weighting = 0
- if self.hasInputFromPort('Weighting') :
- Weighting = self.getInputFromPort('Weighting')
- Flow = 0
- if self.hasInputFromPort('Flow') :
- Flow = self.getInputFromPort('Flow')
- Compare = 0
- if self.hasInputFromPort('Compare') :
- Compare = self.getInputFromPort('Compare')
- Seed_points = 0
- if self.hasInputFromPort('Seed points') :
- Seed_points = self.getInputFromPort('Seed points')
- results = p.execute(Source, Weighting, Flow, Compare, Seed_points)
- self.setResult('Streamlines', results[0])
- self.setResult('Render', results[1])
-
-class ShowString(Visualization) :
- def compute(self) :
- p = sr_py.ShowStringAlg()
- if self.hasInputFromPort('p_bbox') :
- p.set_p_bbox(self.getInputFromPort('p_bbox'))
- if self.hasInputFromPort('p_size') :
- p.set_p_size(self.getInputFromPort('p_size'))
- if self.hasInputFromPort('p_location_x') :
- p.set_p_location_x(self.getInputFromPort('p_location_x'))
- if self.hasInputFromPort('p_location_y') :
- p.set_p_location_y(self.getInputFromPort('p_location_y'))
- if self.hasInputFromPort('p_color_r') :
- p.set_p_color_r(self.getInputFromPort('p_color_r'))
- if self.hasInputFromPort('p_color_g') :
- p.set_p_color_g(self.getInputFromPort('p_color_g'))
- if self.hasInputFromPort('p_color_b') :
- p.set_p_color_b(self.getInputFromPort('p_color_b'))
- Format_String = ''
- if self.hasInputFromPort('Format String') :
- Format_String = self.getInputFromPort('Format String')
- results = p.execute(Format_String)
- self.setResult('Title', results)
-
-class CreateAndEditColorMap(Visualization) :
- def compute(self) :
- p = sr_py.CreateAndEditColorMapAlg()
- if self.hasInputFromPort('p_rgbhsv') :
- p.set_p_rgbhsv(self.getInputFromPort('p_rgbhsv'))
- if self.hasInputFromPort('p_rgb_points') :
- p.set_p_rgb_points(self.getInputFromPort('p_rgb_points'))
- if self.hasInputFromPort('p_alpha_points') :
- p.set_p_alpha_points(self.getInputFromPort('p_alpha_points'))
- if self.hasInputFromPort('p_resolution') :
- p.set_p_resolution(self.getInputFromPort('p_resolution'))
- ColorMap = 0
- if self.hasInputFromPort('ColorMap') :
- ColorMap = self.getInputFromPort('ColorMap')
- results = p.execute(ColorMap)
- self.setResult('ColorMap', results[0])
- self.setResult('Geometry', results[1])
-
-class ShowMeshBoundingBox(Visualization) :
- def compute(self) :
- p = sr_py.ShowMeshBoundingBoxAlg()
- if self.hasInputFromPort('p_sizex') :
- p.set_p_sizex(self.getInputFromPort('p_sizex'))
- if self.hasInputFromPort('p_sizey') :
- p.set_p_sizey(self.getInputFromPort('p_sizey'))
- if self.hasInputFromPort('p_sizez') :
- p.set_p_sizez(self.getInputFromPort('p_sizez'))
- Field = 0
- if self.hasInputFromPort('Field') :
- Field = self.getInputFromPort('Field')
- results = p.execute(Field)
- self.setResult('Scene Graph', results)
-
-class CreateStandardColorMaps(Visualization) :
- def compute(self) :
- p = sr_py.CreateStandardColorMapsAlg()
- if self.hasInputFromPort('p_mapName') :
- p.set_p_mapName(self.getInputFromPort('p_mapName'))
- if self.hasInputFromPort('p_gamma') :
- p.set_p_gamma(self.getInputFromPort('p_gamma'))
- if self.hasInputFromPort('p_resolution') :
- p.set_p_resolution(self.getInputFromPort('p_resolution'))
- if self.hasInputFromPort('p_reverse') :
- p.set_p_reverse(self.getInputFromPort('p_reverse'))
- if self.hasInputFromPort('p_faux') :
- p.set_p_faux(self.getInputFromPort('p_faux'))
- if self.hasInputFromPort('p_positionList') :
- p.set_p_positionList(self.getInputFromPort('p_positionList'))
- if self.hasInputFromPort('p_nodeList') :
- p.set_p_nodeList(self.getInputFromPort('p_nodeList'))
- if self.hasInputFromPort('p_width') :
- p.set_p_width(self.getInputFromPort('p_width'))
- if self.hasInputFromPort('p_height') :
- p.set_p_height(self.getInputFromPort('p_height'))
- results = p.execute()
- self.setResult('ColorMap', results)
-
-class ShowTextureSlices(Visualization) :
- def compute(self) :
- p = sr_py.ShowTextureSlicesAlg()
- if self.hasInputFromPort('p_control_pos_saved') :
- p.set_p_control_pos_saved(self.getInputFromPort('p_control_pos_saved'))
- if self.hasInputFromPort('p_drawX') :
- p.set_p_drawX(self.getInputFromPort('p_drawX'))
- if self.hasInputFromPort('p_drawY') :
- p.set_p_drawY(self.getInputFromPort('p_drawY'))
- if self.hasInputFromPort('p_drawZ') :
- p.set_p_drawZ(self.getInputFromPort('p_drawZ'))
- if self.hasInputFromPort('p_drawView') :
- p.set_p_drawView(self.getInputFromPort('p_drawView'))
- if self.hasInputFromPort('p_interp_mode') :
- p.set_p_interp_mode(self.getInputFromPort('p_interp_mode'))
- if self.hasInputFromPort('p_draw_phi_0') :
- p.set_p_draw_phi_0(self.getInputFromPort('p_draw_phi_0'))
- if self.hasInputFromPort('p_draw_phi_1') :
- p.set_p_draw_phi_1(self.getInputFromPort('p_draw_phi_1'))
- if self.hasInputFromPort('p_phi_0') :
- p.set_p_phi_0(self.getInputFromPort('p_phi_0'))
- if self.hasInputFromPort('p_phi_1') :
- p.set_p_phi_1(self.getInputFromPort('p_phi_1'))
- if self.hasInputFromPort('p_multi_level') :
- p.set_p_multi_level(self.getInputFromPort('p_multi_level'))
- if self.hasInputFromPort('p_color_changed') :
- p.set_p_color_changed(self.getInputFromPort('p_color_changed'))
- if self.hasInputFromPort('p_colors') :
- p.set_p_colors(self.getInputFromPort('p_colors'))
- if self.hasInputFromPort('p_level_on') :
- p.set_p_level_on(self.getInputFromPort('p_level_on'))
- if self.hasInputFromPort('p_outline_levels') :
- p.set_p_outline_levels(self.getInputFromPort('p_outline_levels'))
- if self.hasInputFromPort('p_use_stencil') :
- p.set_p_use_stencil(self.getInputFromPort('p_use_stencil'))
- Texture = 0
- if self.hasInputFromPort('Texture') :
- Texture = self.getInputFromPort('Texture')
- ColorMap = 0
- if self.hasInputFromPort('ColorMap') :
- ColorMap = self.getInputFromPort('ColorMap')
- ColorMap2 = 0
- if self.hasInputFromPort('ColorMap2') :
- ColorMap2 = self.getInputFromPort('ColorMap2')
- results = p.execute(Texture, ColorMap, ColorMap2)
- self.setResult('Geometry', results[0])
- self.setResult('ColorMap', results[1])
-
-class ShowMatrix(Visualization) :
- def compute(self) :
- p = sr_py.ShowMatrixAlg()
- if self.hasInputFromPort('p_xpos') :
- p.set_p_xpos(self.getInputFromPort('p_xpos'))
- if self.hasInputFromPort('p_ypos') :
- p.set_p_ypos(self.getInputFromPort('p_ypos'))
- if self.hasInputFromPort('p_xscale') :
- p.set_p_xscale(self.getInputFromPort('p_xscale'))
- if self.hasInputFromPort('p_yscale') :
- p.set_p_yscale(self.getInputFromPort('p_yscale'))
- if self.hasInputFromPort('p_3d_mode') :
- p.set_p_3d_mode(self.getInputFromPort('p_3d_mode'))
- if self.hasInputFromPort('p_gmode') :
- p.set_p_gmode(self.getInputFromPort('p_gmode'))
- if self.hasInputFromPort('p_showtext') :
- p.set_p_showtext(self.getInputFromPort('p_showtext'))
- if self.hasInputFromPort('p_row_begin') :
- p.set_p_row_begin(self.getInputFromPort('p_row_begin'))
- if self.hasInputFromPort('p_rows') :
- p.set_p_rows(self.getInputFromPort('p_rows'))
- if self.hasInputFromPort('p_col_begin') :
- p.set_p_col_begin(self.getInputFromPort('p_col_begin'))
- if self.hasInputFromPort('p_cols') :
- p.set_p_cols(self.getInputFromPort('p_cols'))
- if self.hasInputFromPort('p_colormapmode') :
- p.set_p_colormapmode(self.getInputFromPort('p_colormapmode'))
- ColorMap = 0
- if self.hasInputFromPort('ColorMap') :
- ColorMap = self.getInputFromPort('ColorMap')
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(ColorMap, Matrix)
- self.setResult('Geometry', results)
-
-class CreateViewerClockIcon(Visualization) :
- def compute(self) :
- p = sr_py.CreateViewerClockIconAlg()
- if self.hasInputFromPort('p_type') :
- p.set_p_type(self.getInputFromPort('p_type'))
- if self.hasInputFromPort('p_bbox') :
- p.set_p_bbox(self.getInputFromPort('p_bbox'))
- if self.hasInputFromPort('p_format') :
- p.set_p_format(self.getInputFromPort('p_format'))
- if self.hasInputFromPort('p_min') :
- p.set_p_min(self.getInputFromPort('p_min'))
- if self.hasInputFromPort('p_max') :
- p.set_p_max(self.getInputFromPort('p_max'))
- if self.hasInputFromPort('p_current') :
- p.set_p_current(self.getInputFromPort('p_current'))
- if self.hasInputFromPort('p_size') :
- p.set_p_size(self.getInputFromPort('p_size'))
- if self.hasInputFromPort('p_location_x') :
- p.set_p_location_x(self.getInputFromPort('p_location_x'))
- if self.hasInputFromPort('p_location_y') :
- p.set_p_location_y(self.getInputFromPort('p_location_y'))
- if self.hasInputFromPort('p_color_r') :
- p.set_p_color_r(self.getInputFromPort('p_color_r'))
- if self.hasInputFromPort('p_color_g') :
- p.set_p_color_g(self.getInputFromPort('p_color_g'))
- if self.hasInputFromPort('p_color_b') :
- p.set_p_color_b(self.getInputFromPort('p_color_b'))
- Time_Matrix = 0
- if self.hasInputFromPort('Time Matrix') :
- Time_Matrix = self.getInputFromPort('Time Matrix')
- Time_Nrrd = 0
- if self.hasInputFromPort('Time Nrrd') :
- Time_Nrrd = self.getInputFromPort('Time Nrrd')
- results = p.execute(Time_Matrix, Time_Nrrd)
- self.setResult('Clock', results)
-
-class ConvertFieldsToTexture(Visualization) :
- def compute(self) :
- p = sr_py.ConvertFieldsToTextureAlg()
- if self.hasInputFromPort('p_vmin') :
- p.set_p_vmin(self.getInputFromPort('p_vmin'))
- if self.hasInputFromPort('p_vmax') :
- p.set_p_vmax(self.getInputFromPort('p_vmax'))
- if self.hasInputFromPort('p_gmin') :
- p.set_p_gmin(self.getInputFromPort('p_gmin'))
- if self.hasInputFromPort('p_gmax') :
- p.set_p_gmax(self.getInputFromPort('p_gmax'))
- if self.hasInputFromPort('p_is_fixed') :
- p.set_p_is_fixed(self.getInputFromPort('p_is_fixed'))
- if self.hasInputFromPort('p_card_mem') :
- p.set_p_card_mem(self.getInputFromPort('p_card_mem'))
- if self.hasInputFromPort('p_card_mem_auto') :
- p.set_p_card_mem_auto(self.getInputFromPort('p_card_mem_auto'))
- if self.hasInputFromPort('p_histogram') :
- p.set_p_histogram(self.getInputFromPort('p_histogram'))
- if self.hasInputFromPort('p_gamma') :
- p.set_p_gamma(self.getInputFromPort('p_gamma'))
- Value_Field = 0
- if self.hasInputFromPort('Value Field') :
- Value_Field = self.getInputFromPort('Value Field')
- Gradient_Magnitude_Field = 0
- if self.hasInputFromPort('Gradient Magnitude Field') :
- Gradient_Magnitude_Field = self.getInputFromPort('Gradient Magnitude Field')
- results = p.execute(Value_Field, Gradient_Magnitude_Field)
- self.setResult('Texture', results[0])
- self.setResult('JointHistoGram', results[1])
-
-class ColorMap2DSemantics(Visualization) :
- def compute(self) :
- p = sr_py.ColorMap2DSemanticsAlg()
- Input_Colormap = 0
- if self.hasInputFromPort('Input Colormap') :
- Input_Colormap = self.getInputFromPort('Input Colormap')
- results = p.execute(Input_Colormap)
- self.setResult('Output Colormap', results)
-
-class ConvertMatrixToString(Converters) :
- def compute(self) :
- p = sr_py.ConvertMatrixToStringAlg()
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(Matrix)
- self.setResult('String', results)
-
-class ConvertMatrixToField(Converters) :
- def compute(self) :
- p = sr_py.ConvertMatrixToFieldAlg()
- if self.hasInputFromPort('p_datalocation') :
- p.set_p_datalocation(self.getInputFromPort('p_datalocation'))
- Matrix = 0
- if self.hasInputFromPort('Matrix') :
- Matrix = self.getInputFromPort('Matrix')
- results = p.execute(Matrix)
- self.setResult('Field', results)
-
-class TimeControls(Time) :
- def compute(self) :
- p = sr_py.TimeControlsAlg()
- if self.hasInputFromPort('p_execmode') :
- p.set_p_execmode(self.getInputFromPort('p_execmode'))
- if self.hasInputFromPort('p_scale_factor') :
- p.set_p_scale_factor(self.getInputFromPort('p_scale_factor'))
- results = p.execute()
- self.setResult('time', results)
-
-
-def initialize(*args, **keywords):
-
- env = []
- for k in os.environ.keys() :
- estr = "%s=%s" % (k, os.environ[k])
- env.append(estr)
- sr_py.init_sr_py(env)
-
- reg = core.modules.module_registry
-
- reg.add_module(Time, abstract=True)
- reg.add_module(Converters, abstract=True)
- reg.add_module(Texture, abstract=True)
- reg.add_module(Visualization, abstract=True)
- reg.add_module(MiscField, abstract=True)
- reg.add_module(DataArrayMath, abstract=True)
- reg.add_module(Math, abstract=True)
- reg.add_module(ChangeMesh, abstract=True)
- reg.add_module(ChangeFieldData, abstract=True)
- reg.add_module(Geometry, abstract=True)
- reg.add_module(NewField, abstract=True)
- reg.add_module(ColorMap, abstract=True)
- reg.add_module(Field, abstract=True)
- reg.add_module(Nrrd, abstract=True)
- reg.add_module(Matrix, abstract=True)
- reg.add_module(ColorMap2, abstract=True)
- reg.add_module(Path, abstract=True)
- reg.add_module(String, abstract=True)
- reg.add_module(Bundle, abstract=True)
- reg.add_module(DataIO, abstract=True)
- reg.add_module(WriteBundle)
- reg.add_input_port(WriteBundle, 'p_filetype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteBundle, 'p_confirm',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteBundle, 'p_confirm_once',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_input_port(WriteBundle, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(WritePath)
- reg.add_input_port(WritePath, 'p_filetype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WritePath, 'p_confirm',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WritePath, 'p_confirm_once',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WritePath, 'Input Data',
- (Path, "Path"))
- reg.add_input_port(WritePath, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(WriteColorMap2D)
- reg.add_input_port(WriteColorMap2D, 'p_filetype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteColorMap2D, 'p_confirm',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteColorMap2D, 'p_confirm_once',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteColorMap2D, 'p_exporttype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteColorMap2D, 'Input Data',
- (ColorMap2, "ColorMap2"))
- reg.add_input_port(WriteColorMap2D, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(ReadHDF5File)
- reg.add_input_port(ReadHDF5File, 'p_have_HDF5',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_power_app',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_datasets',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_dumpname',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_ports',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_ndims',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_mergeData',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_assumeSVT',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_animate',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_animate_tab',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_basic_tab',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_extended_tab',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_playmode_tab',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_selectable_min',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_selectable_max',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_selectable_inc',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_range_min',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_range_max',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_playmode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_current',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_execmode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_delay',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_inc_amount',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_update_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_have_group',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_have_attributes',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_have_datasets',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_continuous',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_selectionString',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_regexp',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_allow_selection',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_read_error',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_max_dims',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_0_dim',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_0_start',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_0_start2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_0_count',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_0_count2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_0_stride',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_0_stride2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_1_dim',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_1_start',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_1_start2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_1_count',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_1_count2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_1_stride',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_1_stride2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_2_dim',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_2_start',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_2_start2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_2_count',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_2_count2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_2_stride',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_2_stride2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_3_dim',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_3_start',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_3_start2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_3_count',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_3_count2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_3_stride',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_3_stride2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_4_dim',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_4_start',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_4_start2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_4_count',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_4_count2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_4_stride',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_4_stride2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_5_dim',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_5_start',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_5_start2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_5_count',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_5_count2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_5_stride',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'p_5_stride2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadHDF5File, 'Full filename',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(ReadHDF5File, 'Current Index',
- (Matrix, "Matrix"))
- reg.add_output_port(ReadHDF5File, 'Output 0 Nrrd',
- (Nrrd, "Nrrd"))
- reg.add_output_port(ReadHDF5File, 'Output 1 Nrrd',
- (Nrrd, "Nrrd"))
- reg.add_output_port(ReadHDF5File, 'Output 2 Nrrd',
- (Nrrd, "Nrrd"))
- reg.add_output_port(ReadHDF5File, 'Output 3 Nrrd',
- (Nrrd, "Nrrd"))
- reg.add_output_port(ReadHDF5File, 'Output 4 Nrrd',
- (Nrrd, "Nrrd"))
- reg.add_output_port(ReadHDF5File, 'Output 5 Nrrd',
- (Nrrd, "Nrrd"))
- reg.add_output_port(ReadHDF5File, 'Output 6 Nrrd',
- (Nrrd, "Nrrd"))
- reg.add_output_port(ReadHDF5File, 'Output 7 Nrrd',
- (Nrrd, "Nrrd"))
- reg.add_output_port(ReadHDF5File, 'Selected Index',
- (Matrix, "Matrix"))
-
- reg.add_module(ReadField)
- reg.add_input_port(ReadField, 'p_from_env',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadField, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(ReadField, 'Output Data',
- (Field, "Field"))
- reg.add_output_port(ReadField, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(WriteColorMap)
- reg.add_input_port(WriteColorMap, 'p_filetype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteColorMap, 'p_confirm',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteColorMap, 'p_confirm_once',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteColorMap, 'p_exporttype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteColorMap, 'Input Data',
- (ColorMap, "ColorMap"))
- reg.add_input_port(WriteColorMap, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(ReadColorMap2D)
- reg.add_input_port(ReadColorMap2D, 'p_from_env',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadColorMap2D, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(ReadColorMap2D, 'Output Data',
- (ColorMap2, "ColorMap2"))
- reg.add_output_port(ReadColorMap2D, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(ReadString)
- reg.add_input_port(ReadString, 'p_from_env',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadString, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(ReadString, 'Output Data',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(ReadString, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(ReadColorMap)
- reg.add_input_port(ReadColorMap, 'p_from_env',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadColorMap, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(ReadColorMap, 'Output Data',
- (ColorMap, "ColorMap"))
- reg.add_output_port(ReadColorMap, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(ReadMatrix)
- reg.add_input_port(ReadMatrix, 'p_from_env',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadMatrix, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(ReadMatrix, 'Output Data',
- (Matrix, "Matrix"))
- reg.add_output_port(ReadMatrix, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(WriteString)
- reg.add_input_port(WriteString, 'p_filetype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteString, 'p_confirm',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteString, 'p_confirm_once',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteString, 'String',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(WriteString, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(ReadPath)
- reg.add_input_port(ReadPath, 'p_from_env',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadPath, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(ReadPath, 'Output Data',
- (Path, "Path"))
- reg.add_output_port(ReadPath, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(WriteField)
- reg.add_input_port(WriteField, 'p_filetype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteField, 'p_confirm',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteField, 'p_confirm_once',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteField, 'p_exporttype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteField, 'p_increment',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(WriteField, 'p_current',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(WriteField, 'Input Data',
- (Field, "Field"))
- reg.add_input_port(WriteField, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(ReadBundle)
- reg.add_input_port(ReadBundle, 'p_from_env',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadBundle, 'p_types',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadBundle, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(ReadBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(ReadBundle, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(StreamMatrixFromDisk)
- reg.add_input_port(StreamMatrixFromDisk, 'p_row_or_col',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(StreamMatrixFromDisk, 'p_slider_min',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(StreamMatrixFromDisk, 'p_slider_max',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(StreamMatrixFromDisk, 'p_range_min',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(StreamMatrixFromDisk, 'p_range_max',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(StreamMatrixFromDisk, 'p_playmode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(StreamMatrixFromDisk, 'p_current',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(StreamMatrixFromDisk, 'p_execmode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(StreamMatrixFromDisk, 'p_delay',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(StreamMatrixFromDisk, 'p_inc_amount',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(StreamMatrixFromDisk, 'p_send_amount',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(StreamMatrixFromDisk, 'Indices',
- (Matrix, "Matrix"))
- reg.add_input_port(StreamMatrixFromDisk, 'Weights',
- (Matrix, "Matrix"))
- reg.add_input_port(StreamMatrixFromDisk, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(StreamMatrixFromDisk, 'DataVector',
- (Matrix, "Matrix"))
- reg.add_output_port(StreamMatrixFromDisk, 'Index',
- (Matrix, "Matrix"))
- reg.add_output_port(StreamMatrixFromDisk, 'Scaled Index',
- (Matrix, "Matrix"))
- reg.add_output_port(StreamMatrixFromDisk, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(WriteMatrix)
- reg.add_input_port(WriteMatrix, 'p_filetype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteMatrix, 'p_confirm',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteMatrix, 'p_confirm_once',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteMatrix, 'p_exporttype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(WriteMatrix, 'p_split',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(WriteMatrix, 'Input Data',
- (Matrix, "Matrix"))
- reg.add_input_port(WriteMatrix, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(ReadNrrd)
- reg.add_input_port(ReadNrrd, 'p_from_env',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReadNrrd, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(ReadNrrd, 'Output Data',
- (Field, "Field"))
- reg.add_output_port(ReadNrrd, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(JoinFields)
- reg.add_input_port(JoinFields, 'p_tolerance',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(JoinFields, 'p_force_nodemerge',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(JoinFields, 'p_force_pointcloud',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(JoinFields, 'p_matchval',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(JoinFields, 'p_meshonly',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(JoinFields, 'Field',
- (Field, "Field"))
- reg.add_output_port(JoinFields, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(RefineMeshByIsovalue)
- reg.add_input_port(RefineMeshByIsovalue, 'p_isoval',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(RefineMeshByIsovalue, 'p_lte',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(RefineMeshByIsovalue, 'Input',
- (Field, "Field"))
- reg.add_input_port(RefineMeshByIsovalue, 'Optional Isovalue',
- (Matrix, "Matrix"))
- reg.add_output_port(RefineMeshByIsovalue, 'Refined',
- (Field, "Field"))
- reg.add_output_port(RefineMeshByIsovalue, 'Mapping',
- (Matrix, "Matrix"))
-
- reg.add_module(FairMesh)
- reg.add_input_port(FairMesh, 'p_iterations',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(FairMesh, 'p_method',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(FairMesh, 'Input Mesh',
- (Field, "Field"))
- reg.add_output_port(FairMesh, 'Faired Mesh',
- (Field, "Field"))
-
- reg.add_module(CreateStructHex)
- reg.add_input_port(CreateStructHex, 'p_sizex',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateStructHex, 'p_sizey',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateStructHex, 'p_sizez',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateStructHex, 'p_padpercent',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateStructHex, 'p_data_at',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateStructHex, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(CreateStructHex, 'Output Sample Field',
- (Field, "Field"))
-
- reg.add_module(ClipLatVolByIndicesOrWidget)
- reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_use_text_bbox',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_min_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_min_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_min_z',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_max_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_max_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipLatVolByIndicesOrWidget, 'p_text_max_z',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipLatVolByIndicesOrWidget, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(ClipLatVolByIndicesOrWidget, 'Selection Widget',
- (Geometry, "Geometry"))
- reg.add_output_port(ClipLatVolByIndicesOrWidget, 'Output Field',
- (Field, "Field"))
- reg.add_output_port(ClipLatVolByIndicesOrWidget, 'MaskVector',
- (Nrrd, "Nrrd"))
-
- reg.add_module(GetFieldBoundary)
- reg.add_input_port(GetFieldBoundary, 'Field',
- (Field, "Field"))
- reg.add_output_port(GetFieldBoundary, 'BoundaryField',
- (Field, "Field"))
- reg.add_output_port(GetFieldBoundary, 'Mapping',
- (Matrix, "Matrix"))
-
- reg.add_module(ConvertMatricesToMesh)
- reg.add_input_port(ConvertMatricesToMesh, 'p_fieldname',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertMatricesToMesh, 'p_meshname',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertMatricesToMesh, 'p_fieldbasetype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertMatricesToMesh, 'p_datatype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertMatricesToMesh, 'Mesh Elements',
- (Matrix, "Matrix"))
- reg.add_input_port(ConvertMatricesToMesh, 'Mesh Positions',
- (Matrix, "Matrix"))
- reg.add_input_port(ConvertMatricesToMesh, 'Mesh Normals',
- (Matrix, "Matrix"))
- reg.add_output_port(ConvertMatricesToMesh, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(ClipFieldToFieldOrWidget)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_clip_location',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_clipmode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_autoexecute',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_autoinvert',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_execmode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_center_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_center_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_center_z',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_right_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_right_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_right_z',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_down_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_down_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_down_z',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_in_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_in_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_in_z',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'p_scale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipFieldToFieldOrWidget, 'Input Field',
- (Field, "Field"))
- reg.add_input_port(ClipFieldToFieldOrWidget, 'Clip Field',
- (Field, "Field"))
- reg.add_output_port(ClipFieldToFieldOrWidget, 'Selection Widget',
- (Geometry, "Geometry"))
- reg.add_output_port(ClipFieldToFieldOrWidget, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(RefineMeshByIsovalue2)
- reg.add_input_port(RefineMeshByIsovalue2, 'p_isoval',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(RefineMeshByIsovalue2, 'p_lte',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(RefineMeshByIsovalue2, 'Input',
- (Field, "Field"))
- reg.add_input_port(RefineMeshByIsovalue2, 'Optional Isovalue',
- (Matrix, "Matrix"))
- reg.add_output_port(RefineMeshByIsovalue2, 'Refined',
- (Field, "Field"))
- reg.add_output_port(RefineMeshByIsovalue2, 'Mapping',
- (Matrix, "Matrix"))
-
- reg.add_module(CreateLatVol)
- reg.add_input_port(CreateLatVol, 'p_sizex',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateLatVol, 'p_sizey',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateLatVol, 'p_sizez',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateLatVol, 'p_padpercent',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateLatVol, 'p_data_at',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateLatVol, 'p_element_size',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateLatVol, 'Input Field',
- (Field, "Field"))
- reg.add_input_port(CreateLatVol, 'LatVol Size',
- (Matrix, "Matrix"))
- reg.add_output_port(CreateLatVol, 'Output Sample Field',
- (Field, "Field"))
-
- reg.add_module(InterfaceWithCamal)
- reg.add_input_port(InterfaceWithCamal, 'TriSurf',
- (Field, "Field"))
- reg.add_output_port(InterfaceWithCamal, 'TetVol',
- (Field, "Field"))
-
- reg.add_module(ClipVolumeByIsovalue)
- reg.add_input_port(ClipVolumeByIsovalue, 'p_isoval_min',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipVolumeByIsovalue, 'p_isoval_max',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipVolumeByIsovalue, 'p_isoval',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ClipVolumeByIsovalue, 'p_lte',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ClipVolumeByIsovalue, 'p_update_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ClipVolumeByIsovalue, 'Input',
- (Field, "Field"))
- reg.add_input_port(ClipVolumeByIsovalue, 'Optional Isovalue',
- (Matrix, "Matrix"))
- reg.add_output_port(ClipVolumeByIsovalue, 'Clipped',
- (Field, "Field"))
- reg.add_output_port(ClipVolumeByIsovalue, 'Mapping',
- (Matrix, "Matrix"))
-
- reg.add_module(RefineMesh)
- reg.add_input_port(RefineMesh, 'p_select',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(RefineMesh, 'p_method',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(RefineMesh, 'p_isoval',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(RefineMesh, 'Mesh',
- (Field, "Field"))
- reg.add_input_port(RefineMesh, 'Isovalue',
- (Matrix, "Matrix"))
- reg.add_output_port(RefineMesh, 'RefinedMesh',
- (Field, "Field"))
- reg.add_output_port(RefineMesh, 'Mapping',
- (Matrix, "Matrix"))
-
- reg.add_module(MergeFields)
- reg.add_input_port(MergeFields, 'Container Mesh',
- (Field, "Field"))
- reg.add_input_port(MergeFields, 'Insert Field',
- (Field, "Field"))
- reg.add_output_port(MergeFields, 'Combined Field',
- (Field, "Field"))
- reg.add_output_port(MergeFields, 'Extended Insert Field',
- (Field, "Field"))
- reg.add_output_port(MergeFields, 'Combined To Extended Mapping',
- (Matrix, "Matrix"))
-
- reg.add_module(GetCentroidsFromMesh)
- reg.add_input_port(GetCentroidsFromMesh, 'TetVolField',
- (Field, "Field"))
- reg.add_output_port(GetCentroidsFromMesh, 'PointCloudField',
- (Field, "Field"))
-
- reg.add_module(ExtractIsosurfaceByFunction)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_zero_checks',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value_min',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value_max',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value_typed',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value_quantity',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_quantity_range',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_quantity_clusive',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_quantity_min',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_quantity_max',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_quantity_list',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_slice_value_list',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_matrix_list',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_algorithm',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_active_slice_value_selection_tab',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_active_tab',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'p_update_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurfaceByFunction, 'Input Field',
- (Field, "Field"))
- reg.add_input_port(ExtractIsosurfaceByFunction, 'Optional Slice values',
- (Matrix, "Matrix"))
- reg.add_output_port(ExtractIsosurfaceByFunction, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(MergeTriSurfs)
- reg.add_input_port(MergeTriSurfs, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(MergeTriSurfs, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(InterfaceWithTetGen)
- reg.add_input_port(InterfaceWithTetGen, 'p_switch',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InterfaceWithTetGen, 'Main',
- (Field, "Field"))
- reg.add_input_port(InterfaceWithTetGen, 'Points',
- (Field, "Field"))
- reg.add_input_port(InterfaceWithTetGen, 'Region Attribs',
- (Field, "Field"))
- reg.add_input_port(InterfaceWithTetGen, 'Regions',
- (Field, "Field"))
- reg.add_output_port(InterfaceWithTetGen, 'TetVol',
- (Field, "Field"))
-
- reg.add_module(CreateImage)
- reg.add_input_port(CreateImage, 'p_sizex',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_sizey',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_sizez',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_z_value',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_auto_size',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_axis',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_padpercent',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_pos',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_data_at',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_update_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_corigin_x',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_corigin_y',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_corigin_z',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_cnormal_x',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_cnormal_y',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateImage, 'p_cnormal_z',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateImage, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(CreateImage, 'Output Sample Field',
- (Field, "Field"))
-
- reg.add_module(InsertHexVolSheetAlongSurface)
- reg.add_input_port(InsertHexVolSheetAlongSurface, 'p_side',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertHexVolSheetAlongSurface, 'p_addlayer',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertHexVolSheetAlongSurface, 'HexField',
- (Field, "Field"))
- reg.add_input_port(InsertHexVolSheetAlongSurface, 'TriField',
- (Field, "Field"))
- reg.add_output_port(InsertHexVolSheetAlongSurface, 'Side1Field',
- (Field, "Field"))
- reg.add_output_port(InsertHexVolSheetAlongSurface, 'Side2Field',
- (Field, "Field"))
-
- reg.add_module(GenerateSinglePointProbeFromField)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_main_frame',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_locx',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_locy',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_locz',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_value',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_node',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_edge',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_face',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_cell',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_show_value',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_show_node',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_show_edge',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_show_face',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_show_cell',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'p_probe_scale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateSinglePointProbeFromField, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(GenerateSinglePointProbeFromField, 'GenerateSinglePointProbeFromField Widget',
- (Geometry, "Geometry"))
- reg.add_output_port(GenerateSinglePointProbeFromField, 'GenerateSinglePointProbeFromField Point',
- (Field, "Field"))
- reg.add_output_port(GenerateSinglePointProbeFromField, 'Element Index',
- (Matrix, "Matrix"))
-
- reg.add_module(InterfaceWithCubit)
- reg.add_input_port(InterfaceWithCubit, 'p_cubitdir',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InterfaceWithCubit, 'p_ncdump',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InterfaceWithCubit, 'Field',
- (Field, "Field"))
- reg.add_input_port(InterfaceWithCubit, 'PointCloudField',
- (Field, "Field"))
- reg.add_output_port(InterfaceWithCubit, 'Field',
- (Field, "Field"))
-
- reg.add_module(ClipFieldByFunction)
- reg.add_input_port(ClipFieldByFunction, 'p_mode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ClipFieldByFunction, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ClipFieldByFunction, 'Function',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(ClipFieldByFunction, 'Input',
- (Field, "Field"))
- reg.add_output_port(ClipFieldByFunction, 'Clipped',
- (Field, "Field"))
- reg.add_output_port(ClipFieldByFunction, 'Mapping',
- (Matrix, "Matrix"))
- reg.add_output_port(ClipFieldByFunction, 'MaskVector',
- (Nrrd, "Nrrd"))
-
- reg.add_module(GetDomainBoundary)
- reg.add_input_port(GetDomainBoundary, 'p_userange',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetDomainBoundary, 'p_minrange',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GetDomainBoundary, 'p_maxrange',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GetDomainBoundary, 'p_usevalue',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetDomainBoundary, 'p_value',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GetDomainBoundary, 'p_includeouterboundary',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetDomainBoundary, 'p_innerboundaryonly',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetDomainBoundary, 'p_noinnerboundary',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetDomainBoundary, 'p_disconnect',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetDomainBoundary, 'Field',
- (Field, "Field"))
- reg.add_input_port(GetDomainBoundary, 'MinValueValue',
- (Matrix, "Matrix"))
- reg.add_input_port(GetDomainBoundary, 'MaxValue',
- (Matrix, "Matrix"))
- reg.add_output_port(GetDomainBoundary, 'Field',
- (Field, "Field"))
-
- reg.add_module(CollectFields)
- reg.add_input_port(CollectFields, 'p_buffersize',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CollectFields, 'Field',
- (Field, "Field"))
- reg.add_input_port(CollectFields, 'BufferSize',
- (Matrix, "Matrix"))
- reg.add_output_port(CollectFields, 'Fields',
- (Field, "Field"))
-
- reg.add_module(GeneratePointSamplesFromField)
- reg.add_input_port(GeneratePointSamplesFromField, 'p_num_seeds',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromField, 'p_probe_scale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromField, 'p_send',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromField, 'p_widget',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromField, 'p_red',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromField, 'p_green',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromField, 'p_blue',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromField, 'p_auto_execute',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromField, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(GeneratePointSamplesFromField, 'GeneratePointSamplesFromField Widget',
- (Geometry, "Geometry"))
- reg.add_output_port(GeneratePointSamplesFromField, 'GeneratePointSamplesFromField Point',
- (Field, "Field"))
-
- reg.add_module(GeneratePointSamplesFromFieldOrWidget)
- reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_wtype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_endpoints',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_maxseeds',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_numseeds',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_rngseed',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_rnginc',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_clamp',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_autoexecute',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_dist',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'p_whichtab',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GeneratePointSamplesFromFieldOrWidget, 'Field to Sample',
- (Field, "Field"))
- reg.add_output_port(GeneratePointSamplesFromFieldOrWidget, 'Samples',
- (Field, "Field"))
- reg.add_output_port(GeneratePointSamplesFromFieldOrWidget, 'Sampling Widget',
- (Geometry, "Geometry"))
-
- reg.add_module(DecimateTriSurf)
- reg.add_input_port(DecimateTriSurf, 'TriSurf',
- (Field, "Field"))
- reg.add_output_port(DecimateTriSurf, 'Decimated',
- (Field, "Field"))
-
- reg.add_module(GetSliceFromStructuredFieldByIndices)
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_axis',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_dims',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_dim_i',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_dim_j',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_dim_k',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_index_i',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_index_j',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_index_k',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_update_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'p_continuous',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'Input Field',
- (Field, "Field"))
- reg.add_input_port(GetSliceFromStructuredFieldByIndices, 'Input Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(GetSliceFromStructuredFieldByIndices, 'Output Field',
- (Field, "Field"))
- reg.add_output_port(GetSliceFromStructuredFieldByIndices, 'Output Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(RemoveHexVolSheet)
- reg.add_input_port(RemoveHexVolSheet, 'p_edge_list',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(RemoveHexVolSheet, 'HexField',
- (Field, "Field"))
- reg.add_output_port(RemoveHexVolSheet, 'NewHexField',
- (Field, "Field"))
- reg.add_output_port(RemoveHexVolSheet, 'ExtractedHexes',
- (Field, "Field"))
-
- reg.add_module(SubsampleStructuredFieldByIndices)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_power_app',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_wrap',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_dims',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_dim_i',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_dim_j',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_dim_k',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_start_i',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_start_j',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_start_k',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stop_i',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stop_j',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stop_k',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stride_i',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stride_j',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_stride_k',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_wrap_i',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_wrap_j',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'p_wrap_k',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'Input Field',
- (Field, "Field"))
- reg.add_input_port(SubsampleStructuredFieldByIndices, 'Input Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(SubsampleStructuredFieldByIndices, 'Output Field',
- (Field, "Field"))
- reg.add_output_port(SubsampleStructuredFieldByIndices, 'Output Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(GetAllSegmentationBoundaries)
- reg.add_input_port(GetAllSegmentationBoundaries, 'Segmentations',
- (Nrrd, "Nrrd"))
- reg.add_output_port(GetAllSegmentationBoundaries, 'Boundaries',
- (Field, "Field"))
-
- reg.add_module(ClipFieldWithSeed)
- reg.add_input_port(ClipFieldWithSeed, 'p_mode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ClipFieldWithSeed, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ClipFieldWithSeed, 'Function',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(ClipFieldWithSeed, 'Input',
- (Field, "Field"))
- reg.add_input_port(ClipFieldWithSeed, 'Seeds',
- (Field, "Field"))
- reg.add_output_port(ClipFieldWithSeed, 'Clipped',
- (Field, "Field"))
- reg.add_output_port(ClipFieldWithSeed, 'Mapping',
- (Matrix, "Matrix"))
- reg.add_output_port(ClipFieldWithSeed, 'MaskVector',
- (Nrrd, "Nrrd"))
-
- reg.add_module(SplitNodesByDomain)
- reg.add_input_port(SplitNodesByDomain, 'Field',
- (Field, "Field"))
- reg.add_output_port(SplitNodesByDomain, 'SplitField',
- (Field, "Field"))
-
- reg.add_module(ApplyMappingMatrix)
- reg.add_input_port(ApplyMappingMatrix, 'Source',
- (Field, "Field"))
- reg.add_input_port(ApplyMappingMatrix, 'Destination',
- (Field, "Field"))
- reg.add_input_port(ApplyMappingMatrix, 'Mapping',
- (Matrix, "Matrix"))
- reg.add_output_port(ApplyMappingMatrix, 'Output',
- (Field, "Field"))
-
- reg.add_module(MaskLatVolWithTriSurf)
- reg.add_input_port(MaskLatVolWithTriSurf, 'LatVolField',
- (Field, "Field"))
- reg.add_input_port(MaskLatVolWithTriSurf, 'TriSurfField',
- (Field, "Field"))
- reg.add_output_port(MaskLatVolWithTriSurf, 'LatVol Mask',
- (Field, "Field"))
-
- reg.add_module(ConvertFieldBasis)
- reg.add_input_port(ConvertFieldBasis, 'p_output_basis',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertFieldBasis, 'Input',
- (Field, "Field"))
- reg.add_output_port(ConvertFieldBasis, 'Output',
- (Field, "Field"))
- reg.add_output_port(ConvertFieldBasis, 'Mapping',
- (Matrix, "Matrix"))
-
- reg.add_module(ReportMeshQualityMeasures)
- reg.add_input_port(ReportMeshQualityMeasures, 'Input',
- (Field, "Field"))
- reg.add_output_port(ReportMeshQualityMeasures, 'Checked',
- (Nrrd, "Nrrd"))
-
- reg.add_module(SelectAndSetFieldData)
- reg.add_input_port(SelectAndSetFieldData, 'p_selection1',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData, 'p_function1',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData, 'p_selection2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData, 'p_function2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData, 'p_selection3',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData, 'p_function3',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData, 'p_selection4',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData, 'p_function4',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData, 'p_functiondef',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData, 'p_format',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData, 'Field',
- (Field, "Field"))
- reg.add_input_port(SelectAndSetFieldData, 'Array',
- (Matrix, "Matrix"))
- reg.add_output_port(SelectAndSetFieldData, 'Field',
- (Field, "Field"))
-
- reg.add_module(CalculateFieldData3)
- reg.add_input_port(CalculateFieldData3, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateFieldData3, 'p_format',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateFieldData3, 'Field1',
- (Field, "Field"))
- reg.add_input_port(CalculateFieldData3, 'Field2',
- (Field, "Field"))
- reg.add_input_port(CalculateFieldData3, 'Field3',
- (Field, "Field"))
- reg.add_input_port(CalculateFieldData3, 'Function',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(CalculateFieldData3, 'Array',
- (Matrix, "Matrix"))
- reg.add_output_port(CalculateFieldData3, 'Field',
- (Field, "Field"))
-
- reg.add_module(SetFieldData)
- reg.add_input_port(SetFieldData, 'p_keepscalartype',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SetFieldData, 'Field',
- (Field, "Field"))
- reg.add_input_port(SetFieldData, 'Matrix Data',
- (Matrix, "Matrix"))
- reg.add_input_port(SetFieldData, 'Nrrd Data',
- (Nrrd, "Nrrd"))
- reg.add_output_port(SetFieldData, 'Field',
- (Field, "Field"))
-
- reg.add_module(SwapFieldDataWithMatrixEntries)
- reg.add_input_port(SwapFieldDataWithMatrixEntries, 'p_preserve_scalar_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SwapFieldDataWithMatrixEntries, 'Input Field',
- (Field, "Field"))
- reg.add_input_port(SwapFieldDataWithMatrixEntries, 'Input Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(SwapFieldDataWithMatrixEntries, 'Output Field',
- (Field, "Field"))
- reg.add_output_port(SwapFieldDataWithMatrixEntries, 'Output Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(ConvertLatVolDataFromElemToNode)
- reg.add_input_port(ConvertLatVolDataFromElemToNode, 'Elem Field',
- (Field, "Field"))
- reg.add_output_port(ConvertLatVolDataFromElemToNode, 'Node Field',
- (Field, "Field"))
-
- reg.add_module(CalculateNodeNormals)
- reg.add_input_port(CalculateNodeNormals, 'Input Field',
- (Field, "Field"))
- reg.add_input_port(CalculateNodeNormals, 'Input Point',
- (Field, "Field"))
- reg.add_output_port(CalculateNodeNormals, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(CalculateVectorMagnitudes)
- reg.add_input_port(CalculateVectorMagnitudes, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(CalculateVectorMagnitudes, 'Output CalculateVectorMagnitudes',
- (Field, "Field"))
-
- reg.add_module(ConvertIndicesToFieldData)
- reg.add_input_port(ConvertIndicesToFieldData, 'p_outputtype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertIndicesToFieldData, 'Field',
- (Field, "Field"))
- reg.add_input_port(ConvertIndicesToFieldData, 'Data',
- (Matrix, "Matrix"))
- reg.add_output_port(ConvertIndicesToFieldData, 'Field',
- (Field, "Field"))
-
- reg.add_module(CalculateDistanceToFieldBoundary)
- reg.add_input_port(CalculateDistanceToFieldBoundary, 'Field',
- (Field, "Field"))
- reg.add_output_port(CalculateDistanceToFieldBoundary, 'DistanceField',
- (Field, "Field"))
-
- reg.add_module(MapFieldDataFromSourceToDestination)
- reg.add_input_port(MapFieldDataFromSourceToDestination, 'p_interpolation_basis',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(MapFieldDataFromSourceToDestination, 'p_map_source_to_single_dest',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(MapFieldDataFromSourceToDestination, 'p_exhaustive_search',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(MapFieldDataFromSourceToDestination, 'p_exhaustive_search_max_dist',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(MapFieldDataFromSourceToDestination, 'p_np',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(MapFieldDataFromSourceToDestination, 'Source',
- (Field, "Field"))
- reg.add_input_port(MapFieldDataFromSourceToDestination, 'Destination',
- (Field, "Field"))
- reg.add_output_port(MapFieldDataFromSourceToDestination, 'Remapped Destination',
- (Field, "Field"))
-
- reg.add_module(SelectAndSetFieldData3)
- reg.add_input_port(SelectAndSetFieldData3, 'p_selection1',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData3, 'p_function1',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData3, 'p_selection2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData3, 'p_function2',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData3, 'p_selection3',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData3, 'p_function3',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData3, 'p_selection4',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData3, 'p_function4',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData3, 'p_functiondef',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData3, 'p_format',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SelectAndSetFieldData3, 'Field1',
- (Field, "Field"))
- reg.add_input_port(SelectAndSetFieldData3, 'Field2',
- (Field, "Field"))
- reg.add_input_port(SelectAndSetFieldData3, 'Field3',
- (Field, "Field"))
- reg.add_input_port(SelectAndSetFieldData3, 'Array',
- (Matrix, "Matrix"))
- reg.add_output_port(SelectAndSetFieldData3, 'Field',
- (Field, "Field"))
-
- reg.add_module(CreateFieldData)
- reg.add_input_port(CreateFieldData, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateFieldData, 'p_format',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateFieldData, 'p_basis',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateFieldData, 'Field',
- (Field, "Field"))
- reg.add_input_port(CreateFieldData, 'Function',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(CreateFieldData, 'DataArray',
- (Matrix, "Matrix"))
- reg.add_output_port(CreateFieldData, 'Field',
- (Field, "Field"))
-
- reg.add_module(ConvertLatVolDataFromNodeToElem)
- reg.add_input_port(ConvertLatVolDataFromNodeToElem, 'Node Field',
- (Field, "Field"))
- reg.add_output_port(ConvertLatVolDataFromNodeToElem, 'Elem Field',
- (Field, "Field"))
-
- reg.add_module(CalculateFieldDataCompiled)
- reg.add_input_port(CalculateFieldDataCompiled, 'p_outputdatatype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateFieldDataCompiled, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateFieldDataCompiled, 'p_cache',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CalculateFieldDataCompiled, 'Function',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(CalculateFieldDataCompiled, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(CalculateFieldDataCompiled, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(MapFieldDataFromElemToNode)
- reg.add_input_port(MapFieldDataFromElemToNode, 'p_method',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(MapFieldDataFromElemToNode, 'Field',
- (Field, "Field"))
- reg.add_output_port(MapFieldDataFromElemToNode, 'Field',
- (Field, "Field"))
-
- reg.add_module(ApplyFilterToFieldData)
- reg.add_input_port(ApplyFilterToFieldData, 'p_method',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ApplyFilterToFieldData, 'p_ed_method',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ApplyFilterToFieldData, 'p_ed_iterations',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ApplyFilterToFieldData, 'Field',
- (Field, "Field"))
- reg.add_output_port(ApplyFilterToFieldData, 'Field',
- (Field, "Field"))
-
- reg.add_module(GetFieldData)
- reg.add_input_port(GetFieldData, 'Field',
- (Field, "Field"))
- reg.add_output_port(GetFieldData, 'Data',
- (Matrix, "Matrix"))
-
- reg.add_module(CalculateFieldData2)
- reg.add_input_port(CalculateFieldData2, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateFieldData2, 'p_format',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateFieldData2, 'Field1',
- (Field, "Field"))
- reg.add_input_port(CalculateFieldData2, 'Field2',
- (Field, "Field"))
- reg.add_input_port(CalculateFieldData2, 'Function',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(CalculateFieldData2, 'Array',
- (Matrix, "Matrix"))
- reg.add_output_port(CalculateFieldData2, 'Field',
- (Field, "Field"))
-
- reg.add_module(CalculateLatVolGradientsAtNodes)
- reg.add_input_port(CalculateLatVolGradientsAtNodes, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(CalculateLatVolGradientsAtNodes, 'Output Gradient',
- (Field, "Field"))
-
- reg.add_module(CalculateGradients)
- reg.add_input_port(CalculateGradients, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(CalculateGradients, 'Output CalculateGradients',
- (Field, "Field"))
-
- reg.add_module(CalculateSignedDistanceToField)
- reg.add_input_port(CalculateSignedDistanceToField, 'Field',
- (Field, "Field"))
- reg.add_input_port(CalculateSignedDistanceToField, 'ObjectField',
- (Field, "Field"))
- reg.add_output_port(CalculateSignedDistanceToField, 'SignedDistanceField',
- (Field, "Field"))
-
- reg.add_module(CalculateInsideWhichField)
- reg.add_input_port(CalculateInsideWhichField, 'p_outputbasis',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateInsideWhichField, 'p_outputtype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateInsideWhichField, 'Field',
- (Field, "Field"))
- reg.add_input_port(CalculateInsideWhichField, 'Object',
- (Field, "Field"))
- reg.add_output_port(CalculateInsideWhichField, 'Field',
- (Field, "Field"))
-
- reg.add_module(MapFieldDataFromNodeToElem)
- reg.add_input_port(MapFieldDataFromNodeToElem, 'p_method',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(MapFieldDataFromNodeToElem, 'Field',
- (Field, "Field"))
- reg.add_output_port(MapFieldDataFromNodeToElem, 'Field',
- (Field, "Field"))
-
- reg.add_module(ConvertFieldDataType)
- reg.add_input_port(ConvertFieldDataType, 'p_outputdatatype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertFieldDataType, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(ConvertFieldDataType, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(CalculateIsInsideField)
- reg.add_input_port(CalculateIsInsideField, 'p_outputtype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateIsInsideField, 'p_outval',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CalculateIsInsideField, 'p_inval',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CalculateIsInsideField, 'Field',
- (Field, "Field"))
- reg.add_input_port(CalculateIsInsideField, 'ObjectField',
- (Field, "Field"))
- reg.add_output_port(CalculateIsInsideField, 'Field',
- (Field, "Field"))
-
- reg.add_module(CalculateFieldData)
- reg.add_input_port(CalculateFieldData, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateFieldData, 'p_format',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateFieldData, 'Field',
- (Field, "Field"))
- reg.add_input_port(CalculateFieldData, 'Function',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(CalculateFieldData, 'Array',
- (Matrix, "Matrix"))
- reg.add_output_port(CalculateFieldData, 'Field',
- (Field, "Field"))
-
- reg.add_module(CalculateDistanceToField)
- reg.add_input_port(CalculateDistanceToField, 'Field',
- (Field, "Field"))
- reg.add_input_port(CalculateDistanceToField, 'ObjectField',
- (Field, "Field"))
- reg.add_output_port(CalculateDistanceToField, 'DistanceField',
- (Field, "Field"))
-
- reg.add_module(TransformPlanarMesh)
- reg.add_input_port(TransformPlanarMesh, 'p_axis',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(TransformPlanarMesh, 'p_invert',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(TransformPlanarMesh, 'p_trans_x',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(TransformPlanarMesh, 'p_trans_y',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(TransformPlanarMesh, 'Input Field',
- (Field, "Field"))
- reg.add_input_port(TransformPlanarMesh, 'Index Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(TransformPlanarMesh, 'Transformed Field',
- (Field, "Field"))
-
- reg.add_module(ConvertMeshToUnstructuredMesh)
- reg.add_input_port(ConvertMeshToUnstructuredMesh, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(ConvertMeshToUnstructuredMesh, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(ConvertQuadSurfToTriSurf)
- reg.add_input_port(ConvertQuadSurfToTriSurf, 'QuadSurf',
- (Field, "Field"))
- reg.add_output_port(ConvertQuadSurfToTriSurf, 'TriSurf',
- (Field, "Field"))
-
- reg.add_module(TransformMeshWithFunction)
- reg.add_input_port(TransformMeshWithFunction, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(TransformMeshWithFunction, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(TransformMeshWithFunction, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(ConvertHexVolToTetVol)
- reg.add_input_port(ConvertHexVolToTetVol, 'HexVol',
- (Field, "Field"))
- reg.add_output_port(ConvertHexVolToTetVol, 'TetVol',
- (Field, "Field"))
-
- reg.add_module(ConvertMeshCoordinateSystem)
- reg.add_input_port(ConvertMeshCoordinateSystem, 'p_oldsystem',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertMeshCoordinateSystem, 'p_newsystem',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertMeshCoordinateSystem, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(ConvertMeshCoordinateSystem, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(ConvertMeshToPointCloud)
- reg.add_input_port(ConvertMeshToPointCloud, 'p_datalocation',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ConvertMeshToPointCloud, 'Field',
- (Field, "Field"))
- reg.add_output_port(ConvertMeshToPointCloud, 'Field',
- (Field, "Field"))
-
- reg.add_module(TransformMeshWithTransform)
- reg.add_input_port(TransformMeshWithTransform, 'Input Field',
- (Field, "Field"))
- reg.add_input_port(TransformMeshWithTransform, 'Transform Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(TransformMeshWithTransform, 'Transformed Field',
- (Field, "Field"))
-
- reg.add_module(ConvertRegularMeshToStructuredMesh)
- reg.add_input_port(ConvertRegularMeshToStructuredMesh, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(ConvertRegularMeshToStructuredMesh, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(CalculateMeshNodes)
- reg.add_input_port(CalculateMeshNodes, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateMeshNodes, 'Field',
- (Field, "Field"))
- reg.add_input_port(CalculateMeshNodes, 'Function',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(CalculateMeshNodes, 'Array',
- (Matrix, "Matrix"))
- reg.add_output_port(CalculateMeshNodes, 'Field',
- (Field, "Field"))
-
- reg.add_module(SmoothMesh)
- reg.add_input_port(SmoothMesh, 'Input',
- (Field, "Field"))
- reg.add_input_port(SmoothMesh, 'IsoValue',
- (Matrix, "Matrix"))
- reg.add_output_port(SmoothMesh, 'Smoothed',
- (Field, "Field"))
-
- reg.add_module(EditMeshBoundingBox)
- reg.add_input_port(EditMeshBoundingBox, 'p_outputcenterx',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_outputcentery',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_outputcenterz',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_outputsizex',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_outputsizey',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_outputsizez',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_useoutputcenter',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_useoutputsize',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_scale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_mode',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_real_scale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_center_x',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_center_y',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_center_z',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_right_x',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_right_y',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_right_z',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_down_x',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_down_y',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_down_z',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_in_x',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_in_y',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'p_box_in_z',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EditMeshBoundingBox, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(EditMeshBoundingBox, 'Output Field',
- (Field, "Field"))
- reg.add_output_port(EditMeshBoundingBox, 'Transformation Widget',
- (Geometry, "Geometry"))
- reg.add_output_port(EditMeshBoundingBox, 'Transformation Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(SwapNodeLocationsWithMatrixEntries)
- reg.add_input_port(SwapNodeLocationsWithMatrixEntries, 'Input Field',
- (Field, "Field"))
- reg.add_input_port(SwapNodeLocationsWithMatrixEntries, 'Input Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(SwapNodeLocationsWithMatrixEntries, 'Output Field',
- (Field, "Field"))
- reg.add_output_port(SwapNodeLocationsWithMatrixEntries, 'Output Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(MapFieldDataToNodeCoordinate)
- reg.add_input_port(MapFieldDataToNodeCoordinate, 'p_coord',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(MapFieldDataToNodeCoordinate, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(MapFieldDataToNodeCoordinate, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(ScaleFieldMeshAndData)
- reg.add_input_port(ScaleFieldMeshAndData, 'p_datascale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ScaleFieldMeshAndData, 'p_geomscale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ScaleFieldMeshAndData, 'p_usegeomcenter',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ScaleFieldMeshAndData, 'Field',
- (Field, "Field"))
- reg.add_input_port(ScaleFieldMeshAndData, 'GeomScaleFactor',
- (Matrix, "Matrix"))
- reg.add_input_port(ScaleFieldMeshAndData, 'DataScaleFactor',
- (Matrix, "Matrix"))
- reg.add_output_port(ScaleFieldMeshAndData, 'Field',
- (Field, "Field"))
-
- reg.add_module(ReportColumnMatrixMisfit)
- reg.add_input_port(ReportColumnMatrixMisfit, 'p_have_ui',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReportColumnMatrixMisfit, 'p_methodTCL',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReportColumnMatrixMisfit, 'p_pTCL',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReportColumnMatrixMisfit, 'Vec1',
- (Matrix, "Matrix"))
- reg.add_input_port(ReportColumnMatrixMisfit, 'Vec2',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportColumnMatrixMisfit, 'Error Out',
- (Matrix, "Matrix"))
-
- reg.add_module(EvaluateLinAlgGeneral)
- reg.add_input_port(EvaluateLinAlgGeneral, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EvaluateLinAlgGeneral, 'i1',
- (Matrix, "Matrix"))
- reg.add_input_port(EvaluateLinAlgGeneral, 'i2',
- (Matrix, "Matrix"))
- reg.add_input_port(EvaluateLinAlgGeneral, 'i3',
- (Matrix, "Matrix"))
- reg.add_input_port(EvaluateLinAlgGeneral, 'i4',
- (Matrix, "Matrix"))
- reg.add_input_port(EvaluateLinAlgGeneral, 'i5',
- (Matrix, "Matrix"))
- reg.add_output_port(EvaluateLinAlgGeneral, 'o1',
- (Matrix, "Matrix"))
- reg.add_output_port(EvaluateLinAlgGeneral, 'o2',
- (Matrix, "Matrix"))
- reg.add_output_port(EvaluateLinAlgGeneral, 'o3',
- (Matrix, "Matrix"))
- reg.add_output_port(EvaluateLinAlgGeneral, 'o4',
- (Matrix, "Matrix"))
- reg.add_output_port(EvaluateLinAlgGeneral, 'o5',
- (Matrix, "Matrix"))
-
- reg.add_module(AppendMatrix)
- reg.add_input_port(AppendMatrix, 'p_row_or_column',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(AppendMatrix, 'BaseMatrix',
- (Matrix, "Matrix"))
- reg.add_input_port(AppendMatrix, 'AppendMatrix',
- (Matrix, "Matrix"))
- reg.add_output_port(AppendMatrix, 'Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(EvaluateLinAlgBinary)
- reg.add_input_port(EvaluateLinAlgBinary, 'p_op',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EvaluateLinAlgBinary, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EvaluateLinAlgBinary, 'A',
- (Matrix, "Matrix"))
- reg.add_input_port(EvaluateLinAlgBinary, 'B',
- (Matrix, "Matrix"))
- reg.add_output_port(EvaluateLinAlgBinary, 'Output',
- (Matrix, "Matrix"))
-
- reg.add_module(ConvertMaskVectorToMappingMatrix)
- reg.add_input_port(ConvertMaskVectorToMappingMatrix, 'MaskVector',
- (Nrrd, "Nrrd"))
- reg.add_output_port(ConvertMaskVectorToMappingMatrix, 'MappingMatrix',
- (Matrix, "Matrix"))
-
- reg.add_module(SolveLinearSystem)
- reg.add_input_port(SolveLinearSystem, 'p_target_error',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_flops',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_floprate',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_memrefs',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_memrate',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_orig_error',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_current_error',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_method',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_precond',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_iteration',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_maxiter',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_use_previous_soln',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_emit_partial',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_emit_iter',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_status',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'p_np',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SolveLinearSystem, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_input_port(SolveLinearSystem, 'RHS',
- (Matrix, "Matrix"))
- reg.add_output_port(SolveLinearSystem, 'Solution',
- (Matrix, "Matrix"))
-
- reg.add_module(ReportMatrixColumnMeasure)
- reg.add_input_port(ReportMatrixColumnMeasure, 'p_method',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReportMatrixColumnMeasure, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportMatrixColumnMeasure, 'Vector',
- (Matrix, "Matrix"))
-
- reg.add_module(SortMatrix)
- reg.add_input_port(SortMatrix, 'p_row_or_col',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SortMatrix, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(SortMatrix, 'Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(CreateGeometricTransform)
- reg.add_input_port(CreateGeometricTransform, 'p_rotate_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_rotate_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_rotate_z',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_rotate_theta',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_translate_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_translate_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_translate_z',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_scale_uniform',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_scale_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_scale_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_scale_z',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_shear_plane_a',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_shear_plane_b',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_shear_plane_c',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_widget_resizable',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_permute_x',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_permute_y',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_permute_z',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_pre_transform',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_which_transform',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_widget_scale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'p_ignoring_widget_changes',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateGeometricTransform, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(CreateGeometricTransform, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(CreateGeometricTransform, 'Geometry',
- (Geometry, "Geometry"))
-
- reg.add_module(ChooseMatrix)
- reg.add_input_port(ChooseMatrix, 'p_use_first_valid',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ChooseMatrix, 'p_port_valid_index',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ChooseMatrix, 'p_port_selected_index',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ChooseMatrix, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(ChooseMatrix, 'Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(ConvertMappingMatrixToMaskVector)
- reg.add_input_port(ConvertMappingMatrixToMaskVector, 'MappingMatrix',
- (Matrix, "Matrix"))
- reg.add_output_port(ConvertMappingMatrixToMaskVector, 'MaskVector',
- (Nrrd, "Nrrd"))
-
- reg.add_module(ResizeMatrix)
- reg.add_input_port(ResizeMatrix, 'p_dim_m',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ResizeMatrix, 'p_dim_n',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ResizeMatrix, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_input_port(ResizeMatrix, 'M',
- (Matrix, "Matrix"))
- reg.add_input_port(ResizeMatrix, 'N',
- (Matrix, "Matrix"))
- reg.add_output_port(ResizeMatrix, 'Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(CollectMatrices)
- reg.add_input_port(CollectMatrices, 'p_append',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CollectMatrices, 'p_row',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CollectMatrices, 'p_front',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CollectMatrices, 'Optional BaseMatrix',
- (Matrix, "Matrix"))
- reg.add_input_port(CollectMatrices, 'SubMatrix',
- (Matrix, "Matrix"))
- reg.add_output_port(CollectMatrices, 'CompositeMatrix',
- (Matrix, "Matrix"))
-
- reg.add_module(GetColumnOrRowFromMatrix)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_row_or_col',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_selectable_min',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_selectable_max',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_selectable_inc',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_selectable_units',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_range_min',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_range_max',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_playmode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_current',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_execmode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_delay',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_inc_amount',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_send_amount',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'p_data_series_done',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetColumnOrRowFromMatrix, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_input_port(GetColumnOrRowFromMatrix, 'Weight Vector',
- (Matrix, "Matrix"))
- reg.add_input_port(GetColumnOrRowFromMatrix, 'Current Index',
- (Matrix, "Matrix"))
- reg.add_output_port(GetColumnOrRowFromMatrix, 'Vector',
- (Matrix, "Matrix"))
- reg.add_output_port(GetColumnOrRowFromMatrix, 'Selected Index',
- (Matrix, "Matrix"))
-
- reg.add_module(BuildNoiseColumnMatrix)
- reg.add_input_port(BuildNoiseColumnMatrix, 'p_snr',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(BuildNoiseColumnMatrix, 'Signal',
- (Matrix, "Matrix"))
- reg.add_output_port(BuildNoiseColumnMatrix, 'Noise',
- (Matrix, "Matrix"))
-
- reg.add_module(EvaluateLinAlgUnary)
- reg.add_input_port(EvaluateLinAlgUnary, 'p_op',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EvaluateLinAlgUnary, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(EvaluateLinAlgUnary, 'Input',
- (Matrix, "Matrix"))
- reg.add_output_port(EvaluateLinAlgUnary, 'Output',
- (Matrix, "Matrix"))
-
- reg.add_module(GetSubmatrix)
- reg.add_input_port(GetSubmatrix, 'p_mincol',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetSubmatrix, 'p_maxcol',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetSubmatrix, 'p_minrow',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetSubmatrix, 'p_maxrow',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetSubmatrix, 'p_nrow',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetSubmatrix, 'p_ncol',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetSubmatrix, 'Input Matrix',
- (Matrix, "Matrix"))
- reg.add_input_port(GetSubmatrix, 'Optional Range Bounds',
- (Matrix, "Matrix"))
- reg.add_output_port(GetSubmatrix, 'Output Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(ReorderMatrixByReverseCuthillMcKee)
- reg.add_input_port(ReorderMatrixByReverseCuthillMcKee, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(ReorderMatrixByReverseCuthillMcKee, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(ReorderMatrixByReverseCuthillMcKee, 'Mapping',
- (Matrix, "Matrix"))
- reg.add_output_port(ReorderMatrixByReverseCuthillMcKee, 'InverseMapping',
- (Matrix, "Matrix"))
-
- reg.add_module(CreateMatrix)
- reg.add_input_port(CreateMatrix, 'p_rows',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateMatrix, 'p_cols',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateMatrix, 'p_data',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateMatrix, 'p_clabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateMatrix, 'p_rlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_output_port(CreateMatrix, 'matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(SolveMinNormLeastSqSystem)
- reg.add_input_port(SolveMinNormLeastSqSystem, 'BasisVec1',
- (Matrix, "Matrix"))
- reg.add_input_port(SolveMinNormLeastSqSystem, 'BasisVec2',
- (Matrix, "Matrix"))
- reg.add_input_port(SolveMinNormLeastSqSystem, 'BasisVec3',
- (Matrix, "Matrix"))
- reg.add_input_port(SolveMinNormLeastSqSystem, 'TargetVec',
- (Matrix, "Matrix"))
- reg.add_output_port(SolveMinNormLeastSqSystem, 'WeightVec(Col)',
- (Matrix, "Matrix"))
- reg.add_output_port(SolveMinNormLeastSqSystem, 'ResultVec(Col)',
- (Matrix, "Matrix"))
-
- reg.add_module(ConvertMatrixType)
- reg.add_input_port(ConvertMatrixType, 'p_oldtype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertMatrixType, 'p_newtype',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertMatrixType, 'p_nrow',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertMatrixType, 'p_ncol',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertMatrixType, 'Input',
- (Matrix, "Matrix"))
- reg.add_output_port(ConvertMatrixType, 'Output',
- (Matrix, "Matrix"))
-
- reg.add_module(ReportMatrixRowMeasure)
- reg.add_input_port(ReportMatrixRowMeasure, 'p_method',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReportMatrixRowMeasure, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportMatrixRowMeasure, 'Vector',
- (Matrix, "Matrix"))
-
- reg.add_module(ReorderMatrixByCuthillMcKee)
- reg.add_input_port(ReorderMatrixByCuthillMcKee, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(ReorderMatrixByCuthillMcKee, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(ReorderMatrixByCuthillMcKee, 'Mapping',
- (Matrix, "Matrix"))
- reg.add_output_port(ReorderMatrixByCuthillMcKee, 'InverseMapping',
- (Matrix, "Matrix"))
-
- reg.add_module(ReportMatrixInfo)
- reg.add_input_port(ReportMatrixInfo, 'Input',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportMatrixInfo, 'NumRows',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportMatrixInfo, 'NumCols',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportMatrixInfo, 'NumElements',
- (Matrix, "Matrix"))
-
- reg.add_module(RemoveZerosFromMatrix)
- reg.add_input_port(RemoveZerosFromMatrix, 'p_row_or_col',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(RemoveZerosFromMatrix, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(RemoveZerosFromMatrix, 'Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(RemoveZeroRowsAndColumns)
- reg.add_input_port(RemoveZeroRowsAndColumns, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(RemoveZeroRowsAndColumns, 'ReducedMatrix',
- (Matrix, "Matrix"))
- reg.add_output_port(RemoveZeroRowsAndColumns, 'LeftMapping',
- (Matrix, "Matrix"))
- reg.add_output_port(RemoveZeroRowsAndColumns, 'RightMapping',
- (Matrix, "Matrix"))
-
- reg.add_module(CreateDataArray)
- reg.add_input_port(CreateDataArray, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateDataArray, 'p_format',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateDataArray, 'Size',
- (Matrix, "Matrix"))
- reg.add_input_port(CreateDataArray, 'Function',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(CreateDataArray, 'Array',
- (Matrix, "Matrix"))
- reg.add_output_port(CreateDataArray, 'DataArray',
- (Matrix, "Matrix"))
-
- reg.add_module(CreateDataArrayFromIndices)
- reg.add_input_port(CreateDataArrayFromIndices, 'Indices',
- (Matrix, "Matrix"))
- reg.add_input_port(CreateDataArrayFromIndices, 'Template',
- (Matrix, "Matrix"))
- reg.add_output_port(CreateDataArrayFromIndices, 'DataArray',
- (Matrix, "Matrix"))
-
- reg.add_module(ReportDataArrayInfo)
- reg.add_input_port(ReportDataArrayInfo, 'DataArray',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportDataArrayInfo, 'NumElements',
- (Matrix, "Matrix"))
-
- reg.add_module(CreateVectorArray)
- reg.add_input_port(CreateVectorArray, 'X',
- (Matrix, "Matrix"))
- reg.add_input_port(CreateVectorArray, 'Y',
- (Matrix, "Matrix"))
- reg.add_input_port(CreateVectorArray, 'Z',
- (Matrix, "Matrix"))
- reg.add_output_port(CreateVectorArray, 'Vector',
- (Matrix, "Matrix"))
-
- reg.add_module(ReplicateDataArray)
- reg.add_input_port(ReplicateDataArray, 'p_size',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReplicateDataArray, 'DataArray',
- (Matrix, "Matrix"))
- reg.add_input_port(ReplicateDataArray, 'Size',
- (Matrix, "Matrix"))
- reg.add_output_port(ReplicateDataArray, 'DataArray',
- (Matrix, "Matrix"))
-
- reg.add_module(SplitVectorArrayInXYZ)
- reg.add_input_port(SplitVectorArrayInXYZ, 'VectorArray',
- (Matrix, "Matrix"))
- reg.add_output_port(SplitVectorArrayInXYZ, 'X',
- (Matrix, "Matrix"))
- reg.add_output_port(SplitVectorArrayInXYZ, 'Y',
- (Matrix, "Matrix"))
- reg.add_output_port(SplitVectorArrayInXYZ, 'Z',
- (Matrix, "Matrix"))
-
- reg.add_module(DecomposeTensorArrayIntoEigenVectors)
- reg.add_input_port(DecomposeTensorArrayIntoEigenVectors, 'TensorArray',
- (Matrix, "Matrix"))
- reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenVector1',
- (Matrix, "Matrix"))
- reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenVector2',
- (Matrix, "Matrix"))
- reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenVector3',
- (Matrix, "Matrix"))
- reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenValue1',
- (Matrix, "Matrix"))
- reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenValue2',
- (Matrix, "Matrix"))
- reg.add_output_port(DecomposeTensorArrayIntoEigenVectors, 'EigenValue3',
- (Matrix, "Matrix"))
-
- reg.add_module(CalculateDataArray)
- reg.add_input_port(CalculateDataArray, 'p_function',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateDataArray, 'p_format',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CalculateDataArray, 'DataArray',
- (Matrix, "Matrix"))
- reg.add_input_port(CalculateDataArray, 'Function',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(CalculateDataArray, 'Array',
- (Matrix, "Matrix"))
- reg.add_output_port(CalculateDataArray, 'DataArray',
- (Matrix, "Matrix"))
-
- reg.add_module(ReportDataArrayMeasure)
- reg.add_input_port(ReportDataArrayMeasure, 'p_measure',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReportDataArrayMeasure, 'Array',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportDataArrayMeasure, 'Measure',
- (Matrix, "Matrix"))
-
- reg.add_module(AppendDataArrays)
- reg.add_input_port(AppendDataArrays, 'Array',
- (Matrix, "Matrix"))
- reg.add_output_port(AppendDataArrays, 'Array',
- (Matrix, "Matrix"))
-
- reg.add_module(CreateTensorArray)
- reg.add_input_port(CreateTensorArray, 'EigenVector1',
- (Matrix, "Matrix"))
- reg.add_input_port(CreateTensorArray, 'EigenVector2',
- (Matrix, "Matrix"))
- reg.add_input_port(CreateTensorArray, 'EigenValue1',
- (Matrix, "Matrix"))
- reg.add_input_port(CreateTensorArray, 'EigenValue2',
- (Matrix, "Matrix"))
- reg.add_input_port(CreateTensorArray, 'EigenValue3',
- (Matrix, "Matrix"))
- reg.add_output_port(CreateTensorArray, 'TensorArray',
- (Matrix, "Matrix"))
-
- reg.add_module(PrintMatrixIntoString)
- reg.add_input_port(PrintMatrixIntoString, 'p_formatstring',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(PrintMatrixIntoString, 'Format',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(PrintMatrixIntoString, 'Input',
- (Matrix, "Matrix"))
- reg.add_output_port(PrintMatrixIntoString, 'Output',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(GetFileName)
- reg.add_input_port(GetFileName, 'p_filename_base',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetFileName, 'p_delay',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetFileName, 'p_pinned',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_output_port(GetFileName, 'Full Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(SplitFileName)
- reg.add_input_port(SplitFileName, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(SplitFileName, 'Pathname',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(SplitFileName, 'Filename Base',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(SplitFileName, 'Extension',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(SplitFileName, 'Filename',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(PrintStringIntoString)
- reg.add_input_port(PrintStringIntoString, 'p_formatstring',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(PrintStringIntoString, 'Format',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(PrintStringIntoString, 'Input',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(PrintStringIntoString, 'Output',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(CreateString)
- reg.add_input_port(CreateString, 'p_inputstring',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_output_port(CreateString, 'Output',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(ReportStringInfo)
- reg.add_input_port(ReportStringInfo, 'p_inputstring',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReportStringInfo, 'Input',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(JoinStrings)
- reg.add_input_port(JoinStrings, 'input',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(JoinStrings, 'Output',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(GetNetworkFileName)
- reg.add_output_port(GetNetworkFileName, 'String',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(SetFieldProperty)
- reg.add_input_port(SetFieldProperty, 'p_num_entries',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SetFieldProperty, 'p_property',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SetFieldProperty, 'p_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SetFieldProperty, 'p_value',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SetFieldProperty, 'p_readonly',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SetFieldProperty, 'Field',
- (Field, "Field"))
- reg.add_output_port(SetFieldProperty, 'Field',
- (Field, "Field"))
-
- reg.add_module(ReportScalarFieldStats)
- reg.add_input_port(ReportScalarFieldStats, 'p_min',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ReportScalarFieldStats, 'p_max',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ReportScalarFieldStats, 'p_mean',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ReportScalarFieldStats, 'p_median',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ReportScalarFieldStats, 'p_sigma',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ReportScalarFieldStats, 'p_is_fixed',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReportScalarFieldStats, 'p_nbuckets',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReportScalarFieldStats, 'Input Field',
- (Field, "Field"))
-
- reg.add_module(SelectFieldROIWithBoxWidget)
- reg.add_input_port(SelectFieldROIWithBoxWidget, 'p_stampvalue',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SelectFieldROIWithBoxWidget, 'p_runmode',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SelectFieldROIWithBoxWidget, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(SelectFieldROIWithBoxWidget, 'Selection Widget',
- (Geometry, "Geometry"))
- reg.add_output_port(SelectFieldROIWithBoxWidget, 'Output Field',
- (Field, "Field"))
-
- reg.add_module(BuildMatrixOfSurfaceNormals)
- reg.add_input_port(BuildMatrixOfSurfaceNormals, 'Surface Field',
- (Field, "Field"))
- reg.add_output_port(BuildMatrixOfSurfaceNormals, 'Nodal Surface Normals',
- (Matrix, "Matrix"))
-
- reg.add_module(ReportFieldInfo)
- reg.add_input_port(ReportFieldInfo, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(ReportFieldInfo, 'NumNodes',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportFieldInfo, 'NumElements',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportFieldInfo, 'NumData',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportFieldInfo, 'DataMin',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportFieldInfo, 'DataMax',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportFieldInfo, 'FieldSize',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportFieldInfo, 'FieldCenter',
- (Matrix, "Matrix"))
- reg.add_output_port(ReportFieldInfo, 'Dimensions',
- (Matrix, "Matrix"))
-
- reg.add_module(ReportFieldGeometryMeasures)
- reg.add_input_port(ReportFieldGeometryMeasures, 'p_simplexString',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReportFieldGeometryMeasures, 'p_xFlag',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReportFieldGeometryMeasures, 'p_yFlag',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReportFieldGeometryMeasures, 'p_zFlag',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReportFieldGeometryMeasures, 'p_idxFlag',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReportFieldGeometryMeasures, 'p_sizeFlag',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReportFieldGeometryMeasures, 'p_normalsFlag',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ReportFieldGeometryMeasures, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(ReportFieldGeometryMeasures, 'Output Measures Matrix',
- (Matrix, "Matrix"))
-
- reg.add_module(SetFieldOrMeshStringProperty)
- reg.add_input_port(SetFieldOrMeshStringProperty, 'p_prop',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SetFieldOrMeshStringProperty, 'p_val',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(SetFieldOrMeshStringProperty, 'p_meshprop',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(SetFieldOrMeshStringProperty, 'Input',
- (Field, "Field"))
- reg.add_output_port(SetFieldOrMeshStringProperty, 'Output',
- (Field, "Field"))
-
- reg.add_module(ManageFieldSeries)
- reg.add_input_port(ManageFieldSeries, 'p_num_ports',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ManageFieldSeries, 'Input',
- (Field, "Field"))
- reg.add_output_port(ManageFieldSeries, 'Output 0',
- (Field, "Field"))
- reg.add_output_port(ManageFieldSeries, 'Output 1',
- (Field, "Field"))
- reg.add_output_port(ManageFieldSeries, 'Output 2',
- (Field, "Field"))
- reg.add_output_port(ManageFieldSeries, 'Output 3',
- (Field, "Field"))
-
- reg.add_module(ReportSearchGridInfo)
- reg.add_input_port(ReportSearchGridInfo, 'Input Field',
- (Field, "Field"))
- reg.add_output_port(ReportSearchGridInfo, 'Output Sample Field',
- (Field, "Field"))
-
- reg.add_module(ChooseField)
- reg.add_input_port(ChooseField, 'p_use_first_valid',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ChooseField, 'p_port_valid_index',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ChooseField, 'p_port_selected_index',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ChooseField, 'Field',
- (Field, "Field"))
- reg.add_output_port(ChooseField, 'Field',
- (Field, "Field"))
-
- reg.add_module(BuildPointCloudToLatVolMappingMatrix)
- reg.add_input_port(BuildPointCloudToLatVolMappingMatrix, 'p_epsilon',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(BuildPointCloudToLatVolMappingMatrix, 'PointCloudField',
- (Field, "Field"))
- reg.add_input_port(BuildPointCloudToLatVolMappingMatrix, 'LatVolField',
- (Field, "Field"))
- reg.add_output_port(BuildPointCloudToLatVolMappingMatrix, 'MappingMatrix',
- (Matrix, "Matrix"))
-
- reg.add_module(BuildMappingMatrix)
- reg.add_input_port(BuildMappingMatrix, 'p_interpolation_basis',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(BuildMappingMatrix, 'p_map_source_to_single_dest',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(BuildMappingMatrix, 'p_exhaustive_search',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(BuildMappingMatrix, 'p_exhaustive_search_max_dist',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(BuildMappingMatrix, 'p_np',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(BuildMappingMatrix, 'Source',
- (Field, "Field"))
- reg.add_input_port(BuildMappingMatrix, 'Destination',
- (Field, "Field"))
- reg.add_output_port(BuildMappingMatrix, 'Mapping',
- (Matrix, "Matrix"))
-
- reg.add_module(CoregisterPointClouds)
- reg.add_input_port(CoregisterPointClouds, 'p_allowScale',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CoregisterPointClouds, 'p_allowRotate',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CoregisterPointClouds, 'p_allowTranslate',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CoregisterPointClouds, 'p_seed',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CoregisterPointClouds, 'p_iters',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CoregisterPointClouds, 'p_misfitTol',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CoregisterPointClouds, 'p_method',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CoregisterPointClouds, 'Fixed PointCloudField',
- (Field, "Field"))
- reg.add_input_port(CoregisterPointClouds, 'Mobile PointCloudField',
- (Field, "Field"))
- reg.add_input_port(CoregisterPointClouds, 'DistanceField From Fixed',
- (Field, "Field"))
- reg.add_output_port(CoregisterPointClouds, 'Transform',
- (Matrix, "Matrix"))
-
- reg.add_module(CollectPointClouds)
- reg.add_input_port(CollectPointClouds, 'p_num_fields',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CollectPointClouds, 'Point Cloud',
- (Field, "Field"))
- reg.add_output_port(CollectPointClouds, 'Curve',
- (Field, "Field"))
-
- reg.add_module(GetColorMapsFromBundle)
- reg.add_input_port(GetColorMapsFromBundle, 'p_colormap1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMapsFromBundle, 'p_colormap2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMapsFromBundle, 'p_colormap3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMapsFromBundle, 'p_colormap4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMapsFromBundle, 'p_colormap5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMapsFromBundle, 'p_colormap6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMapsFromBundle, 'p_colormap_selection',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMapsFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetColorMapsFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetColorMapsFromBundle, 'colormap1',
- (ColorMap, "ColorMap"))
- reg.add_output_port(GetColorMapsFromBundle, 'colormap2',
- (ColorMap, "ColorMap"))
- reg.add_output_port(GetColorMapsFromBundle, 'colormap3',
- (ColorMap, "ColorMap"))
- reg.add_output_port(GetColorMapsFromBundle, 'colormap4',
- (ColorMap, "ColorMap"))
- reg.add_output_port(GetColorMapsFromBundle, 'colormap5',
- (ColorMap, "ColorMap"))
- reg.add_output_port(GetColorMapsFromBundle, 'colormap6',
- (ColorMap, "ColorMap"))
-
- reg.add_module(InsertFieldsIntoBundle)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_field1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_field2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_field3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_field4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_field5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_field6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_replace1',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_replace2',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_replace3',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_replace4',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_replace5',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_replace6',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'p_bundlename',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertFieldsIntoBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertFieldsIntoBundle, 'field1',
- (Field, "Field"))
- reg.add_input_port(InsertFieldsIntoBundle, 'field2',
- (Field, "Field"))
- reg.add_input_port(InsertFieldsIntoBundle, 'field3',
- (Field, "Field"))
- reg.add_input_port(InsertFieldsIntoBundle, 'field4',
- (Field, "Field"))
- reg.add_input_port(InsertFieldsIntoBundle, 'field5',
- (Field, "Field"))
- reg.add_input_port(InsertFieldsIntoBundle, 'field6',
- (Field, "Field"))
- reg.add_output_port(InsertFieldsIntoBundle, 'bundle',
- (Bundle, "Bundle"))
-
- reg.add_module(GetFieldsFromBundle)
- reg.add_input_port(GetFieldsFromBundle, 'p_field1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetFieldsFromBundle, 'p_field2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetFieldsFromBundle, 'p_field3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetFieldsFromBundle, 'p_field4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetFieldsFromBundle, 'p_field5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetFieldsFromBundle, 'p_field6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetFieldsFromBundle, 'p_field_selection',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetFieldsFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetFieldsFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetFieldsFromBundle, 'field1',
- (Field, "Field"))
- reg.add_output_port(GetFieldsFromBundle, 'field2',
- (Field, "Field"))
- reg.add_output_port(GetFieldsFromBundle, 'field3',
- (Field, "Field"))
- reg.add_output_port(GetFieldsFromBundle, 'field4',
- (Field, "Field"))
- reg.add_output_port(GetFieldsFromBundle, 'field5',
- (Field, "Field"))
- reg.add_output_port(GetFieldsFromBundle, 'field6',
- (Field, "Field"))
-
- reg.add_module(InsertColorMap2sIntoBundle)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap21_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap22_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap23_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap24_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap25_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_colormap26_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace1',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace2',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace3',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace4',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace5',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_replace6',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'p_bundlename',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMap2sIntoBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap21',
- (ColorMap2, "ColorMap2"))
- reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap22',
- (ColorMap2, "ColorMap2"))
- reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap23',
- (ColorMap2, "ColorMap2"))
- reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap24',
- (ColorMap2, "ColorMap2"))
- reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap25',
- (ColorMap2, "ColorMap2"))
- reg.add_input_port(InsertColorMap2sIntoBundle, 'colormap26',
- (ColorMap2, "ColorMap2"))
- reg.add_output_port(InsertColorMap2sIntoBundle, 'bundle',
- (Bundle, "Bundle"))
-
- reg.add_module(GetBundlesFromBundle)
- reg.add_input_port(GetBundlesFromBundle, 'p_bundle1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetBundlesFromBundle, 'p_bundle2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetBundlesFromBundle, 'p_bundle3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetBundlesFromBundle, 'p_bundle4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetBundlesFromBundle, 'p_bundle5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetBundlesFromBundle, 'p_bundle6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetBundlesFromBundle, 'p_bundle_selection',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetBundlesFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetBundlesFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetBundlesFromBundle, 'bundle1',
- (Bundle, "Bundle"))
- reg.add_output_port(GetBundlesFromBundle, 'bundle2',
- (Bundle, "Bundle"))
- reg.add_output_port(GetBundlesFromBundle, 'bundle3',
- (Bundle, "Bundle"))
- reg.add_output_port(GetBundlesFromBundle, 'bundle4',
- (Bundle, "Bundle"))
- reg.add_output_port(GetBundlesFromBundle, 'bundle5',
- (Bundle, "Bundle"))
- reg.add_output_port(GetBundlesFromBundle, 'bundle6',
- (Bundle, "Bundle"))
-
- reg.add_module(GetPathsFromBundle)
- reg.add_input_port(GetPathsFromBundle, 'p_path1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetPathsFromBundle, 'p_path2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetPathsFromBundle, 'p_path3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetPathsFromBundle, 'p_path4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetPathsFromBundle, 'p_path5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetPathsFromBundle, 'p_path6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetPathsFromBundle, 'p_path_selection',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetPathsFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetPathsFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetPathsFromBundle, 'path1',
- (Path, "Path"))
- reg.add_output_port(GetPathsFromBundle, 'path2',
- (Path, "Path"))
- reg.add_output_port(GetPathsFromBundle, 'path3',
- (Path, "Path"))
- reg.add_output_port(GetPathsFromBundle, 'path4',
- (Path, "Path"))
- reg.add_output_port(GetPathsFromBundle, 'path5',
- (Path, "Path"))
- reg.add_output_port(GetPathsFromBundle, 'path6',
- (Path, "Path"))
-
- reg.add_module(InsertStringsIntoBundle)
- reg.add_input_port(InsertStringsIntoBundle, 'p_string1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'p_string2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'p_string3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'p_string4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'p_string5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'p_string6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'p_replace1',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'p_replace2',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'p_replace3',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'p_replace4',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'p_replace5',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'p_replace6',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertStringsIntoBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertStringsIntoBundle, 'string1',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(InsertStringsIntoBundle, 'string2',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(InsertStringsIntoBundle, 'string3',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(InsertStringsIntoBundle, 'string4',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(InsertStringsIntoBundle, 'string5',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_input_port(InsertStringsIntoBundle, 'string6',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(InsertStringsIntoBundle, 'bundle',
- (Bundle, "Bundle"))
-
- reg.add_module(GetNrrdsFromBundle)
- reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd1',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd2',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd3',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd4',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd5',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_transposenrrd6',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'p_nrrd_selection',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetNrrdsFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetNrrdsFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetNrrdsFromBundle, 'nrrd1',
- (Nrrd, "Nrrd"))
- reg.add_output_port(GetNrrdsFromBundle, 'nrrd2',
- (Nrrd, "Nrrd"))
- reg.add_output_port(GetNrrdsFromBundle, 'nrrd3',
- (Nrrd, "Nrrd"))
- reg.add_output_port(GetNrrdsFromBundle, 'nrrd4',
- (Nrrd, "Nrrd"))
- reg.add_output_port(GetNrrdsFromBundle, 'nrrd5',
- (Nrrd, "Nrrd"))
- reg.add_output_port(GetNrrdsFromBundle, 'nrrd6',
- (Nrrd, "Nrrd"))
-
- reg.add_module(GetMatricesFromBundle)
- reg.add_input_port(GetMatricesFromBundle, 'p_matrix1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_matrix2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_matrix3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_matrix4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_matrix5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_matrix6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd1',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd2',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd3',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd4',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd5',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_transposenrrd6',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'p_matrix_selection',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetMatricesFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetMatricesFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetMatricesFromBundle, 'matrix1',
- (Matrix, "Matrix"))
- reg.add_output_port(GetMatricesFromBundle, 'matrix2',
- (Matrix, "Matrix"))
- reg.add_output_port(GetMatricesFromBundle, 'matrix3',
- (Matrix, "Matrix"))
- reg.add_output_port(GetMatricesFromBundle, 'matrix4',
- (Matrix, "Matrix"))
- reg.add_output_port(GetMatricesFromBundle, 'matrix5',
- (Matrix, "Matrix"))
- reg.add_output_port(GetMatricesFromBundle, 'matrix6',
- (Matrix, "Matrix"))
-
- reg.add_module(JoinBundles)
- reg.add_input_port(JoinBundles, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(JoinBundles, 'bundle',
- (Bundle, "Bundle"))
-
- reg.add_module(ReportBundleInfo)
- reg.add_input_port(ReportBundleInfo, 'p_tclinfostring',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ReportBundleInfo, 'bundle',
- (Bundle, "Bundle"))
-
- reg.add_module(InsertPathsIntoBundle)
- reg.add_input_port(InsertPathsIntoBundle, 'p_path1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_path2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_path3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_path4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_path5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_path6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_replace1',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_replace2',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_replace3',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_replace4',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_replace5',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_replace6',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'p_bundlename',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertPathsIntoBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertPathsIntoBundle, 'path1',
- (Path, "Path"))
- reg.add_input_port(InsertPathsIntoBundle, 'path2',
- (Path, "Path"))
- reg.add_input_port(InsertPathsIntoBundle, 'path3',
- (Path, "Path"))
- reg.add_input_port(InsertPathsIntoBundle, 'path4',
- (Path, "Path"))
- reg.add_input_port(InsertPathsIntoBundle, 'path5',
- (Path, "Path"))
- reg.add_input_port(InsertPathsIntoBundle, 'path6',
- (Path, "Path"))
- reg.add_output_port(InsertPathsIntoBundle, 'bundle',
- (Bundle, "Bundle"))
-
- reg.add_module(GetColorMap2sFromBundle)
- reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap21_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap22_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap23_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap24_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap25_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap26_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMap2sFromBundle, 'p_colormap2_selection',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetColorMap2sFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetColorMap2sFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetColorMap2sFromBundle, 'colormap21',
- (ColorMap2, "ColorMap2"))
- reg.add_output_port(GetColorMap2sFromBundle, 'colormap22',
- (ColorMap2, "ColorMap2"))
- reg.add_output_port(GetColorMap2sFromBundle, 'colormap23',
- (ColorMap2, "ColorMap2"))
- reg.add_output_port(GetColorMap2sFromBundle, 'colormap24',
- (ColorMap2, "ColorMap2"))
- reg.add_output_port(GetColorMap2sFromBundle, 'colormap25',
- (ColorMap2, "ColorMap2"))
- reg.add_output_port(GetColorMap2sFromBundle, 'colormap26',
- (ColorMap2, "ColorMap2"))
-
- reg.add_module(InsertMatricesIntoBundle)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_matrix6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_replace1',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_replace2',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_replace3',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_replace4',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_replace5',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_replace6',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'p_bundlename',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertMatricesIntoBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertMatricesIntoBundle, 'matrix1',
- (Matrix, "Matrix"))
- reg.add_input_port(InsertMatricesIntoBundle, 'matrix2',
- (Matrix, "Matrix"))
- reg.add_input_port(InsertMatricesIntoBundle, 'matrix3',
- (Matrix, "Matrix"))
- reg.add_input_port(InsertMatricesIntoBundle, 'matrix4',
- (Matrix, "Matrix"))
- reg.add_input_port(InsertMatricesIntoBundle, 'matrix5',
- (Matrix, "Matrix"))
- reg.add_input_port(InsertMatricesIntoBundle, 'matrix6',
- (Matrix, "Matrix"))
- reg.add_output_port(InsertMatricesIntoBundle, 'bundle',
- (Bundle, "Bundle"))
-
- reg.add_module(InsertNrrdsIntoBundle)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_nrrd6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace1',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace2',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace3',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace4',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace5',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_replace6',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'p_bundlename',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertNrrdsIntoBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd1',
- (Nrrd, "Nrrd"))
- reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd2',
- (Nrrd, "Nrrd"))
- reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd3',
- (Nrrd, "Nrrd"))
- reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd4',
- (Nrrd, "Nrrd"))
- reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd5',
- (Nrrd, "Nrrd"))
- reg.add_input_port(InsertNrrdsIntoBundle, 'nrrd6',
- (Nrrd, "Nrrd"))
- reg.add_output_port(InsertNrrdsIntoBundle, 'bundle',
- (Bundle, "Bundle"))
-
- reg.add_module(InsertBundlesIntoBundle)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_bundle6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_replace1',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_replace2',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_replace3',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_replace4',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_replace5',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_replace6',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'p_bundlename',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertBundlesIntoBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertBundlesIntoBundle, 'bundle1',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertBundlesIntoBundle, 'bundle2',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertBundlesIntoBundle, 'bundle3',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertBundlesIntoBundle, 'bundle4',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertBundlesIntoBundle, 'bundle5',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertBundlesIntoBundle, 'bundle6',
- (Bundle, "Bundle"))
- reg.add_output_port(InsertBundlesIntoBundle, 'bundle',
- (Bundle, "Bundle"))
-
- reg.add_module(GetStringsFromBundle)
- reg.add_input_port(GetStringsFromBundle, 'p_string1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetStringsFromBundle, 'p_string2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetStringsFromBundle, 'p_string3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetStringsFromBundle, 'p_string4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetStringsFromBundle, 'p_string5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetStringsFromBundle, 'p_string6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetStringsFromBundle, 'p_string_selection',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(GetStringsFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetStringsFromBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_output_port(GetStringsFromBundle, 'string1',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(GetStringsFromBundle, 'string2',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(GetStringsFromBundle, 'string3',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(GetStringsFromBundle, 'string4',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(GetStringsFromBundle, 'string5',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(GetStringsFromBundle, 'string6',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(InsertColorMapsIntoBundle)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap1_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap2_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap3_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap4_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap5_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_colormap6_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace1',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace2',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace3',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace4',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace5',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_replace6',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'p_bundlename',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(InsertColorMapsIntoBundle, 'bundle',
- (Bundle, "Bundle"))
- reg.add_input_port(InsertColorMapsIntoBundle, 'colormap1',
- (ColorMap, "ColorMap"))
- reg.add_input_port(InsertColorMapsIntoBundle, 'colormap2',
- (ColorMap, "ColorMap"))
- reg.add_input_port(InsertColorMapsIntoBundle, 'colormap3',
- (ColorMap, "ColorMap"))
- reg.add_input_port(InsertColorMapsIntoBundle, 'colormap4',
- (ColorMap, "ColorMap"))
- reg.add_input_port(InsertColorMapsIntoBundle, 'colormap5',
- (ColorMap, "ColorMap"))
- reg.add_input_port(InsertColorMapsIntoBundle, 'colormap6',
- (ColorMap, "ColorMap"))
- reg.add_output_port(InsertColorMapsIntoBundle, 'bundle',
- (Bundle, "Bundle"))
-
- reg.add_module(CreateParameterBundle)
- reg.add_input_port(CreateParameterBundle, 'p_data',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateParameterBundle, 'p_new_field_count',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateParameterBundle, 'p_update_all',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_output_port(CreateParameterBundle, 'ParameterList',
- (Bundle, "Bundle"))
-
- reg.add_module(InsertEnvironmentIntoBundle)
- reg.add_output_port(InsertEnvironmentIntoBundle, 'Environment',
- (Bundle, "Bundle"))
-
- reg.add_module(ShowColorMap)
- reg.add_input_port(ShowColorMap, 'p_length',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowColorMap, 'p_side',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowColorMap, 'p_numlabels',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowColorMap, 'p_scale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowColorMap, 'p_numsigdigits',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowColorMap, 'p_units',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowColorMap, 'p_color_r',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowColorMap, 'p_color_g',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowColorMap, 'p_color_b',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowColorMap, 'p_text_fontsize',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowColorMap, 'p_extra_padding',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowColorMap, 'ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_output_port(ShowColorMap, 'Geometry',
- (Geometry, "Geometry"))
-
- reg.add_module(CreateAndEditColorMap2D)
- reg.add_input_port(CreateAndEditColorMap2D, 'p_histo',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateAndEditColorMap2D, 'p_selected_widget',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateAndEditColorMap2D, 'p_selected_object',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateAndEditColorMap2D, 'p_num_entries',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateAndEditColorMap2D, 'p_marker',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateAndEditColorMap2D, 'p_cm2view_targ',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateAndEditColorMap2D, 'p_id',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateAndEditColorMap2D, 'Input Colormap',
- (ColorMap2, "ColorMap2"))
- reg.add_input_port(CreateAndEditColorMap2D, 'Histogram',
- (Nrrd, "Nrrd"))
- reg.add_output_port(CreateAndEditColorMap2D, 'Output Colormap',
- (ColorMap2, "ColorMap2"))
-
- reg.add_module(ShowField)
- reg.add_input_port(ShowField, 'p_nodes_on',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_nodes_transparency',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_nodes_color_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_nodes_display_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowField, 'p_edges_on',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_edges_transparency',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_edges_color_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_edges_display_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowField, 'p_faces_on',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_faces_transparency',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_faces_color_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_faces_normals',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_faces_usetexture',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_on',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_color_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_color_r',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_color_g',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_color_b',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_backface_cull',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_always_visible',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_fontsize',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_precision',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_render_locations',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_show_data',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_show_nodes',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_show_edges',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_show_faces',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_text_show_cells',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_def_color_r',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowField, 'p_def_color_g',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowField, 'p_def_color_b',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowField, 'p_def_color_a',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowField, 'p_nodes_scale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowField, 'p_nodes_scaleNV',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowField, 'p_edges_scale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowField, 'p_edges_scaleNV',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowField, 'p_active_tab',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowField, 'p_interactive_mode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowField, 'p_show_progress',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_field_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowField, 'p_field_name_override',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_nodes_resolution',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_edges_resolution',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_approx_div',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'p_use_default_size',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowField, 'Mesh',
- (Field, "Field"))
- reg.add_input_port(ShowField, 'ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_output_port(ShowField, 'Scene Graph',
- (Geometry, "Geometry"))
-
- reg.add_module(ExtractIsosurface)
- reg.add_input_port(ExtractIsosurface, 'p_isoval_min',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_isoval_max',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_isoval',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_isoval_typed',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_isoval_quantity',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_quantity_range',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_quantity_clusive',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_quantity_min',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_quantity_max',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_quantity_list',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_isoval_list',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_matrix_list',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_algorithm',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_build_trisurf',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_build_geom',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_transparency',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_np',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_active_isoval_selection_tab',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_active_tab',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_update_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_color_r',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_color_g',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_color_b',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'p_color_a',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ExtractIsosurface, 'Field',
- (Field, "Field"))
- reg.add_input_port(ExtractIsosurface, 'Optional Color Map',
- (ColorMap, "ColorMap"))
- reg.add_input_port(ExtractIsosurface, 'Optional Isovalues',
- (Matrix, "Matrix"))
- reg.add_output_port(ExtractIsosurface, 'Surface',
- (Field, "Field"))
- reg.add_output_port(ExtractIsosurface, 'Geometry',
- (Geometry, "Geometry"))
- reg.add_output_port(ExtractIsosurface, 'Mapping',
- (Matrix, "Matrix"))
-
- reg.add_module(CreateViewerAxes)
- reg.add_input_port(CreateViewerAxes, 'p_precision',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_squash',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_valuerez',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_labelrez',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_divisions',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_offset',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_range_first',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_range_second',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_min_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_max_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_minplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_maxplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_lines',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_minticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_maxticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_minlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_maxlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_minvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_maxvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_width',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_tickangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_ticktilt',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_ticksize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_labelangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_labelheight',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_valuesize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_0_Axis_valuesquash',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_divisions',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_offset',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_range_first',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_range_second',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_min_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_max_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_minplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_maxplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_lines',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_minticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_maxticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_minlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_maxlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_minvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_maxvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_width',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_tickangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_ticktilt',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_ticksize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_labelangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_labelheight',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_valuesize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_01_1_Axis_valuesquash',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_divisions',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_offset',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_range_first',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_range_second',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_min_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_max_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_minplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_maxplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_lines',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_minticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_maxticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_minlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_maxlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_minvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_maxvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_width',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_tickangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_ticktilt',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_ticksize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_labelangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_labelheight',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_valuesize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_0_Axis_valuesquash',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_divisions',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_offset',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_range_first',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_range_second',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_min_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_max_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_minplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_maxplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_lines',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_minticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_maxticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_minlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_maxlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_minvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_maxvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_width',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_tickangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_ticktilt',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_ticksize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_labelangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_labelheight',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_valuesize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_02_2_Axis_valuesquash',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_divisions',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_offset',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_range_first',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_range_second',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_min_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_max_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_minplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_maxplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_lines',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_minticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_maxticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_minlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_maxlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_minvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_maxvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_width',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_tickangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_ticktilt',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_ticksize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_labelangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_labelheight',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_valuesize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_1_Axis_valuesquash',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_divisions',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_offset',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_range_first',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_range_second',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_min_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_max_absolute',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_minplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_maxplane',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_lines',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_minticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_maxticks',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_minlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_maxlabel',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_minvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_maxvalue',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_width',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_tickangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_ticktilt',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_ticksize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_labelangle',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_labelheight',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_valuesize',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'p_Plane_12_2_Axis_valuesquash',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerAxes, 'Field',
- (Field, "Field"))
- reg.add_output_port(CreateViewerAxes, 'Axes',
- (Geometry, "Geometry"))
-
- reg.add_module(RescaleColorMap)
- reg.add_input_port(RescaleColorMap, 'p_main_frame',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(RescaleColorMap, 'p_isFixed',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(RescaleColorMap, 'p_min',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(RescaleColorMap, 'p_max',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(RescaleColorMap, 'p_makeSymmetric',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(RescaleColorMap, 'ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_input_port(RescaleColorMap, 'Field',
- (Field, "Field"))
- reg.add_output_port(RescaleColorMap, 'ColorMap',
- (ColorMap, "ColorMap"))
-
- reg.add_module(ConvertNrrdsToTexture)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_vmin',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_vmax',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_gmin',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_gmax',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_mmin',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_mmax',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_is_fixed',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_card_mem',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_card_mem_auto',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_is_uchar',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_histogram',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'p_gamma',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertNrrdsToTexture, 'Value Nrrd',
- (Nrrd, "Nrrd"))
- reg.add_input_port(ConvertNrrdsToTexture, 'Gradient Magnitude Nrrd',
- (Nrrd, "Nrrd"))
- reg.add_output_port(ConvertNrrdsToTexture, 'Texture',
- (Texture, "Texture"))
- reg.add_output_port(ConvertNrrdsToTexture, 'JointHistoGram',
- (Nrrd, "Nrrd"))
-
- reg.add_module(ChooseColorMap)
- reg.add_input_port(ChooseColorMap, 'p_use_first_valid',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ChooseColorMap, 'p_port_valid_index',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ChooseColorMap, 'p_port_selected_index',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ChooseColorMap, 'ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_output_port(ChooseColorMap, 'ColorMap',
- (ColorMap, "ColorMap"))
-
- reg.add_module(CreateLightForViewer)
- reg.add_input_port(CreateLightForViewer, 'p_control_pos_saved',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateLightForViewer, 'p_control_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateLightForViewer, 'p_control_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateLightForViewer, 'p_control_z',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateLightForViewer, 'p_at_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateLightForViewer, 'p_at_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateLightForViewer, 'p_at_z',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateLightForViewer, 'p_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateLightForViewer, 'p_on',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_output_port(CreateLightForViewer, 'Geometry',
- (Geometry, "Geometry"))
-
- reg.add_module(ShowTextureVolume)
- reg.add_input_port(ShowTextureVolume, 'p_sampling_rate_hi',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_sampling_rate_lo',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_gradient_min',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_gradient_max',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_adaptive',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_cmap_size',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_sw_raster',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_render_style',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_alpha_scale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_interp_mode',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_shading',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_ambient',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_diffuse',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_specular',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_shine',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_light',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_blend_res',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_multi_level',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_use_stencil',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_invert_opacity',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_num_clipping_planes',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_show_clipping_widgets',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_level_on',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_level_vals',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'p_id',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowTextureVolume, 'Texture',
- (Texture, "Texture"))
- reg.add_input_port(ShowTextureVolume, 'ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_input_port(ShowTextureVolume, 'ColorMap2',
- (ColorMap2, "ColorMap2"))
- reg.add_output_port(ShowTextureVolume, 'Geometry',
- (Geometry, "Geometry"))
- reg.add_output_port(ShowTextureVolume, 'ColorMap',
- (ColorMap, "ColorMap"))
-
- reg.add_module(ShowFieldGlyphs)
- reg.add_input_port(ShowFieldGlyphs, 'p_scalars_has_data',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_scalars_on',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_scalars_display_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_scalars_transparency',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_scalars_normalize',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_scalars_color_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_scalars_resolution',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_vectors_has_data',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_vectors_on',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_vectors_display_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_vectors_transparency',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_vectors_normalize',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_vectors_bidirectional',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_vectors_color_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_vectors_resolution',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tensors_has_data',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tensors_on',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tensors_display_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tensors_transparency',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tensors_normalize',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tensors_color_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tensors_resolution',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tensors_emphasis',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_secondary_has_data',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_secondary_on',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_secondary_display_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_secondary_color_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_secondary_alpha',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_secondary_value',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_has_data',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_on',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_display_type',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_color_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_alpha',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_tertiary_value',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_on',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_color_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_color_r',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_color_g',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_color_b',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_backface_cull',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_always_visible',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_fontsize',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_precision',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_render_locations',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_show_data',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_show_nodes',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_show_edges',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_show_faces',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_text_show_cells',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_def_color_r',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_def_color_g',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_def_color_b',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_def_color_a',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_active_tab',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_interactive_mode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_show_progress',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_field_name',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_field_name_override',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_approx_div',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'p_use_default_size',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowFieldGlyphs, 'Primary Data',
- (Field, "Field"))
- reg.add_input_port(ShowFieldGlyphs, 'Primary ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_input_port(ShowFieldGlyphs, 'Secondary Data',
- (Field, "Field"))
- reg.add_input_port(ShowFieldGlyphs, 'Secondary ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_input_port(ShowFieldGlyphs, 'Tertiary Data',
- (Field, "Field"))
- reg.add_input_port(ShowFieldGlyphs, 'Tertiary ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_output_port(ShowFieldGlyphs, 'Scene Graph',
- (Geometry, "Geometry"))
-
- reg.add_module(GenerateStreamLines)
- reg.add_input_port(GenerateStreamLines, 'p_stepsize',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateStreamLines, 'p_tolerance',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateStreamLines, 'p_maxsteps',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLines, 'p_direction',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLines, 'p_value',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLines, 'p_remove_colinear_pts',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLines, 'p_method',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLines, 'p_nthreads',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLines, 'p_auto_parameterize',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLines, 'Vector Field',
- (Field, "Field"))
- reg.add_input_port(GenerateStreamLines, 'Seed Points',
- (Field, "Field"))
- reg.add_output_port(GenerateStreamLines, 'Streamlines',
- (Field, "Field"))
-
- reg.add_module(GenerateStreamLinesWithPlacementHeuristic)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_numsl',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_numpts',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_minper',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_maxper',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_ming',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_maxg',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_numsamples',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_method',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_stepsize',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_stepout',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_maxsteps',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_minmag',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'p_direction',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'Source',
- (Field, "Field"))
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'Weighting',
- (Field, "Field"))
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'Flow',
- (Field, "Field"))
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'Compare',
- (Field, "Field"))
- reg.add_input_port(GenerateStreamLinesWithPlacementHeuristic, 'Seed points',
- (Field, "Field"))
- reg.add_output_port(GenerateStreamLinesWithPlacementHeuristic, 'Streamlines',
- (Field, "Field"))
- reg.add_output_port(GenerateStreamLinesWithPlacementHeuristic, 'Render',
- (Field, "Field"))
-
- reg.add_module(ShowString)
- reg.add_input_port(ShowString, 'p_bbox',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowString, 'p_size',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowString, 'p_location_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowString, 'p_location_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowString, 'p_color_r',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowString, 'p_color_g',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowString, 'p_color_b',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowString, 'Format String',
- (core.modules.basic_modules.String, 'tip'))
- reg.add_output_port(ShowString, 'Title',
- (Geometry, "Geometry"))
-
- reg.add_module(CreateAndEditColorMap)
- reg.add_input_port(CreateAndEditColorMap, 'p_rgbhsv',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateAndEditColorMap, 'p_rgb_points',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateAndEditColorMap, 'p_alpha_points',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateAndEditColorMap, 'p_resolution',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateAndEditColorMap, 'ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_output_port(CreateAndEditColorMap, 'ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_output_port(CreateAndEditColorMap, 'Geometry',
- (Geometry, "Geometry"))
-
- reg.add_module(ShowMeshBoundingBox)
- reg.add_input_port(ShowMeshBoundingBox, 'p_sizex',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowMeshBoundingBox, 'p_sizey',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowMeshBoundingBox, 'p_sizez',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowMeshBoundingBox, 'Field',
- (Field, "Field"))
- reg.add_output_port(ShowMeshBoundingBox, 'Scene Graph',
- (Geometry, "Geometry"))
-
- reg.add_module(CreateStandardColorMaps)
- reg.add_input_port(CreateStandardColorMaps, 'p_mapName',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateStandardColorMaps, 'p_gamma',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateStandardColorMaps, 'p_resolution',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateStandardColorMaps, 'p_reverse',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateStandardColorMaps, 'p_faux',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateStandardColorMaps, 'p_positionList',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateStandardColorMaps, 'p_nodeList',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateStandardColorMaps, 'p_width',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateStandardColorMaps, 'p_height',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_output_port(CreateStandardColorMaps, 'ColorMap',
- (ColorMap, "ColorMap"))
-
- reg.add_module(ShowTextureSlices)
- reg.add_input_port(ShowTextureSlices, 'p_control_pos_saved',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_drawX',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_drawY',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_drawZ',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_drawView',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_interp_mode',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_draw_phi_0',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_draw_phi_1',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_phi_0',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_phi_1',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_multi_level',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_color_changed',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_colors',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_level_on',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_outline_levels',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'p_use_stencil',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowTextureSlices, 'Texture',
- (Texture, "Texture"))
- reg.add_input_port(ShowTextureSlices, 'ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_input_port(ShowTextureSlices, 'ColorMap2',
- (ColorMap2, "ColorMap2"))
- reg.add_output_port(ShowTextureSlices, 'Geometry',
- (Geometry, "Geometry"))
- reg.add_output_port(ShowTextureSlices, 'ColorMap',
- (ColorMap, "ColorMap"))
-
- reg.add_module(ShowMatrix)
- reg.add_input_port(ShowMatrix, 'p_xpos',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'p_ypos',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'p_xscale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'p_yscale',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'p_3d_mode',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'p_gmode',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'p_showtext',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'p_row_begin',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'p_rows',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'p_col_begin',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'p_cols',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'p_colormapmode',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ShowMatrix, 'ColorMap',
- (ColorMap, "ColorMap"))
- reg.add_input_port(ShowMatrix, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(ShowMatrix, 'Geometry',
- (Geometry, "Geometry"))
-
- reg.add_module(CreateViewerClockIcon)
- reg.add_input_port(CreateViewerClockIcon, 'p_type',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'p_bbox',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'p_format',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'p_min',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'p_max',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'p_current',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'p_size',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'p_location_x',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'p_location_y',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'p_color_r',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'p_color_g',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'p_color_b',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(CreateViewerClockIcon, 'Time Matrix',
- (Matrix, "Matrix"))
- reg.add_input_port(CreateViewerClockIcon, 'Time Nrrd',
- (Nrrd, "Nrrd"))
- reg.add_output_port(CreateViewerClockIcon, 'Clock',
- (Geometry, "Geometry"))
-
- reg.add_module(ConvertFieldsToTexture)
- reg.add_input_port(ConvertFieldsToTexture, 'p_vmin',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertFieldsToTexture, 'p_vmax',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertFieldsToTexture, 'p_gmin',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertFieldsToTexture, 'p_gmax',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertFieldsToTexture, 'p_is_fixed',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ConvertFieldsToTexture, 'p_card_mem',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ConvertFieldsToTexture, 'p_card_mem_auto',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ConvertFieldsToTexture, 'p_histogram',
- (core.modules.basic_modules.Integer, 'tip'), True)
- reg.add_input_port(ConvertFieldsToTexture, 'p_gamma',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_input_port(ConvertFieldsToTexture, 'Value Field',
- (Field, "Field"))
- reg.add_input_port(ConvertFieldsToTexture, 'Gradient Magnitude Field',
- (Field, "Field"))
- reg.add_output_port(ConvertFieldsToTexture, 'Texture',
- (Texture, "Texture"))
- reg.add_output_port(ConvertFieldsToTexture, 'JointHistoGram',
- (Nrrd, "Nrrd"))
-
- reg.add_module(ColorMap2DSemantics)
- reg.add_input_port(ColorMap2DSemantics, 'Input Colormap',
- (ColorMap2, "ColorMap2"))
- reg.add_output_port(ColorMap2DSemantics, 'Output Colormap',
- (ColorMap2, "ColorMap2"))
-
- reg.add_module(ConvertMatrixToString)
- reg.add_input_port(ConvertMatrixToString, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(ConvertMatrixToString, 'String',
- (core.modules.basic_modules.String, 'tip'))
-
- reg.add_module(ConvertMatrixToField)
- reg.add_input_port(ConvertMatrixToField, 'p_datalocation',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(ConvertMatrixToField, 'Matrix',
- (Matrix, "Matrix"))
- reg.add_output_port(ConvertMatrixToField, 'Field',
- (Field, "Field"))
-
- reg.add_module(TimeControls)
- reg.add_input_port(TimeControls, 'p_execmode',
- (core.modules.basic_modules.String, 'tip'), True)
- reg.add_input_port(TimeControls, 'p_scale_factor',
- (core.modules.basic_modules.Float, 'tip'), True)
- reg.add_output_port(TimeControls, 'time',
- (Time, "Time"))
-
-
-
- import viewercell
- viewercell.registerSelf()
- import cm2viewcell
- cm2viewcell.registerSelf()
-
-
-def package_dependencies():
- return ['edu.utah.sci.vistrails.spreadsheet']
-
-
-def finalize():
- sr_py.terminate()
- time.sleep(.5)
diff --git a/contrib/SCIRun/cm2viewcell.py b/contrib/SCIRun/cm2viewcell.py
deleted file mode 100644
index 7c19e29..0000000
--- a/contrib/SCIRun/cm2viewcell.py
+++ /dev/null
@@ -1,285 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-from PyQt4 import QtCore, QtGui, QtOpenGL
-import sip
-from core import system
-from core.modules.module_registry import registry
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
-import gc
-from gui.qt import qt_super
-from core.vistrail.action import Action
-from core.vistrail.port import Port
-from core.vistrail import module
-from core.vistrail import connection
-from core.vistrail.module_function import ModuleFunction
-from core.vistrail.module_param import ModuleParam
-from core.modules.vistrails_module import Module, ModuleError
-import db.services.action
-import copy
-import sr_py
-import time
-import uuid
-from renderbase import Render
-
-################################################################################
-class CM2ViewCell(Render):
- """
- CM2ViewCell is a VisTrails Module that can display SCIRun Viewer.
-
- """
- def compute(self):
- """ compute() -> None
- Dispatch the SCIRun scene graph to the Viewer
- """
- sg = self.forceGetInputListFromPort('ColorMap2')
- self.display(QCM2ViewWidget, (sg))
-
-
-
-class QCM2ViewWidget(QtOpenGL.QGLWidget) :
- """
- QCM2ViewWidget is the actual rendering widget that can display
- a SCIRun scene graph inside a Qt QWidget
-
- """
- def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
- """ QCM2ViewWidget(parent: QWidget, f: WindowFlags) -> QCM2ViewWidget
- Initialize QCM2ViewWidget.
- context
-
- """
- QtOpenGL.QGLWidget.__init__(self, parent)
-
- self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
- self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
- self.setMouseTracking(True)
- self.setFocusPolicy(QtCore.Qt.StrongFocus)
- self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
- QtGui.QSizePolicy.Expanding))
-
-
-
- self.sci_context = sr_py.CallbackOpenGLContext()
- self.sci_context.set_pymake_current_func(self.make_current)
- self.sci_context.set_pyswap_func(self.swap)
- self.sci_context.set_pywidth_func(self.get_width)
- self.sci_context.set_pyheight_func(self.get_height)
- self.sci_context.set_pyrelease_func(self.release)
- unique_id = uuid.uuid4()
- self._id = "sr_viewer_%s" % str(unique_id)
- #print self._id
- self.full_speed = False
- self.timer = QtCore.QTimer()
- self.connect(self.timer,
- QtCore.SIGNAL("timeout()"), self.updateGL)
-
- def make_current(self) :
- if self.isValid() :
- self.makeCurrent()
- return 1
- return 0
-
- def swap(self) :
- if self.isValid() :
- self.swapBuffers()
- return 1
- return 0
-
- def get_width(self) :
- if self.isValid() :
- w = self.width()
- return w
- return 0
-
- def get_height(self) :
- if self.isValid() :
- h = self.height()
- return h
- return 0
-
- def release(self) :
- #self.doneCurrent()
- pass
-
- def pointer_event(self, e, event) :
- e.set_x(event.x())
- e.set_y(event.y())
-
- mask = e.get_modifiers()
- mask = self.get_sr_py_modifier_mask(event, mask)
- e.set_modifiers(mask)
-
- state = e.get_pointer_state()
- state, n = self.get_sr_py_pointer_modifier_mask(event, state)
- e.set_pointer_state(state)
- sr_py.add_pointer_event(e, self._id)
-
- def get_sr_py_modifier_mask(self, event, mask) :
- if event.modifiers() & QtCore.Qt.ShiftModifier :
- mask |= sr_py.EventModifiers.SHIFT_E
- if event.modifiers() & QtCore.Qt.ControlModifier :
- mask |= sr_py.EventModifiers.CONTROL_E
- if event.modifiers() & QtCore.Qt.AltModifier :
- mask |= sr_py.EventModifiers.ALT_E
- if event.modifiers() & QtCore.Qt.MetaModifier :
- mask |= sr_py.EventModifiers.M1_E
- return mask
-
- def get_sr_py_pointer_modifier_mask(self, event, mask) :
- n = 0
-
- if event.buttons() & QtCore.Qt.LeftButton :
- mask |= sr_py.PointerEvent.BUTTON_1_E
- n = 1
- if event.buttons() & QtCore.Qt.MidButton :
- mask |= sr_py.PointerEvent.BUTTON_2_E
- n = 2
- if event.buttons() & QtCore.Qt.RightButton :
- mask |= sr_py.PointerEvent.BUTTON_3_E
- n = 3
- return mask, n
-
- def initializeGL(self):
- # create the viewer
- self.vid = sr_py.create_cm2view(self.sci_context, self._id)
- #start the timer
- #self.timer.start(33)
-
-## def paintGL(self):
-## #self.doneCurrent()
-## pass
-
- def glDraw(self):
- sr_py.update_cm2view(self.vid);
-
- if self.timer.isActive() and not self.full_speed :
- self.full_speed = True
- self.timer.start(55)
-
- if not self.timer.isActive() :
- self.timer.start(1000)
-
-
-
- def mousePressEvent(self, event):
- """ mousePressEvent(e: QMouseEvent) -> None
- Echo mouse event to SCIRun event system.
-
- """
- e = sr_py.PointerEvent()
- e.set_pointer_state(sr_py.PointerEvent.BUTTON_PRESS_E)
- self.pointer_event(e, event)
-
- def mouseReleaseEvent(self, event):
- """ mouseReleaseEvent(e: QEvent) -> None
- Echo mouse event to SCIRun event system.
-
- """
- e = sr_py.PointerEvent()
- #e.set_time(long(event.time))
- e.set_pointer_state(sr_py.PointerEvent.BUTTON_RELEASE_E)
- self.pointer_event(e, event)
-
- def mouseMoveEvent(self, event):
- """ mouseMoveEvent(e: QMouseEvent) -> None
- Echo mouse event to SCIRun event system.
-
- """
- e = sr_py.PointerEvent()
- #e.set_time(long(event.time))
- e.set_pointer_state(sr_py.PointerEvent.MOTION_E)
- self.pointer_event(e, event)
-
- def enterEvent(self,e):
- """ enterEvent(e: QEvent) -> None
-
- """
-
- def leaveEvent(self,e):
- """ leaveEvent(e: QEvent) -> None
-
- """
-
-
- def keyPressEvent(self, event):
- """ keyPressEvent(e: QKeyEvent) -> None
- Echo the key event to the SCIRun event system.
-
- """
-
- ascii_key = None
- if event.text().length()>0:
- ascii_key = event.text().toLatin1()[0]
- else:
- ascii_key = chr(0)
-
- #for now use native...
- keysym = event.nativeVirtualKey()
- e = sr_py.KeyEvent()
- #e.set_time(long(event.time))
- # translate qt modifiers to sci modifiers
- mask = e.get_modifiers()
- e.set_modifiers(self.get_sr_py_modifier_mask(event, mask))
- e.set_keyval(keysym)
- e.set_key_string(ascii_key)
- e.set_key_state(sr_py.KeyEvent.KEY_PRESS_E)
- sr_py.add_key_event(e, self._id)
-
-
- def keyReleaseEvent(self,e):
- """ keyReleaseEvent(e: QKeyEvent) -> None
-
- """
- #print "keyReleaseEvent"
-
- def wheelEvent(self,e):
- """ wheelEvent(e: QWheelEvent) -> None
- Zoom in/out while scrolling the mouse
-
- """
- print "wheelEvent"
-
- def updateContents(self, inputPorts):
- """ updateContents(inputPorts: tuple)
- Connects the input scene graph to this viewer
-
- """
-
-## p = inputPorts[0]
-## for i in p:
-## if i != 0 :
-## sr_py.send_scene(i, self._id);
-
-def registerSelf():
- """ registerSelf() -> None
- Registry module with the registry
- """
- identifier = "edu.utah.sci.vistrails.scirun"
-# registry.add_module(Render, abstract=True)
- registry.add_module(CM2ViewCell)
- registry.add_input_port(CM2ViewCell, "Location", CellLocation)
- registry.add_input_port(CM2ViewCell, "Scene Graph",
- registry.get_module_by_name(identifier,
- 'Geometry'),
- 'Scene Graph')
-
diff --git a/contrib/SCIRun/renderbase.py b/contrib/SCIRun/renderbase.py
deleted file mode 100644
index a4363f0..0000000
--- a/contrib/SCIRun/renderbase.py
+++ /dev/null
@@ -1,10 +0,0 @@
-from core import system
-from core.modules.module_registry import registry
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-
-class Render(SpreadsheetCell):
- def compute(self):
- pass
-
-def registerRender():
- registry.add_module(Render, abstract=True)
diff --git a/contrib/SCIRun/viewercell.py b/contrib/SCIRun/viewercell.py
deleted file mode 100644
index 0c4053b..0000000
--- a/contrib/SCIRun/viewercell.py
+++ /dev/null
@@ -1,289 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-from PyQt4 import QtCore, QtGui, QtOpenGL
-import sip
-from core import system
-from core.modules.module_registry import registry
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
-import gc
-from gui.qt import qt_super
-from core.vistrail.action import Action
-from core.vistrail.port import Port
-from core.vistrail import module
-from core.vistrail import connection
-from core.vistrail.module_function import ModuleFunction
-from core.vistrail.module_param import ModuleParam
-from core.modules.vistrails_module import Module, ModuleError
-import db.services.action
-import copy
-import sr_py
-import time
-import uuid
-from renderbase import Render, registerRender
-
-
-################################################################################
-class ViewerCell(Render):
- """
- ViewerCell is a VisTrails Module that can display SCIRun Viewer.
-
- """
- def compute(self):
- """ compute() -> None
- Dispatch the SCIRun scene graph to the Viewer
- """
- sg = self.forceGetInputListFromPort('Scene Graph')
- self.display(QViewerWidget, (sg))
-
-
-
-class QViewerWidget(QtOpenGL.QGLWidget) :
- """
- QViewerWidget is the actual rendering widget that can display
- a SCIRun scene graph inside a Qt QWidget
-
- """
- def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
- """ QViewerWidget(parent: QWidget, f: WindowFlags) -> QViewerWidget
- Initialize QViewerWidget.
- context
-
- """
- QtOpenGL.QGLWidget.__init__(self, parent)
-
- self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
- self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
- self.setMouseTracking(True)
- self.setFocusPolicy(QtCore.Qt.StrongFocus)
- self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
- QtGui.QSizePolicy.Expanding))
-
-
-
- self.sci_context = sr_py.CallbackOpenGLContext()
- self.sci_context.set_pymake_current_func(self.make_current)
- self.sci_context.set_pyswap_func(self.swap)
- self.sci_context.set_pywidth_func(self.get_width)
- self.sci_context.set_pyheight_func(self.get_height)
- self.sci_context.set_pyrelease_func(self.release)
- unique_id = uuid.uuid4()
- self._id = "sr_viewer_%s" % str(unique_id)
- #print self._id
- self.full_speed = False
- self.timer = QtCore.QTimer()
- self.connect(self.timer,
- QtCore.SIGNAL("timeout()"), self.updateGL)
-
- def make_current(self) :
- if self.isValid() :
- self.makeCurrent()
- return 1
- return 0
-
- def swap(self) :
- if self.isValid() :
- self.swapBuffers()
- return 1
- return 0
-
- def get_width(self) :
- if self.isValid() :
- w = self.width()
- return w
- return 0
-
- def get_height(self) :
- if self.isValid() :
- h = self.height()
- return h
- return 0
-
- def release(self) :
- #self.doneCurrent()
- pass
-
- def pointer_event(self, e, event) :
- e.set_x(event.x())
- e.set_y(event.y())
-
- mask = e.get_modifiers()
- mask = self.get_sr_py_modifier_mask(event, mask)
- e.set_modifiers(mask)
-
- state = e.get_pointer_state()
- state, n = self.get_sr_py_pointer_modifier_mask(event, state)
- e.set_pointer_state(state)
- sr_py.add_pointer_event(e, self._id)
-
- def get_sr_py_modifier_mask(self, event, mask) :
- if event.modifiers() & QtCore.Qt.ShiftModifier :
- mask |= sr_py.EventModifiers.SHIFT_E
- if event.modifiers() & QtCore.Qt.ControlModifier :
- mask |= sr_py.EventModifiers.CONTROL_E
- if event.modifiers() & QtCore.Qt.AltModifier :
- mask |= sr_py.EventModifiers.ALT_E
- if event.modifiers() & QtCore.Qt.MetaModifier :
- mask |= sr_py.EventModifiers.M1_E
- return mask
-
- def get_sr_py_pointer_modifier_mask(self, event, mask) :
- n = 0
-
- if event.buttons() & QtCore.Qt.LeftButton :
- mask |= sr_py.PointerEvent.BUTTON_1_E
- n = 1
- if event.buttons() & QtCore.Qt.MidButton :
- mask |= sr_py.PointerEvent.BUTTON_2_E
- n = 2
- if event.buttons() & QtCore.Qt.RightButton :
- mask |= sr_py.PointerEvent.BUTTON_3_E
- n = 3
- return mask, n
-
- def initializeGL(self):
- # create the viewer
- self.vid = sr_py.create_viewer(self.sci_context, self._id)
- #start the timer
- #self.timer.start(33)
-
-## def paintGL(self):
-## #self.doneCurrent()
-## pass
-
- def glDraw(self):
- sr_py.update_viewer(self.vid);
-
- if self.timer.isActive() and not self.full_speed :
- self.full_speed = True
- self.timer.start(55)
-
- if not self.timer.isActive() :
- self.timer.start(1000)
-
-
-
- def mousePressEvent(self, event):
- """ mousePressEvent(e: QMouseEvent) -> None
- Echo mouse event to SCIRun event system.
-
- """
- e = sr_py.PointerEvent()
- e.set_pointer_state(sr_py.PointerEvent.BUTTON_PRESS_E)
- self.pointer_event(e, event)
-
- def mouseReleaseEvent(self, event):
- """ mouseReleaseEvent(e: QEvent) -> None
- Echo mouse event to SCIRun event system.
-
- """
- e = sr_py.PointerEvent()
- #e.set_time(long(event.time))
- e.set_pointer_state(sr_py.PointerEvent.BUTTON_RELEASE_E)
- self.pointer_event(e, event)
-
- def mouseMoveEvent(self, event):
- """ mouseMoveEvent(e: QMouseEvent) -> None
- Echo mouse event to SCIRun event system.
-
- """
- e = sr_py.PointerEvent()
- #e.set_time(long(event.time))
- e.set_pointer_state(sr_py.PointerEvent.MOTION_E)
- self.pointer_event(e, event)
-
- def enterEvent(self,e):
- """ enterEvent(e: QEvent) -> None
-
- """
-
- def leaveEvent(self,e):
- """ leaveEvent(e: QEvent) -> None
-
- """
-
-
- def keyPressEvent(self, event):
- """ keyPressEvent(e: QKeyEvent) -> None
- Echo the key event to the SCIRun event system.
-
- """
-
- ascii_key = None
- if event.text().length()>0:
- ascii_key = event.text().toLatin1()[0]
- else:
- ascii_key = chr(0)
-
- #for now use native...
- keysym = event.nativeVirtualKey()
- e = sr_py.KeyEvent()
- #e.set_time(long(event.time))
- # translate qt modifiers to sci modifiers
- mask = e.get_modifiers()
- e.set_modifiers(self.get_sr_py_modifier_mask(event, mask))
- e.set_keyval(keysym)
- e.set_key_string(ascii_key)
- e.set_key_state(sr_py.KeyEvent.KEY_PRESS_E)
- sr_py.add_key_event(e, self._id)
-
-
- def keyReleaseEvent(self,e):
- """ keyReleaseEvent(e: QKeyEvent) -> None
-
- """
- #print "keyReleaseEvent"
-
- def wheelEvent(self,e):
- """ wheelEvent(e: QWheelEvent) -> None
- Zoom in/out while scrolling the mouse
-
- """
- print "wheelEvent"
-
- def updateContents(self, inputPorts):
- """ updateContents(inputPorts: tuple)
- Connects the input scene graph to this viewer
-
- """
- for p in inputPorts :
- try:
- for i in p:
- if i != 0 :
- print i
- sr_py.send_scene(i, self._id);
- except:
- if p != 0 :
- sr_py.send_scene(p, self._id);
-def registerSelf():
- """ registerSelf() -> None
- Registry module with the registry
- """
- identifier = "edu.utah.sci.vistrails.scirun"
- registerRender()
- registry.add_module(ViewerCell)
- registry.add_input_port(ViewerCell, "Location", CellLocation)
- registry.add_input_port(ViewerCell, "Scene Graph",
- registry.get_module_by_name(identifier,
- 'Geometry'),
- 'Scene Graph')
-
diff --git a/contrib/SciPy/DSP.py b/contrib/SciPy/DSP.py
deleted file mode 100644
index 7cf5c69..0000000
--- a/contrib/SciPy/DSP.py
+++ /dev/null
@@ -1,150 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from SciPy import SciPy
-from Matrix import *
-import scipy
-from scipy import sparse, fftpack
-import numpy
-
-#################################################################
-
-class DSP(SciPy):
- def compute(self):
- pass
-
-class FFT(DSP):
- def compute(self):
- mat = self.getInputFromPort("Signals")
- pts = self.getInputFromPort("FFT Samples")
-
- phasors = fftpack.fft(mat.matrix.data, pts)
- outmat = sparse.csc_matrix(phasors)
- out = SparseMatrix()
- out.matrix = outmat
- self.setResult("FFT Output", out)
-
-class FFT2(DSP):
- def compute(self):
- mat = self.getInputFromPort("Signals")
-
- phasors = fftpack.fftn(mat.matrix.data)
- outmat = sparse.csc_matrix(phasors)
- out = SparseMatrix()
- out.matrix = outmat
- self.setResult("FFT Output", out)
-
-class WindowedFourierTransform(DSP):
- def compute(self):
- mat = self.getInputFromPort("Signal")
-
- sr = self.getInputFromPort("Sampling Rate")
- if self.hasInputFromPort("Window Size"):
- window = self.getInputFromPort("Window Size")
- else:
- window = sr
-
- if self.hasInputFromPort("Stride"):
- stride = self.getInputFromPort("Stride")
- else:
- stride = int(sr / 2)
-
-
- signal_array = mat.matrix.toarray().ravel()
-
- # We now have a 1-D array that we can have good indexing into
- pad = signal_array[0:int(window/2)]
- signal_array = numpy.concatenate((pad,signal_array))
- win_low = 0
- win_hi = window - 1
- phasors = fftpack.fft(signal_array[win_low:win_hi])
- out_array = phasors.ravel()
-
- win_low += stride
- win_hi += stride
-
- while win_hi < signal_array.shape[0]:
- phasors = fftpack.fft(signal_array[win_low:win_hi])
- win_low += stride
- win_hi += stride
- out_array = numpy.vstack([out_array, phasors.ravel()])
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(out_array)
- self.setResult("FFT Output", out)
-
-class ShortTimeFourierTransform(DSP):
- def get_signal(self, sigs, window, offset, size):
- win = scipy.zeros(sigs.shape[0]).ravel()
- win[offset:offset+size] = window.ravel()
- part = sigs * win
- return part
-
- def compute(self):
- mat = self.getInputFromPort("Signal")
- sr = self.getInputFromPort("Sampling Rate")
-
- if self.hasInputFromPort("Window"):
- window = self.getInputFromPort("Window").matrix.toarray()
- win_size = window.shape[1]
- else:
- win_size = self.getInputFromPort("WindowSize")
- window = scipy.signal.hamming(win_size)
-
- if self.hasInputFromPort("Stride"):
- stride = self.getInputFromPort("Stride")
- else:
- stride = int(win_size / 2)
-
- signal_array = mat.matrix.transpose().toarray().ravel()
-
- samples = signal_array.shape[0]
-
- offset = 0
- sig = self.get_signal(signal_array, window, offset, win_size)
- phasors = fftpack.fft(sig).ravel()
- out_array = phasors
- offset += stride
-
- i = 1
- while 1:
- try:
- sig = self.get_signal(signal_array, window, offset, win_size)
- phasors = fftpack.fft(sig)
- offset += stride
- out_array = numpy.vstack([out_array, phasors.ravel()])
- i += 1
- except:
- break
-
- (slices, freqs) = out_array.shape
- ar = out_array[0:,0:sr*2]
- ar = ar[0:,::-1]
-
- out = SparseMatrix()
- sigout = SparseMatrix()
- sigout.matrix = sparse.csc_matrix(signal_array)
- out.matrix = sparse.csc_matrix(ar)
- self.setResult("Signal Output", sigout)
- self.setResult("FFT Output", out)
diff --git a/contrib/SciPy/Filters.py b/contrib/SciPy/Filters.py
deleted file mode 100644
index 9ddb308..0000000
--- a/contrib/SciPy/Filters.py
+++ /dev/null
@@ -1,118 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from SciPy import SciPy
-from Matrix import *
-import scipy
-import scipy.signal
-from scipy import sparse, fftpack
-import numpy
-
-class DSPFilters(SciPy):
- def compute(self):
- pass
-
-class HanningWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.hanning(size))
- self.setResult("Window", out)
-
-class TriangularWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.triang(size))
- self.setResult("Window", out)
-
-class BlackmanWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.blackman(size))
- self.setResult("Window", out)
-
-class BlackmanHarrisWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.blackmanharris(size))
- self.setResult("Window", out)
-
-class ParzenWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.parzen(size))
- self.setResult("Window", out)
-
-class HammingWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.hamming(size))
- self.setResult("Window", out)
-
-class KaiserWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- beta = self.getInputFromPort("Beta")
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.kaiser(size, beta))
- self.setResult("Window", out)
-
-class BartlettHannWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.barthann(size))
- self.setResult("Window", out)
-
-class GaussianWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
- sigma = self.getInputFromPort("Sigma")
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.gaussian(size, sigma))
- self.setResult("Window", out)
-
-class BoxcarWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.boxcar(size))
- self.setResult("Window", out)
-
-class BohmanWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.bohman(size))
- self.setResult("Window", out)
-
-class BartlettWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.bartlett(size))
- self.setResult("Window", out)
-
-class NuttallBlackmanHarrisWindow(DSPFilters):
- def compute(self):
- size = self.getInputFromPort("Window Size")
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.signal.nuttall(size))
- self.setResult("Window", out)
-
diff --git a/contrib/SciPy/MatlabReader.py b/contrib/SciPy/MatlabReader.py
deleted file mode 100644
index 38e2ced..0000000
--- a/contrib/SciPy/MatlabReader.py
+++ /dev/null
@@ -1,51 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from SciPy import SciPy
-from Matrix import *
-from scipy import io, sparse
-import numpy
-
-#######################################################################
-
-class MatlabReader(SciPy):
-
- def compute(self):
- if self.hasInputFromPort("Filename"):
- fname = self.getInputFromPort("Filename")
- else:
- fname = self.getInputFromPort("File").name
- self.readFileAsCSC(fname)
-
- def readFileAsCSC(self, filename):
- m = io.loadmat(filename, None, 0)
- vals = m.values()
- for t in vals:
- if type(t) == numpy.ndarray:
- mat = t
-
- cscmat = sparse.csr_matrix(mat)
- self.matrix = SparseMatrix()
- self.matrix.matrix = cscmat
- self.setResult("sparseoutput", self.matrix)
diff --git a/contrib/SciPy/Matrix.py b/contrib/SciPy/Matrix.py
deleted file mode 100644
index 9c4d9f4..0000000
--- a/contrib/SciPy/Matrix.py
+++ /dev/null
@@ -1,121 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from SciPy import SciPy
-
-from numpy import allclose, arange, eye, linalg, ones
-from scipy import linsolve, sparse
-
-#######################################################################
-class Matrix(SciPy):
-
- def setSize(self, size):
- pass
-
- def setMatrix(self, m):
- self.matrix = m
-
- def numElements(self):
- return self.matrix.getnnz()
-
- def maxNumElements(self):
- return self.matrix.nzmax
-
- def rows(self):
- return self.matrix.shape[0]
-
- def cols(self):
- return self.matrix.shape[1]
-
- def Reals(self):
- out = SparseMatrix()
- tmp = self.matrix.copy()
- out.matrix = tmp._real()
- return out
-
- def Imaginaries(self):
- out = SparseMatrix()
- tmp = self.matrix.copy()
- out.matrix = tmp._imag()
- return out
-
- def Conjugate(self):
- out = SparseMatrix()
- out.matrix = self.matrix.conjugate().copy()
- return out
-
- def GetRow(self, i):
- return self.matrix.getrow(i)
-
- def GetCol(self, i):
- return self.matrix.getcol(i)
-
-class SparseMatrix(Matrix):
-
- def setSize(self, size):
- self.matrix = sparse.csc_matrix((size, size))
- self.matrix.setdiag(ones(size))
-
-class DenseMatrix(Matrix):
-
- def setSize(self, size):
- self.matrix = sparse.csc_matrix((size, size))
- self.matrix.setdiag(ones(size))
- self.matrix.todense()
-
-
-class DOKMatrix(Matrix):
-
- def setSize(self, size):
- self.matrix = sparse.dok_matrix((size, size))
- self.matrix.setdiag(ones(size))
-
-class COOMatrix(Matrix):
-
- def __init__(self, mat):
- self.matrix=mat
-
- def setSize(self, size):
- self.matrix = sparse.coo_matrix((size, size))
- self.matrix.setdiag(ones(size))
-
-class CSRMatrix(Matrix):
-
- def __init__(self, mat):
- self.matrix=mat
-
- def setSize(self, size):
- self.matrix = sparse.csr_matrix((size, size))
- self.matrix.setdiag(ones(size))
-
-class LILMatrix(Matrix):
-
- def __init__(self, mat):
- self.matrix=mat
-
- def setSize(self, size):
- self.matrix = sparse.lil_matrix((size, size))
- self.matrix.setdiag(ones(size))
-
-#######################################################################
diff --git a/contrib/SciPy/MatrixConvert.py b/contrib/SciPy/MatrixConvert.py
deleted file mode 100644
index bacc865..0000000
--- a/contrib/SciPy/MatrixConvert.py
+++ /dev/null
@@ -1,150 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from SciPy import SciPy
-from Matrix import Matrix, COOMatrix, SparseMatrix, CSRMatrix
-from scipy import sparse
-import numpy, scipy
-
-class MatrixConvert(SciPy):
-
- def compute(self):
- m = self.getInputFromPort("InputMatrix")
- to = self.getInputFromPort("OutputType")
-
- to = to.upper()
- if to == 'Dense':
- self.matrix = DenseMatrix(m.matrix.todense())
- self.setResult("SparseOutput", self.matrix)
- else:
- self.matrix = SparseMatrix(m.matrix.tocsc())
- self.setResult("SparseOutput", self.matrix)
-
-class vtkDataSetToMatrix(SciPy):
- ''' In some cases, particularly in terms of user-defined VTK Filters, the
- output of the filter is a vtk datatype representing '''
-
- def from_unstructured_grid(self, vtkalgout):
- import vtk
- prod = vtkalgout.vtkInstance.GetProducer()
- prod.Update()
- grid = prod.GetOutput()
- pt_set = grid.GetPoints()
- scalars = grid.GetPointData().GetScalars()
-
- ''' Points in vtk are always 3D... so we must assume this. '''
- self.matrix_ = SparseMatrix()
- self.matrix_.matrix = sparse.csc_matrix((grid.GetNumberOfPoints(), 3))
-
- i = 0
- while i < grid.GetNumberOfPoints():
- (x,y,z) = pt_set.GetPoint(i)
- self.matrix_.matrix[i,0] = x
- self.matrix_.matrix[i,1] = y
- self.matrix_.matrix[i,2] = z
- print x, y, z
- i += 1
-
-
- def compute(self):
- if self.hasInputFromPort("vtkUnstructuredGrid"):
- self.from_unstructured_grid(self.getInputFromPort("vtkUnstructuredGrid"))
- else:
- pass
-
- self.setResult("Output Matrix", self.matrix_)
-
-class PhaseHistogramToVTKPoints(SciPy):
-
- def form_point_set(self, histo, point_set):
- (slices, numbins) = histo.shape
- phases = numpy.arange(numbins)
- phases = phases * (360. / numbins)
- phases += phases[1] / 2.
- phi_step = phases[0]
-
- for time in xrange(slices):
- z = float(time)
- for bin in xrange(numbins):
- r = histo[time,bin]
- theta = phi_step * (bin+1)
- theta *= (scipy.pi / 180.)
- x = r*scipy.cos(theta)
- y = r*scipy.sin(theta)
- point_set.InsertNextPoint(x, y, z)
-
- for bin in xrange(numbins):
- curbin = bin
- lastbin = bin-1
- if lastbin < 0:
- lastbin = numbins-1
-
- r = (histo[time,bin] - histo[time,lastbin]) / 2.
- theta = curbin * 360. / numbins
- x = r*scipy.cos(theta)
- y = r*scipy.sin(theta)
- point_set.InsertNextPoint(x, y, z)
-
-
- def compute(self):
- import vtk
-
- phasors = self.getInputFromPort("FFT Input")
- numbins = self.getInputFromPort("Num Bins")
- phasor_matrix = phasors.matrix.toarray()
- (timeslices,phases) = phasor_matrix.shape
-
- point_set = vtk.vtkPoints()
-
- histo = numpy.zeros((timeslices, numbins))
-
- for time in xrange(timeslices):
- phase_slice = phasor_matrix[time,:]
- reals = phase_slice.real
- imaginary = phase_slice.imag
- phases = scipy.arctan2(imaginary, reals)
- phases = phases * (180. / scipy.pi)
- bins = phases % numbins
- for b in bins:
- histo[time,b] += 1
-
- self.form_point_set(histo, point_set)
-
- pointdata = vtk.vtkUnstructuredGrid()
- pointdata.SetPoints(point_set)
-
- self.surf_filter = vtk.vtkSurfaceReconstructionFilter()
-
- self.surf_filter.SetInput(0,pointdata)
-# self.surf_filter.Update()
- reg = core.modules.module_registry
- vtk_set = reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkAlgorithmOutput').module()
- vtk_set.vtkInstance = self.surf_filter.GetOutputPort()
-
- histo_mat = SparseMatrix()
- histo_mat.matrix = sparse.csc_matrix(histo)
-
- self.setResult("Num Slices", timeslices)
- self.setResult("Phase Histogram", histo_mat)
- self.setResult("Phase Geometry", vtk_set)
diff --git a/contrib/SciPy/MatrixInfo.py b/contrib/SciPy/MatrixInfo.py
deleted file mode 100644
index 223e40c..0000000
--- a/contrib/SciPy/MatrixInfo.py
+++ /dev/null
@@ -1,45 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import core.modules
-from core.modules.vistrails_module import Module, ModuleError
-from SciPy import SciPy
-from Matrix import Matrix
-
-class MatrixInfo(SciPy):
-
- def getString(self, m):
- numrows = m.rows()
- numcols = m.cols()
- numel = m.numElements()
- maxel = m.maxNumElements()
-
- out = "Matrix Info:\n\tNumber of Rows: " + str(numrows) + \
- "\n\tNumber of Columns: " + str(numcols) + \
- "\n\tNumber of Elements: " + str(numel) + \
- "\n\tMaximum Number of Elements for compressed matrix: " + \
- str(maxel)
-
- return out
-
- def compute(self):
- m = self.getInputFromPort("InputMatrix")
- self.setResult("output", self.getString(m))
diff --git a/contrib/SciPy/MatrixOperations.py b/contrib/SciPy/MatrixOperations.py
deleted file mode 100644
index e18aebe..0000000
--- a/contrib/SciPy/MatrixOperations.py
+++ /dev/null
@@ -1,139 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import core.modules
-import core.modules.module_registry
-
-from core.modules.vistrails_module import Module, ModuleError
-from SciPy import SciPy
-from Matrix import *
-import math
-import scipy
-
-class MatrixOperation(SciPy):
- def compute(self):
- pass
-
-class GetReals(MatrixOperation):
- def compute(self):
- m = self.getInputFromPort("InputMatrix")
- self.setResult("OutputMatrix", m.Reals())
-
-class GetImaginaries(MatrixOperation):
- def compute(self):
- m = self.getInputFromPort("InputMatrix")
- self.setResult("OutputMatrix", m.Imaginaries())
-
-class Conjugate(MatrixOperation):
- def compute(self):
- m = self.getInputFromPort("InputMatrix")
- self.setResult("OutputMatrix", m.Conjugate())
-
-class GetRow(MatrixOperation):
- def compute(self):
- m = self.getInputFromPort("InputMatrix")
- c = self.getInputFromPort("RowIndex")
- row = m.GetRow(c)
- mat = SparseMatrix()
- mat.matrix = row
- self.setResult("OutputMatrix", mat)
-
-class GetCol(MatrixOperation):
- def compute(self):
- m = self.getInputFromPort("InputMatrix")
- c = self.getInputFromPort("ColIndex")
- col = m.GetCol(c)
- mat = SparseMatrix()
- mat.matrix = col
- self.setResult("OutputMatrix", mat)
-
-class MatrixMultiply(MatrixOperation):
- def compute(self):
- a = self.getInputFromPort("InputMatrix1")
- b = self.getInputFromPort("InputMatrix2")
- c = a.matrix * b.matrix
- out = SparseMatrix()
- out.matrix = c
- return out
-
-class ScalarMultiply(MatrixOperation):
- def compute(self):
- m = self.getInputFromPort("InputMatrix")
- s = self.getInputFromPort("Scalar")
- m.matrix = m.matrix * s
- self.setResult("OutputMatrix", m)
-
-class ElementMultiply(MatrixOperation):
- def compute(self):
- from numpy import array
- a = self.getInputFromPort("InputMatrix1")
- b = self.getInputFromPort("InputMatrix2")
- if a.matrix.shape != b.matrix.shape:
- raise ModuleError(self, 'Mismatching input dimensions!')
- c = SparseMatrix()
- c.matrix = sparse.csc_matrix(array(a.matrix.toarray())*array(b.matrix.toarray()))
- self.setResult("OutputMatrix", c)
-
-class Transpose(MatrixOperation):
- def compute(self):
- m = self.getInputFromPort("InputMatrix")
- m.matrix = m.matrix.transpose()
- self.setResult("OutputMatrix", m)
-
-class PrintMatrix(Matrix):
- def compute(self):
- m = self.getInputFromPort("InputMatrix")
- s = m.matrix.__str__()
- self.setResult("Output", s)
-
-class GetColumnRange(Matrix):
- def compute(self):
- m = self.getInputFromPort("InputMatrix")
- start = self.getInputFromPort("StartIndex")
- end = self.getInputFromPort("EndIndex")
- size = end - start
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix((m.matrix.shape[0], size))
-
- i = 0
- j = 0
- while j < m.matrix.shape[0]:
- while i < size:
- val = m.matrix[j,start+i]
- out.matrix[j,i] = val
- i = i + 1
- j = j + 1
-
- self.setResult("Output", out)
-
-class ATan2(MatrixOperation):
- def compute(self):
- if self.hasInputFromPort("InputMatrix"):
- m = self.getInputFromPort("InputMatrix")
- r = m.Reals().matrix
- im = m.Imaginaries().matrix
- else:
- r = self.getInputFromPort("RealMatrix").matrix
- im = self.getInputFromPort("ImaginaryMatrix").matrix
-
- out = SparseMatrix()
- out.matrix = sparse.csc_matrix(scipy.arctan2(im.toarray(),r.toarray()))
- self.setResult("Output", out)
diff --git a/contrib/SciPy/SciPy.py b/contrib/SciPy/SciPy.py
deleted file mode 100644
index 6ab54ea..0000000
--- a/contrib/SciPy/SciPy.py
+++ /dev/null
@@ -1,36 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-
-################################################################################
-
-class SciPy(Module):
- def compute(self):
- pass
-# def __init__(self):
-# Module.__init__(self)
-
- # The compute method is passed on as this is functioning only as a base class.
-
-################################################################################
diff --git a/contrib/SciPy/__init__.py b/contrib/SciPy/__init__.py
deleted file mode 100644
index ba18208..0000000
--- a/contrib/SciPy/__init__.py
+++ /dev/null
@@ -1,226 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from SciPy import SciPy
-from Matrix import *
-from MatlabReader import MatlabReader
-from MatrixInfo import MatrixInfo
-from MatrixConvert import *
-from MatrixOperations import *
-from DSP import *
-from Filters import *
-import core.modules.basic_modules
-
-version = '0.9.0'
-name = 'SciPy'
-identifier = 'edu.utah.sci.vistrails.scipy'
-
-##############################################################################
-
-from scipy import sparse
-
-def initialize(*args, **keywords):
- reg = core.modules.module_registry.get_module_registry()
- basic = core.modules.basic_modules
-
- reg.add_module(SciPy)
- reg.add_module(Matrix)
- reg.add_module(MatrixOperation)
- reg.add_module(DSP)
- reg.add_module(DSPFilters, name="DSP Window Filters")
-
- reg.add_module(SparseMatrix)
- reg.add_input_port(SparseMatrix, "size", (basic.Integer, 'Matrix Size'))
- reg.add_output_port(SparseMatrix, "output", (SparseMatrix, 'Output Matrix'))
-
- reg.add_module(HanningWindow)
- reg.add_input_port(HanningWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(HanningWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(TriangularWindow)
- reg.add_input_port(TriangularWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(TriangularWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(BlackmanWindow)
- reg.add_input_port(BlackmanWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(BlackmanWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(BlackmanHarrisWindow)
- reg.add_input_port(BlackmanHarrisWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(BlackmanHarrisWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(ParzenWindow)
- reg.add_input_port(ParzenWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(ParzenWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(HammingWindow)
- reg.add_input_port(HammingWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(HammingWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(KaiserWindow)
- reg.add_input_port(KaiserWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_input_port(KaiserWindow, "Beta", (basic.Float, 'Beta'))
- reg.add_output_port(KaiserWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(BartlettHannWindow)
- reg.add_input_port(BartlettHannWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(BartlettHannWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(GaussianWindow)
- reg.add_input_port(GaussianWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_input_port(GaussianWindow, "Sigma", (basic.Integer, 'Sigma (Std. Deviation)'))
- reg.add_output_port(GaussianWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(BoxcarWindow)
- reg.add_input_port(BoxcarWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(BoxcarWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(BohmanWindow)
- reg.add_input_port(BohmanWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(BohmanWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(BartlettWindow)
- reg.add_input_port(BartlettWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(BartlettWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(NuttallBlackmanHarrisWindow)
- reg.add_input_port(NuttallBlackmanHarrisWindow, "Window Size", (basic.Integer, 'Window Size'))
- reg.add_output_port(NuttallBlackmanHarrisWindow, "Window", (SparseMatrix, 'Window'))
-
- reg.add_module(PrintMatrix)
- reg.add_input_port(PrintMatrix, "InputMatrix", (Matrix, 'Matrix'))
- reg.add_output_port(PrintMatrix, "Output", (basic.String, 'Output String'))
-
- reg.add_module(MatrixConvert)
- reg.add_input_port(MatrixConvert, "InputMatrix", (Matrix, 'Matrix'))
- reg.add_input_port(MatrixConvert, "OutputType", (basic.String, 'Output Type'))
- reg.add_output_port(MatrixConvert, "SparseOutput", (SparseMatrix, 'Output Sparse Matrix'))
-# reg.add_output_port(MatrixConvert, "COOOutput", (COOMatrix, 'Output COO Matrix'))
-# reg.add_output_port(MatrixConvert, "CSCOutput", (CSCMatrix, 'Output CSC Matrix'))
-
- reg.add_module(MatlabReader)
- reg.add_input_port(MatlabReader, "Filename", (basic.String, 'Filename'))
- reg.add_output_port(MatlabReader, "sparseoutput", (SparseMatrix, 'Output Sparse Matrix'))
- reg.add_input_port(MatlabReader, "File", (basic.File, 'File'))
-
- reg.add_module(MatrixInfo)
- reg.add_input_port(MatrixInfo, "InputMatrix", (Matrix, 'Matrix'))
- reg.add_output_port(MatrixInfo, "output", (basic.String, 'Output String'))
-
- reg.add_module(GetReals)
- reg.add_input_port(GetReals, "InputMatrix", (SparseMatrix, 'Input Matrix'))
- reg.add_output_port(GetReals, "OutputMatrix", (SparseMatrix, 'Result'))
-
- reg.add_module(GetImaginaries)
- reg.add_input_port(GetImaginaries, "InputMatrix", (SparseMatrix, 'Input Matrix'))
- reg.add_output_port(GetImaginaries, "OutputMatrix", (SparseMatrix, 'Result'))
-
- reg.add_module(Conjugate)
- reg.add_input_port(Conjugate, "InputMatrix", (SparseMatrix, 'Input Matrix'))
- reg.add_output_port(Conjugate, "OutputMatrix", (SparseMatrix, 'Result'))
-
- reg.add_module(GetRow)
- reg.add_input_port(GetRow, "InputMatrix", (Matrix, 'Input Matrix'))
- reg.add_input_port(GetRow, "RowIndex", (basic.Integer, 'Row Index'))
- reg.add_output_port(GetRow, "OutputMatrix", (SparseMatrix, 'Result'))
-
- reg.add_module(GetCol)
- reg.add_input_port(GetCol, "InputMatrix", (Matrix, 'Input Matrix'))
- reg.add_input_port(GetCol, "ColIndex", (basic.Integer, 'Col Index'))
- reg.add_output_port(GetCol, "OutputMatrix", (SparseMatrix, 'Result'))
-
- reg.add_module(GetColumnRange)
- reg.add_input_port(GetColumnRange, "InputMatrix", (SparseMatrix, 'Input Matrix'))
- reg.add_input_port(GetColumnRange, "StartIndex", (basic.Integer, 'Start Index'))
- reg.add_input_port(GetColumnRange, "EndIndex", (basic.Integer, 'End Index'))
- reg.add_output_port(GetColumnRange, "Output", (SparseMatrix, 'Result'))
-
- reg.add_module(ScalarMultiply)
- reg.add_input_port(ScalarMultiply, "InputMatrix", (Matrix, 'Input Matrix'))
- reg.add_input_port(ScalarMultiply, "Scalar", (basic.Float, 'Scalar'))
- reg.add_output_port(ScalarMultiply, "OutputMatrix", (SparseMatrix, 'Result'))
-
- reg.add_module(Transpose)
- reg.add_input_port(Transpose, "InputMatrix", (Matrix, 'Input Matrix'))
- reg.add_output_port(Transpose, "OutputMatrix", (Matrix, 'Output Matrix'))
-
- reg.add_module(MatrixMultiply)
- reg.add_input_port(MatrixMultiply, "InputMatrix1", (Matrix, 'Input Matrix 1'))
- reg.add_input_port(MatrixMultiply, "InputMatrix2", (Matrix, 'Input Matrix 2'))
- reg.add_output_port(MatrixMultiply, "OutputMatrix", (Matrix, 'Output Matrix'))
-
- reg.add_module(ElementMultiply)
- reg.add_input_port(ElementMultiply, "InputMatrix1", (Matrix, 'Input Matrix 1'))
- reg.add_input_port(ElementMultiply, "InputMatrix2", (Matrix, 'Input Matrix 2'))
- reg.add_output_port(ElementMultiply, "OutputMatrix", (SparseMatrix, 'Output Matrix'))
-
- reg.add_module(ATan2)
- reg.add_input_port(ATan2, "InputMatrix", (SparseMatrix, 'Complex Matrix'))
- reg.add_input_port(ATan2, "RealMatrix", (SparseMatrix, 'Real Matrix'), True)
- reg.add_input_port(ATan2, "ImaginaryMatrix", (SparseMatrix, 'Imaginary Matrix'), True)
- reg.add_output_port(ATan2, "Output", (SparseMatrix, 'Output Matrix'))
-
- reg.add_module(FFT)
- reg.add_input_port(FFT, "Signals", (Matrix, 'Input Signal Matrix'))
- reg.add_input_port(FFT, "FFT Samples", (basic.Integer, 'FFT Samples'))
- reg.add_output_port(FFT, "FFT Output", (SparseMatrix, 'FFT Output'))
-
- reg.add_module(FFT2)
- reg.add_input_port(FFT2, "Signals", (Matrix, 'Input Signal Matrix'))
- reg.add_output_port(FFT2, "FFT Output", (SparseMatrix, 'FFT Output'))
-
- reg.add_module(WindowedFourierTransform)
- reg.add_input_port(WindowedFourierTransform, "Signal", (Matrix, 'Input Signal'))
- reg.add_input_port(WindowedFourierTransform, "Sampling Rate", (basic.Integer, 'Sampling Rate'))
- reg.add_input_port(WindowedFourierTransform, "Window Size", (basic.Integer, 'Window Size'), True)
- reg.add_input_port(WindowedFourierTransform, "Stride", (basic.Integer, 'Window Stride'), True)
- reg.add_output_port(WindowedFourierTransform, "FFT Output", (SparseMatrix, 'FFT Output'))
-
- reg.add_module(ShortTimeFourierTransform)
- reg.add_input_port(ShortTimeFourierTransform, "Signal", (Matrix, 'Input Signal'))
- reg.add_input_port(ShortTimeFourierTransform, "Sampling Rate", (basic.Integer, 'Sampling Rate'))
- reg.add_input_port(ShortTimeFourierTransform, "Stride", (basic.Integer, 'Window Stride'))
- reg.add_input_port(ShortTimeFourierTransform, "Window", (Matrix, 'Window Function'), True)
- reg.add_input_port(ShortTimeFourierTransform, "WindowSize", (basic.Integer, 'Window Size'))
- reg.add_output_port(ShortTimeFourierTransform, "FFT Output", (SparseMatrix, 'FFT Output'))
- reg.add_output_port(ShortTimeFourierTransform, "Signal Output", (SparseMatrix, 'Signal Output'), True)
-
- reg.add_module(vtkDataSetToMatrix)
- reg.add_input_port(vtkDataSetToMatrix, "vtkUnstructuredGrid", (reg.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkAlgorithmOutput').module, 'Input Unstructured Grid'))
- reg.add_output_port(vtkDataSetToMatrix, "Output Matrix", (SparseMatrix, 'Output Matrix'))
-
- reg.add_module(PhaseHistogramToVTKPoints)
- reg.add_input_port(PhaseHistogramToVTKPoints, "FFT Input", (SparseMatrix, 'FFT Input'))
- reg.add_input_port(PhaseHistogramToVTKPoints, "Num Bins", (basic.Integer, 'Number of Phase Bins'))
- reg.add_output_port(PhaseHistogramToVTKPoints, "Num Slices", (basic.Integer, 'Number of Histogram Timeslices'), True)
- reg.add_output_port(PhaseHistogramToVTKPoints, "Phase Histogram", (SparseMatrix, 'Phase Histogram'), True)
- reg.add_output_port(PhaseHistogramToVTKPoints, "Phase Geometry", (reg.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkAlgorithmOutput').module, 'Phase Geometry Connection'))
-
-def package_dependencies():
- import core.packagemanager
- manager = core.packagemanager.get_package_manager()
- if manager.has_package('edu.utah.sci.vistrails.vtk'):
- return ['edu.utah.sci.vistrails.vtk']
- else:
- return []
diff --git a/contrib/TetGenBridge/CreateTestSurf.py b/contrib/TetGenBridge/CreateTestSurf.py
deleted file mode 100644
index 6a5f356..0000000
--- a/contrib/TetGenBridge/CreateTestSurf.py
+++ /dev/null
@@ -1,102 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-import packages.TetGenBridge
-import TetGen
-import re
-import os
-
-# TetGen output on this mesh. -pqAz
-## Statistics:
-
-## Input points: 149
-## Input facets: 294
-## Input holes: 0
-## Input regions: 0
-
-## Mesh points: 2184
-## Mesh tetrahedra: 7462
-## Mesh faces: 16726
-## Mesh subfaces: 3604
-## Mesh subsegments: 2037
-
-nodes_exp = re.compile('([\d\-\.]+)\s+([\d\-\.]+)\s+([\d\-\.]+)')
-def getTestNodes() :
- nodes = []
- p = "%spackages%sTetGenBridge%s" % (os.sep, os.sep, os.sep)
- f = open('%s%spill.nodes' % (os.getcwd(), p))
- for l in f.readlines() :
- mo = nodes_exp.match(l)
- if mo != None :
- nodes.append((float(mo.group(1)), float(mo.group(2)),
- float(mo.group(3))))
- return nodes
-
-tris_exp = re.compile('(\d+)\s+(\d+)\s+(\d+)')
-def getTestTris() :
- tris = []
- p = "%spackages%sTetGenBridge%s" % (os.sep, os.sep, os.sep)
- f = open('%s%spill.tri' % (os.getcwd(), p))
- for l in f.readlines() :
- mo = tris_exp.match(l)
- if mo != None :
- tris.append((int(mo.group(1)), int(mo.group(2)),
- int(mo.group(3))))
- return tris
-
-def addSurfaceInfo(tgio, marker = 0) :
-
- #iterate over nodes and add the points.
- nodes = getTestNodes()
- sz = len(nodes)
- tgio.pointlist = TetGen.allocate_array(sz * 3)
- tgio.numberofpoints = sz
- idx = 0
- for n in nodes :
- TetGen.set_val(tgio.pointlist, idx * 3, n[0])
- TetGen.set_val(tgio.pointlist, idx * 3 + 1, n[1])
- TetGen.set_val(tgio.pointlist, idx * 3 + 2, n[2])
- idx = idx + 1
-
- #iterate over faces and add the facets.
- tris = getTestTris()
- fsz = len(tris)
- tgio.facetlist = TetGen.allocate_facet_array(fsz)
- tgio.numberoffacets = fsz;
- idx = 0
- for t in tris :
- TetGen.add_tri(tgio.facetlist, idx, t[0], t[1], t[2])
- idx = idx + 1
-
-class CreateTestSurf(Module):
- def compute(self):
- out = packages.TetGenBridge.tetgenio_wrapper()
- addSurfaceInfo(out.data, 0)
- self.setResult("tgio out", out)
-
-def initialize(reg):
- reg.add_module(CreateTestSurf)
- reg.add_output_port(CreateTestSurf, "tgio out",
- (packages.TetGenBridge.tetgenio_wrapper,
- 'output test surface'))
diff --git a/contrib/TetGenBridge/Makefile b/contrib/TetGenBridge/Makefile
deleted file mode 100644
index 6ed25f4..0000000
--- a/contrib/TetGenBridge/Makefile
+++ /dev/null
@@ -1,19 +0,0 @@
-SRCS := tetgen_wrap.cc
-
-INCLUDES := -I/usr/include/python2.4 -I/scratch/mjc/tetgen-dev
-
-CC := g++
-CXXFLAGS := -fPIC
-LIBS := -lpython2.4 -ltet
-
-%.o :: %.cc
- $(CC) $(CXXFLAGS) -c -o $@ $(INCLUDES) $<
-
-
-_TetGen.so: tetgen_wrap.o
- $(CC) $(CXXFLAGS) -shared -o _TetGen.so tetgen_wrap.o $(INCLUDES) -L . $(LIBS)
-
-tetgen_wrap.cc:tetgen.i
- swig -v -o tetgen_wrap.cc $(INCLUDES) -python -c++ tetgen.i
-
-
diff --git a/contrib/TetGenBridge/TetGen.py b/contrib/TetGenBridge/TetGen.py
deleted file mode 100644
index 8794b17..0000000
--- a/contrib/TetGenBridge/TetGen.py
+++ /dev/null
@@ -1,313 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-# This file was created automatically by SWIG 1.3.27.
-# Don't modify this file, modify the SWIG interface instead.
-
-import _TetGen
-
-# This file is compatible with both classic and new-style classes.
-def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
- if (name == "this"):
- if isinstance(value, class_type):
- self.__dict__[name] = value.this
- if hasattr(value,"thisown"): self.__dict__["thisown"] = value.thisown
- del value.thisown
- return
- method = class_type.__swig_setmethods__.get(name,None)
- if method: return method(self,value)
- if (not static) or hasattr(self,name) or (name == "thisown"):
- self.__dict__[name] = value
- else:
- raise AttributeError("You cannot add attributes to %s" % self)
-
-def _swig_setattr(self,class_type,name,value):
- return _swig_setattr_nondynamic(self,class_type,name,value,0)
-
-def _swig_getattr(self,class_type,name):
- method = class_type.__swig_getmethods__.get(name,None)
- if method: return method(self)
- raise AttributeError,name
-
-import types
-try:
- _object = types.ObjectType
- _newclass = 1
-except AttributeError:
- class _object : pass
- _newclass = 0
-del types
-
-
-class tetgenio(_object):
- __swig_setmethods__ = {}
- __setattr__ = lambda self, name, value: _swig_setattr(self, tetgenio, name, value)
- __swig_getmethods__ = {}
- __getattr__ = lambda self, name: _swig_getattr(self, tetgenio, name)
- def __repr__(self):
- return "<%s.%s; proxy of C++ tetgenio instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
- FILENAMESIZE = _TetGen.tetgenio_FILENAMESIZE
- INPUTLINESIZE = _TetGen.tetgenio_INPUTLINESIZE
- __swig_getmethods__["init"] = lambda x: _TetGen.tetgenio_init
- if _newclass:init = staticmethod(_TetGen.tetgenio_init)
- __swig_setmethods__["firstnumber"] = _TetGen.tetgenio_firstnumber_set
- __swig_getmethods__["firstnumber"] = _TetGen.tetgenio_firstnumber_get
- if _newclass:firstnumber = property(_TetGen.tetgenio_firstnumber_get, _TetGen.tetgenio_firstnumber_set)
- __swig_setmethods__["mesh_dim"] = _TetGen.tetgenio_mesh_dim_set
- __swig_getmethods__["mesh_dim"] = _TetGen.tetgenio_mesh_dim_get
- if _newclass:mesh_dim = property(_TetGen.tetgenio_mesh_dim_get, _TetGen.tetgenio_mesh_dim_set)
- __swig_setmethods__["pointlist"] = _TetGen.tetgenio_pointlist_set
- __swig_getmethods__["pointlist"] = _TetGen.tetgenio_pointlist_get
- if _newclass:pointlist = property(_TetGen.tetgenio_pointlist_get, _TetGen.tetgenio_pointlist_set)
- __swig_setmethods__["pointattributelist"] = _TetGen.tetgenio_pointattributelist_set
- __swig_getmethods__["pointattributelist"] = _TetGen.tetgenio_pointattributelist_get
- if _newclass:pointattributelist = property(_TetGen.tetgenio_pointattributelist_get, _TetGen.tetgenio_pointattributelist_set)
- __swig_setmethods__["addpointlist"] = _TetGen.tetgenio_addpointlist_set
- __swig_getmethods__["addpointlist"] = _TetGen.tetgenio_addpointlist_get
- if _newclass:addpointlist = property(_TetGen.tetgenio_addpointlist_get, _TetGen.tetgenio_addpointlist_set)
- __swig_setmethods__["addpointattributelist"] = _TetGen.tetgenio_addpointattributelist_set
- __swig_getmethods__["addpointattributelist"] = _TetGen.tetgenio_addpointattributelist_get
- if _newclass:addpointattributelist = property(_TetGen.tetgenio_addpointattributelist_get, _TetGen.tetgenio_addpointattributelist_set)
- __swig_setmethods__["pointmarkerlist"] = _TetGen.tetgenio_pointmarkerlist_set
- __swig_getmethods__["pointmarkerlist"] = _TetGen.tetgenio_pointmarkerlist_get
- if _newclass:pointmarkerlist = property(_TetGen.tetgenio_pointmarkerlist_get, _TetGen.tetgenio_pointmarkerlist_set)
- __swig_setmethods__["numberofpoints"] = _TetGen.tetgenio_numberofpoints_set
- __swig_getmethods__["numberofpoints"] = _TetGen.tetgenio_numberofpoints_get
- if _newclass:numberofpoints = property(_TetGen.tetgenio_numberofpoints_get, _TetGen.tetgenio_numberofpoints_set)
- __swig_setmethods__["numberofpointattributes"] = _TetGen.tetgenio_numberofpointattributes_set
- __swig_getmethods__["numberofpointattributes"] = _TetGen.tetgenio_numberofpointattributes_get
- if _newclass:numberofpointattributes = property(_TetGen.tetgenio_numberofpointattributes_get, _TetGen.tetgenio_numberofpointattributes_set)
- __swig_setmethods__["numberofaddpoints"] = _TetGen.tetgenio_numberofaddpoints_set
- __swig_getmethods__["numberofaddpoints"] = _TetGen.tetgenio_numberofaddpoints_get
- if _newclass:numberofaddpoints = property(_TetGen.tetgenio_numberofaddpoints_get, _TetGen.tetgenio_numberofaddpoints_set)
- __swig_setmethods__["tetrahedronlist"] = _TetGen.tetgenio_tetrahedronlist_set
- __swig_getmethods__["tetrahedronlist"] = _TetGen.tetgenio_tetrahedronlist_get
- if _newclass:tetrahedronlist = property(_TetGen.tetgenio_tetrahedronlist_get, _TetGen.tetgenio_tetrahedronlist_set)
- __swig_setmethods__["tetrahedronattributelist"] = _TetGen.tetgenio_tetrahedronattributelist_set
- __swig_getmethods__["tetrahedronattributelist"] = _TetGen.tetgenio_tetrahedronattributelist_get
- if _newclass:tetrahedronattributelist = property(_TetGen.tetgenio_tetrahedronattributelist_get, _TetGen.tetgenio_tetrahedronattributelist_set)
- __swig_setmethods__["tetrahedronvolumelist"] = _TetGen.tetgenio_tetrahedronvolumelist_set
- __swig_getmethods__["tetrahedronvolumelist"] = _TetGen.tetgenio_tetrahedronvolumelist_get
- if _newclass:tetrahedronvolumelist = property(_TetGen.tetgenio_tetrahedronvolumelist_get, _TetGen.tetgenio_tetrahedronvolumelist_set)
- __swig_setmethods__["neighborlist"] = _TetGen.tetgenio_neighborlist_set
- __swig_getmethods__["neighborlist"] = _TetGen.tetgenio_neighborlist_get
- if _newclass:neighborlist = property(_TetGen.tetgenio_neighborlist_get, _TetGen.tetgenio_neighborlist_set)
- __swig_setmethods__["numberoftetrahedra"] = _TetGen.tetgenio_numberoftetrahedra_set
- __swig_getmethods__["numberoftetrahedra"] = _TetGen.tetgenio_numberoftetrahedra_get
- if _newclass:numberoftetrahedra = property(_TetGen.tetgenio_numberoftetrahedra_get, _TetGen.tetgenio_numberoftetrahedra_set)
- __swig_setmethods__["numberofcorners"] = _TetGen.tetgenio_numberofcorners_set
- __swig_getmethods__["numberofcorners"] = _TetGen.tetgenio_numberofcorners_get
- if _newclass:numberofcorners = property(_TetGen.tetgenio_numberofcorners_get, _TetGen.tetgenio_numberofcorners_set)
- __swig_setmethods__["numberoftetrahedronattributes"] = _TetGen.tetgenio_numberoftetrahedronattributes_set
- __swig_getmethods__["numberoftetrahedronattributes"] = _TetGen.tetgenio_numberoftetrahedronattributes_get
- if _newclass:numberoftetrahedronattributes = property(_TetGen.tetgenio_numberoftetrahedronattributes_get, _TetGen.tetgenio_numberoftetrahedronattributes_set)
- __swig_setmethods__["facetlist"] = _TetGen.tetgenio_facetlist_set
- __swig_getmethods__["facetlist"] = _TetGen.tetgenio_facetlist_get
- if _newclass:facetlist = property(_TetGen.tetgenio_facetlist_get, _TetGen.tetgenio_facetlist_set)
- __swig_setmethods__["facetmarkerlist"] = _TetGen.tetgenio_facetmarkerlist_set
- __swig_getmethods__["facetmarkerlist"] = _TetGen.tetgenio_facetmarkerlist_get
- if _newclass:facetmarkerlist = property(_TetGen.tetgenio_facetmarkerlist_get, _TetGen.tetgenio_facetmarkerlist_set)
- __swig_setmethods__["numberoffacets"] = _TetGen.tetgenio_numberoffacets_set
- __swig_getmethods__["numberoffacets"] = _TetGen.tetgenio_numberoffacets_get
- if _newclass:numberoffacets = property(_TetGen.tetgenio_numberoffacets_get, _TetGen.tetgenio_numberoffacets_set)
- __swig_setmethods__["holelist"] = _TetGen.tetgenio_holelist_set
- __swig_getmethods__["holelist"] = _TetGen.tetgenio_holelist_get
- if _newclass:holelist = property(_TetGen.tetgenio_holelist_get, _TetGen.tetgenio_holelist_set)
- __swig_setmethods__["numberofholes"] = _TetGen.tetgenio_numberofholes_set
- __swig_getmethods__["numberofholes"] = _TetGen.tetgenio_numberofholes_get
- if _newclass:numberofholes = property(_TetGen.tetgenio_numberofholes_get, _TetGen.tetgenio_numberofholes_set)
- __swig_setmethods__["regionlist"] = _TetGen.tetgenio_regionlist_set
- __swig_getmethods__["regionlist"] = _TetGen.tetgenio_regionlist_get
- if _newclass:regionlist = property(_TetGen.tetgenio_regionlist_get, _TetGen.tetgenio_regionlist_set)
- __swig_setmethods__["numberofregions"] = _TetGen.tetgenio_numberofregions_set
- __swig_getmethods__["numberofregions"] = _TetGen.tetgenio_numberofregions_get
- if _newclass:numberofregions = property(_TetGen.tetgenio_numberofregions_get, _TetGen.tetgenio_numberofregions_set)
- __swig_setmethods__["facetconstraintlist"] = _TetGen.tetgenio_facetconstraintlist_set
- __swig_getmethods__["facetconstraintlist"] = _TetGen.tetgenio_facetconstraintlist_get
- if _newclass:facetconstraintlist = property(_TetGen.tetgenio_facetconstraintlist_get, _TetGen.tetgenio_facetconstraintlist_set)
- __swig_setmethods__["numberoffacetconstraints"] = _TetGen.tetgenio_numberoffacetconstraints_set
- __swig_getmethods__["numberoffacetconstraints"] = _TetGen.tetgenio_numberoffacetconstraints_get
- if _newclass:numberoffacetconstraints = property(_TetGen.tetgenio_numberoffacetconstraints_get, _TetGen.tetgenio_numberoffacetconstraints_set)
- __swig_setmethods__["segmentconstraintlist"] = _TetGen.tetgenio_segmentconstraintlist_set
- __swig_getmethods__["segmentconstraintlist"] = _TetGen.tetgenio_segmentconstraintlist_get
- if _newclass:segmentconstraintlist = property(_TetGen.tetgenio_segmentconstraintlist_get, _TetGen.tetgenio_segmentconstraintlist_set)
- __swig_setmethods__["numberofsegmentconstraints"] = _TetGen.tetgenio_numberofsegmentconstraints_set
- __swig_getmethods__["numberofsegmentconstraints"] = _TetGen.tetgenio_numberofsegmentconstraints_get
- if _newclass:numberofsegmentconstraints = property(_TetGen.tetgenio_numberofsegmentconstraints_get, _TetGen.tetgenio_numberofsegmentconstraints_set)
- __swig_setmethods__["nodeconstraintlist"] = _TetGen.tetgenio_nodeconstraintlist_set
- __swig_getmethods__["nodeconstraintlist"] = _TetGen.tetgenio_nodeconstraintlist_get
- if _newclass:nodeconstraintlist = property(_TetGen.tetgenio_nodeconstraintlist_get, _TetGen.tetgenio_nodeconstraintlist_set)
- __swig_setmethods__["numberofnodeconstraints"] = _TetGen.tetgenio_numberofnodeconstraints_set
- __swig_getmethods__["numberofnodeconstraints"] = _TetGen.tetgenio_numberofnodeconstraints_get
- if _newclass:numberofnodeconstraints = property(_TetGen.tetgenio_numberofnodeconstraints_get, _TetGen.tetgenio_numberofnodeconstraints_set)
- __swig_setmethods__["pbcgrouplist"] = _TetGen.tetgenio_pbcgrouplist_set
- __swig_getmethods__["pbcgrouplist"] = _TetGen.tetgenio_pbcgrouplist_get
- if _newclass:pbcgrouplist = property(_TetGen.tetgenio_pbcgrouplist_get, _TetGen.tetgenio_pbcgrouplist_set)
- __swig_setmethods__["numberofpbcgroups"] = _TetGen.tetgenio_numberofpbcgroups_set
- __swig_getmethods__["numberofpbcgroups"] = _TetGen.tetgenio_numberofpbcgroups_get
- if _newclass:numberofpbcgroups = property(_TetGen.tetgenio_numberofpbcgroups_get, _TetGen.tetgenio_numberofpbcgroups_set)
- __swig_setmethods__["trifacelist"] = _TetGen.tetgenio_trifacelist_set
- __swig_getmethods__["trifacelist"] = _TetGen.tetgenio_trifacelist_get
- if _newclass:trifacelist = property(_TetGen.tetgenio_trifacelist_get, _TetGen.tetgenio_trifacelist_set)
- __swig_setmethods__["adjtetlist"] = _TetGen.tetgenio_adjtetlist_set
- __swig_getmethods__["adjtetlist"] = _TetGen.tetgenio_adjtetlist_get
- if _newclass:adjtetlist = property(_TetGen.tetgenio_adjtetlist_get, _TetGen.tetgenio_adjtetlist_set)
- __swig_setmethods__["trifacemarkerlist"] = _TetGen.tetgenio_trifacemarkerlist_set
- __swig_getmethods__["trifacemarkerlist"] = _TetGen.tetgenio_trifacemarkerlist_get
- if _newclass:trifacemarkerlist = property(_TetGen.tetgenio_trifacemarkerlist_get, _TetGen.tetgenio_trifacemarkerlist_set)
- __swig_setmethods__["numberoftrifaces"] = _TetGen.tetgenio_numberoftrifaces_set
- __swig_getmethods__["numberoftrifaces"] = _TetGen.tetgenio_numberoftrifaces_get
- if _newclass:numberoftrifaces = property(_TetGen.tetgenio_numberoftrifaces_get, _TetGen.tetgenio_numberoftrifaces_set)
- __swig_setmethods__["edgelist"] = _TetGen.tetgenio_edgelist_set
- __swig_getmethods__["edgelist"] = _TetGen.tetgenio_edgelist_get
- if _newclass:edgelist = property(_TetGen.tetgenio_edgelist_get, _TetGen.tetgenio_edgelist_set)
- __swig_setmethods__["edgemarkerlist"] = _TetGen.tetgenio_edgemarkerlist_set
- __swig_getmethods__["edgemarkerlist"] = _TetGen.tetgenio_edgemarkerlist_get
- if _newclass:edgemarkerlist = property(_TetGen.tetgenio_edgemarkerlist_get, _TetGen.tetgenio_edgemarkerlist_set)
- __swig_setmethods__["numberofedges"] = _TetGen.tetgenio_numberofedges_set
- __swig_getmethods__["numberofedges"] = _TetGen.tetgenio_numberofedges_get
- if _newclass:numberofedges = property(_TetGen.tetgenio_numberofedges_get, _TetGen.tetgenio_numberofedges_set)
- def initialize(*args): return _TetGen.tetgenio_initialize(*args)
- def deinitialize(*args): return _TetGen.tetgenio_deinitialize(*args)
- def load_node_call(*args): return _TetGen.tetgenio_load_node_call(*args)
- def load_node(*args): return _TetGen.tetgenio_load_node(*args)
- def load_addnodes(*args): return _TetGen.tetgenio_load_addnodes(*args)
- def load_pbc(*args): return _TetGen.tetgenio_load_pbc(*args)
- def load_var(*args): return _TetGen.tetgenio_load_var(*args)
- def load_mtr(*args): return _TetGen.tetgenio_load_mtr(*args)
- def load_poly(*args): return _TetGen.tetgenio_load_poly(*args)
- def load_off(*args): return _TetGen.tetgenio_load_off(*args)
- def load_ply(*args): return _TetGen.tetgenio_load_ply(*args)
- def load_stl(*args): return _TetGen.tetgenio_load_stl(*args)
- def load_medit(*args): return _TetGen.tetgenio_load_medit(*args)
- def load_plc(*args): return _TetGen.tetgenio_load_plc(*args)
- def load_tetmesh(*args): return _TetGen.tetgenio_load_tetmesh(*args)
- def save_nodes(*args): return _TetGen.tetgenio_save_nodes(*args)
- def save_elements(*args): return _TetGen.tetgenio_save_elements(*args)
- def save_faces(*args): return _TetGen.tetgenio_save_faces(*args)
- def save_edges(*args): return _TetGen.tetgenio_save_edges(*args)
- def save_neighbors(*args): return _TetGen.tetgenio_save_neighbors(*args)
- def save_poly(*args): return _TetGen.tetgenio_save_poly(*args)
- def readline(*args): return _TetGen.tetgenio_readline(*args)
- def findnextfield(*args): return _TetGen.tetgenio_findnextfield(*args)
- def readnumberline(*args): return _TetGen.tetgenio_readnumberline(*args)
- def findnextnumber(*args): return _TetGen.tetgenio_findnextnumber(*args)
- def __init__(self, *args):
- _swig_setattr(self, tetgenio, 'this', _TetGen.new_tetgenio(*args))
- _swig_setattr(self, tetgenio, 'thisown', 1)
- def __del__(self, destroy=_TetGen.delete_tetgenio):
- try:
- if self.thisown: destroy(self)
- except: pass
-
-
-class tetgenioPtr(tetgenio):
- def __init__(self, this):
- _swig_setattr(self, tetgenio, 'this', this)
- if not hasattr(self,"thisown"): _swig_setattr(self, tetgenio, 'thisown', 0)
- self.__class__ = tetgenio
-_TetGen.tetgenio_swigregister(tetgenioPtr)
-
-tetgenio_init = _TetGen.tetgenio_init
-
-class polygon(_object):
- __swig_setmethods__ = {}
- __setattr__ = lambda self, name, value: _swig_setattr(self, polygon, name, value)
- __swig_getmethods__ = {}
- __getattr__ = lambda self, name: _swig_getattr(self, polygon, name)
- def __repr__(self):
- return "<%s.%s; proxy of C++ tetgenio::polygon instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
- def __init__(self, *args):
- _swig_setattr(self, polygon, 'this', _TetGen.new_polygon(*args))
- _swig_setattr(self, polygon, 'thisown', 1)
- def __del__(self, destroy=_TetGen.delete_polygon):
- try:
- if self.thisown: destroy(self)
- except: pass
-
-
-class polygonPtr(polygon):
- def __init__(self, this):
- _swig_setattr(self, polygon, 'this', this)
- if not hasattr(self,"thisown"): _swig_setattr(self, polygon, 'thisown', 0)
- self.__class__ = polygon
-_TetGen.polygon_swigregister(polygonPtr)
-
-class facet(_object):
- __swig_setmethods__ = {}
- __setattr__ = lambda self, name, value: _swig_setattr(self, facet, name, value)
- __swig_getmethods__ = {}
- __getattr__ = lambda self, name: _swig_getattr(self, facet, name)
- def __repr__(self):
- return "<%s.%s; proxy of C++ tetgenio::facet instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
- def __init__(self, *args):
- _swig_setattr(self, facet, 'this', _TetGen.new_facet(*args))
- _swig_setattr(self, facet, 'thisown', 1)
- def __del__(self, destroy=_TetGen.delete_facet):
- try:
- if self.thisown: destroy(self)
- except: pass
-
-
-class facetPtr(facet):
- def __init__(self, this):
- _swig_setattr(self, facet, 'this', this)
- if not hasattr(self,"thisown"): _swig_setattr(self, facet, 'thisown', 0)
- self.__class__ = facet
-_TetGen.facet_swigregister(facetPtr)
-
-class pbcgroup(_object):
- __swig_setmethods__ = {}
- __setattr__ = lambda self, name, value: _swig_setattr(self, pbcgroup, name, value)
- __swig_getmethods__ = {}
- __getattr__ = lambda self, name: _swig_getattr(self, pbcgroup, name)
- def __repr__(self):
- return "<%s.%s; proxy of C++ tetgenio::pbcgroup instance at %s>" % (self.__class__.__module__, self.__class__.__name__, self.this,)
- def __init__(self, *args):
- _swig_setattr(self, pbcgroup, 'this', _TetGen.new_pbcgroup(*args))
- _swig_setattr(self, pbcgroup, 'thisown', 1)
- def __del__(self, destroy=_TetGen.delete_pbcgroup):
- try:
- if self.thisown: destroy(self)
- except: pass
-
-
-class pbcgroupPtr(pbcgroup):
- def __init__(self, this):
- _swig_setattr(self, pbcgroup, 'this', this)
- if not hasattr(self,"thisown"): _swig_setattr(self, pbcgroup, 'thisown', 0)
- self.__class__ = pbcgroup
-_TetGen.pbcgroup_swigregister(pbcgroupPtr)
-
-
-tetrahedralize = _TetGen.tetrahedralize
-
-allocate_array = _TetGen.allocate_array
-
-set_val = _TetGen.set_val
-
-get_val = _TetGen.get_val
-
-allocate_facet_array = _TetGen.allocate_facet_array
-
-add_tri = _TetGen.add_tri
-
-
diff --git a/contrib/TetGenBridge/__init__.py b/contrib/TetGenBridge/__init__.py
deleted file mode 100644
index e9abd51..0000000
--- a/contrib/TetGenBridge/__init__.py
+++ /dev/null
@@ -1,90 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-"""The TetGenBridge package wraps the TetGen library, exposing the tetrahedralize function as well as the input/output classes."""
-
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-import TetGen
-import CreateTestSurf
-
-identifier = 'edu.utah.sci.vistrails.tetget'
-version = '0.9.0'
-name = 'tetgen'
-
-
-# The port that wraps a tetgenio class.
-class tetgenio_wrapper(Module):
- def __init__(self) :
- self.data = TetGen.tetgenio()
-
-
-class tetrahedralize(Module):
- """tetrahedralize corresponds to the TetGen function of the same name"""
-
-
- def __init__(self):
- Module.__init__(self)
-
-
- def compute(self):
- switches = None
- if self.hasInputFromPort("switches") :
- switches = self.getInputFromPort("switches")
- print switches
- if self.hasInputFromPort("tgio in") :
- tgio_in = self.getInputFromPort("tgio in").data
-
- print "input has %d nodes!" % tgio_in.numberofpoints
- tgio_in.save_nodes("/tmp/tgIN.vt")
- tgio_in.save_poly("/tmp/tgIN.vt")
- out = tetgenio_wrapper()
- TetGen.tetrahedralize(switches, tgio_in, out.data)
- print "Done making tets"
-
- self.setResult("tgio out", out)
-
-
-
-
-def initialize(*args, **keywords):
- reg = core.modules.module_registry
-
- #calls the lib with function of the same name.
- reg.add_module(tetrahedralize)
-
- # command line switches that tell tetrahedralize what to do.
- reg.add_input_port(tetrahedralize, "switches",
- (core.modules.basic_modules.String, 'tetgen options'))
- # input mesh information.
- reg.add_input_port(tetrahedralize, "tgio in",
- (tetgenio_wrapper, 'input data'))
- # output mesh information.
- reg.add_output_port(tetrahedralize, "tgio out",
- (tetgenio_wrapper, 'output data'))
-
- #holds the tetgenio class, and acts as a port.
- reg.add_module(tetgenio_wrapper)
-
- # get support and testing modules registered.
- CreateTestSurf.initialize(reg)
-
diff --git a/contrib/TetGenBridge/pill.nodes b/contrib/TetGenBridge/pill.nodes
deleted file mode 100644
index c5f5a68..0000000
--- a/contrib/TetGenBridge/pill.nodes
+++ /dev/null
@@ -1,150 +0,0 @@
-149
-0.033647 -0.306675 3.748440
--0.347509 -0.075738 3.535168
-0.092023 -0.614814 3.779968
-0.021385 -2.885010 0.977596
--0.112491 -2.852496 1.096028
--0.056638 -2.866179 0.515760
--0.503132 -2.472678 0.886320
--0.570188 -2.306610 1.016956
--0.586178 -2.308524 0.017460
--0.301889 1.910949 -2.821956
-0.026409 2.723172 -1.229416
--0.041798 1.964835 -2.904396
-0.235241 1.313400 3.407456
--0.020073 2.394933 2.122384
--0.302936 1.265127 3.373072
--0.245984 1.872435 2.512964
--0.210951 2.390691 1.760696
--0.524534 1.672173 2.541640
--0.442159 2.569212 0.792744
--0.007979 2.949366 0.036412
--0.488698 2.325690 -1.341472
-0.637188 1.756113 1.543692
-0.643783 2.118804 1.000968
-0.417678 2.189415 2.027796
-0.252642 0.061152 -3.837976
-0.401088 -0.941775 -3.308704
-0.134762 -0.928620 -3.737112
--0.711742 1.731426 -0.562400
--0.618031 -1.548495 -2.366948
--0.347366 -2.194776 -1.896868
--0.612231 -2.235354 -0.725212
-0.572145 -1.887516 -2.036456
-0.745612 -1.357884 -1.878496
-0.649281 -2.099940 -0.895152
--0.337037 -1.593987 3.065784
-0.074563 -1.640271 3.317000
--0.281961 -1.323942 3.246140
--0.146002 -1.326615 -3.412476
--0.165076 -1.883532 -2.705452
--0.306512 -1.491813 -2.993896
-0.020136 -2.161710 2.709012
--0.489976 -2.243619 1.636224
-0.284432 2.442969 1.844652
--0.066112 2.724162 1.218828
-0.135661 2.443317 1.887448
-0.134471 2.926203 0.385164
-0.051413 -1.948131 2.941104
--0.991643 -0.293256 0.280112
--0.845646 -1.203078 1.264624
--0.943756 0.206325 1.250476
-0.788734 -1.553430 -0.459912
-0.640943 -2.188170 0.116052
-0.328358 1.404426 3.190840
-0.311628 2.189739 2.399064
-0.078507 0.405717 3.669368
--0.406630 1.108497 -3.283724
--0.462487 1.065186 -3.209104
-0.757712 0.363909 -2.180700
-0.509538 0.514614 -3.372692
-0.629818 1.439865 -2.343808
-0.938141 0.705099 -0.924884
-0.847130 1.072203 -0.892852
-0.832034 1.334268 0.360916
-0.953819 0.182691 -0.453084
-0.900561 -0.730938 -1.147268
-0.909254 0.021477 1.332048
-0.894119 0.524982 0.917536
-0.859944 1.065861 1.453580
-0.072408 -2.553180 1.854312
--0.971071 -0.338877 -0.813692
--0.982599 -0.013476 -0.438032
--0.922431 0.217410 -1.428816
--0.301798 -2.768169 0.602832
--0.233951 -2.786538 0.838784
-0.220680 -2.769438 -1.055128
-0.278649 -2.745525 -0.099352
--0.209502 0.347388 -3.556680
--0.304391 -0.668637 -3.454268
--0.485787 -0.508335 -3.386584
--0.880478 1.168008 -0.597384
--0.852596 1.179015 -0.796288
--0.893187 0.458553 -1.359004
-0.539223 -0.414942 -3.133860
-0.541222 1.678707 1.848644
-0.844172 0.822438 -1.569772
-0.791937 0.829539 -1.815540
-0.702219 1.616712 -1.745900
-0.786245 -0.454056 -2.003272
-0.854364 -0.697968 -1.578756
-0.709524 -1.070706 -2.390708
-0.847056 -0.797703 -1.550640
-0.623879 -0.843942 -2.831528
--0.924460 1.128144 0.201020
--0.484701 2.386260 1.167624
--0.556188 2.165889 0.787772
--0.614616 1.827243 1.600812
-0.425120 2.042298 -2.363344
-0.586647 0.180975 -3.115508
-0.007301 1.722885 -3.253400
--0.269774 0.969108 -3.365348
-0.720678 -1.888437 0.818816
-0.626801 -1.465182 2.371240
-0.522424 -0.210393 3.393136
-0.442195 -0.874248 3.237860
-0.755334 -0.866100 2.246260
--0.709054 -1.841262 1.158012
--0.836380 -1.581552 0.439960
--0.584255 0.320208 -3.105980
-0.558459 1.375503 1.836948
--0.337053 -2.676717 0.016568
-0.418370 -2.390439 -1.579916
-0.161297 -2.369046 -2.258808
--0.733779 -1.508079 -1.580732
-0.335703 1.129452 -3.371780
--0.610116 -1.853631 1.812860
--0.330328 -1.796346 2.745868
-0.451876 -1.652637 2.765888
--0.744153 -1.489014 1.735160
--0.636224 -1.239411 -2.476316
-0.508024 -0.797406 -3.097188
--0.986026 -0.181818 -0.337200
-0.773520 1.519650 0.382688
-0.585568 2.377557 0.586440
-0.193621 -1.782402 -3.080188
--0.706445 0.066513 -2.487392
--0.016795 -2.830479 -1.287572
-0.156494 -2.740728 -1.255484
-0.700143 0.339690 2.424976
-0.918999 -0.719838 1.145084
-0.478251 -2.369100 1.506828
-0.838386 0.258438 1.949544
-0.382820 2.363100 -1.709844
-0.264992 -0.980940 3.385348
--0.713670 1.119309 2.298100
-0.429838 -2.178912 1.944372
-0.372454 2.616471 -0.233160
-0.427271 2.372673 -1.077952
-0.533478 -1.502943 -2.593560
--0.727316 0.083877 2.581624
--0.598577 2.023176 -1.645036
-0.720693 1.742499 -0.045540
-0.382893 2.556219 0.614812
-0.773121 -0.039462 2.169820
--0.546753 2.201277 0.690560
--0.645896 -1.471629 2.062720
--0.556976 0.475389 2.863348
--0.831044 1.370163 -0.748872
-0.889934 -1.112343 0.023912
-0.920718 -0.648489 0.324428
diff --git a/contrib/TetGenBridge/pill.tri b/contrib/TetGenBridge/pill.tri
deleted file mode 100644
index ebd3206..0000000
--- a/contrib/TetGenBridge/pill.tri
+++ /dev/null
@@ -1,295 +0,0 @@
-294
-0 1 2
-3 4 5
-6 7 8
-9 10 11
-12 13 14
-15 14 13
-13 16 17
-15 13 17
-18 19 20
-21 22 23
-24 25 26
-18 20 27
-28 29 30
-31 32 33
-34 35 36
-37 38 39
-4 40 41
-42 43 44
-45 43 42
-46 35 40
-34 40 35
-47 48 49
-33 50 51
-12 52 53
-34 36 1
-0 54 1
-9 55 56
-57 58 59
-60 61 62
-63 64 60
-65 66 67
-4 68 40
-28 38 29
-28 39 38
-64 50 32
-69 70 71
-72 5 4
-73 72 4
-3 5 74
-3 74 75
-76 77 78
-79 80 81
-18 16 43
-24 58 82
-21 23 83
-59 84 85
-59 86 84
-87 88 89
-90 89 88
-90 88 64
-87 89 91
-92 93 94
-92 95 93
-59 96 86
-57 87 97
-98 76 99
-14 1 54
-60 64 88
-100 51 50
-37 77 26
-20 10 9
-101 102 103
-104 102 101
-105 106 7
-8 7 106
-71 81 56
-107 71 56
-108 67 83
-21 83 67
-53 23 42
-60 86 61
-60 84 86
-72 8 109
-72 6 8
-31 110 111
-57 59 85
-57 97 58
-28 30 112
-41 7 6
-24 98 113
-58 97 82
-34 114 41
-115 34 41
-53 42 44
-46 116 35
-114 117 105
-28 118 78
-28 78 39
-119 82 91
-69 47 120
-101 103 116
-22 67 62
-121 22 62
-31 33 110
-41 114 7
-122 23 22
-37 123 38
-47 106 48
-124 78 118
-123 111 38
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-125 126 74
-126 111 74
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-69 118 112
-52 83 23
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-57 88 87
-21 67 22
-65 67 130
-90 32 89
-75 51 129
-96 11 131
-117 106 105
-48 106 117
-30 8 106
-103 2 132
-95 133 17
-134 68 129
-63 60 66
-135 122 136
-15 17 14
-25 91 137
-119 91 25
-26 77 76
-96 131 86
-55 76 78
-138 34 1
-92 133 95
-69 120 70
-115 41 40
-92 70 47
-107 78 124
-40 68 134
-33 32 50
-139 56 81
-82 97 91
-87 91 97
-12 53 13
-33 51 75
-69 71 118
-36 2 1
-24 113 58
-122 22 140
-138 133 49
-127 130 67
-55 78 56
-107 56 78
-108 83 52
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-122 141 42
-127 102 142
-45 19 43
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-69 106 47
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-110 33 74
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-60 67 66
-13 44 43
-96 113 98
-139 27 20
-125 30 29
-125 109 30
-45 141 122
-135 45 122
-92 49 133
-36 35 2
-114 105 7
-138 1 145
-135 136 131
-131 11 10
-123 26 25
-104 130 142
-40 134 116
-46 40 116
-104 142 102
-136 86 131
-73 6 72
-3 75 129
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-139 146 27
-147 64 148
-18 27 143
-53 52 23
-138 48 117
-60 88 84
-57 84 88
-140 61 86
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-90 64 32
-147 50 64
-132 2 35
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-127 142 130
-145 1 14
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-37 78 77
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-34 144 117
-34 117 114
-103 35 116
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-9 11 98
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-79 71 70
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-128 147 148
-3 68 4
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-17 133 14
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-92 27 146
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-138 49 48
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-89 137 91
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-73 41 6
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-31 137 89
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-24 82 25
-24 26 76
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-47 70 120
-100 50 147
-146 81 80
-139 81 146
-45 42 141
-92 94 143
-92 143 27
diff --git a/contrib/TetGenBridge/tetgen.i b/contrib/TetGenBridge/tetgen.i
deleted file mode 100644
index 72da66a..0000000
--- a/contrib/TetGenBridge/tetgen.i
+++ /dev/null
@@ -1,284 +0,0 @@
-%module TetGen
-%{
-#include <tetgen.h>
-%}
-
-class tetgenio {
-
- public:
-
- // Maximum number of characters in a file name (including the null).
- enum {FILENAMESIZE = 1024};
-
- // Maxi. numbers of chars in a line read from a file (incl. the null).
- enum {INPUTLINESIZE = 1024};
-
- // The polygon data structure. A "polygon" is a planar polygon. It can
- // be arbitrary shaped (convex or non-convex) and bounded by non-
- // crossing segments, i.e., the number of vertices it has indictes the
- // same number of edges.
- // 'vertexlist' is a list of vertex indices (integers), its length is
- // indicated by 'numberofvertices'. The vertex indices are odered in
- // either counterclockwise or clockwise way.
-
- class polygon;
-
- static void init(polygon* p) {
- p->vertexlist = (int *) NULL;
- p->numberofvertices = 0;
- }
-
- // The facet data structure. A "facet" is a planar facet. It is used
- // to represent a planar straight line graph (PSLG) in two dimension.
- // A PSLG contains a list of polygons. It also may conatin holes in it,
- // indicated by a list of hole points (their coordinates).
- class facet;
-
- static void init(facet* f) {
- f->polygonlist = (polygon *) NULL;
- f->numberofpolygons = 0;
- f->holelist = (REAL *) NULL;
- f->numberofholes = 0;
- }
-
- // The periodic boundary condition group data structure. A "pbcgroup"
- // contains the definition of a pbc and the list of pbc point pairs.
- // 'fmark1' and 'fmark2' are the facetmarkers of the two pbc facets f1
- // and f2, respectively. 'transmat' is the transformation matrix which
- // maps a point in f1 into f2. An array of pbc point pairs are saved
- // in 'pointpairlist'. The first point pair is at indices [0] and [1],
- // followed by remaining pairs. Two integers per pair.
- class pbcgroup;
- public:
-
- // Items are numbered starting from 'firstnumber' (0 or 1), default is 0.
- int firstnumber;
-
- // Dimension of the mesh (2 or 3), default is 3.
- int mesh_dim;
-
- // `pointlist': An array of point coordinates. The first point's x
- // coordinate is at index [0] and its y coordinate at index [1], its
- // z coordinate is at index [2], followed by the coordinates of the
- // remaining points. Each point occupies three REALs.
- // `pointattributelist': An array of point attributes. Each point's
- // attributes occupy `numberofpointattributes' REALs.
- // 'addpointlist': An array of additional point coordinates.
- // 'addpointattributelist': An array of attributes for addition points.
- // `pointmarkerlist': An array of point markers; one int per point.
- REAL *pointlist;
- REAL *pointattributelist;
- REAL *addpointlist;
- REAL *addpointattributelist;
- int *pointmarkerlist;
- int numberofpoints;
- int numberofpointattributes;
- int numberofaddpoints;
-
- // `elementlist': An array of element (triangle or tetrahedron) corners.
- // The first element's first corner is at index [0], followed by its
- // other corners in counterclockwise order, followed by any other
- // nodes if the element represents a nonlinear element. Each element
- // occupies `numberofcorners' ints.
- // `elementattributelist': An array of element attributes. Each
- // element's attributes occupy `numberofelementattributes' REALs.
- // `elementconstraintlist': An array of constraints, i.e. triangle's
- // area or tetrahedron's volume; one REAL per element. Input only.
- // `neighborlist': An array of element neighbors; 3 or 4 ints per
- // element. Output only.
- int *tetrahedronlist;
- REAL *tetrahedronattributelist;
- REAL *tetrahedronvolumelist;
- int *neighborlist;
- int numberoftetrahedra;
- int numberofcorners;
- int numberoftetrahedronattributes;
-
- // `facetlist': An array of facets. Each entry is a structure of facet.
- // `facetmarkerlist': An array of facet markers; one int per facet.
- facet *facetlist;
- int *facetmarkerlist;
- int numberoffacets;
-
- // `holelist': An array of holes. The first hole's x, y and z
- // coordinates are at indices [0], [1] and [2], followed by the
- // remaining holes. Three REALs per hole.
- REAL *holelist;
- int numberofholes;
-
- // `regionlist': An array of regional attributes and volume constraints.
- // The first constraint's x, y and z coordinates are at indices [0],
- // [1] and [2], followed by the regional attribute at index [3], foll-
- // owed by the maximum volume at index [4]. Five REALs per constraint.
- // Note that each regional attribute is used only if you select the `A'
- // switch, and each volume constraint is used only if you select the
- // `a' switch (with no number following).
- REAL *regionlist;
- int numberofregions;
-
- // `facetconstraintlist': An array of facet maximal area constraints.
- // Two REALs per constraint. The first one is the facet marker (cast
- // it to int), the second is its maximum area bound.
- // Note the 'facetconstraintlist' is used only for the 'q' switch.
- REAL *facetconstraintlist;
- int numberoffacetconstraints;
-
- // `segmentconstraintlist': An array of segment max. length constraints.
- // Three REALs per constraint. The first two are the indices (pointing
- // into 'pointlist') of the endpoints of the segment, the third is its
- // maximum length bound.
- // Note the 'segmentconstraintlist' is used only for the 'q' switch.
- REAL *segmentconstraintlist;
- int numberofsegmentconstraints;
-
- // `nodeconstraintlist': An array of segment length constraints. Two
- // REALs per constraint. The first one is the index (pointing into
- // 'pointlist') of the node, the second is its edge length bound.
- // Note the 'nodeconstraintlist' is used only for the 'q' switch.
- REAL *nodeconstraintlist;
- int numberofnodeconstraints;
-
- // 'pbcgrouplist': An array of periodic boundary condition groups.
- pbcgroup *pbcgrouplist;
- int numberofpbcgroups;
-
- // `trifacelist': An array of triangular face endpoints. The first
- // face's endpoints are at indices [0], [1] and [2], followed by the
- // remaining faces. Three ints per face.
- // `adjtetlist': An array of adjacent tetrahedra to the faces of
- // trifacelist. Each face has at most two adjacent tets, the first
- // face's adjacent tets are at [0], [1]. Two ints per face. A '-1'
- // indicates outside (no adj. tet). This list is output when '-n'
- // switch is used.
- // `trifacemarkerlist': An array of face markers; one int per face.
- int *trifacelist;
- int *adjtetlist;
- int *trifacemarkerlist;
- int numberoftrifaces;
-
- // `edgelist': An array of edge endpoints. The first edge's endpoints
- // are at indices [0] and [1], followed by the remaining edges. Two
- // ints per edge.
- // `edgemarkerlist': An array of edge markers; one int per edge.
- int *edgelist;
- int *edgemarkerlist;
- int numberofedges;
-
- public:
-
- // Initialize routine.
- void initialize();
- void deinitialize();
-
- // Input & output routines.
- bool load_node_call(FILE* infile, int markers, char* nodefilename);
- bool load_node(char* filename);
- bool load_addnodes(char* filename);
- bool load_pbc(char* filename);
- bool load_var(char* filename);
- bool load_mtr(char* filename);
- bool load_poly(char* filename);
- bool load_off(char* filename);
- bool load_ply(char* filename);
- bool load_stl(char* filename);
- bool load_medit(char* filename);
- bool load_plc(char* filename, int object);
- bool load_tetmesh(char* filename);
- void save_nodes(char* filename);
- void save_elements(char* filename);
- void save_faces(char* filename);
- void save_edges(char* filename);
- void save_neighbors(char* filename);
- void save_poly(char* filename);
-
- // Read line and parse string functions.
- char *readline(char* string, FILE* infile, int *linenumber);
- char *findnextfield(char* string);
- char *readnumberline(char* string, FILE* infile, char* infilename);
- char *findnextnumber(char* string);
-
- // Constructor and destructor.
- tetgenio() {initialize();}
- ~tetgenio() {deinitialize();}
-};
-
-%rename(polygon) tetgenio::polygon;
-%rename(facet) tetgenio::facet;
-%rename(pbcgroup) tetgenio::pbcgroup;
-
-class tetgenio::polygon {
- int *vertexlist;
- int numberofvertices;
-};
-
-class tetgenio::facet {
- polygon *polygonlist;
- int numberofpolygons;
- REAL *holelist;
- int numberofholes;
-};
-
-class tetgenio::pbcgroup {
- int fmark1, fmark2;
- REAL transmat[4][4];
- int numberofpointpairs;
- int *pointpairlist;
-};
-
-
-void tetrahedralize(char *switches, tetgenio &in, tetgenio &out);
-
-
-// additional interface for data loading.
-REAL* allocate_array(unsigned int sz);
-void set_val(REAL*arr, unsigned int idx, float val);
-float get_val(REAL*arr, unsigned int idx);
-tetgenio::facet* allocate_facet_array(unsigned int sz);
-void add_tri(tetgenio::facet*arr, int fidx, int nidx0, int nidx1, int nidx2);
-
-%{
-#include <iostream>
-using namespace std;
-
-REAL* allocate_array(unsigned int sz)
-{
- return new REAL[sz];
-}
-
-void set_val(REAL*arr, unsigned int idx, float val)
-{
- arr[idx] = val;
-}
-float get_val(REAL*arr, unsigned int idx)
-{
- return arr[idx];
-}
-
-tetgenio::facet* allocate_facet_array(unsigned int sz)
-{
- return new tetgenio::facet[sz];
-}
-
-void add_tri(tetgenio::facet*arr, int fidx, int nidx0, int nidx1, int nidx2)
-{
- tetgenio::facet *f = &arr[fidx];
- f->numberofpolygons = 1;
- f->polygonlist = new tetgenio::polygon[f->numberofpolygons];
- f->numberofholes = 0;
- f->holelist = 0;
- tetgenio::polygon *p = &f->polygonlist[0];
- p->numberofvertices = 3;
- p->vertexlist = new int[p->numberofvertices];
- p->vertexlist[0] = nidx0;
- p->vertexlist[1] = nidx1;
- p->vertexlist[2] = nidx2;
-}
-
-
-
-void tetrahedralize(char* switches, tetgenio &in, tetgenio &out)
-{
- tetrahedralize(switches, &in, &out);
-}
-
-%}
\ No newline at end of file
diff --git a/contrib/cdat/NOTES b/contrib/cdat/NOTES
deleted file mode 100644
index 8a27f3b..0000000
--- a/contrib/cdat/NOTES
+++ /dev/null
@@ -1,17 +0,0 @@
-Issues:
-
-When the user closes vistrails or uses command + q to quit, the close event
-doesn't seem to be passed to vcdat so we won't execute functionality that we
-want to run before we close vcdat. Right now the only thing we want to do
-when we quit is to kill the process that is running the editor to view the
-teaching commands if it exists.
-
-Any operation that relies on data from a defined variable such as 'altered
-weighted average' doesn't work because the vistrails module must have access
-to all of the defined variables to execute these commands and it doesn't have
-that yet.
-
-Clicking on the plot will show the tooltip but the tooltip will disappear very
-fast. Right now there is a hardcoded wait(1) so the tooltip shows up for
-1 second, otherwise the tooltip usually doesn't appear.
-
diff --git a/contrib/cdat/__init__.py b/contrib/cdat/__init__.py
deleted file mode 100644
index e99857e..0000000
--- a/contrib/cdat/__init__.py
+++ /dev/null
@@ -1,10094 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2008 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-""" Do not edit this file!
-
-File automatically generated by scripts/gen_init.py
-Change History:
-version : description
- 0.2 : Integrated quickplot module that displays the CDAT plot
- widget inside the spreadsheet
- 0.1 : First automatically generated package based on xml descriptions
-
-"""
-from PyQt4 import QtCore, QtGui
-import sip
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import (Module, NotCacheable,
- ModuleError, new_module)
-from core.bundles import py_import
-import os, sys, re
-
-#cdat specific packages
-vcs = py_import('vcs',{})
-cdms2 = py_import('cdms2', {})
-cdutil = py_import('cdutil', {})
-import MV2
-import genutil
-
-#local python modules
-from cdat_window import QCDATWindow
-from cdat_cell import QCDATWidget, CDATCell, Variable, GraphicsMethod, Quickplot
-#from quickplot import quickplot
-from packages.spreadsheet.basic_widgets import CellLocation
-from packages.spreadsheet.basic_widgets import SpreadsheetCell
-
-version = "0.2"
-identifier = "edu.utah.sci.vistrails.cdat"
-name = "CDAT"
-
-vt_type_dict = {}
-def get_late_type(type):
- return vt_type_dict[type]
-
-Canvas = new_module(Module,'Canvas')
-Dp = new_module(Module,'Dp')
-vt_type_dict['vcs.displayplot.Dp'] = Dp
-Gfb = new_module(Module,'Gfb')
-vt_type_dict['vcs.boxfill.Gfb'] = Gfb
-Gfi = new_module(Module,'Gfi')
-vt_type_dict['vcs.isofill.Gfi'] = Gfi
-Gi = new_module(Module,'Gi')
-vt_type_dict['vcs.isoline.Gi'] = Gi
-Gfo = new_module(Module,'Gfo')
-vt_type_dict['vcs.outfill.Gfo'] = Gfo
-Go = new_module(Module,'Go')
-vt_type_dict['vcs.outline.Go'] = Go
-GSp = new_module(Module,'GSp')
-vt_type_dict['vcs.scatter.GSp'] = GSp
-GXY = new_module(Module,'GXY')
-vt_type_dict['vcs.xvsy.GXY'] = GXY
-GXy = new_module(Module,'GXy')
-vt_type_dict['vcs.xyvsy.GXy'] = GXy
-GYx = new_module(Module,'GYx')
-vt_type_dict['vcs.yxvsx.GYx'] = GYx
-CdmsFile = new_module(Module,'CdmsFile')
-vt_type_dict['cdms2.dataset.CdmsFile'] = CdmsFile
-TransientVariable = new_module(Module,'TransientVariable')
-vt_type_dict['cdms2.tvariable.TransientVariable'] = TransientVariable
-
-
-class boxfill(SpreadsheetCell,NotCacheable):
- """
- Function: boxfill # Generate a boxfill plot
-
- Description of Function:
- Generate a boxfill plot given the data, boxfill graphics method, and
- template. If no boxfill class object is given, then the 'default' boxfill
- graphics method is used. Similarly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('boxfill') # Show all the existing boxfill graphics methods
- box=a.getboxfill('quick') # Create instance of 'quick'
- a.boxfill(array,box) # Plot array using specified box and default
- # template
- templt=a.gettemplate('AMIP') # Create an instance of template 'AMIP'
- a.clear() # Clear VCS canvas
- a.boxfill(array,box,template) # Plot array using specified box and template
- a.boxfill(box,array,template) # Plot array using specified box and template
- a.boxfill(template,array,box) # Plot array using specified box and template
- a.boxfill(template,array,box) # Plot array using specified box and template
- a.boxfill(array,'AMIP','quick') # Use 'AMIP' template and 'quick' boxfill
- a.boxfill('AMIP',array,'quick') # Use 'AMIP' template and 'quick' boxfill
- a.boxfill('AMIP','quick',array) # Use 'AMIP' template and 'quick' boxfill
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End boxfill Description ################################################
-######################################### #################################################
-###################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- print 'got canvas'
- print canvas
- else:
- print 'no canvas'
- canvas = vcs.init()
-
- # Build the argument list
- args = []
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- args.append(slab)
- # slab is a required port
- if slab is None:
- raise ModuleError(self, "'slab' is a mandatory port")
-
- template = None
- if self.hasInputFromPort('template'):
- template = self.getInputFromPort('template')
- args.append(template)
- # template is a required port
- if template is None:
- raise ModuleError(self, "'template' is a mandatory port")
-
- args.append('Boxfill')
-
- gm_name = None
- if self.hasInputFromPort('gm_name'):
- gm_name = self.getInputFromPort('gm_name')
- args.append(gm_name)
- # gm_name is a required port
- if gm_name is None:
- raise ModuleError(self, "'template' is a mandatory port")
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- # force images to be created in the background
- # kwargs['bg'] = 1
-
- # TODO
-
- #res = canvas.boxfill(*args,**kwargs)
- #res = canvas.plot(slab, 'ASD', 'Boxfill', 'ASD')
-
- #plotArgs = (graphics_method, 'ASD', dataset)
- inputPorts = (canvas, args, kwargs)
- self.displayAndWait(QCDATWidget, inputPorts)
-
- # self.setResult('display', res)
- self.setResult('canvas',canvas)
-
-class createboxfill(Module):
- """
- Function: createboxfill # Construct a new boxfill graphics method
-
- Description of Function:
- Create a new boxfill graphics method given the the name and the existing
- boxfill graphics method to copy the attributes from. If no existing
- boxfill graphics method name is given, then the default boxfill graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
- a=vcs.init()
- a.show('boxfill')
- box=a.createboxfill('example1',)
- a.show('boxfill')
- box=a.createboxfill('example2','quick')
- a.show('boxfill')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createboxfill Description ################################################
-######################################### #################################################
-#########################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- new_GM_name = None
- if self.hasInputFromPort('new_GM_name'):
- new_GM_name = self.getInputFromPort('new_GM_name')
- args.append(new_GM_name)
-
- source_GM_name = None
- if self.hasInputFromPort('source_GM_name'):
- source_GM_name = self.getInputFromPort('source_GM_name')
- args.append(source_GM_name)
-
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- self.setResult('slab_0_out', slab)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- gm = canvas.createboxfill(*args,**kwargs)
- self.setResult('boxfill', gm)
- self.setResult('canvas', canvas)
-
-class createisofill(Module):
- """
- Function: createisofill # Construct a new isofill graphics method
-
- Description of Function:
- Create a new isofill graphics method given the the name and the existing
- isofill graphics method to copy the attributes from. If no existing
- isofill graphics method name is given, then the default isofill graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
- a=vcs.init()
- a.show('isofill')
- iso=a.createisofill('example1',)
- a.show('isofill')
- iso=a.createisofill('example2','quick')
- a.show('isofill')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createisofill Description ################################################
-######################################### #################################################
-#########################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- new_GM_name = None
- if self.hasInputFromPort('new_GM_name'):
- new_GM_name = self.getInputFromPort('new_GM_name')
- args.append(new_GM_name)
-
- source_GM_name = None
- if self.hasInputFromPort('source_GM_name'):
- source_GM_name = self.getInputFromPort('source_GM_name')
- args.append(source_GM_name)
-
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- self.setResult('slab_0_out', slab)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- #kwargs['bg'] = 1
- res = canvas.createisofill(*args,**kwargs)
- self.setResult('isofill',res)
- self.setResult('canvas',canvas)
-
-class createisoline(Module):
- """
- Function: createisoline # Construct a new isoline graphics method
-
- Description of Function:
- Create a new isoline graphics method given the the name and the existing
- isoline graphics method to copy the attributes from. If no existing
- isoline graphics method name is given, then the default isoline graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
-
- a=vcs.init()
- a.show('isoline')
- iso=a.createisoline('example1',)
- a.show('isoline')
- iso=a.createisoline('example2','quick')
- a.show('isoline')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createisoline Description ################################################
-######################################### #################################################
-#########################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- new_GM_name = None
- if self.hasInputFromPort('new_GM_name'):
- new_GM_name = self.getInputFromPort('new_GM_name')
- args.append(new_GM_name)
- source_GM_name = None
-
- if self.hasInputFromPort('source_GM_name'):
- source_GM_name = self.getInputFromPort('source_GM_name')
- args.append(source_GM_name)
-
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- self.setResult('slab_0_out', slab)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- #kwargs['bg'] = 1
- res = canvas.createisoline(*args,**kwargs)
- self.setResult('isoline',res)
- self.setResult('canvas',canvas)
-
-class createoutfill(Module):
- """
- Function: createoutfill # Construct a new outfill graphics method
-
- Description of Function:
- Create a new outfill graphics method given the the name and the existing
- outfill graphics method to copy the attributes from. If no existing
- outfill graphics method name is given, then the default outfill graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
-
- a=vcs.init()
- a.show('outfill')
- out=a.createoutfill('example1',)
- a.show('outfill')
- out=a.createoutfill('example2','quick')
- a.show('outfill')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createoutfill Description ################################################
-######################################### #################################################
-#########################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
-
- args = []
- new_GM_name = None
- if self.hasInputFromPort('new_GM_name'):
- new_GM_name = self.getInputFromPort('new_GM_name')
- args.append(new_GM_name)
-
- source_GM_name = None
- if self.hasInputFromPort('source_GM_name'):
- source_GM_name = self.getInputFromPort('source_GM_name')
- args.append(source_GM_name)
-
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- self.setResult('slab_0_out', slab)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- #kwargs['bg'] = 1
- res = canvas.createoutfill(*args,**kwargs)
- self.setResult('outfill',res)
- self.setResult('canvas',canvas)
-
-class createoutline(Module):
- """
- Function: createoutline # Construct a new outline graphics method
-
- Description of Function:
- Create a new outline graphics method given the the name and the existing
- outline graphics method to copy the attributes from. If no existing
- outline graphics method name is given, then the default outline graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
-
- a=vcs.init()
- a.show('outline')
- out=a.createoutline('example1',)
- a.show('outline')
- out=a.createoutline('example2','quick')
- a.show('outline')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createoutline Description ################################################
-######################################### #################################################
-#########################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- new_GM_name = None
- if self.hasInputFromPort('new_GM_name'):
- new_GM_name = self.getInputFromPort('new_GM_name')
- args.append(new_GM_name)
- source_GM_name = None
-
- if self.hasInputFromPort('source_GM_name'):
- source_GM_name = self.getInputFromPort('source_GM_name')
- args.append(source_GM_name)
-
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- self.setResult('slab_0_out', slab)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- #kwargs['bg'] = 1
- res = canvas.createoutline(*args,**kwargs)
- self.setResult('outline',res)
- self.setResult('canvas',canvas)
-
-class createscatter(Module):
- """
- Function: createscatter # Construct a new scatter graphics method
-
- Description of Function:
- Create a new scatter graphics method given the the name and the existing
- scatter graphics method to copy the attributes from. If no existing
- scatter graphics method name is given, then the default scatter graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
- a=vcs.init()
- a.show('scatter')
- sct=a.createscatter('example1',)
- a.show('scatter')
- sct=a.createscatter('example2','quick')
- a.show('scatter')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createscatter Description ################################################
-######################################### #################################################
-#########################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- new_GM_name = None
- if self.hasInputFromPort('new_GM_name'):
- new_GM_name = self.getInputFromPort('new_GM_name')
- args.append(new_GM_name)
-
- source_GM_name = None
- if self.hasInputFromPort('source_GM_name'):
- source_GM_name = self.getInputFromPort('source_GM_name')
- args.append(source_GM_name)
-
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- self.setResult('slab_0_out', slab)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- #kwargs['bg'] = 1
- res = canvas.createscatter(*args,**kwargs)
- self.setResult('scatter',res)
- self.setResult('canvas',canvas)
-
-class createxvsy(Module):
- """
- Function: createxvsy # Construct a new XvsY graphics method
-
- Description of Function:
- Create a new XvsY graphics method given the the name and the existing
- XvsY graphics method to copy the attributes from. If no existing
- XvsY graphics method name is given, then the default XvsY graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
- a=vcs.init()
- a.show('xvsy')
- xy=a.createxvsy('example1',)
- a.show('xvsy')
- xy=a.createxvsy('example2','quick')
- a.show('xvsy')
-
-######################################################################################################################
-########################################### ###############################################
-########################################## End createxvsy Description ################################################
-######################################### #################################################
-######################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- new_GM_name = None
- if self.hasInputFromPort('new_GM_name'):
- new_GM_name = self.getInputFromPort('new_GM_name')
- args.append(new_GM_name)
- source_GM_name = None
-
- if self.hasInputFromPort('source_GM_name'):
- source_GM_name = self.getInputFromPort('source_GM_name')
- args.append(source_GM_name)
-
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- self.setResult('slab_0_out', slab)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- #kwargs['bg'] = 1
- res = canvas.createxvsy(*args,**kwargs)
- self.setResult('xvsy',res)
- self.setResult('canvas',canvas)
-
-class createxyvsy(Module):
- """
- Function: createxyvsy # Construct a new Xyvsy graphics method
-
- Description of Function:
- Create a new Xyvsy graphics method given the the name and the existing
- Xyvsy graphics method to copy the attributes from. If no existing
- Xyvsy graphics method name is given, then the default Xyvsy graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
-
- a=vcs.init()
- a.show('xyvsy')
- xyy=a.createxyvsy('example1',)
- a.show('xyvsy')
- xyy=a.createxyvsy('example2','quick')
- a.show('xyvsy')
-
-#######################################################################################################################
-########################################### ###############################################
-########################################## End createxyvsy Description ################################################
-######################################### #################################################
-#######################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- new_GM_name = None
- if self.hasInputFromPort('new_GM_name'):
- new_GM_name = self.getInputFromPort('new_GM_name')
- args.append(new_GM_name)
- source_GM_name = None
-
- if self.hasInputFromPort('source_GM_name'):
- source_GM_name = self.getInputFromPort('source_GM_name')
- args.append(source_GM_name)
-
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- self.setResult('slab_0_out', slab)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- #kwargs['bg'] = 1
- res = canvas.createxyvsy(*args,**kwargs)
- self.setResult('xyvsy',res)
- self.setResult('canvas',canvas)
-
-class createyxvsx(Module):
- """
- Function: createyxvsx # Construct a new Yxvsx graphics method
-
- Description of Function:
- Create a new Yxvsx graphics method given the the name and the existing
- Yxvsx graphics method to copy the attributes from. If no existing
- Yxvsx graphics method name is given, then the default Yxvsx graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
-
- a=vcs.init()
- a.show('yxvsx')
- yxx=a.createyxvsx('example1',)
- a.show('yxvsx')
- yxx=a.createyxvsx('example2','quick')
- a.show('yxvsx')
-
-#######################################################################################################################
-########################################### ###############################################
-########################################## End createyxvsx Description ################################################
-######################################### #################################################
-#######################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- new_GM_name = None
- if self.hasInputFromPort('new_GM_name'):
- new_GM_name = self.getInputFromPort('new_GM_name')
- args.append(new_GM_name)
- source_GM_name = None
-
- if self.hasInputFromPort('source_GM_name'):
- source_GM_name = self.getInputFromPort('source_GM_name')
- args.append(source_GM_name)
-
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- self.setResult('slab_0_out', slab)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- #kwargs['bg'] = 1
-
- res = canvas.createyxvsx(*args,**kwargs)
- self.setResult('yxvsx',res)
- self.setResult('canvas',canvas)
-
-class getboxfill(Module):
- """
- Function: getboxfill # Construct a new boxfill graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- boxfill class object from an existing VCS boxfill graphics method. If
- no boxfill name is given, then boxfill 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createboxfill function.)
-
- Example of Use:
- a=vcs.init()
- a.show('boxfill') # Show all the existing boxfill graphics methods
- box=a.getboxfill() # box instance of 'default' boxfill graphics
- # method
- box2=a.getboxfill('quick') # box2 instance of existing 'quick' boxfill
- # graphics method
-######################################################################################################################
-########################################### ###############################################
-########################################## End getboxfill Description ################################################
-######################################### #################################################
-######################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
-
- GM_name = None
- if self.hasInputFromPort('GM_name'):
- GM_name = self.getInputFromPort('GM_name')
- args.append(GM_name)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- res = canvas.getboxfill(*args)
- self.setResult('boxfill',res)
- self.setResult('canvas',canvas)
-
-class getisofill(Module):
- """
- Function: getisofill Construct a new isofill graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- isofill class object from an existing VCS isofill graphics method. If
- no isofill name is given, then isofill 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createisofill function.)
-
- Example of Use:
- a=vcs.init()
- a.show('isofill') # Show all the existing isofill graphics methods
- iso=a.getisofill() # iso instance of 'default' isofill graphics
- # method
- iso2=a.getisofill('quick') # iso2 instance of existing 'quick' isofill
- # graphics method
-######################################################################################################################
-########################################### ###############################################
-########################################## End getisofill Description ################################################
-######################################### #################################################
-######################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- GM_name = None
- if self.hasInputFromPort('GM_name'):
- GM_name = self.getInputFromPort('GM_name')
- args.append(GM_name)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- res = canvas.getisofill(*args)
-
- self.setResult('isofill',res)
- self.setResult('canvas',canvas)
-
-class getisoline(Module):
- """
- Function: getisoline # Construct a new isoline graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- isoline class object from an existing VCS isoline graphics method. If
- no isoline name is given, then isoline 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createisoline function.)
-
- Example of Use:
- a=vcs.init()
- a.show('isoline') # Show all the existing isoline graphics methods
- iso=a.getisoline() # iso instance of 'default' isoline graphics
- # method
- iso2=a.getisoline('quick') # iso2 instance of existing 'quick' isoline
- # graphics method
-######################################################################################################################
-########################################### ###############################################
-########################################## End getisoline Description ################################################
-######################################### #################################################
-######################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- GM_name = None
- if self.hasInputFromPort('GM_name'):
- GM_name = self.getInputFromPort('GM_name')
- args.append(GM_name)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- res = canvas.getisoline(*args)
- self.setResult('isoline',res)
- self.setResult('canvas',canvas)
-
-class getoutfill(Module):
- """
- Function: getoutfill # Construct a new outfill graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- outfill class object from an existing VCS outfill graphics method. If
- no outfill name is given, then outfill 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createoutfill function.)
-
- Example of Use:
- a=vcs.init()
- a.show('outfill') # Show all the existing outfill graphics methods
- out=a.getoutfill() # out instance of 'default' outfill graphics
- # method
- out2=a.getoutfill('quick') # out2 instance of existing 'quick' outfill
- # graphics method
-
-######################################################################################################################
-########################################### ###############################################
-########################################## End getoutfill Description ################################################
-######################################### #################################################
-######################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- GM_name = None
- if self.hasInputFromPort('GM_name'):
- GM_name = self.getInputFromPort('GM_name')
- args.append(GM_name)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- res = canvas.getoutfill(*args,**kwargs)
- self.setResult('outfill',res)
- self.setResult('canvas',canvas)
-
-class getoutline(Module):
- """
- Function: getoutline # Construct a new outline graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- outline class object from an existing VCS outline graphics method. If
- no outline name is given, then outline 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createoutline function.)
-
- Example of Use:
- a=vcs.init()
- a.show('outline') # Show all the existing outline graphics methods
- out=a.getoutline() # out instance of 'default' outline graphics
- # method
- out2=a.getoutline('quick') # out2 instance of existing 'quick' outline
- # graphics method
-
-######################################################################################################################
-########################################### ###############################################
-########################################## End getoutline Description ################################################
-######################################### #################################################
-######################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- GM_name = None
- if self.hasInputFromPort('GM_name'):
- GM_name = self.getInputFromPort('GM_name')
- args.append(GM_name)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- res = canvas.getoutline(*args)
- self.setResult('outline',res)
- self.setResult('canvas',canvas)
-
-class getscatter(Module):
- """
- Function: getscatter # Construct a new scatter graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- scatter class object from an existing VCS scatter graphics method. If
- no scatter name is given, then scatter 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createscatter function.)
-
- Example of Use:
- a=vcs.init()
- a.show('scatter') # Show all the existing scatter graphics methods
- sct=a.getscatter() # sct instance of 'default' scatter graphics
- # method
- sct2=a.getscatter('quick') # sct2 instance of existing 'quick' scatter
- # graphics method
-
-######################################################################################################################
-########################################### ###############################################
-########################################## End getscatter Description ################################################
-######################################### #################################################
-######################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- GM_name = None
- if self.hasInputFromPort('GM_name'):
- GM_name = self.getInputFromPort('GM_name')
- args.append(GM_name)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- res = canvas.getscatter(*args)
- self.setResult('scatter',res)
- self.setResult('canvas',canvas)
-
-class getxvsy(Module):
- """
- Function: getxvsy # Construct a new XvsY graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- XvsY class object from an existing VCS XvsY graphics method. If
- no XvsY name is given, then XvsY 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createxvsy function.)
-
- Example of Use:
- a=vcs.init()
- a.show('xvsy') # Show all the existing XvsY graphics methods
- xy=a.getxvsy() # xy instance of 'default' XvsY graphics
- # method
- xy2=a.getxvsy('quick') # xy2 instance of existing 'quick' XvsY
- # graphics method
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End getxvsy Description ################################################
-######################################### #################################################
-###################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- GM_name = None
- if self.hasInputFromPort('GM_name'):
- GM_name = self.getInputFromPort('GM_name')
- args.append(GM_name)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- res = canvas.getxvsy(*args)
- self.setResult('xvsy',res)
- self.setResult('canvas',canvas)
-
-class getxyvsy(Module):
- """
- Function: getxyvsy # Construct a new Xyvsy graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- Xyvsy class object from an existing VCS Xyvsy graphics method. If
- no Xyvsy name is given, then Xyvsy 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createxyvsy function.)
-
- Example of Use:
- a=vcs.init()
- a.show('xyvsy') # Show all the existing Xyvsy graphics methods
- xyy=a.getxyvsy() # xyy instance of 'default' Xyvsy graphics
- # method
- xyy2=a.getxyvsy('quick') # xyy2 instance of existing 'quick' Xyvsy
- # graphics method
-####################################################################################################################
-########################################### ###############################################
-########################################## End getxyvsy Description ################################################
-######################################### #################################################
-####################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- GM_name = None
- if self.hasInputFromPort('GM_name'):
- GM_name = self.getInputFromPort('GM_name')
- args.append(GM_name)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- res = canvas.getxyvsy(*args)
- self.setResult('xyvsy',res)
- self.setResult('canvas',canvas)
-
-class getyxvsx(Module):
- """
- Function: getyxvsx # Construct a new Yxvsx graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- Yxvsx class object from an existing VCS Yxvsx graphics method. If
- no Yxvsx name is given, then Yxvsx 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createyxvsx function.)
-
- Example of Use:
- a=vcs.init()
- a.show('yxvsx') # Show all the existing Yxvsx graphics methods
- yxx=a.getyxvsx() # yxx instance of 'default' Yxvsx graphics
- # method
- yxx2=a.getyxvsx('quick') # yxx2 instance of existing 'quick' Yxvsx
- # graphics method
-####################################################################################################################
-########################################### ###############################################
-########################################## End getyxvsx Description ################################################
-######################################### #################################################
-####################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- GM_name = None
- if self.hasInputFromPort('GM_name'):
- GM_name = self.getInputFromPort('GM_name')
- args.append(GM_name)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- res = canvas.getyxvsx(*args,**kwargs)
- self.setResult('yxvsx',res)
- self.setResult('canvas',canvas)
-
-class isofill(Module,NotCacheable):
- """
- Function: isofill # Generate an isofill plot
-
- Description of Function:
- Generate a isofill plot given the data, isofill graphics method, and
- template. If no isofill class object is given, then the 'default' isofill
- graphics method is used. Similarly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('isofill') # Show all the existing isofill graphics methods
- iso=a.getisofill('quick') # Create instance of 'quick'
- a.isofill(array,iso) # Plot array using specified iso and default
- # template
- a.clear() # Clear VCS canvas
- a.isofill(array,iso,template) # Plot array using specified iso and template
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End isofill Description ################################################
-######################################### #################################################
-###################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
-
- args = []
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- args.append(slab)
-
- template = None
- if self.hasInputFromPort('template'):
- template = self.getInputFromPort('template')
- args.append(template)
- # template is a required port
- if template is None:
- raise ModuleError(self, "'template' is a mandatory port")
-
- args.append('Isofill')
-
- gm_name = None
- if self.hasInputFromPort('gm_name'):
- gm_name = self.getInputFromPort('gm_name')
- args.append(gm_name)
- # gm_name is a required port
- if gm_name is None:
- raise ModuleError(self, "'template' is a mandatory port")
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- kwargs['bg'] = 1
- res = canvas.isofill(*args,**kwargs)
- self.setResult('display',res)
- self.setResult('canvas',canvas)
-
-class isoline(Module,NotCacheable):
- """
- Function: isoline # Generate an isoline plot
-
- Description of Function:
- Generate a isoline plot given the data, isoline graphics method, and
- template. If no isoline class object is given, then the 'default' isoline
- graphics method is used. Similarly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('isoline') # Show all the existing isoline graphics methods
- iso=a.getisoline('quick') # Create instance of 'quick'
- a.isoline(array,iso) # Plot array using specified iso and default
- # template
- a.clear() # Clear VCS canvas
- a.isoline(array,iso,template) # Plot array using specified iso and template
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End isoline Description ################################################
-######################################### #################################################
-###################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
-
- args = []
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- args.append(slab)
-
- template = None
- if self.hasInputFromPort('template'):
- template = self.getInputFromPort('template')
- args.append(template)
- # template is a required port
- if template is None:
- raise ModuleError(self, "'template' is a mandatory port")
-
- args.append('Isoline')
-
- gm_name = None
- if self.hasInputFromPort('gm_name'):
- gm_name = self.getInputFromPort('gm_name')
- args.append(gm_name)
- # gm_name is a required port
- if gm_name is None:
- raise ModuleError(self, "'template' is a mandatory port")
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- kwargs['bg'] = 1
- res = canvas.isoline(*args,**kwargs)
- self.setResult('display',res)
- self.setResult('canvas',canvas)
-
-class outfill(Module):
- """
- Function: outfill # Generate an outfill plot
-
- Description of Function:
- Generate a outfill plot given the data, outfill graphics method, and
- template. If no outfill class object is given, then the 'default' outfill
- graphics method is used. Simerly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('outfill') # Show all the existing outfill graphics methods
- out=a.getoutfill('quick') # Create instance of 'quick'
- a.outfill(array,out) # Plot array using specified out and default
- # template
- a.clear() # Clear VCS canvas
- a.outfill(array,out,template) # Plot array using specified out and template
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End outfill Description ################################################
-######################################### #################################################
-###################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
-
- args = []
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- args.append(slab)
-
- template = None
- if self.hasInputFromPort('template'):
- template = self.getInputFromPort('template')
- args.append(template)
- # template is a required port
- if template is None:
- raise ModuleError(self, "'template' is a mandatory port")
-
- args.append('Outfill')
-
- gm_name = None
- if self.hasInputFromPort('gm_name'):
- gm_name = self.getInputFromPort('gm_name')
- args.append(gm_name)
- # gm_name is a required port
- if gm_name is None:
- raise ModuleError(self, "'template' is a mandatory port")
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- kwargs['bg'] = 1
- res = canvas.outfill(*args,**kwargs)
- self.setResult('display',res)
- self.setResult('canvas',canvas)
-
-class outline(Module):
- """
- Function: outline # Generate an outline plot
-
- Description of Function:
- Generate a outline plot given the data, outline graphics method, and
- template. If no outline class object is given, then the 'default' outline
- graphics method is used. Simerly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('outline') # Show all the existing outline graphics methods
- out=a.getoutline('quick') # Create instance of 'quick'
- a.outline(array,out) # Plot array using specified out and default
- # template
- a.clear() # Clear VCS canvas
- a.outline(array,out,template) # Plot array using specified out and template
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End outline Description ################################################
-######################################### #################################################
-###################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
-
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- args.append(slab)
-
- template = None
- if self.hasInputFromPort('template'):
- template = self.getInputFromPort('template')
- args.append(template)
- # template is a required port
- if template is None:
- raise ModuleError(self, "'template' is a mandatory port")
-
- args.append('Outline')
-
- gm_name = None
- if self.hasInputFromPort('gm_name'):
- gm_name = self.getInputFromPort('gm_name')
- args.append(gm_name)
- # gm_name is a required port
- if gm_name is None:
- raise ModuleError(self, "'template' is a mandatory port")
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- kwargs['bg'] = 1
- res = canvas.outline(*args,**kwargs)
- self.setResult('display',res)
- self.setResult('canvas',canvas)
-
-class plot(SpreadsheetCell,NotCacheable):
- """
- Function: plot
-
- Description of plot:
- Plot an array(s) of data given a template and graphics method. The VCS template is
- used to define where the data and variable attributes will be displayed on the VCS
- Canvas. The VCS graphics method is used to define how the array(s) will be shown
- on the VCS Canvas.
-
- The form of the call is:
- plot(array1=None, array2=None, template_name=None, graphics_method=None,
- graphics_name=None, [key=value [, key=value [, ...]]])
-
- where array1 and array2 are NumPy arrays.
-
- Plot keywords:
- ratio [default is none]
- None: let the self.ratio attribute decide
- 0,'off': overwritte self.ratio and do nothing about the ratio
- 'auto': computes an automatic ratio
- '3',3: y dim will be 3 times bigger than x dim (restricted to original tempalte.data area
- Adding a 't' at the end of the ratio, makes the tickmarks and boxes move along.
-
- Variable attribute keys:
- comment1 = string #Comment plotted above file_comment
- comment2 = string #Comment plotted above comment1
- comment3 = string #Comment plotted above comment2
- comment4 = string #Comment plotted above comment4
- file_comment = string #Comment (defaults to file.comment)
- hms = string (hh:mm:ss) #Hour, minute, second
- long_name = string #Descriptive variable name
- name = string #Variable name (defaults to var.id)
- time = cdtime #instance (relative or absolute),
- cdtime, reltime or abstime value
- units = string #Variable units
- ymd = string (yy/mm/dd) #Year, month, day
-
- Dimension attribute keys (dimension length=n):
- [x|y|z|t|w]array = NumPy array of length n # x or y Dimension values
- [x|y|z|t|w]array = NumPy array of length n # x or y Dimension values
- [x|y]bounds = NumPy array of shape (n,2) # x or y Dimension boundaries
- [x|y|z|t|w]name = string # x or y Dimension name
- [x|y|z|t|w]units = string # x or y Dimension units
- [x|y]weights = NumPy array of length n # x or y Dimension weights (used to
- calculate area-weighted mean)
-
- CDMS object:
- [x|y|z|t|w]axis = CDMS axis object # x or y Axis
- grid = CDMS grid object # Grid object (e.g. grid=var.getGrid()
- variable = CDMS variable object # Variable object
-
- Other:
- [x|y]rev = 0|1 # if ==1, reverse the direction of the x
- or y axis
- continents = 0,1,2,3,4,5,6,7,8,9,10,11 # if >=1, plot continental outlines
- (default: plot if xaxis is
- longitude, yaxis is latitude -or-
- xname is 'longitude' and yname is
- 'latitude'
- # The continents-type values are integers
- # ranging from 0 to 11, where:
- # 0 signifies "No Continents"
- # 1 signifies "Fine Continents"
- # 2 signifies "Coarse Continents"
- # 3 signifies "United States"
- # 4 signifies "Political Borders"
- # 5 signifies "Rivers"
-
- # Values 6 through 11 signify the line type
- # defined by the files data_continent_other7
- # through data_continent_other12.
-
- Graphics Output in Background Mode:
- bg = 0|1 # if ==1, create images in the background
- (Don't display the VCS Canvas)
-
- Note:
- More specific attributes take precedence over general attributes. In particular,
- specifie attributes override variable object attributes, dimension attributes and
- arrays override axis objects, which override grid objects, which override variable
- objects.
-
- For example, if both 'file_comment' and 'variable' keywords are specified, the value of
- 'file_comment' is used instead of the file comment in the parent of variable. Similarly,
- if both 'xaxis' and 'grid' keywords are specified, the value of 'xaxis' takes precedence
- over the x-axis of grid.
-
- Example of Use:
- x=vcs.init() # x is an instance of the VCS class object (constructor)
- x.plot(array) # this call will use default settings for template and boxfill
- x.plot(array, 'AMIP', 'isofill','AMIP_psl') # this is specifying the template and
- graphics method
- t=x.gettemplate('AMIP') # get a predefined the template 'AMIP'
- vec=x.getvector('quick') # get a predefined the vector graphics method 'quick'
- x.plot(array1, array2, t, vec) # plot the data as a vector using the 'AMIP' template
- x.clear() # clear the VCS Canvas of all plots
- box=x.createboxfill('new') # create boxfill graphics method 'new'
- x.plot(box,t,array) # plot array data using box 'new' and template 't'
-
-###############################################################################################################
-########################################### ##############################################
-########################################## End plot Description ###############################################
-######################################### ################################################
-###############################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
-
- # Build up the argument list
- args = []
- slab2 = None
- if self.hasInputFromPort('slab2_0'):
- slab2 = self.getInputFromPort('slab2_0')
- args.append(slab2)
- slab1 = None
- if self.hasInputFromPort('slab1_0'):
- slab1 = self.getInputFromPort('slab1_0')
- args.append(slab1)
- template = None
- if self.hasInputFromPort('template'):
- template = self.getInputFromPort('template')
- args.append(template)
- plot_type = None
- if self.hasInputFromPort('plot_type'):
- plot_type = self.getInputFromPort('plot_type')
- args.append(plot_type)
- gm_name = None
- if self.hasInputFromPort('gm_name'):
- gm_name = self.getInputFromPort('gm_name')
- args.append(gm_name)
-
- # slab1 is a required port
- if slab1 is None:
- raise ModuleError(self, "'slab1' is a mandatory port")
- # template is a required port
- if template is None:
- raise ModuleError(self, "'template' is a mandatory port")
- # plot_type is a required port
- if plot_type is None:
- raise ModuleError(self, "'plot_type' is a mandatory port")
- # gm_name is a required port
- if gm_name is None:
- raise ModuleError(self, "'gm_name' is a mandatory port")
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
-
- # Set the cell row / col
- self.location = CellLocation()
- if self.hasInputFromPort('row'):
- self.location.row = self.getInputFromPort('row')
- if self.hasInputFromPort('col'):
- self.location.col = self.getInputFromPort('col')
-
- # Plot into the cell
- inputPorts = (canvas, args, kwargs)
- self.displayAndWait(QCDATWidget, inputPorts)
-
- self.setResult('canvas',canvas)
-
-class scatter(Module):
- """
- Function: scatter # Generate a scatter plot
-
- Description of Function:
- Generate a scatter plot given the data, scatter graphics method, and
- template. If no scatter class object is given, then the 'default' scatter
- graphics method is used. Similarly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('scatter') # Show all the existing scatter graphics methods
- sct=a.getscatter('quick') # Create instance of 'quick'
- a.scatter(array,sct) # Plot array using specified sct and default
- # template
- a.clear() # Clear VCS canvas
- a.scatter(array,sct,template) # Plot array using specified sct and template
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End scatter Description ################################################
-######################################### #################################################
-###################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- slab2 = None
- if self.hasInputFromPort('slab2_0'):
- slab2 = self.getInputFromPort('slab2_0')
- args.append(slab2)
- slab1 = None
- if self.hasInputFromPort('slab1_0'):
- slab1 = self.getInputFromPort('slab1_0')
- args.append(slab1)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- kwargs['bg'] = 1
- res = canvas.scatter(*args,**kwargs)
- self.setResult('display',res)
- self.setResult('canvas',canvas)
-
-class xvsy(Module):
- """
- Function: xvsy # Generate a XvsY plot
-
- Description of Function:
- Generate a XvsY plot given the data, XvsY graphics method, and
- template. If no XvsY class object is given, then the 'default' XvsY
- graphics method is used. Similarly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('xvsy') # Show all the existing XvsY graphics methods
- xy=a.getxvsy('quick') # Create instance of 'quick'
- a.xvsy(array,xy) # Plot array using specified xy and default
- # template
- a.clear() # Clear VCS canvas
- a.xvsy(array,xy,template) # Plot array using specified xy and template
-
-#################################################################################################################
-########################################### ###############################################
-########################################## End xvsy Description ################################################
-######################################### #################################################
-#################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- slab2 = None
- if self.hasInputFromPort('slab2_0'):
- slab2 = self.getInputFromPort('slab2_0')
- args.append(slab2)
- slab1 = None
- if self.hasInputFromPort('slab1_0'):
- slab1 = self.getInputFromPort('slab1_0')
- args.append(slab1)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('yaxisconvert'):
- kwargs['yaxisconvert'] = self.getInputFromPort('yaxisconvert')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- kwargs['bg'] = 1
- res = canvas.xvsy(*args,**kwargs)
- self.setResult('display',res)
- self.setResult('canvas',canvas)
-
-class xyvsy(Module):
- """
- Function: xyvsy # Generate a Xyvsy plot
-
- Description of Function:
- Generate a Xyvsy plot given the data, Xyvsy graphics method, and
- template. If no Xyvsy class object is given, then the 'default' Xyvsy
- graphics method is used. Simerly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('xyvsy') # Show all the existing Xyvsy graphics methods
- xyy=a.getxyvsy('quick') # Create instance of 'quick'
- a.xyvsy(array,xyy) # Plot array using specified xyy and default
- # template
- a.clear() # Clear VCS canvas
- a.xyvsy(array,xyy,template) # Plot array using specified xyy and template
-
-#################################################################################################################
-########################################### ###############################################
-########################################## End xyvsy Description ################################################
-######################################### #################################################
-#################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- args.append(slab)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- kwargs['bg'] = 1
- res = canvas.xyvsy(*args,**kwargs)
- self.setResult('display',res)
- self.setResult('canvas',canvas)
-
-class yxvsx(Module):
- """
- Function: yxvsx # Generate a Yxvsx plot
-
- Description of Function:
- Generate a Yxvsx plot given the data, Yxvsx graphics method, and
- template. If no Yxvsx class object is given, then the 'default' Yxvsx
- graphics method is used. Simerly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('yxvsx') # Show all the existing Yxvsx graphics methods
- yxx=a.getyxvsx('quick') # Create instance of 'quick'
- a.yxvsx(array,yxx) # Plot array using specified yxx and default
- # template
- a.clear() # Clear VCS canvas
- a.yxvsx(array,yxx,template) # Plot array using specified yxx and template
-
-#################################################################################################################
-########################################### ###############################################
-########################################## End yxvsx Description ################################################
-######################################### #################################################
-#################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- slab = None
- if self.hasInputFromPort('slab_0'):
- slab = self.getInputFromPort('slab_0')
- args.append(slab)
-
- # build up the keyword arguments from the optional inputs.
- kwargs = {}
- if self.hasInputFromPort('datawc_timeunits'):
- kwargs['datawc_timeunits'] = self.getInputFromPort('datawc_timeunits')
- if self.hasInputFromPort('long_name'):
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('projection_0'):
- kwargs['projection'] = self.getInputFromPort('projection_0')
- if self.hasInputFromPort('xticlabels2_0'):
- kwargs['xticlabels2'] = self.getInputFromPort('xticlabels2_0')
- if self.hasInputFromPort('xarray_0'):
- kwargs['xarray'] = self.getInputFromPort('xarray_0')
- if self.hasInputFromPort('yweights_0'):
- kwargs['yweights'] = self.getInputFromPort('yweights_0')
- if self.hasInputFromPort('xweights_0'):
- kwargs['xweights'] = self.getInputFromPort('xweights_0')
- if self.hasInputFromPort('warray_0'):
- kwargs['warray'] = self.getInputFromPort('warray_0')
- if self.hasInputFromPort('tunits'):
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('ymtics1_0'):
- kwargs['ymtics1'] = self.getInputFromPort('ymtics1_0')
- if self.hasInputFromPort('ymtics2_0'):
- kwargs['ymtics2'] = self.getInputFromPort('ymtics2_0')
- if self.hasInputFromPort('datawc_x1'):
- kwargs['datawc_x1'] = self.getInputFromPort('datawc_x1')
- if self.hasInputFromPort('datawc_x2'):
- kwargs['datawc_x2'] = self.getInputFromPort('datawc_x2')
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
- if self.hasInputFromPort('xmtics1_0'):
- kwargs['xmtics1'] = self.getInputFromPort('xmtics1_0')
- if self.hasInputFromPort('xmtics2_0'):
- kwargs['xmtics2'] = self.getInputFromPort('xmtics2_0')
- if self.hasInputFromPort('xbounds_0'):
- kwargs['xbounds'] = self.getInputFromPort('xbounds_0')
- if self.hasInputFromPort('ybounds_0'):
- kwargs['ybounds'] = self.getInputFromPort('ybounds_0')
- if self.hasInputFromPort('datawc_y2'):
- kwargs['datawc_y2'] = self.getInputFromPort('datawc_y2')
- if self.hasInputFromPort('wname'):
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('file_comment'):
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('datawc_calendar'):
- kwargs['datawc_calendar'] = self.getInputFromPort('datawc_calendar')
- if self.hasInputFromPort('wunits'):
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xrev'):
- kwargs['xrev'] = self.getInputFromPort('xrev')
- if self.hasInputFromPort('ymd'):
- kwargs['ymd'] = self.getInputFromPort('ymd')
- if self.hasInputFromPort('yarray_0'):
- kwargs['yarray'] = self.getInputFromPort('yarray_0')
- if self.hasInputFromPort('units'):
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('yunits'):
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zarray_0'):
- kwargs['zarray'] = self.getInputFromPort('zarray_0')
- if self.hasInputFromPort('xname'):
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('tarray_0'):
- kwargs['tarray'] = self.getInputFromPort('tarray_0')
- if self.hasInputFromPort('bg_0'):
- kwargs['bg'] = self.getInputFromPort('bg_0')
- elif self.hasInputFromPort('bg_1'):
- kwargs['bg'] = self.getInputFromPort('bg_1')
- if self.hasInputFromPort('xaxisconvert'):
- kwargs['xaxisconvert'] = self.getInputFromPort('xaxisconvert')
- if self.hasInputFromPort('zname'):
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('hms'):
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('tname'):
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('yname'):
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('ratio_0'):
- kwargs['ratio'] = self.getInputFromPort('ratio_0')
- elif self.hasInputFromPort('ratio_1'):
- kwargs['ratio'] = self.getInputFromPort('ratio_1')
- if self.hasInputFromPort('datawc_y1'):
- kwargs['datawc_y1'] = self.getInputFromPort('datawc_y1')
- if self.hasInputFromPort('xunits'):
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('name'):
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('yticlabels1_0'):
- kwargs['yticlabels1'] = self.getInputFromPort('yticlabels1_0')
- if self.hasInputFromPort('yticlabels2_0'):
- kwargs['yticlabels2'] = self.getInputFromPort('yticlabels2_0')
- if self.hasInputFromPort('comment1'):
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('zunits'):
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('comment3'):
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment2'):
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('xticlabels1_0'):
- kwargs['xticlabels1'] = self.getInputFromPort('xticlabels1_0')
- if self.hasInputFromPort('comment4'):
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('yrev'):
- kwargs['yrev'] = self.getInputFromPort('yrev')
- #force images to be created in the background
- kwargs['bg'] = 1
- res = canvas.yxvsx(*args,**kwargs)
- self.setResult('display',res)
- self.setResult('canvas',canvas)
-
-class png(Module,NotCacheable):
- """
- Function: png
-
- Description of Function:
- Png output is another form of raster graphics.
-
- Example of Use:
- a=vcs.init()
- a.plot(array)
- a.png('example') # Overwrite a png file
- a.png('example', width=11.5, height= 8.5) # US Legal
- a.png('example', width=21, height=29.7, units='cm') # A4
-#################################################################################################################
-########################################### ###############################################
-########################################## End png Description ################################################
-######################################### #################################################
-#################################################################################################################
-
- """
- def compute(self):
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- canvas = vcs.init()
- args = []
- file = None
- if self.hasInputFromPort('file'):
- file = self.getInputFromPort('file')
- args.append(file)
-
- # file is a required port
- if file is None:
- raise ModuleError(self, "'file' is a mandatory port")
- width = None
- if self.hasInputFromPort('width'):
- width = self.getInputFromPort('width')
- args.append(width)
- height = None
- if self.hasInputFromPort('height'):
- height = self.getInputFromPort('height')
- args.append(height)
- units = None
- if self.hasInputFromPort('units'):
- units = self.getInputFromPort('units')
- args.append(units)
- ofile = core.modules.basic_modules.File()
- ofile.name = file
- canvas.png(*args)
- self.setResult('file',ofile)
-
-class open(Module):
- """
- Function: open # Open an existing dataset
-
-Description of Function:
- 'uri' is a Uniform Resource Identifier, referring to a cdunif file, XML file,
- or LDAP URL of a catalog dataset entry.
- 'mode' is 'r', 'r+', 'a', or 'w'
-###################################################################################################################
-########################################### ###############################################
-########################################## End open Description ################################################
-######################################### #################################################
-###################################################################################################################
-
- """
- def compute(self):
- args = []
- uri = None
- if self.hasInputFromPort('uri'):
- uri = self.getInputFromPort('uri')
- args.append(uri)
-
- # uri is a required port
- if uri is None:
- raise ModuleError(self, "'uri' is a mandatory port")
- mode = None
- if self.hasInputFromPort('mode'):
- mode = self.getInputFromPort('mode')
- args.append(mode)
- template = None
- if self.hasInputFromPort('template'):
- template = self.getInputFromPort('template')
- args.append(template)
- dods = None
- if self.hasInputFromPort('dods'):
- dods = self.getInputFromPort('dods')
- args.append(dods)
- res = cdms2.open(*args)
- self.setResult('dataset',res)
-
-class __call__(Module):
- """
- Function: __call__ # Call a variable object with the given id
-
-Description of Function:
- Call a variable object with the given id
- Exception if not found.
- Call the variable with the other arguments.
-###################################################################################################################
-########################################### ###############################################
-########################################## End _call_ Description ################################################
-######################################### #################################################
-###################################################################################################################
-
- """
- def compute(self):
- # Check ports
- if not self.hasInputFromPort('cdmsfile'):
- raise ModuleError(self, "'cdmsfile' is mandatory.")
- if not self.hasInputFromPort('type'):
- raise ModuleError(self, "'type' is mandatory.")
- if not self.hasInputFromPort('id'):
- raise ModuleError(self, "'id' is mandatory.")
- if not self.hasInputFromPort('axes'):
- raise ModuleError(self, "'axes' is mandatory.")
- if not self.hasInputFromPort('axesOperations'):
- raise ModuleError(self, "'axesOperations' is mandatory.")
-
- # Get input from ports
- cdmsfile = self.getInputFromPort('cdmsfile')
- varType = self.getInputFromPort('type')
- id = self.getInputFromPort('id')
- axes = self.getInputFromPort('axes')
- axesOperations = self.getInputFromPort('axesOperations')
-
- # Get the variable
- if (varType == 'variable'):
- var = cdmsfile.__call__(id)
- elif (varType == 'axis'):
- varID = self.getAxisID(id)
- axis = getattr(cdmsfile, 'axes')[varID]
- var = MV2.array(axis)
- var.setAxis(0, axis)
- elif (varType == 'weighted-axis'):
- varID, axisID = self.getVarAndAxisID(id)
- var = cdmsfile.__call__(varID)
- var = genutil.getAxisWeightByName(var, axisID)
- var.id = varID +'_' + axisID + '_weight'
- else:
- var = None
-
- # Get the updated variable
- if axes is not None and var is not None:
- try:
- kwargs = eval(axes)
- var = var(**kwargs)
- except:
- raise ModuleError(self, "Invalid 'axes' specification", axes)
-
- # Apply axes ops to the variable
- var = self.applyAxesOperations(var, axesOperations)
-
- self.setResult('variable', var)
-
- def applyAxesOperations(self, var, axesOperations):
- """ Apply kwargs / axis operations to update the dataset """
- try:
- axesOperations = eval(axesOperations)
- except:
- raise TypeError("Invalid string 'axesOperations'")
-
- for axis in list(axesOperations):
- if axesOperations[axis] == 'sum':
- var = cdutil.averager(var, axis="(%s)" % axis, weight='equal',
- action='sum')
- elif axesOperations[axis] == 'avg':
- var = cdutil.averager(var, axis="(%s)" % axis, weight='equal')
- elif axesOperations[axis] == 'wgt':
- var = cdutil.averager(var, axis="(%s)" % axis)
- elif axesOperations[axis] == 'gtm':
- var = genutil.statistics.geometricmean(var, axis="(%s)" % axis)
- elif axesOperations[axis] == 'std':
- var = genutil.statistics.std(var, axis="(%s)" % axis)
-
- return var
-
- def getVarAndAxisID(self, varID):
- """ get the varID and axisID from a string with format
- varID_axisID_weight """
-
- match = re.compile('(.+)(_)(.+)(_)(weight)').match(varID)
- if match:
- return (match.group(1), match.group(3))
-
- return None
-
- def getAxisID(self, varID):
- """ get the axisID from a string with format varID_axisID_axis """
-
- match = re.compile('(.+)(_)(.+)(_)(axis)').match(varID)
- if match:
- return match.group(3)
-
- return varID
-
-def initialize(*args, **keywords):
- reg = core.modules.module_registry.get_module_registry()
-
- reg.add_module(Canvas,namespace='vcs|Canvas')
- reg.add_module(GSp,namespace='vcs|scatter')
- reg.add_module(CdmsFile,namespace='cdms2|dataset')
- reg.add_module(TransientVariable,namespace='cdms2|tvariable')
- reg.add_module(GXy,namespace='vcs|xyvsy')
- reg.add_module(Go,namespace='vcs|outline')
- reg.add_module(Gfi,namespace='vcs|isofill')
- reg.add_module(Dp,namespace='vcs|displayplot')
- reg.add_module(Gfb,namespace='vcs|boxfill')
- reg.add_module(GYx,namespace='vcs|yxvsx')
- reg.add_module(GXY,namespace='vcs|xvsy')
- reg.add_module(Gi,namespace='vcs|isoline')
- reg.add_module(Gfo,namespace='vcs|outfill')
-
-
- ##########################################################################
- # included from cdatwindow_init_inc.py
- #display = sip.unwrapinstance(QtGui.QX11Info.display())
- #vcs._vcs.setdisplay(display)
-
- #cdat GUI modules
- global cdatWindow
- cdatWindow = QCDATWindow()
- cdatWindow.show()
-
-
- reg.add_module(CDATCell,namespace='cdat')
- reg.add_input_port(CDATCell, 'slab1',
- (TransientVariable, "variable to be plotted"))
- reg.add_input_port(CDATCell, 'slab2',
- (TransientVariable, "variable to be plotted"))
- reg.add_input_port(CDATCell, 'plotType',
- (core.modules.basic_modules.String, "Plot type"))
- reg.add_input_port(CDATCell, 'template',
- (core.modules.basic_modules.String, "template name"))
- reg.add_input_port(CDATCell, 'gmName',
- (core.modules.basic_modules.String, "graphics method name"))
- reg.add_input_port(CDATCell, 'canvas',
- (Canvas, "Canvas object"))
- reg.add_input_port(CDATCell, 'col',
- (core.modules.basic_modules.Integer, "Cell Col"))
- reg.add_input_port(CDATCell, 'row',
- (core.modules.basic_modules.Integer, "Cell Row"))
- reg.add_input_port(CDATCell, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_output_port(CDATCell, 'canvas',
- (Canvas, ""), True)
-
- reg.add_module(Variable, namespace='cdat')
- reg.add_module(Quickplot, namespace='cdat')
- reg.add_input_port(Variable, 'id',
- (core.modules.basic_modules.String,
- ""))
- reg.add_input_port(Variable, 'type',
- (core.modules.basic_modules.String,
- "variable, axis, or weighted-axis"))
- reg.add_input_port(Variable, 'inputVariable',
- (core.modules.basic_modules.List,
- ""))
- reg.add_output_port(Variable, 'variable',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- ""))
- reg.add_input_port(Variable, 'axes',
- (core.modules.basic_modules.String, "Axes of variables"))
- reg.add_input_port(Variable, 'axesOperations',
- (core.modules.basic_modules.String, "Axes Operations"))
- reg.add_input_port(Variable, 'cdmsfile',
- (CdmsFile, "cdmsfile"))
-
- reg.add_module(GraphicsMethod, namespace='cdat')
- reg.add_input_port(GraphicsMethod, 'gmName',
- (core.modules.basic_modules.String,
- "Get the graphics method object of the given name."))
- reg.add_input_port(GraphicsMethod, 'plotType',
- (core.modules.basic_modules.String, "Plot type"))
- reg.add_input_port(GraphicsMethod, 'slab1',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "slab1"))
- reg.add_input_port(GraphicsMethod, 'slab2',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "slab2"))
- reg.add_input_port(GraphicsMethod, 'color_1',
- (core.modules.basic_modules.Integer, "color_1"), True)
- reg.add_input_port(GraphicsMethod, 'color_2',
- (core.modules.basic_modules.Integer, "color_2"), True)
- reg.add_input_port(GraphicsMethod, 'level_1',
- (core.modules.basic_modules.Float, "level_1"), True)
- reg.add_input_port(GraphicsMethod, 'level_2',
- (core.modules.basic_modules.Float, "level_2"), True)
- reg.add_output_port(GraphicsMethod, 'slab1',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "slab1"))
- reg.add_output_port(GraphicsMethod, 'slab2',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "slab2"))
- reg.add_output_port(GraphicsMethod, 'canvas', (Canvas, "Canvas object"))
-
- # end of cdatwindow_init_inc.py
- ##########################################################################
-
-
- #Module boxfill
- reg.add_module(boxfill,namespace='vcs|Canvas')
- reg.add_input_port(boxfill, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(boxfill, 'template',
- (core.modules.basic_modules.String,
- "Name of the template"))
- reg.add_input_port(boxfill, 'gm_name',
- (core.modules.basic_modules.String,
- "Name of the graphics method"))
- reg.add_input_port(boxfill, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(boxfill, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(boxfill, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(boxfill, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(boxfill, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(boxfill, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(boxfill, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(boxfill, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(boxfill, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(boxfill, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(boxfill, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(boxfill, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(boxfill, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(boxfill, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(boxfill, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(boxfill, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(boxfill, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(boxfill, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(boxfill, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(boxfill, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(boxfill, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(boxfill, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(boxfill, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(boxfill, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(boxfill, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(boxfill, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(boxfill, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(boxfill, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(boxfill, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(boxfill, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(boxfill, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(boxfill, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(boxfill, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(boxfill, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(boxfill, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(boxfill, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(boxfill, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(boxfill, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(boxfill, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(boxfill, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(boxfill, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(boxfill, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(boxfill, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(boxfill, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(boxfill, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(boxfill, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(boxfill, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(boxfill, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(boxfill, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(boxfill, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(boxfill, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(boxfill, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(boxfill, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(boxfill, 'display',
- (get_late_type('vcs.displayplot.Dp'),
- "no default"))
-
- #Module createboxfill
- reg.add_module(createboxfill,namespace='vcs|Canvas')
- reg.add_input_port(createboxfill, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_output_port(createboxfill, 'slab_0_out',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(createboxfill, 'new_GM_name',
- (core.modules.basic_modules.String,
- "name of the new graphics method object. If no name is given, then one will be created for use."))
- reg.add_input_port(createboxfill, 'source_GM_name',
- (core.modules.basic_modules.String,
- "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
- reg.add_input_port(createboxfill, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(createboxfill, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(createboxfill, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(createboxfill, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(createboxfill, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(createboxfill, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createboxfill, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createboxfill, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(createboxfill, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(createboxfill, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createboxfill, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createboxfill, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(createboxfill, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(createboxfill, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(createboxfill, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createboxfill, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createboxfill, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(createboxfill, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(createboxfill, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(createboxfill, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(createboxfill, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(createboxfill, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(createboxfill, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(createboxfill, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(createboxfill, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(createboxfill, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(createboxfill, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(createboxfill, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(createboxfill, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(createboxfill, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(createboxfill, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(createboxfill, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(createboxfill, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(createboxfill, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createboxfill, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(createboxfill, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(createboxfill, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(createboxfill, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(createboxfill, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createboxfill, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createboxfill, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(createboxfill, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createboxfill, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(createboxfill, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(createboxfill, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(createboxfill, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(createboxfill, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(createboxfill, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(createboxfill, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(createboxfill, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(createboxfill, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(createboxfill, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(createboxfill, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(createboxfill, 'boxfill',
- (get_late_type('vcs.boxfill.Gfb'),
- "no default"))
-
- #Module createisofill
- reg.add_module(createisofill,namespace='vcs|Canvas')
- reg.add_input_port(createisofill, 'new_GM_name',
- (core.modules.basic_modules.String,
- "name of the new graphics method object. If no name is given, then one will be created for use."))
- reg.add_input_port(createisofill, 'source_GM_name',
- (core.modules.basic_modules.String,
- "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
- reg.add_input_port(createisofill, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_output_port(createisofill, 'slab_0_out',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(createisofill, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(createisofill, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(createisofill, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(createisofill, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(createisofill, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(createisofill, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createisofill, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createisofill, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(createisofill, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(createisofill, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createisofill, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createisofill, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(createisofill, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(createisofill, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(createisofill, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createisofill, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createisofill, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(createisofill, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(createisofill, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(createisofill, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(createisofill, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(createisofill, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(createisofill, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(createisofill, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(createisofill, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(createisofill, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(createisofill, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(createisofill, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(createisofill, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(createisofill, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(createisofill, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(createisofill, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(createisofill, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(createisofill, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createisofill, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(createisofill, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(createisofill, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(createisofill, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(createisofill, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createisofill, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createisofill, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(createisofill, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createisofill, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(createisofill, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(createisofill, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(createisofill, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(createisofill, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(createisofill, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(createisofill, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(createisofill, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(createisofill, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(createisofill, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(createisofill, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(createisofill, 'isofill',
- (get_late_type('vcs.isofill.Gfi'),
- "no default"))
-
- #Module createisoline
- reg.add_module(createisoline,namespace='vcs|Canvas')
- reg.add_input_port(createisoline, 'new_GM_name',
- (core.modules.basic_modules.String,
- "name of the new graphics method object. If no name is given, then one will be created for use."))
- reg.add_input_port(createisoline, 'source_GM_name',
- (core.modules.basic_modules.String,
- "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
- reg.add_input_port(createisoline, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_output_port(createisoline, 'slab_0_out',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(createisoline, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(createisoline, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(createisoline, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(createisoline, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(createisoline, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(createisoline, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createisoline, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createisoline, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(createisoline, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(createisoline, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createisoline, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createisoline, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(createisoline, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(createisoline, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(createisoline, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createisoline, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createisoline, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(createisoline, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(createisoline, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(createisoline, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(createisoline, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(createisoline, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(createisoline, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(createisoline, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(createisoline, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(createisoline, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(createisoline, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(createisoline, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(createisoline, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(createisoline, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(createisoline, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(createisoline, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(createisoline, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(createisoline, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createisoline, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(createisoline, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(createisoline, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(createisoline, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(createisoline, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createisoline, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createisoline, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(createisoline, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createisoline, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(createisoline, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(createisoline, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(createisoline, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(createisoline, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(createisoline, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(createisoline, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(createisoline, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(createisoline, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(createisoline, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(createisoline, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(createisoline, 'isoline',
- (get_late_type('vcs.isoline.Gi'),
- "no default"))
-
- #Module createoutfill
- reg.add_module(createoutfill,namespace='vcs|Canvas')
- reg.add_input_port(createoutfill, 'new_GM_name',
- (core.modules.basic_modules.String,
- "name of the new graphics method object. If no name is given, then one will be created for use."))
- reg.add_input_port(createoutfill, 'source_GM_name',
- (core.modules.basic_modules.String,
- "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
- reg.add_input_port(createoutfill, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_output_port(createoutfill, 'slab_0_out',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(createoutfill, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(createoutfill, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(createoutfill, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(createoutfill, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(createoutfill, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(createoutfill, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createoutfill, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createoutfill, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(createoutfill, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(createoutfill, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createoutfill, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createoutfill, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(createoutfill, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(createoutfill, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(createoutfill, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createoutfill, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createoutfill, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(createoutfill, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(createoutfill, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(createoutfill, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(createoutfill, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(createoutfill, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(createoutfill, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(createoutfill, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(createoutfill, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(createoutfill, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(createoutfill, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(createoutfill, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(createoutfill, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(createoutfill, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(createoutfill, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(createoutfill, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(createoutfill, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(createoutfill, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createoutfill, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(createoutfill, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(createoutfill, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(createoutfill, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(createoutfill, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createoutfill, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createoutfill, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(createoutfill, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createoutfill, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(createoutfill, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(createoutfill, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(createoutfill, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(createoutfill, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(createoutfill, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(createoutfill, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(createoutfill, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(createoutfill, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(createoutfill, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(createoutfill, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(createoutfill, 'outfill',
- (get_late_type('vcs.outfill.Gfo'),
- "no default"))
-
- #Module createoutline
- reg.add_module(createoutline,namespace='vcs|Canvas')
- reg.add_input_port(createoutline, 'new_GM_name',
- (core.modules.basic_modules.String,
- "name of the new graphics method object. If no name is given, then one will be created for use."))
- reg.add_input_port(createoutline, 'source_GM_name',
- (core.modules.basic_modules.String,
- "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
- reg.add_input_port(createoutline, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_output_port(createoutline, 'slab_0_out',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(createoutline, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(createoutline, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(createoutline, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(createoutline, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(createoutline, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(createoutline, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createoutline, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createoutline, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(createoutline, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(createoutline, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createoutline, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createoutline, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(createoutline, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(createoutline, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(createoutline, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createoutline, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createoutline, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(createoutline, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(createoutline, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(createoutline, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(createoutline, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(createoutline, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(createoutline, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(createoutline, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(createoutline, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(createoutline, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(createoutline, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(createoutline, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(createoutline, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(createoutline, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(createoutline, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(createoutline, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(createoutline, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(createoutline, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createoutline, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(createoutline, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(createoutline, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(createoutline, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(createoutline, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createoutline, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createoutline, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(createoutline, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createoutline, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(createoutline, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(createoutline, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(createoutline, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(createoutline, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(createoutline, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(createoutline, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(createoutline, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(createoutline, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(createoutline, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(createoutline, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(createoutline, 'outline',
- (get_late_type('vcs.outline.Go'),
- "no default"))
-
- #Module createscatter
- reg.add_module(createscatter,namespace='vcs|Canvas')
- reg.add_input_port(createscatter, 'new_GM_name',
- (core.modules.basic_modules.String,
- "name of the new graphics method object. If no name is given, then one will be created for use."))
- reg.add_input_port(createscatter, 'source_GM_name',
- (core.modules.basic_modules.String,
- "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
- reg.add_input_port(createscatter, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_output_port(createscatter, 'slab_0_out',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(createscatter, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(createscatter, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(createscatter, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(createscatter, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(createscatter, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(createscatter, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createscatter, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createscatter, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(createscatter, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(createscatter, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createscatter, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createscatter, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(createscatter, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(createscatter, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(createscatter, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createscatter, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createscatter, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(createscatter, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(createscatter, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(createscatter, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(createscatter, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(createscatter, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(createscatter, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(createscatter, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(createscatter, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(createscatter, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(createscatter, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(createscatter, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(createscatter, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(createscatter, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(createscatter, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(createscatter, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(createscatter, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(createscatter, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createscatter, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(createscatter, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(createscatter, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(createscatter, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(createscatter, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createscatter, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createscatter, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(createscatter, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createscatter, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(createscatter, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(createscatter, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(createscatter, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(createscatter, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(createscatter, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(createscatter, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(createscatter, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(createscatter, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(createscatter, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(createscatter, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(createscatter, 'scatter',
- (get_late_type('vcs.scatter.GSp'),
- "no default"))
-
- #Module createxvsy
- reg.add_module(createxvsy,namespace='vcs|Canvas')
- reg.add_input_port(createxvsy, 'new_GM_name',
- (core.modules.basic_modules.String,
- "name of the new graphics method object. If no name is given, then one will be created for use."))
- reg.add_input_port(createxvsy, 'source_GM_name',
- (core.modules.basic_modules.String,
- "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
- reg.add_input_port(createxvsy, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_output_port(createxvsy, 'slab_0_out',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(createxvsy, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(createxvsy, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(createxvsy, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(createxvsy, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(createxvsy, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(createxvsy, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createxvsy, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createxvsy, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(createxvsy, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(createxvsy, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createxvsy, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createxvsy, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(createxvsy, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(createxvsy, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(createxvsy, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createxvsy, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createxvsy, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(createxvsy, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(createxvsy, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(createxvsy, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(createxvsy, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(createxvsy, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(createxvsy, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(createxvsy, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(createxvsy, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(createxvsy, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(createxvsy, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(createxvsy, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(createxvsy, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(createxvsy, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(createxvsy, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(createxvsy, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(createxvsy, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(createxvsy, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createxvsy, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(createxvsy, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(createxvsy, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(createxvsy, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(createxvsy, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createxvsy, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createxvsy, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(createxvsy, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createxvsy, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(createxvsy, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(createxvsy, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(createxvsy, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(createxvsy, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(createxvsy, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(createxvsy, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(createxvsy, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(createxvsy, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(createxvsy, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(createxvsy, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(createxvsy, 'xvsy',
- (get_late_type('vcs.xvsy.GXY'),
- "no default"))
-
- #Module createxyvsy
- reg.add_module(createxyvsy,namespace='vcs|Canvas')
- reg.add_input_port(createxyvsy, 'new_GM_name',
- (core.modules.basic_modules.String,
- "name of the new graphics method object. If no name is given, then one will be created for use."))
- reg.add_input_port(createxyvsy, 'source_GM_name',
- (core.modules.basic_modules.String,
- "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
- reg.add_input_port(createxyvsy, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_output_port(createxyvsy, 'slab_0_out',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(createxyvsy, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(createxyvsy, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(createxyvsy, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(createxyvsy, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(createxyvsy, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(createxyvsy, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createxyvsy, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createxyvsy, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(createxyvsy, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(createxyvsy, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createxyvsy, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createxyvsy, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(createxyvsy, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(createxyvsy, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(createxyvsy, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createxyvsy, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createxyvsy, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(createxyvsy, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(createxyvsy, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(createxyvsy, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(createxyvsy, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(createxyvsy, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(createxyvsy, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(createxyvsy, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(createxyvsy, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(createxyvsy, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(createxyvsy, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(createxyvsy, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(createxyvsy, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(createxyvsy, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(createxyvsy, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(createxyvsy, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(createxyvsy, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(createxyvsy, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createxyvsy, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(createxyvsy, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(createxyvsy, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(createxyvsy, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(createxyvsy, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createxyvsy, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createxyvsy, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(createxyvsy, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createxyvsy, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(createxyvsy, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(createxyvsy, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(createxyvsy, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(createxyvsy, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(createxyvsy, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(createxyvsy, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(createxyvsy, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(createxyvsy, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(createxyvsy, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(createxyvsy, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(createxyvsy, 'xyvsy',
- (get_late_type('vcs.xyvsy.GXy'),
- "no default"))
-
- #Module createyxvsx
- reg.add_module(createyxvsx,namespace='vcs|Canvas')
- reg.add_input_port(createyxvsx, 'new_GM_name',
- (core.modules.basic_modules.String,
- "name of the new graphics method object. If no name is given, then one will be created for use."))
- reg.add_input_port(createyxvsx, 'source_GM_name',
- (core.modules.basic_modules.String,
- "copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object."))
- reg.add_input_port(createyxvsx, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_output_port(createyxvsx, 'slab_0_out',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(createyxvsx, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(createyxvsx, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(createyxvsx, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(createyxvsx, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(createyxvsx, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(createyxvsx, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createyxvsx, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(createyxvsx, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(createyxvsx, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(createyxvsx, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createyxvsx, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createyxvsx, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(createyxvsx, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(createyxvsx, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(createyxvsx, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(createyxvsx, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(createyxvsx, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(createyxvsx, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(createyxvsx, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(createyxvsx, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(createyxvsx, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(createyxvsx, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(createyxvsx, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(createyxvsx, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(createyxvsx, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(createyxvsx, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(createyxvsx, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(createyxvsx, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(createyxvsx, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(createyxvsx, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(createyxvsx, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(createyxvsx, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(createyxvsx, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(createyxvsx, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createyxvsx, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(createyxvsx, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(createyxvsx, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(createyxvsx, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(createyxvsx, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createyxvsx, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(createyxvsx, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(createyxvsx, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(createyxvsx, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(createyxvsx, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(createyxvsx, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(createyxvsx, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(createyxvsx, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(createyxvsx, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(createyxvsx, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(createyxvsx, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(createyxvsx, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(createyxvsx, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(createyxvsx, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(createyxvsx, 'yxvsx',
- (get_late_type('vcs.yxvsx.GYx'),
- "no default"))
-
- #Module getboxfill
- reg.add_module(getboxfill,namespace='vcs|Canvas')
- reg.add_input_port(getboxfill, 'GM_name',
- (core.modules.basic_modules.String,
- "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
- reg.add_input_port(getboxfill, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(getboxfill, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(getboxfill, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(getboxfill, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(getboxfill, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(getboxfill, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getboxfill, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getboxfill, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(getboxfill, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(getboxfill, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getboxfill, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getboxfill, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(getboxfill, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(getboxfill, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(getboxfill, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getboxfill, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getboxfill, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(getboxfill, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(getboxfill, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(getboxfill, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(getboxfill, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(getboxfill, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(getboxfill, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(getboxfill, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(getboxfill, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(getboxfill, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(getboxfill, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(getboxfill, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(getboxfill, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(getboxfill, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(getboxfill, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(getboxfill, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(getboxfill, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(getboxfill, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getboxfill, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(getboxfill, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(getboxfill, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(getboxfill, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(getboxfill, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getboxfill, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getboxfill, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(getboxfill, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getboxfill, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(getboxfill, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(getboxfill, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(getboxfill, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(getboxfill, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(getboxfill, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(getboxfill, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(getboxfill, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(getboxfill, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(getboxfill, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(getboxfill, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(getboxfill, 'boxfill',
- (get_late_type('vcs.boxfill.Gfb'),
- "no default"))
-
- #Module getisofill
- reg.add_module(getisofill,namespace='vcs|Canvas')
- reg.add_input_port(getisofill, 'GM_name',
- (core.modules.basic_modules.String,
- "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
- reg.add_input_port(getisofill, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(getisofill, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(getisofill, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(getisofill, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(getisofill, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(getisofill, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getisofill, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getisofill, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(getisofill, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(getisofill, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getisofill, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getisofill, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(getisofill, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(getisofill, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(getisofill, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getisofill, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getisofill, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(getisofill, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(getisofill, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(getisofill, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(getisofill, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(getisofill, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(getisofill, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(getisofill, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(getisofill, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(getisofill, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(getisofill, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(getisofill, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(getisofill, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(getisofill, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(getisofill, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(getisofill, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(getisofill, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(getisofill, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getisofill, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(getisofill, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(getisofill, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(getisofill, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(getisofill, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getisofill, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getisofill, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(getisofill, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getisofill, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(getisofill, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(getisofill, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(getisofill, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(getisofill, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(getisofill, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(getisofill, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(getisofill, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(getisofill, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(getisofill, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(getisofill, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(getisofill, 'isofill',
- (get_late_type('vcs.isofill.Gfi'),
- "no default"))
-
- #Module getisoline
- reg.add_module(getisoline,namespace='vcs|Canvas')
- reg.add_input_port(getisoline, 'GM_name',
- (core.modules.basic_modules.String,
- "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
- reg.add_input_port(getisoline, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(getisoline, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(getisoline, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(getisoline, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(getisoline, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(getisoline, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getisoline, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getisoline, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(getisoline, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(getisoline, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getisoline, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getisoline, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(getisoline, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(getisoline, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(getisoline, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getisoline, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getisoline, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(getisoline, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(getisoline, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(getisoline, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(getisoline, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(getisoline, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(getisoline, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(getisoline, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(getisoline, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(getisoline, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(getisoline, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(getisoline, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(getisoline, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(getisoline, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(getisoline, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(getisoline, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(getisoline, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(getisoline, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getisoline, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(getisoline, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(getisoline, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(getisoline, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(getisoline, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getisoline, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getisoline, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(getisoline, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getisoline, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(getisoline, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(getisoline, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(getisoline, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(getisoline, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(getisoline, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(getisoline, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(getisoline, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(getisoline, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(getisoline, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(getisoline, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(getisoline, 'isoline',
- (get_late_type('vcs.isoline.Gi'),
- "no default"))
-
- #Module getoutfill
- reg.add_module(getoutfill,namespace='vcs|Canvas')
- reg.add_input_port(getoutfill, 'GM_name',
- (core.modules.basic_modules.String,
- "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
- reg.add_input_port(getoutfill, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(getoutfill, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(getoutfill, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(getoutfill, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(getoutfill, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(getoutfill, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getoutfill, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getoutfill, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(getoutfill, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(getoutfill, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getoutfill, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getoutfill, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(getoutfill, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(getoutfill, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(getoutfill, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getoutfill, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getoutfill, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(getoutfill, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(getoutfill, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(getoutfill, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(getoutfill, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(getoutfill, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(getoutfill, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(getoutfill, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(getoutfill, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(getoutfill, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(getoutfill, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(getoutfill, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(getoutfill, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(getoutfill, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(getoutfill, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(getoutfill, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(getoutfill, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(getoutfill, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getoutfill, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(getoutfill, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(getoutfill, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(getoutfill, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(getoutfill, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getoutfill, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getoutfill, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(getoutfill, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getoutfill, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(getoutfill, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(getoutfill, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(getoutfill, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(getoutfill, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(getoutfill, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(getoutfill, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(getoutfill, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(getoutfill, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(getoutfill, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(getoutfill, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(getoutfill, 'outfill',
- (get_late_type('vcs.outfill.Gfo'),
- "no default"))
-
- #Module getoutline
- reg.add_module(getoutline,namespace='vcs|Canvas')
- reg.add_input_port(getoutline, 'GM_name',
- (core.modules.basic_modules.String,
- "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
- reg.add_input_port(getoutline, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(getoutline, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(getoutline, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(getoutline, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(getoutline, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(getoutline, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getoutline, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getoutline, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(getoutline, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(getoutline, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getoutline, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getoutline, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(getoutline, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(getoutline, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(getoutline, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getoutline, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getoutline, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(getoutline, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(getoutline, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(getoutline, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(getoutline, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(getoutline, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(getoutline, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(getoutline, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(getoutline, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(getoutline, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(getoutline, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(getoutline, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(getoutline, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(getoutline, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(getoutline, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(getoutline, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(getoutline, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(getoutline, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getoutline, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(getoutline, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(getoutline, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(getoutline, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(getoutline, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getoutline, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getoutline, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(getoutline, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getoutline, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(getoutline, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(getoutline, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(getoutline, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(getoutline, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(getoutline, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(getoutline, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(getoutline, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(getoutline, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(getoutline, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(getoutline, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(getoutline, 'outline',
- (get_late_type('vcs.outline.Go'),
- "no default"))
-
- #Module getscatter
- reg.add_module(getscatter,namespace='vcs|Canvas')
- reg.add_input_port(getscatter, 'GM_name',
- (core.modules.basic_modules.String,
- "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
- reg.add_input_port(getscatter, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(getscatter, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(getscatter, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(getscatter, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(getscatter, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(getscatter, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getscatter, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getscatter, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(getscatter, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(getscatter, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getscatter, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getscatter, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(getscatter, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(getscatter, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(getscatter, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getscatter, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getscatter, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(getscatter, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(getscatter, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(getscatter, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(getscatter, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(getscatter, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(getscatter, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(getscatter, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(getscatter, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(getscatter, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(getscatter, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(getscatter, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(getscatter, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(getscatter, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(getscatter, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(getscatter, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(getscatter, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(getscatter, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getscatter, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(getscatter, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(getscatter, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(getscatter, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(getscatter, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getscatter, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getscatter, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(getscatter, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getscatter, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(getscatter, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(getscatter, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(getscatter, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(getscatter, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(getscatter, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(getscatter, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(getscatter, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(getscatter, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(getscatter, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(getscatter, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(getscatter, 'scatter',
- (get_late_type('vcs.scatter.GSp'),
- "no default"))
-
- #Module getxvsy
- reg.add_module(getxvsy,namespace='vcs|Canvas')
- reg.add_input_port(getxvsy, 'GM_name',
- (core.modules.basic_modules.String,
- "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
- reg.add_input_port(getxvsy, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(getxvsy, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(getxvsy, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(getxvsy, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(getxvsy, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(getxvsy, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getxvsy, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getxvsy, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(getxvsy, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(getxvsy, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getxvsy, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getxvsy, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(getxvsy, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(getxvsy, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(getxvsy, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getxvsy, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getxvsy, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(getxvsy, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(getxvsy, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(getxvsy, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(getxvsy, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(getxvsy, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(getxvsy, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(getxvsy, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(getxvsy, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(getxvsy, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(getxvsy, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(getxvsy, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(getxvsy, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(getxvsy, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(getxvsy, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(getxvsy, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(getxvsy, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(getxvsy, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getxvsy, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(getxvsy, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(getxvsy, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(getxvsy, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(getxvsy, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getxvsy, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getxvsy, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(getxvsy, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getxvsy, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(getxvsy, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(getxvsy, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(getxvsy, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(getxvsy, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(getxvsy, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(getxvsy, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(getxvsy, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(getxvsy, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(getxvsy, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(getxvsy, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(getxvsy, 'xvsy',
- (get_late_type('vcs.xvsy.GXY'),
- "no default"))
-
- #Module getxyvsy
- reg.add_module(getxyvsy,namespace='vcs|Canvas')
- reg.add_input_port(getxyvsy, 'GM_name',
- (core.modules.basic_modules.String,
- "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
- reg.add_input_port(getxyvsy, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(getxyvsy, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(getxyvsy, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(getxyvsy, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(getxyvsy, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(getxyvsy, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getxyvsy, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getxyvsy, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(getxyvsy, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(getxyvsy, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getxyvsy, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getxyvsy, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(getxyvsy, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(getxyvsy, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(getxyvsy, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getxyvsy, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getxyvsy, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(getxyvsy, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(getxyvsy, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(getxyvsy, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(getxyvsy, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(getxyvsy, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(getxyvsy, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(getxyvsy, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(getxyvsy, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(getxyvsy, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(getxyvsy, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(getxyvsy, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(getxyvsy, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(getxyvsy, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(getxyvsy, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(getxyvsy, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(getxyvsy, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(getxyvsy, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getxyvsy, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(getxyvsy, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(getxyvsy, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(getxyvsy, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(getxyvsy, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getxyvsy, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getxyvsy, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(getxyvsy, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getxyvsy, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(getxyvsy, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(getxyvsy, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(getxyvsy, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(getxyvsy, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(getxyvsy, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(getxyvsy, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(getxyvsy, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(getxyvsy, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(getxyvsy, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(getxyvsy, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(getxyvsy, 'xyvsy',
- (get_late_type('vcs.xyvsy.GXy'),
- "no default"))
-
- #Module getyxvsx
- reg.add_module(getyxvsx,namespace='vcs|Canvas')
- reg.add_input_port(getyxvsx, 'GM_name',
- (core.modules.basic_modules.String,
- "retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method."))
- reg.add_input_port(getyxvsx, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(getyxvsx, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(getyxvsx, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(getyxvsx, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(getyxvsx, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(getyxvsx, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getyxvsx, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(getyxvsx, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(getyxvsx, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(getyxvsx, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getyxvsx, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getyxvsx, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(getyxvsx, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(getyxvsx, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(getyxvsx, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(getyxvsx, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(getyxvsx, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(getyxvsx, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(getyxvsx, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(getyxvsx, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(getyxvsx, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(getyxvsx, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(getyxvsx, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(getyxvsx, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(getyxvsx, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(getyxvsx, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(getyxvsx, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(getyxvsx, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(getyxvsx, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(getyxvsx, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(getyxvsx, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(getyxvsx, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(getyxvsx, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(getyxvsx, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getyxvsx, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(getyxvsx, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(getyxvsx, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(getyxvsx, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(getyxvsx, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getyxvsx, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(getyxvsx, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(getyxvsx, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(getyxvsx, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(getyxvsx, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(getyxvsx, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(getyxvsx, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(getyxvsx, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(getyxvsx, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(getyxvsx, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(getyxvsx, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(getyxvsx, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(getyxvsx, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(getyxvsx, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(getyxvsx, 'yxvsx',
- (get_late_type('vcs.yxvsx.GYx'),
- "no default"))
-
- #Module isofill
- reg.add_module(isofill,namespace='vcs|Canvas')
- reg.add_input_port(isofill, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(isofill, 'template',
- (core.modules.basic_modules.String,
- "Name of the template"))
- reg.add_input_port(isofill, 'gm_name',
- (core.modules.basic_modules.String,
- "Name of the graphics method"))
- reg.add_input_port(isofill, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(isofill, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(isofill, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(isofill, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(isofill, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(isofill, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(isofill, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(isofill, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(isofill, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(isofill, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(isofill, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(isofill, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(isofill, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(isofill, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(isofill, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(isofill, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(isofill, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(isofill, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(isofill, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(isofill, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(isofill, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(isofill, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(isofill, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(isofill, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(isofill, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(isofill, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(isofill, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(isofill, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(isofill, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(isofill, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(isofill, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(isofill, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(isofill, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(isofill, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(isofill, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(isofill, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(isofill, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(isofill, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(isofill, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(isofill, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(isofill, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(isofill, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(isofill, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(isofill, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(isofill, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(isofill, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(isofill, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(isofill, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(isofill, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(isofill, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(isofill, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(isofill, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(isofill, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(isofill, 'display',
- (get_late_type('vcs.displayplot.Dp'),
- "no default"))
-
- #Module isoline
- reg.add_module(isoline,namespace='vcs|Canvas')
- reg.add_input_port(isoline, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(isoline, 'template',
- (core.modules.basic_modules.String,
- "Name of the template"))
- reg.add_input_port(isoline, 'gm_name',
- (core.modules.basic_modules.String,
- "Name of the graphics method"))
- reg.add_input_port(isoline, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(isoline, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(isoline, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(isoline, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(isoline, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(isoline, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(isoline, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(isoline, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(isoline, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(isoline, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(isoline, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(isoline, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(isoline, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(isoline, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(isoline, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(isoline, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(isoline, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(isoline, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(isoline, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(isoline, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(isoline, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(isoline, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(isoline, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(isoline, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(isoline, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(isoline, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(isoline, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(isoline, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(isoline, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(isoline, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(isoline, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(isoline, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(isoline, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(isoline, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(isoline, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(isoline, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(isoline, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(isoline, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(isoline, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(isoline, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(isoline, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(isoline, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(isoline, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(isoline, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(isoline, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(isoline, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(isoline, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(isoline, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(isoline, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(isoline, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(isoline, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(isoline, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(isoline, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(isoline, 'display',
- (get_late_type('vcs.displayplot.Dp'),
- "no default"))
-
- #Module outfill
- reg.add_module(outfill,namespace='vcs|Canvas')
- reg.add_input_port(outfill, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(outfill, 'template',
- (core.modules.basic_modules.String,
- "Name of the template"))
- reg.add_input_port(outfill, 'gm_name',
- (core.modules.basic_modules.String,
- "Name of the graphics method"))
- reg.add_input_port(outfill, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(outfill, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(outfill, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(outfill, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(outfill, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(outfill, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(outfill, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(outfill, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(outfill, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(outfill, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(outfill, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(outfill, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(outfill, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(outfill, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(outfill, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(outfill, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(outfill, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(outfill, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(outfill, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(outfill, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(outfill, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(outfill, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(outfill, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(outfill, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(outfill, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(outfill, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(outfill, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(outfill, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(outfill, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(outfill, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(outfill, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(outfill, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(outfill, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(outfill, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(outfill, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(outfill, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(outfill, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(outfill, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(outfill, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(outfill, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(outfill, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(outfill, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(outfill, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(outfill, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(outfill, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(outfill, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(outfill, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(outfill, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(outfill, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(outfill, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(outfill, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(outfill, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(outfill, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(outfill, 'display',
- (get_late_type('vcs.displayplot.Dp'),
- "no default"))
-
- #Module outline
- reg.add_module(outline,namespace='vcs|Canvas')
- reg.add_input_port(outline, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 2D, last 2 dimensions will be plotted"))
- reg.add_input_port(outline, 'template',
- (core.modules.basic_modules.String,
- "Name of the template"))
- reg.add_input_port(outline, 'gm_name',
- (core.modules.basic_modules.String,
- "Name of the graphics method"))
- reg.add_input_port(outline, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(outline, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(outline, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(outline, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(outline, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(outline, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(outline, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(outline, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(outline, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(outline, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(outline, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(outline, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(outline, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(outline, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(outline, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(outline, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(outline, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(outline, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(outline, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(outline, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(outline, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(outline, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(outline, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(outline, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(outline, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(outline, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(outline, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(outline, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(outline, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(outline, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(outline, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(outline, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(outline, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(outline, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(outline, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(outline, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(outline, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(outline, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(outline, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(outline, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(outline, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(outline, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(outline, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(outline, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(outline, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(outline, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(outline, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(outline, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(outline, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(outline, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(outline, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(outline, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(outline, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(outline, 'display',
- (get_late_type('vcs.displayplot.Dp'),
- "no default"))
-
- #Module plot
- reg.add_module(plot,namespace='vcs|Canvas')
- reg.add_input_port(plot, 'row',
- (core.modules.basic_modules.Integer, "Cell Row"))
- reg.add_input_port(plot, 'col',
- (core.modules.basic_modules.Integer, "Cell Col"))
- reg.add_input_port(plot, 'template',
- (core.modules.basic_modules.String,
- "Name of the template"))
- reg.add_input_port(plot, 'gm_name',
- (core.modules.basic_modules.String,
- "Name of the graphics method"))
- reg.add_input_port(plot, 'plot_type',
- (core.modules.basic_modules.String,
- "Type of plot - boxfill, isoline, etc"))
- reg.add_input_port(plot, 'slab2_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 1D, last dimension will be plotted"))
- reg.add_input_port(plot, 'slab1_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 1D, last dimension will be plotted"))
-
- reg.add_input_port(plot, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(plot, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(plot, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(plot, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(plot, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(plot, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(plot, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(plot, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(plot, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(plot, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(plot, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(plot, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(plot, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(plot, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(plot, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(plot, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(plot, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(plot, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(plot, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(plot, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(plot, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(plot, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(plot, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(plot, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(plot, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(plot, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(plot, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(plot, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(plot, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(plot, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(plot, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(plot, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(plot, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(plot, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(plot, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(plot, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(plot, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(plot, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(plot, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(plot, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(plot, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(plot, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(plot, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(plot, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(plot, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(plot, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(plot, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(plot, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(plot, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(plot, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(plot, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(plot, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(plot, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(plot, 'display',
- (get_late_type('vcs.displayplot.Dp'),
- "no default"))
-
- #Module scatter
- reg.add_module(scatter,namespace='vcs|Canvas')
- reg.add_input_port(scatter, 'template',
- (core.modules.basic_modules.String,
- "Name of the template"))
- reg.add_input_port(scatter, 'gm_name',
- (core.modules.basic_modules.String,
- "Name of the graphics method"))
- reg.add_input_port(scatter, 'slab2_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 1D, last dimension will be plotted"))
- reg.add_input_port(scatter, 'slab1_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 1D, last dimension will be plotted"))
- reg.add_input_port(scatter, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(scatter, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(scatter, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(scatter, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(scatter, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(scatter, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(scatter, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(scatter, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(scatter, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(scatter, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(scatter, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(scatter, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(scatter, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(scatter, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(scatter, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(scatter, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(scatter, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(scatter, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(scatter, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(scatter, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(scatter, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(scatter, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(scatter, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(scatter, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(scatter, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(scatter, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(scatter, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(scatter, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(scatter, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(scatter, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(scatter, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(scatter, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(scatter, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(scatter, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(scatter, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(scatter, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(scatter, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(scatter, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(scatter, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(scatter, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(scatter, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(scatter, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(scatter, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(scatter, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(scatter, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(scatter, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(scatter, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(scatter, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(scatter, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(scatter, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(scatter, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(scatter, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(scatter, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(scatter, 'display',
- (get_late_type('vcs.displayplot.Dp'),
- "no default"))
-
- #Module xvsy
- reg.add_module(xvsy,namespace='vcs|Canvas')
- reg.add_input_port(xvsy, 'template',
- (core.modules.basic_modules.String,
- "Name of the template"))
- reg.add_input_port(xvsy, 'gm_name',
- (core.modules.basic_modules.String,
- "Name of the graphics method"))
- reg.add_input_port(xvsy, 'slab2_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 1D, last dimension will be plotted"))
- reg.add_input_port(xvsy, 'slab1_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 1D, last dimension will be plotted"))
- reg.add_input_port(xvsy, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(xvsy, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(xvsy, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(xvsy, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(xvsy, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(xvsy, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(xvsy, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(xvsy, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(xvsy, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(xvsy, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(xvsy, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(xvsy, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(xvsy, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(xvsy, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(xvsy, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(xvsy, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(xvsy, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(xvsy, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(xvsy, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(xvsy, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(xvsy, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(xvsy, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(xvsy, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(xvsy, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(xvsy, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(xvsy, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(xvsy, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(xvsy, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(xvsy, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(xvsy, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(xvsy, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(xvsy, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(xvsy, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(xvsy, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(xvsy, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(xvsy, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(xvsy, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(xvsy, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(xvsy, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(xvsy, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(xvsy, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(xvsy, 'yaxisconvert',
- (core.modules.basic_modules.String,
- "converting yaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(xvsy, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(xvsy, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(xvsy, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(xvsy, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(xvsy, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(xvsy, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(xvsy, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(xvsy, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(xvsy, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(xvsy, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(xvsy, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(xvsy, 'display',
- (get_late_type('vcs.displayplot.Dp'),
- "no default"))
-
- #Module xyvsy
- reg.add_module(xyvsy,namespace='vcs|Canvas')
- reg.add_input_port(xyvsy, 'template',
- (core.modules.basic_modules.String,
- "Name of the template"))
- reg.add_input_port(xyvsy, 'gm_name',
- (core.modules.basic_modules.String,
- "Name of the graphics method"))
- reg.add_input_port(xyvsy, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 1D, last dimension will be plotted"))
- reg.add_input_port(xyvsy, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(xyvsy, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(xyvsy, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(xyvsy, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(xyvsy, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(xyvsy, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(xyvsy, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(xyvsy, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(xyvsy, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(xyvsy, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(xyvsy, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(xyvsy, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(xyvsy, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(xyvsy, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(xyvsy, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(xyvsy, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(xyvsy, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(xyvsy, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(xyvsy, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(xyvsy, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(xyvsy, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(xyvsy, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(xyvsy, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(xyvsy, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(xyvsy, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(xyvsy, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(xyvsy, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(xyvsy, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(xyvsy, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(xyvsy, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(xyvsy, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(xyvsy, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(xyvsy, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(xyvsy, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(xyvsy, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(xyvsy, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(xyvsy, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(xyvsy, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(xyvsy, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(xyvsy, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(xyvsy, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(xyvsy, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(xyvsy, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(xyvsy, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(xyvsy, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(xyvsy, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(xyvsy, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(xyvsy, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(xyvsy, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(xyvsy, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(xyvsy, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(xyvsy, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(xyvsy, 'display',
- (get_late_type('vcs.displayplot.Dp'),
- "no default"))
-
- #Module yxvsx
- reg.add_module(yxvsx,namespace='vcs|Canvas')
- reg.add_input_port(yxvsx, 'template',
- (core.modules.basic_modules.String,
- "Name of the template"))
- reg.add_input_port(yxvsx, 'gm_name',
- (core.modules.basic_modules.String,
- "Name of the graphics method"))
- reg.add_input_port(yxvsx, 'slab_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Data at least 1D, last dimension will be plotted"))
- reg.add_input_port(yxvsx, 'datawc_timeunits',
- (core.modules.basic_modules.String,
- "units to use when disaplaying time dimension auto tick"), True)
- reg.add_input_port(yxvsx, 'long_name',
- (core.modules.basic_modules.String,
- "replaces long_name on plot"), True)
- reg.add_input_port(yxvsx, 'projection_0',
- (core.modules.basic_modules.String,
- "projection to use, name or object"), True)
- reg.add_input_port(yxvsx, 'xticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of x axis"), True)
- reg.add_input_port(yxvsx, 'xarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis"), True)
- reg.add_input_port(yxvsx, 'yweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(yxvsx, 'xweights_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "replace xaxis weights used for computing mean"), True)
- reg.add_input_port(yxvsx, 'warray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of w axis, only if var has more than 4D"), True)
- reg.add_input_port(yxvsx, 'tunits',
- (core.modules.basic_modules.String,
- "replace taxis units on plot (if exists)"), True)
- reg.add_input_port(yxvsx, 'ymtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(yxvsx, 'ymtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(yxvsx, 'datawc_x1',
- (core.modules.basic_modules.Float,
- "first value of xaxis on plot"), True)
- reg.add_input_port(yxvsx, 'datawc_x2',
- (core.modules.basic_modules.Float,
- "second value of xaxis on plot"), True)
- reg.add_input_port(yxvsx, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
- reg.add_input_port(yxvsx, 'xmtics1_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 1st side of y axis"), True)
- reg.add_input_port(yxvsx, 'xmtics2_0',
- (core.modules.basic_modules.String,
- "dictionary with location of intermediate tics as keys for 2nd side of y axis"), True)
- reg.add_input_port(yxvsx, 'xbounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of x axis bounds values"), True)
- reg.add_input_port(yxvsx, 'ybounds_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis bounds values (if exist)"), True)
- reg.add_input_port(yxvsx, 'datawc_y2',
- (core.modules.basic_modules.Float,
- "second value of yaxis on plot"), True)
- reg.add_input_port(yxvsx, 'wname',
- (core.modules.basic_modules.String,
- "replace waxis name on plot (if exists)"), True)
- reg.add_input_port(yxvsx, 'file_comment',
- (core.modules.basic_modules.String,
- "replaces file_comment on plot"), True)
- reg.add_input_port(yxvsx, 'datawc_calendar',
- (core.modules.basic_modules.Integer,
- "calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar"), True)
- reg.add_input_port(yxvsx, 'wunits',
- (core.modules.basic_modules.String,
- "replace waxis units on plot (if exists)"), True)
- reg.add_input_port(yxvsx, 'xrev',
- (core.modules.basic_modules.Boolean,
- "reverse x axis"), True)
- reg.add_input_port(yxvsx, 'ymd',
- (core.modules.basic_modules.String,
- "replaces year/month/day on plot"), True)
- reg.add_input_port(yxvsx, 'yarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of y axis, only if var has more than 1D"), True)
- reg.add_input_port(yxvsx, 'units',
- (core.modules.basic_modules.String,
- "replaces units value on plot"), True)
- reg.add_input_port(yxvsx, 'yunits',
- (core.modules.basic_modules.String,
- "replace yaxis units on plot (if exists)"), True)
- reg.add_input_port(yxvsx, 'zarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of z axis, only if var has more than 2D"), True)
- reg.add_input_port(yxvsx, 'xname',
- (core.modules.basic_modules.String,
- "replace xaxis name on plot"), True)
- reg.add_input_port(yxvsx, 'tarray_0',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "Values to use instead of t axis, only if var has more than 3D"), True)
- reg.add_input_port(yxvsx, 'bg_0',
- (core.modules.basic_modules.Boolean,
- "plots in background mode"), True)
- reg.add_input_port(yxvsx, 'bg_1',
- (core.modules.basic_modules.Integer,
- "plots in background mode"), True)
- reg.add_input_port(yxvsx, 'xaxisconvert',
- (core.modules.basic_modules.String,
- "converting xaxis linear/log/log10/ln/exp/area_wt"), True)
- reg.add_input_port(yxvsx, 'zname',
- (core.modules.basic_modules.String,
- "replace zaxis name on plot (if exists)"), True)
- reg.add_input_port(yxvsx, 'hms',
- (core.modules.basic_modules.String,
- "replaces hh/mm/ss on plot"), True)
- reg.add_input_port(yxvsx, 'tname',
- (core.modules.basic_modules.String,
- "replace taxis name on plot (if exists)"), True)
- reg.add_input_port(yxvsx, 'yname',
- (core.modules.basic_modules.String,
- "replace yaxis name on plot (if exists)"), True)
- reg.add_input_port(yxvsx, 'ratio_0',
- (core.modules.basic_modules.Integer,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(yxvsx, 'ratio_1',
- (core.modules.basic_modules.String,
- "sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks"), True)
- reg.add_input_port(yxvsx, 'datawc_y1',
- (core.modules.basic_modules.Float,
- "first value of yaxis on plot"), True)
- reg.add_input_port(yxvsx, 'xunits',
- (core.modules.basic_modules.String,
- "replace xaxis units on plot"), True)
- reg.add_input_port(yxvsx, 'name',
- (core.modules.basic_modules.String,
- "replaces variable name on plot time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot"), True)
- reg.add_input_port(yxvsx, 'yticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of y axis"), True)
- reg.add_input_port(yxvsx, 'yticlabels2_0',
- (core.modules.basic_modules.String,
- "values for labels on 2nd side of y axis"), True)
- reg.add_input_port(yxvsx, 'comment1',
- (core.modules.basic_modules.String,
- "replaces comment1 on plot"), True)
- reg.add_input_port(yxvsx, 'zunits',
- (core.modules.basic_modules.String,
- "replace zaxis units on plot (if exists)"), True)
- reg.add_input_port(yxvsx, 'comment3',
- (core.modules.basic_modules.String,
- "replaces comment3 on plot"), True)
- reg.add_input_port(yxvsx, 'comment2',
- (core.modules.basic_modules.String,
- "replaces comment2 on plot"), True)
- reg.add_input_port(yxvsx, 'xticlabels1_0',
- (core.modules.basic_modules.String,
- "values for labels on 1st side of x axis"), True)
- reg.add_input_port(yxvsx, 'comment4',
- (core.modules.basic_modules.String,
- "replaces comment4 on plot"), True)
- reg.add_input_port(yxvsx, 'yrev',
- (core.modules.basic_modules.Boolean,
- "reverse y axis, only if slab has more than 1D"), True)
- reg.add_output_port(yxvsx, 'display',
- (get_late_type('vcs.displayplot.Dp'),
- "no default"))
-
- #Module png
- reg.add_module(png,namespace='vcs|Canvas')
- reg.add_input_port(png, 'file',
- (core.modules.basic_modules.String,
- ""))
- reg.add_input_port(png, 'width',
- (core.modules.basic_modules.Float,
- ""))
- reg.add_input_port(png, 'height',
- (core.modules.basic_modules.Float,
- ""))
- reg.add_input_port(png, 'units',
- (core.modules.basic_modules.String,
- ""))
- reg.add_output_port(png, 'file',
- (core.modules.basic_modules.File,
- "File output"))
-
- #extra input ports not available in the xml file
- reg.add_input_port(boxfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(createboxfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(createisofill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(createisoline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(createoutfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(createoutline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(createscatter, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(createxvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(createxyvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(createyxvsx, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(getboxfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(getisofill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(getisoline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(getoutfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(getoutline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(getscatter, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(getxvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(getxyvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(getyxvsx, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(isofill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(isoline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(outfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(outline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(plot, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(scatter, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(xvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(xyvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(yxvsx, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_input_port(png, 'canvas',
- (Canvas,
- "Canvas object"))
-
- #extra output ports not available in the xml file
- reg.add_output_port(boxfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(createboxfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(createisofill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(createisoline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(createoutfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(createoutline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(createscatter, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(createxvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(createxyvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(createyxvsx, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(getboxfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(getisofill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(getisoline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(getoutfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(getoutline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(getscatter, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(getxvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(getxyvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(getyxvsx, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(isofill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(isoline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(outfill, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(outline, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(plot, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(scatter, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(xvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(xyvsy, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(yxvsx, 'canvas',
- (Canvas,
- "Canvas object"))
- reg.add_output_port(png, 'canvas',
- (Canvas,
- "Canvas object"))
-
- #Module open
- reg.add_module(open,namespace='cdms2')
- reg.add_input_port(open, 'uri',
- (core.modules.basic_modules.String,
- ""))
- reg.add_input_port(open, 'mode',
- (core.modules.basic_modules.String,
- ""))
- reg.add_input_port(open, 'template',
- (core.modules.basic_modules.String,
- ""))
- reg.add_input_port(open, 'dods',
- (core.modules.basic_modules.Integer,
- ""))
- reg.add_output_port(open, 'dataset',
- (get_late_type('cdms2.dataset.CdmsFile'),
- ""))
-
- #Module __call__
- reg.add_module(__call__,namespace='cdms2|dataset')
- reg.add_input_port(__call__, 'id',
- (core.modules.basic_modules.String,
- ""))
- reg.add_input_port(__call__, 'type',
- (core.modules.basic_modules.String,
- "variable, axis, or weighted-axis"))
- reg.add_output_port(__call__, 'variable',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- ""))
-
- #extra input ports not available in the xml file
- reg.add_input_port(__call__, 'axes',
- (core.modules.basic_modules.String, "Axes of variables"))
- reg.add_input_port(__call__, 'axesOperations',
- (core.modules.basic_modules.String, "Axes Operations"))
- reg.add_input_port(__call__, 'cdmsfile',
- (CdmsFile, "cdmsfile"))
-
-def package_dependencies():
- return []
-
-def package_requirements():
- import core.requirements
- if not core.requirements.python_module_exists('vcs'):
- raise core.requirements.MissingRequirements('vcs')
- if not core.requirements.python_module_exists('cdms2'):
- raise core.requirements.MissingRequirements('cdms2')
- if not core.requirements.python_module_exists('cdutil'):
- raise core.requirements.MissingRequirements('cdutil')
- import vcs, cdms2, cdutil
-
-
diff --git a/contrib/cdat/cdat.sip b/contrib/cdat/cdat.sip
deleted file mode 100644
index f36d87f..0000000
--- a/contrib/cdat/cdat.sip
+++ /dev/null
@@ -1,36 +0,0 @@
-%Module coreappwrap 0
-
-%Import QtGui/QtGuimod.sip
-
-class MainWindow : QMainWindow {
-%TypeHeaderCode
-#include <Qt/mainwindow.h>
-%End
-
-public:
- void paintEvent(QPaintEvent *);
- virtual bool event(QEvent *);
- void setupCairo();
- void unsetupCairo();
-
-public slots:
- void actionTriggered(QAction*);
-};
-
-class VCSQtManager {
-
-%TypeHeaderCode
-#include <Qt/qti.h>
-%End
-
-public:
- static bool isCreated();
- static MainWindow* window(int id);
- static void sendEvent(int index, QEvent::Type eventType);
-
-public slots:
-
-signals:
-
-};
-
diff --git a/contrib/cdat/cdat.vt b/contrib/cdat/cdat.vt
deleted file mode 100644
index c375fec..0000000
Binary files a/contrib/cdat/cdat.vt and /dev/null differ
diff --git a/contrib/cdat/cdat_cell.py b/contrib/cdat/cdat_cell.py
deleted file mode 100644
index 24fbd54..0000000
--- a/contrib/cdat/cdat_cell.py
+++ /dev/null
@@ -1,291 +0,0 @@
-from PyQt4 import QtCore, QtGui
-from core.modules.vistrails_module import Module, ModuleError, NotCacheable
-from core.modules.basic_modules import Constant
-from packages.spreadsheet.spreadsheet_controller import spreadsheetController
-from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-from packages.spreadsheet.spreadsheet_event import DisplayCellEvent
-#from cdatwrap.coreappwrap import VCSQtManager
-import vcs
-import genutil
-import cdutil
-import time
-import api
-import re
-import MV2
-
-""" This file contains all of the classes related to the Vistrails Modules (the
-boxes). Eventually Variable and GraphicsMethod should be replaced by generating
-the proper graphics method, cdms2, MV2, etc... modules """
-
-# Index into the VCSQtManager window array so we can communicate with the
-# C++ Qt windows which the plots show up in. If this number is no longer
-# consistent with the number of C++ Qt windows due to adding or removing
-# vcs.init() calls, then when you plot, it will plot into a
-# separate window instead of in the cell and may crash.
-windowIndex = 1
-
-class Variable(Module):
- """ Get the updated transient variable """
-
- def compute(self):
- # *** IMPORTANT ***
- # Once someone figures out how to pass the tvariable object, to this
- # module none of the computation in this method is necessary
-
- # Check ports
- if not self.hasInputFromPort('cdmsfile'):
- raise ModuleError(self, "'cdmsfile' is mandatory.")
- if not self.hasInputFromPort('id'):
- raise ModuleError(self, "'id' is mandatory.")
-
- # Get input from ports
- cdmsfile = self.getInputFromPort('cdmsfile')
- id = self.getInputFromPort('id')
- axes = self.forceGetInputFromPort('axes') # None if no input
- axesOperations = self.forceGetInputFromPort('axesOperations') # None if no input
-
- # Get the variable
- varType = self.getVarType(id, cdmsfile)
- if (varType == 'variable'):
- var = cdmsfile.__call__(id)
- elif (varType == 'axis'):
- varID = self.getAxisID(id)
- axis = getattr(cdmsfile, 'axes')[varID]
- var = MV2.array(axis)
- var.setAxis(0, axis)
- elif (varType == 'weighted-axis'):
- varID, axisID = self.getVarAndAxisID(id)
- var = cdmsfile.__call__(varID)
- var = genutil.getAxisWeightByName(var, axisID)
- var.id = varID +'_' + axisID + '_weight'
- else:
- var = None
-
- # Eval the variable with the axes
- if axes is not None and var is not None:
- try:
- kwargs = eval(axes)
- var = var(**kwargs)
- except:
- raise ModuleError(self, "Invalid 'axes' specification", axes)
-
- # Apply axes ops to the variable
- if axesOperations is not None:
- var = self.applyAxesOperations(var, axesOperations)
-
- self.setResult('variable', var)
-
- def applyAxesOperations(self, var, axesOperations):
- """ Apply axes operations to update the slab """
- try:
- axesOperations = eval(axesOperations)
- except:
- raise TypeError("Invalid string 'axesOperations'")
-
- for axis in list(axesOperations):
- if axesOperations[axis] == 'sum':
- var = cdutil.averager(var, axis="(%s)" % axis, weight='equal',
- action='sum')
- elif axesOperations[axis] == 'avg':
- var = cdutil.averager(var, axis="(%s)" % axis, weight='equal')
- elif axesOperations[axis] == 'wgt':
- var = cdutil.averager(var, axis="(%s)" % axis)
- elif axesOperations[axis] == 'gtm':
- var = genutil.statistics.geometricmean(var, axis="(%s)" % axis)
- elif axesOperations[axis] == 'std':
- var = genutil.statistics.std(var, axis="(%s)" % axis)
-
- return var
-
- def getVarType(self, varID, file):
- if varID in list(getattr(file, 'variables')):
- return 'variable'
- elif varID in list(getattr(file, 'axes')):
- return 'axis'
- elif re.compile('(.+)(_)(.+)(_)axis').match(varID):
- return 'axis'
- elif re.compile('(.+)(_)(.+)(_)weight').match(varID):
- return 'weighted-axis'
-
- def getVarAndAxisID(self, varID):
- """ Get the varID and axisID from a string with format:
- varID_axisID_weight """
-
- match = re.compile('(.+)(_)(.+)(_)(weight)').match(varID)
- if match:
- return (match.group(1), match.group(3))
-
- return None
-
- def getAxisID(self, varID):
- """ Get the axisID from a string with format: varID_axisID_axis """
-
- match = re.compile('(.+)(_)(.+)(_)(axis)').match(varID)
- if match:
- return match.group(3)
-
- return varID
-
-class Quickplot(Variable):
- """ Quickplot is identical to Variable except we will only have a single
- quickplot module in a pipeline. """
-
- def foo(self):
- return
-
-class GraphicsMethod(Module, NotCacheable):
- """ GraphicsMethod initializes the vcs canvas and gets the graphics method
- and modify it's attributes """
-
- def compute(self):
- # Check required input ports
- if not self.hasInputFromPort('gmName'):
- return
- if not self.hasInputFromPort('plotType'):
- return
- if not self.hasInputFromPort('slab1'):
- return
-
- # Get required input
- gmName = self.getInputFromPort('gmName')
- plotType = self.getInputFromPort('plotType')
-
- # GraphicsMethod doesn't need slab1/slab2 as input. It can be passed
- # directly to CDATCell but I pass it to graphics method so it looks
- # nicer in the pipeline.
- slab1 = self.getInputFromPort('slab1')
- if self.hasInputFromPort('slab2'):
- self.setResult('slab2', self.getInputFromPort('slab2'))
-
- # Initialize the canvas and get the graphics method
- canvas = vcs.init()
- gm = canvas.get_gm(plotType.lower(), gmName)
-
- # Modify the graphics method's attributes
- if self.hasInputFromPort('color_1'):
- gm.color_1 = self.getInputFromPort('color_1')
- if self.hasInputFromPort('color_2'):
- gm.color_2 = self.getInputFromPort('color_2')
- if self.hasInputFromPort('level_1'):
- gm.level_1 = self.getInputFromPort('level_1')
- if self.hasInputFromPort('level_2'):
- gm.level_2 = self.getInputFromPort('level_2')
- # TODO: more gm attributes ...
-
- # Add canvas / slab to output Ports
- self.setResult('slab1', slab1)
- self.setResult('canvas', canvas)
-
-class CDATCell(SpreadsheetCell, NotCacheable):
- def __init__(self):
- SpreadsheetCell.__init__(self)
- self.cellWidget = None
-
- def compute(self):
- """ compute() -> None
- Dispatch the vtkRenderer to the actual rendering widget
- """
- # Check required input ports
- if self.hasInputFromPort('canvas'):
- canvas = self.getInputFromPort('canvas')
- else:
- self.cellWidget = self.displayAndWait(QCDATWidget, (None,))
- self.setResult('canvas', self.cellWidget.canvas)
- return
- self.setResult('canvas', canvas)
- if not self.hasInputFromPort('gmName'):
- return
- if not self.hasInputFromPort('plotType'):
- return
- if not self.hasInputFromPort('slab1'):
- return
- if not self.hasInputFromPort('template'):
- return
-
- # Build up the argument list
- args = []
- slab1 = self.getInputFromPort('slab1')
- args.append(self.getInputFromPort('slab1'))
- if self.hasInputFromPort('slab2'):
- args.append(self.getInputFromPort('slab2'))
- args.append(self.getInputFromPort('template'))
- args.append(self.getInputFromPort('plotType'))
- args.append(self.getInputFromPort('gmName'))
-
- # Build up plot keyword args ...
- kwargs = {}
- if self.hasInputFromPort('continents'):
- kwargs['continents'] = self.getInputFromPort('continents')
-
- # Set the cell row / col
- self.location = CellLocation()
- if self.hasInputFromPort('row'):
- self.location.row = self.getInputFromPort('row')
- if self.hasInputFromPort('col'):
- self.location.col = self.getInputFromPort('col')
-
- # Plot into the cell
- inputPorts = (canvas, args, kwargs)
- self.displayAndWait(QCDATWidget, inputPorts)
-
-class QCDATWidget(QCellWidget):
- """ QCDATWidget is the spreadsheet cell widget where the plots are displayed.
- The widget interacts with the underlying C++, VCSQtManager through SIP.
- This enables QCDATWidget to get a reference to the Qt MainWindow that the
- plot will be displayed in and send signals (events) to that window widget.
- """
-
- def __init__(self, parent=None):
- QCellWidget.__init__(self, parent)
- self.window = None
- self.canvas = None
- self.windowIndex = self.getWindowIndex() #index to get QT Window from VCSQtManager
-
- def getWindowIndex(self):
- """ Return the index into the VCSQtManager's array of Qt Windows which
- plots will be displayed in.
- """
- global windowIndex
-
- windowIndex += 1
- maxWindows = 8
- if windowIndex > maxWindows:
- windowIndex = 1
- return windowIndex
-
- def updateContents(self, inputPorts):
- """ Get the vcs canvas, setup the cell's layout, and plot """
- spreadsheetWindow = spreadsheetController.findSpreadsheetWindow()
- spreadsheetWindow.setUpdatesEnabled(False)
-
- # Set the canvas
- self.canvas = inputPorts[0]
- if self.canvas is None:
- self.canvas = vcs.init()
- self.canvas.clear()
-
- # Place the mainwindow that the plot will be displayed in, into this
- # cell widget's layout
- self.window = VCSQtManager.window(self.windowIndex)
- layout = QtGui.QVBoxLayout()
- layout.addWidget(self.window)
- self.setLayout(layout)
-
- # Plot
- if len(inputPorts) > 2:
- args = inputPorts[1]
- kwargs = inputPorts[2]
- self.canvas.plot(*args, **kwargs)
-
- spreadsheetWindow.setUpdatesEnabled(True)
-
- def deleteLater(self):
- """ deleteLater() -> None
- Make sure to free render window resource when
- deallocating. Overriding PyQt deleteLater to free up
- resources
- """
- self.canvas = None
- QCellWidget.deleteLater(self)
-
diff --git a/contrib/cdat/cdat_window.py b/contrib/cdat/cdat_window.py
deleted file mode 100644
index 03ade10..0000000
--- a/contrib/cdat/cdat_window.py
+++ /dev/null
@@ -1,2356 +0,0 @@
-from PyQt4 import QtCore, QtGui
-from cdat_cell import QCDATWidget
-from gui_controller import *
-from graphics_method_controller import QGraphicsMethodAttributeWindow
-import cdutil
-import genutil
-import cdms2
-import MV2
-import os
-import re
-import api
-import vcs
-
-class QCDATWindow(QtGui.QWidget):
- """ Main class for VCDAT Window. Contains a menu widget, file widget,
- defined variable widget, and variable widget """
-
- def __init__(self, parent=None):
- """ Instantiate the child widgets of the main VCDAT window and setup
- the overall layout """
- QtGui.QWidget.__init__(self, parent)
-
- self.setWindowTitle('The Visual Climate Data Analysis Tools - (VCDAT)')
- layout = QtGui.QVBoxLayout()
- self.setLayout(layout)
-
- # Init Menu Widget
- self.menuWidget = QMenuWidget(self)
-
- # Init File Widget
- vsplitter = QtGui.QSplitter(QtCore.Qt.Vertical)
- fileWidget = QLabeledWidgetContainer(QCDATFileWidget(),
- 'FILE VARIABLES')
- vsplitter.addWidget(fileWidget)
-
- # Init Defined Variables Widget
- definedVar = QLabeledWidgetContainer(QDefinedVariable(),
- 'DEFINED VARIABLES')
- vsplitter.addWidget(definedVar)
- hsplitter = QtGui.QSplitter(QtCore.Qt.Horizontal)
- hsplitter.addWidget(vsplitter)
-
- # Init Var Plotting Widget
- varView = QLabeledWidgetContainer(QVariableView(),
- 'PLOTTING')
- hsplitter.addWidget(varView)
- hsplitter.setStretchFactor(1, 1)
- layout.addWidget(hsplitter)
-
- # Init guiController
- guiController = GuiController(fileWidget.getWidget(),
- definedVar.getWidget(),
- varView.getWidget())
- guiController.initTeachingCommands()
- self.guiController = guiController # So guicontroller doesn't get garbage collected
-
- # Connect signals between self & GuiController
- self.connect(self, QtCore.SIGNAL('setRecordCommands'),
- guiController.setRecordCommands)
- self.connect(self, QtCore.SIGNAL('viewTeachingCommands'),
- guiController.viewTeachingCommands)
- self.connect(self, QtCore.SIGNAL('closeTeachingCommands'),
- guiController.closeTeachingCommands)
-
- # Connect Signals between QVariableView & QDefinedVariable
- varView.connect(definedVar.getWidget(), QtCore.SIGNAL('selectDefinedVariableEvent'),
- varView.getWidget().selectDefinedVariableEvent)
- varView.connect(definedVar.getWidget(), QtCore.SIGNAL('setupDefinedVariableAxes'),
- varView.getWidget().setupDefinedVariableAxes)
- definedVar.connect(varView.getWidget(), QtCore.SIGNAL('plotPressed'),
- definedVar.getWidget().defineQuickplot)
- definedVar.connect(varView.getWidget(), QtCore.SIGNAL('defineVariable'),
- definedVar.getWidget().defineVariable)
-
- # Connect Signals between QFileWidget & QVariableView
- varView.connect(fileWidget.getWidget(), QtCore.SIGNAL('variableChanged'),
- varView.getWidget().setupDefinedVariableAxes)
- varView.connect(fileWidget.getWidget(), QtCore.SIGNAL('defineVariableEvent'),
- varView.getWidget().defineVariableEvent)
-
- def closeEvent(self, event):
- # TODO
- # closeEvent() isn't called vistrails is closed,
- # perhaps because the event isn't propagated by vistrails? Therefore,
- # any functionality we want to execute when vistrails exits is not done
- # unless the user specifically closes this gui.
-
- self.emit(QtCore.SIGNAL('closeTeachingCommands'))
-
- def sizeHint(self):
- return QtCore.QSize(1024, 600)
-
-class QFileDialogWidget(QtGui.QFileDialog):
-
- def __init__(self, parent=None):
- QtGui.QFileDialog.__init__(self, parent, QtCore.Qt.Widget)
- self.setModal(False)
- self.setSizeGripEnabled(False)
- self.setFileMode(QtGui.QFileDialog.ExistingFile)
- self.setLabelText(QtGui.QFileDialog.LookIn, 'Directory')
- self.setSidebarUrls([QtCore.QUrl('file://')])
-
- gridLayout = self.findChild(QtGui.QGridLayout, 'gridLayout')
- if gridLayout:
- gridLayout.setMargin(0)
- gridLayout.setVerticalSpacing(0)
- gridLayout.setColumnStretch(1, 1)
- hBoxLayout = gridLayout.itemAtPosition(0, 1).layout()
- if hBoxLayout:
- hBoxLayout.setSpacing(0)
-
- # Hide the Back and Forward button
- backButton = self.findChild(QtGui.QToolButton, 'backButton')
- if backButton: backButton.hide()
- forwardButton = self.findChild(QtGui.QToolButton, 'forwardButton')
- if forwardButton: forwardButton.hide()
-
- # Hide the File Name indicators
- fileNameLabel = self.findChild(QtGui.QLabel, 'fileNameLabel')
- if fileNameLabel: fileNameLabel.hide()
- fileNameEdit = self.findChild(QtGui.QLineEdit, 'fileNameEdit')
- if fileNameEdit: fileNameEdit.hide()
-
- # Hide the File Type indicators
- fileTypeLabel = self.findChild(QtGui.QLabel, 'fileTypeLabel')
- if fileTypeLabel: fileTypeLabel.hide()
- fileTypeCombo = self.findChild(QtGui.QComboBox, 'fileTypeCombo')
- if fileTypeCombo: fileTypeCombo.hide()
-
- # Hide the dialog buttons
- buttonBox = self.findChild(QtGui.QDialogButtonBox, 'buttonBox')
- buttonBox.hide()
-
- # Adjust the sidebar width
- splitter = self.findChild(QtGui.QSplitter, 'splitter')
- splitter.setSizes([0, 1])
-
- # Simplify the Details view to List View
- stackedWidget = splitter.widget(1).findChild(QtGui.QStackedWidget, 'stackedWidget')
- listView = stackedWidget.widget(0).findChild(QtGui.QListView, 'listView')
- listView.setAlternatingRowColors(True)
- listView.setWrapping(False)
- self.setViewMode(QtGui.QFileDialog.List)
-
- def done(self, result):
- pass
-
- def sizeHint(self):
- return QtCore.QSize(384, 150)
-
-class QCDATFileWidget(QtGui.QWidget):
- """ QCDATFileWidget contains a line-edit to enter the file name and a file
- selection button. It also has a combo box to choose variables once a file
- is specified. """
-
- FILTER = "CDAT data (*.cdms *.ctl *.dic *.hdf *.nc *.xml)"
-
- def __init__(self, parent=None):
- QtGui.QWidget.__init__(self, parent)
-
- self.cdmsFile = None
-
- # Start the layout
- layout = QtGui.QVBoxLayout()
- self.setLayout(layout)
- layout.setMargin(0)
-
- self.fileDialog = QFileDialogWidget()
- self.fileDialog.setNameFilter(QCDATFileWidget.FILTER)
- layout.addWidget(self.fileDialog)
-
- # A shared layout of the bottom half
- vbox = QtGui.QVBoxLayout()
- vbox.setMargin(0)
- vbox.setSpacing(0)
- layout.addLayout(vbox)
- self.fileVarLayout = vbox
-
- # Create the bottom horizontal indicator
- hbox = QtGui.QHBoxLayout()
-
- self.drawerButton = QtGui.QToolButton()
- self.drawerButton.setArrowType(QtCore.Qt.UpArrow)
- self.drawerButton.setAutoRaise(True)
- self.drawerButton.setIconSize(QtCore.QSize(8, 8))
- hbox.addWidget(self.drawerButton)
-
- hline = QtGui.QFrame()
- hline.setFrameStyle(QtGui.QFrame.HLine | QtGui.QFrame.Sunken)
- hbox.addWidget(hline)
-
- self.connect(self.drawerButton, QtCore.SIGNAL('clicked(bool)'),
- self.toggleFileDialog)
-
- vbox.addLayout(hbox)
-
- # Create the file name box
- grid = QtGui.QGridLayout()
- grid.setHorizontalSpacing(10)
- vbox.addLayout(grid)
-
- # First line: File
- fileNameLabel = QtGui.QLabel('File')
- grid.addWidget(fileNameLabel)
-
- hbox = QtGui.QHBoxLayout()
- hbox.setSpacing(6)
- self.fileNameEdit = QtGui.QLineEdit()
- self.fileNameEdit.setToolTip('Enter file name or click on button on the right to select a file')
- hbox.addWidget(self.fileNameEdit, 1)
-
- self.fileSelectButton = QtGui.QToolButton()
- self.fileSelectButton.setText('...')
- self.fileSelectButton.setToolTip('View and select files')
- hbox.addWidget(self.fileSelectButton)
-
- grid.addLayout(hbox, 0, 1)
-
- # Second line: Var
- varNameLabel = QtGui.QLabel('Variable')
- grid.addWidget(varNameLabel, 1, 0)
-
- hbox = QtGui.QHBoxLayout()
- hbox.setSpacing(6)
-
- # Init combo box
- self.varCombo = QtGui.QComboBox()
- self.varCombo.setToolTip('View and select variables in file')
- self.varCombo.setMinimumContentsLength(10)
- comboPalette = self.varCombo.view().palette()
- comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
- comboPalette.setColor(QtGui.QPalette.Highlight, QtCore.Qt.blue)
- self.varCombo.view().setPalette(comboPalette)
-
- hbox.addWidget(self.varCombo, 1)
-
- self.defineVarButton = QtGui.QPushButton('&Define')
- self.defineVarButton.setToolTip('Define variable into memory')
- hbox.addWidget(self.defineVarButton)
-
- grid.addLayout(hbox, 1, 1)
-
- # Connect signals
- self.connect(self.fileDialog, QtCore.SIGNAL('filesSelected(const QStringList&)'),
- self.filesSelected)
- self.connect(self.fileNameEdit, QtCore.SIGNAL('returnPressed()'),
- self.updateCDMSFile)
- self.connect(self.fileSelectButton, QtCore.SIGNAL('clicked(bool)'),
- self.openSelectFileDialog)
- self.connect(self.varCombo, QtCore.SIGNAL('currentIndexChanged(const QString&)'),
- self.variableChanged)
- self.connect(self.defineVarButton, QtCore.SIGNAL('clicked(bool)'),
- self.defineVariablePressed)
-
- # Init the widget with its file dialog hidden
- self.fileDialog.hide()
- self.setFileName('')
- self.varCombo.setCurrentIndex(1)
-
- def updateSizeConstraints(self):
- isDialogVisible = self.fileDialog.isVisible()
- if isDialogVisible:
- self.drawerButton.setArrowType(QtCore.Qt.UpArrow)
- self.setMaximumHeight(16777215)
- else:
- self.drawerButton.setArrowType(QtCore.Qt.DownArrow)
- self.setMaximumHeight(self.fileVarLayout.contentsRect().height())
- self.fileSelectButton.setVisible(not isDialogVisible)
-
- def toggleFileDialog(self, ignored=False):
- self.fileDialog.setVisible(not self.fileDialog.isVisible())
- self.updateSizeConstraints()
-
- def showEvent(self, e):
- self.updateSizeConstraints()
- self.variableChanged(self.varCombo.currentText())
-
- def setFileName(self, fn):
- self.fileNameEdit.setText(fn)
- self.updateCDMSFile()
-
- def updateCDMSFile(self):
- fn = str(self.fileNameEdit.text())
- fi = QtCore.QFileInfo(fn)
- if fi.exists():
- self.fileDialog.setDirectory(fi.dir())
- self.cdmsFile = cdms2.open(fn)
- self.recordOpenFileTeachingCommand(fn)
- # Create and update the open module
- self.emit(QtCore.SIGNAL('createModule'), open_name)
- self.emit(QtCore.SIGNAL('updateModule'), open_name, 'uri', fn)
- else:
- self.cdmsFile = None
- self.updateVariableList()
-
- def recordOpenFileTeachingCommand(self, file):
- openFileComment = '\n# Open CDMS File\n'
- varName = 'fid2'
- command = "%s = cdms2.open('%s')\n" %(varName, file)
-
- self.emit(QtCore.SIGNAL('recordTeachingCommand'), openFileComment)
- self.emit(QtCore.SIGNAL('recordTeachingCommand'), command)
-
- def filesSelected(self, files):
- if files.count()>0:
- self.setFileName(files[0])
-
- def updateVariableList(self):
- self.varCombo.clear()
- if self.cdmsFile!=None:
- # Add Variables sorted based on their dimensions
- curDim = -1
- for (dim, varId) in sorted([(len(var.listdimnames()), var.id)
- for var in self.cdmsFile.variables.itervalues()]):
- if dim!=curDim:
- curDim = dim
- count = self.varCombo.count()
- self.varCombo.insertSeparator(count)
- self.varCombo.model().item(count, 0).setText('%dD VARIABLES' % dim)
- var = self.cdmsFile.variables[varId]
- varName = var.id + ' ' + str(var.shape) + ' ['
-
- if hasattr(var, 'long_name'):
- varName += var.long_name
- if hasattr(var, 'units') and var.units!='':
- if varName[-1]!='[': varName += ' '
- varName += var.units
- varName += ']'
- self.varCombo.addItem(varName, QtCore.QVariant(QtCore.QStringList(['variables', var.id])))
-
- # Add Axis List
- count = self.varCombo.count()
- self.varCombo.insertSeparator(count)
- self.varCombo.model().item(count, 0).setText('AXIS LIST')
- for axis in self.cdmsFile.axes.itervalues():
- axisName = axis.id + " (" + str(len(axis)) + ") - [" + axis.units + ": (" + str(axis[0]) + ", " + str(axis[-1]) + ")]"
- self.varCombo.addItem(axisName, QtCore.QVariant(QtCore.QStringList(['axes', axis.id])))
-
- # By default, not selecting anything
- self.varCombo.setCurrentIndex(-1)
-
- def openSelectFileDialog(self):
- file = QtGui.QFileDialog.getOpenFileName(self, 'Open CDAT data file...',
- self.fileDialog.directory().absolutePath(),
- QCDATFileWidget.FILTER + ';;All files (*.*)')
- if not file.isNull():
- self.setFileName(file)
-
- def variableChanged(self, varName):
- if varName == '':
- return
-
- self.defineVarButton.setEnabled(not varName.isNull()) # Enable define button
-
- # Send signal to setup axisList in 'quickplot' tab
- self.emit(QtCore.SIGNAL('variableChanged'), self.getCDMSFile(),
- self.getCDMSVariable(), 'quickplot')
-
- def defineVariablePressed(self):
- self.emit(QtCore.SIGNAL('defineVariableEvent'))
-
- def getCDMSFile(self):
- return self.cdmsFile
-
- def getCDMSVariable(self):
- if not self.cdmsFile is None:
- data = self.varCombo.itemData(self.varCombo.currentIndex()).toStringList()
- if data.count() > 0:
- if data[0] == 'variables':
- return getattr(self.cdmsFile, str(data[0]))[str(data[1])]
- elif data[0] == 'axes':
- axis = getattr(self.cdmsFile, str(data[0]))[str(data[1])]
- var = MV2.array(axis)
- var.setAxis(0, axis)
- var.id = axis.id
- return var
- return None
-
-class QLabeledWidgetContainer(QtGui.QWidget):
- """ Container widget for the 3 main widgets: QVariableView, QCDATFileWidget,
- and QDefinedVariable """
-
- def __init__(self, widget, label='', parent=None):
- QtGui.QWidget.__init__(self, parent)
-
- vbox = QtGui.QVBoxLayout()
- vbox.setMargin(0)
-
- self.label = QtGui.QLabel(label)
- self.label.setAutoFillBackground(True)
- self.label.setAlignment(QtCore.Qt.AlignCenter)
- self.label.setFrameStyle(QtGui.QFrame.Panel | QtGui.QFrame.Raised)
- vbox.addWidget(self.label, 0)
-
- if widget!=None:
- self.widget = widget
- else:
- self.widget = QtGui.QWidget()
- vbox.addWidget(self.widget, 1)
-
- self.setLayout(vbox)
-
- def getWidget(self):
- return self.widget
-
- def event(self, e):
- if e.type()==76: #QtCore.QEvent.LayoutRequest:
- self.setMaximumHeight(min(self.label.height()+self.layout().spacing()+
- self.widget.maximumHeight(), 16777215))
- return False
-
-class QDefinedVariable(QtGui.QWidget):
- """ QDefinedVariable contains a list of the user defined variables and allows the
- user to apply functions on defined variables """
-
- def __init__(self, parent=None):
- QtGui.QWidget.__init__(self, parent)
- self.warningWidget = QDefVarWarningBox(self) # Popup box to warn var is already defined
- self.quickplotItem = None
- self.numVarsSelected = 0
-
- # Create Layout
- vbox = QtGui.QVBoxLayout()
- vbox.setMargin(0)
- self.setLayout(vbox)
-
- # Create Toolbar and add it to the layout
- self.createToolbar()
- vbox.addWidget(self.toolBar)
-
- # Create List for defined variables and add it to the layout
- self.varList = QtGui.QListWidget()
- self.varList.setAlternatingRowColors(True)
- self.varList.setSelectionMode(QtGui.QAbstractItemView.MultiSelection)
- vbox.addWidget(self.varList)
-
- # Connect Signals
- self.connect(self.varList, QtCore.SIGNAL('clicked(const QModelIndex&)'),
- self.selectVariableFromListEvent)
- self.connect(self.warningWidget, QtCore.SIGNAL('newVarID'),
- self.addVariable)
-
- def defineQuickplot(self, file, var):
- """ When a user plots a variable that isn't explicitly defined a signal
- is emitted and this function is called to define the variable under
- the name 'quickplot'. Replace the 'quickplot' variable if it
- already exists
- """
- if self.quickplotItem is None:
- self.quickplotItem = QDefinedVariableItem(file, var, 'quickplot')
- self.varList.addItem(self.quickplotItem)
- else:
- self.quickplotItem.setVariable(var)
- self.quickplotItem.setFile(file)
-
- def defineVariable(self, file, var, axesArgString):
- """ Check if a variable with the same name has already been defined.
- If so, warn user and prompt for a new variable name. Otherwise,
- add the variable to the ListWidget
- """
- if self.isVariableDefined(var.id):
- self.warningWidget.showWarning(var.id, file, var, axesArgString)
- else:
- self.addVariable(var.id, file, var, axesArgString)
-
- def addVariable(self, varName, file, var, axesArgString):
- """ Add variable into dict / list & emit signal to create
- a tab for the variable
- """
- # If the variable is defined, replace existing variable, else create a new variable
- if self.isVariableDefined(varName):
- item = self.getItem(varName)
- item.setVariable(var)
- item.setFile(file)
- else:
- item = QDefinedVariableItem(file, var, varName)
- self.varList.addItem(item)
-
- # Recording define variable teaching command
- self.recordDefineVariableTeachingCommand(varName, var.id, file, axesArgString)
-
- # emit signal to QVariableView to create a new axisList / tab
- self.emit(QtCore.SIGNAL('setupDefinedVariableAxes'), file, var, varName)
-
- def selectVariableFromListEvent(self, modelIndex):
- """ Update the number next to the selected defined variable and
- send a signal to QVariableView to display the selected variable
- """
- item = self.varList.item(modelIndex.row())
- selectedItems = self.varList.selectedItems()
-
- # If the item is unselected then change the selection str back to '--'
- # and decrement all the numbers of the other selected vars that are
- # less than the number of the item that was unselected
- if item not in selectedItems:
- unselectedNum = item.getSelectNum()
- item.updateVariableString(None)
- self.numVarsSelected -= 1
-
- for item in selectedItems:
- num = item.getSelectNum()
- if num > unselectedNum:
- item.updateVariableString(item.getSelectNum() - 1)
- # If item is selected, change the selection str to a number
- else:
- self.numVarsSelected += 1
- item.updateVariableString(self.numVarsSelected)
-
- # Send signal of all selected vars to qvariableview and bring up the
- # most recently selected variable's tab
- var = item.getVariable()
- cdmsFile = item.getFile()
- selectedVars = [item.getVariable() for item in selectedItems]
- tabName = item.getVarName()
-
- if item.isQuickplotItem():
- self.emit(QtCore.SIGNAL('selectDefinedVariableEvent'), 'quickplot',
- cdmsFile, selectedVars)
- else:
- self.emit(QtCore.SIGNAL('selectDefinedVariableEvent'), tabName,
- cdmsFile, selectedVars)
-
- def isVariableDefined(self, varID):
- """ Return true if a variable with the given id is defined (this does
- not include 'quickplot' """
-
- for i in range(self.varList.count()):
- item = self.varList.item(i)
- if varID == item.getVariable().id and not item.isQuickplotItem():
- return True
- return False
-
- def getItem(self, varID):
- """ Return the item with the defined variable with name = varID """
- for i in range(self.varList.count()):
- listItem = self.varList.item(i)
- if varID == listItem.getVariable().id:
- return listItem
- return None
-
- def recordDefineVariableTeachingCommand(self, name, varName, file, axesArgString):
- if varName in list(getattr(file, 'variables')):
- fileID = "fid2"
- command = '\n# Get new slab\n'
- command += "%s = %s('%s', %s)\n" %(name, fileID, varName, axesArgString)
-
- self.emit(QtCore.SIGNAL('recordTeachingCommand'), command)
-
- def createToolbar(self):
- ICONPATH = os.path.join(cdms2.__path__[0], '..', '..', '..', '..', 'bin')
-
- # Create options bar
- self.toolBar = QtGui.QToolBar()
- self.toolBar.setIconSize(QtCore.QSize(16, 16))
- actionInfo = [
- ('edit_20.gif', 'Edit (in memory) selected defined variable.'),
- ('save_20.gif', 'Save selected defined variable to a netCDF file.'),
- ('info_20.gif', 'Display selected defined variable information.'),
- ('editdelete_20.gif', 'Move selected defined variable(s) to trashcan for disposal.'),
- ('recycle_20.gif', 'Move [ALL] defined variables to trashcan for disposal.'),
- ('log_20.gif', 'Logged information about the defined variables.'),
- ('trashcan_empty_20.gif', 'Defined variable items that can be disposed of permanetly or restored.'),
- ]
-
- for info in actionInfo:
- icon = QtGui.QIcon(os.path.join(ICONPATH, info[0]))
- action = self.toolBar.addAction(icon, '')
- action.setStatusTip(info[1])
- action.setToolTip(info[1])
- self.toolBar.addSeparator()
-
- self.opButton = QtGui.QToolButton()
- self.opButton.setText('Ops')
-
- # Create Operations Menu
- menu = QtGui.QMenu(self)
- grid = QtGui.QGridLayout()
- grid.setMargin(0)
- grid.setSpacing(0)
- menu.setLayout(grid)
- opDefs =[
- ['Add a number or two (or more)\nselected Defined Variables.\n(Can be used as "or")','add.gif','add'],
- ['Subtract a number or two (or more)\nselected Defined Variables.','subtract.gif','subtract'],
- ['Multiply a number or two (or more)\nselected Defined Variables.\n(Can be used as "and")','multiply.gif','multiply'],
- ['Divide a number or two (or more)\nselected Defined Variables.','divide.gif','divide'],
- ['"Grows" variable 1 and variable 2 so that they end up having the same dimensions\n(order of variable 1 plus any extra dims)','grower.gif','grower'],
- ['Spatially regrid the first selected Defined Variable\nto the second selected Defined Variable.','regrid.gif','regrid'],
- ['Mask variable 2 where variable 1 is "true".','mask.gif','mask'],
- ['Get variable mask','getmask.gif','getmask'],
- ['Return true where variable 1 is less than variable 2 (or number)','less.gif','less'],
- ['Return true where variable 1 is greater than variable 2 (or number)','greater.gif','greater'],
- ['Return true where variable 1 is equal than variable 2 (or number)','equal.gif','equal'],
- ['Return not of variable','not.gif','not'],
- ['Compute the standard deviation\n(over first axis)','std.gif','std'],
- ['Power (i.e., x ** y) of the most recently\nselected two Defined Variables, where\nx = variable 1 and y = variable 2 or float number.','power.gif','power'],
- ['Exp (i.e., e ** x) of the most recently\nselected Defined Variable.','exp.gif','exp'],
- ['Log (i.e., natural log) of the most recently\nselected Defined Variable.','mlog.gif','log'],
- ['Base10 (i.e., 10 ** x) of the most recently\nselected Defined Variable.','base10.gif','base10'],
- ['Log10 (i.e., log base 10) of the most\nrecently selected Defined Variable. ','mlog10.gif','log10'],
- ['Inverse (i.e., 1/x) of the most recently\nselected Defined Variable.','inverse.gif','inverse'],
- ['Abs (i.e., absolute value of x) of the most\nrecently selected Defined Variable.','fabs.gif','fabs'],
- ['Sine (i.e., sin) of the most recently\nselected Defined Variable.','sin.gif','sin'],
- ['Hyperbolic sine (i.e., sinh) of the most recently\nselected Defined Variable.','sinh.gif','sinh'],
- ['Cosine (i.e., cos) of the most recently\nselected Defined Variable.','cos.gif', 'cos'],
- ['Hyperbolic cosine (i.e., cosh) of the most recently\nselected Defined Variable.','cosh.gif','cosh'],
- ['Tangent (i.e., tan) of the most recently\nselected Defined Variable.','tan.gif','tan'],
- ['Hyperbolic tangent (i.e., tanh) of the most recently\nselected Defined Variable.','tanh.gif','tanh'],
- ]
- self.opActions = []
- for i in xrange(len(opDefs)):
- action = QtGui.QAction(QtGui.QIcon(os.path.join(ICONPATH, opDefs[i][1])), opDefs[i][2], menu)
- action.setStatusTip(opDefs[i][0])
- action.setToolTip(opDefs[i][0])
- self.opActions.append(action)
- b = QtGui.QToolButton()
- b.setDefaultAction(action)
- grid.addWidget(b, i/2, i%2)
-
- self.opButton.setMenu(menu)
- self.opButton.setPopupMode(QtGui.QToolButton.InstantPopup)
- self.connect(self.opButton, QtCore.SIGNAL('clicked(bool)'), self.opButton.showMenu)
-
- self.toolBar.addWidget(self.opButton)
-
-class QDefinedVariableItem(QtGui.QListWidgetItem):
- """ Item to be stored by QDefinedVariable's list widget """
-
- def __init__(self, cdmsFile, variable, varName, parent=None):
- QtGui.QListWidgetItem.__init__(self, parent)
- self.varName = varName # This is also the tabname
- self.cdmsFile = cdmsFile
- self.variable = variable
-
- self.updateVariableString()
-
- def getVariable(self):
- return self.variable
-
- def getVarName(self):
- return self.varName
-
- def getFile(self):
- return self.cdmsFile
-
- def getSelectNum(self):
- return self.selectNum
-
- def isQuickplotItem(self):
- return self.varName == 'quickplot'
-
- def updateVariableString(self, num=None):
- """ updateVariableString(num: int)
-
- Update the variable string that is shown to the user in the list.
- format = '-- variableName (shape)', where num is the selection number
- """
- if num is None:
- self.selectNum = -1
- numString = '-- '
- elif 0 < num < 10:
- self.selectNum = num
- numString = "-%s " % num
- else:
- self.selectNum = num
- numString = "%s " % num
-
- varString = numString + self.varName + ' ' + str(self.variable.shape)
- self.setData(0, QtCore.QVariant(QtCore.QString(varString)))
-
- def setFile(self, cdmsFile):
- self.cdmsFile = cdmsFile
-
- def setVariable(self, variable):
- """ Set the variable and update the variable string that is shown to the
- user in the list
- """
- self.variable = variable
- self.updateVariableString()
-
-class QDefVarWarningBox(QtGui.QDialog):
- """ Popup box to warn a user that a variable with same name is already
- defined. Contains a line edit to allow a user to enter a new variable
- name or to replace the existing defined variable """
-
- def __init__(self, parent=None):
- QtGui.QDialog.__init__(self, parent)
- self.varID = None
-
- # Init layout
- vbox = QtGui.QVBoxLayout()
- hbox = QtGui.QHBoxLayout()
- hbox.setDirection(QtGui.QBoxLayout.RightToLeft)
- vbox.setSpacing(10)
-
- # Add LineEdit
- self.text = QtGui.QLabel()
- self.lineEdit = QtGui.QLineEdit()
-
- # Add OK / Cancel Buttons
- okButton = QtGui.QPushButton('OK')
- cancelButton = QtGui.QPushButton('Cancel')
- hbox.addWidget(cancelButton)
- hbox.addWidget(okButton)
-
- vbox.addWidget(self.text)
- vbox.addWidget(self.lineEdit)
- vbox.addLayout(hbox)
- self.setLayout(vbox)
-
- # Connect Signals
- self.connect(okButton, QtCore.SIGNAL('pressed()'), self.okPressedEvent)
- self.connect(cancelButton, QtCore.SIGNAL('pressed()'), self.close)
- self.connect(self.lineEdit, QtCore.SIGNAL('returnPressed()'), self.okPressedEvent)
-
- def showWarning(self, varID, file, var, axesArgString):
- """ Show warning message and prompt user for a new variable name. Or use
- the same var name to replace the existing defined variable """
-
- self.varID = varID
- self.file = file
- self.var = var
- self.axesArgString = axesArgString
-
- message = "'%s' has already been defined. Enter a new variable name \n or press 'OK' to replace '%s'" %(varID, varID)
- self.text.setText(message)
- self.lineEdit.setText(varID)
-
- self.open()
-
- def okPressedEvent(self):
- self.varID = self.lineEdit.text() # get the user entered variable name
- self.close()
-
- # Emit signal to QDefinedVar to indicate it's ok to add the variable to defined list
- self.emit(QtCore.SIGNAL('newVarID'),
- self.varID, self.file, self.var, self.axesArgString)
-
-class QSliderCombo(QtGui.QWidget):
- """ Widget containing min slider, max slider, min label, max label, and a
- corresponding combo box. The comboBox, labels, sliders must always be in
- sync with each other """
-
- def __init__(self, axis, parent=None):
- QtGui.QWidget.__init__(self, parent)
- self.isTime = axis.isTime()
- self.indexMode = False
- self.startIndex = 0
-
- # Init Layout
- hbox = QtGui.QHBoxLayout()
- vbox = QtGui.QVBoxLayout()
- vbox.setSpacing(0)
- vbox.setMargin(0)
- self.setLayout(hbox)
-
- # Init combo box
- self.axisCombo = QAxisComboWidget()
- hbox.addWidget(self.axisCombo)
-
- # Init sliders
- hbox.addLayout(vbox)
- self.topSlider = QtGui.QSlider(QtCore.Qt.Horizontal)
- self.bottomSlider = QtGui.QSlider(QtCore.Qt.Horizontal)
- vbox.addWidget(self.topSlider)
- vbox.addWidget(self.bottomSlider)
-
- # Init axis slider value labels
- self.bottomLabel = QtGui.QLabel('To', self)
- self.topLabel = QtGui.QLabel('From', self)
- hbox = QtGui.QHBoxLayout()
- hbox.addWidget(self.topLabel)
- hbox.addWidget(self.bottomLabel)
- vbox.addLayout(hbox)
-
- # Initialize the sliders' and comboBox's values
- self.initAxisValues(axis)
- self.setSlidersMinMax()
- self.topSlider.setValue(self.minIndex)
- self.bottomSlider.setValue(self.maxIndex)
- self.axisCombo.initValues(self.axisValues)
-
- # Connect Signals
- self.connect(self.topSlider, QtCore.SIGNAL('valueChanged (int)'),
- self.updateMin)
- self.connect(self.bottomSlider, QtCore.SIGNAL('valueChanged (int)'),
- self.updateMax)
- self.connect(self.axisCombo,
- QtCore.SIGNAL('axisComboMinValueChanged (int)'),
- self.updateTopSlider)
- self.connect(self.axisCombo,
- QtCore.SIGNAL('axisComboMaxValueChanged (int)'),
- self.updateBottomSlider)
-
- def initAxisValues(self, axis):
- """ Initialize list containing the axis values and set the top slider /
- combobox value to be the min value and the bottom slider / combobox
- value to be the max value"""
-
- if (axis != None):
- if self.isTime:
- self.axisValues = [repr(t.tocomponent())
- for t in axis.asRelativeTime()]
- else:
- self.axisValues = axis.getValue()
- else:
- raise TypeError("Error: axis is not defined")
-
- self.axisIndices = range(len(self.axisValues))
- self.updateMin(0)
- self.updateMax(len(self.axisValues) - 1)
-
- def setStartIndex(self, index):
- self.startIndex = index
-
- def setIndexMode(self, mode):
- """ Set the indexMode to True or False. If indexMode is True the widget
- will display indices. If indexMode is False the widget will display
- actual values """
- self.indexMode = mode
-
- def setSlidersMinMax(self):
- self.topSlider.setMinimum(self.minIndex)
- self.bottomSlider.setMinimum(self.minIndex)
- self.topSlider.setMaximum(self.maxIndex)
- self.bottomSlider.setMaximum(self.maxIndex)
-
- def updateMin(self, minIndex=None):
- """ Set min value, update the slider label and the comboBox line edit
- to show the new min value"""
-
- if not minIndex is None:
- self.minIndex = minIndex
-
- if (self.indexMode == True):
- minValue = self.minIndex + self.startIndex
- else:
- minValue = self.axisValues[self.minIndex]
-
- self.topLabel.setText(str(minValue))
- self.axisCombo.setMinValue(minValue)
-
- def updateMax(self, maxIndex=None):
- """ Set max value, update the slider label and the comboBox line edit
- to show the new max value"""
-
- if not maxIndex is None:
- self.maxIndex = maxIndex
-
- if (self.indexMode == True):
- maxValue = self.maxIndex + self.startIndex
- else:
- maxValue = self.axisValues[self.maxIndex]
-
- self.bottomLabel.setText(str(maxValue))
- self.axisCombo.setMaxValue(maxValue)
-
- def updateTopSlider(self, index):
- self.minIndex = index
- self.topSlider.setValue(index)
-
- def updateBottomSlider(self, index):
- self.maxIndex = index
- self.bottomSlider.setValue(index)
-
- def replaceComboBoxValues(self, values):
- self.axisCombo.replaceComboBoxValues(values)
-
- def getAxisIndices(self):
- return self.axisIndices
-
- def getAxisValues(self):
- return self.axisValues
-
- def getCurrentValues(self):
- return (self.axisValues[self.minIndex], self.axisValues[self.maxIndex])
-
- def getCurrentValuesAsStr(self):
- if self.isTime:
- return "('%s', '%s')" % (self.axisValues[self.minIndex],
- self.axisValues[self.maxIndex])
- else:
- return "(%s, %s)" % (self.axisValues[self.minIndex],
- self.axisValues[self.maxIndex])
-
- def numValues(self):
- return len(self.axisValues)
-
- def getIndex(self):
- return (self.minIndex, self.maxIndex)
-
-class QAxis(QtGui.QWidget):
- """ Axis widget containing: a button + popup-menu for modifying an axis, combobox
- and sliders for setting axis values, and a function def button + popup-menu """
-
- def __init__(self, axis, axisName, axisIndex, parent=None):
- QtGui.QWidget.__init__(self, parent)
- self.myParent = parent
- self.axis = axis
- self.axisName = axisName # Axis name including the label
- self.axisIndex = axisIndex
-
- hbox = QtGui.QHBoxLayout()
- hbox.setSpacing(0)
- hbox.setMargin(0)
- self.sliderCombo = QSliderCombo(axis, self)
- hbox.addWidget(self.sliderCombo)
- self.setLayout(hbox)
-
- # These buttons aren't added to the layout here, instead they are added
- # in QAxisList which has a grid layout so they can line up properly
- self.axisOperationsButton = self.createAxisOperationsButtonAndMenu()
- self.axisButton = self.createAxisButtonAndMenu()
-
- # Connect signals such that when the value of the axis slider is changed,
- # a signal will be emitted to update the value in the corresponding
- # Vistrails 'Variable' or 'Quickplot' box.
- self.connect(self.sliderCombo.topSlider,
- QtCore.SIGNAL('valueChanged (int)'),
- parent.setVistrailsVariableAxes)
- self.connect(self.sliderCombo.bottomSlider,
- QtCore.SIGNAL('valueChanged (int)'),
- parent.setVistrailsVariableAxes)
-
- def createAxisOperationsButtonAndMenu(self):
- """ Initialize the button to the right of the axis sliders and it's menu
- with operations: def, sum, avg, wgt, gtm, awt, std
- """
- button = QtGui.QToolButton()
- menu = QtGui.QMenu(self)
-
- opDefs = ['def default axis points',
- 'sum summation of selected axis points',
- 'avg average of selected axis points',
- 'wgt weighted average of selected axis points',
- 'awt altered weighted average of selected axis points',
- 'gtm geometrical mean of selected axis points',
- 'std standard deviation of selected axis points',]
-
- for op in opDefs:
- action = menu.addAction(op)
- self.connect(action, QtCore.SIGNAL('triggered ()'),
- self.selectAxesOperationEvent)
-
- button.setText(' def ')
- button.setMenu(menu)
- button.setPopupMode(QtGui.QToolButton.InstantPopup)
-
- # Connect Signals
- self.connect(button, QtCore.SIGNAL('clicked(bool)'),
- button.showMenu)
-
- return button
-
- def selectAxesOperationEvent(self):
- """ Event handler for when a user selects an operation from the
- axes operations popup menu (located to right of the sliders):
- sum, avg, awt, gtm, etc ...
- """
- # Get the operation selected by getting the text of who sent the signal
- op = self.sender().text()[:3] # def, sum, avg, wgt, awt, gtm, or std
-
- # If the operation is 'awt' ask the user for an alternate weight var
- if op == 'awt':
- definedVars = self.myParent.getParent().getDefinedVars()
- QReplaceAxisWeightsDialog(definedVars, self).show()
- return
-
- # Set button text to what the user selected
- self.axisOperationsButton.setText(" %s " % op)
-
- # Update the vistrails 'Variable' module's axesOperations input
- axesOperations = self.myParent.getAxesOperations()
- varWidget = self.myParent.getParent()
- varWidget.emit(QtCore.SIGNAL('updateModule'),
- self.myParent.currentTabName(), 'axesOperations',
- str(axesOperations))
-
- def createAxisButtonAndMenu(self):
- """ createAxisButtonAndMenu(axesNames: list)
-
- Initialize the button to the left of the sliders / combo box and
- it's menu which currently has options: index, raw, get axis values,
- get axis weight values, replace axis values, re-order dimensions.
- """
- axisMenu = QtGui.QMenu(self)
- menuVbox = QtGui.QVBoxLayout()
- axisMenu.setLayout(menuVbox)
-
-
- # Add index options to the menu
- indexAction = axisMenu.addAction(self.axis.id + '_index')
- indexAction.setCheckable(True)
-
- # Add raw index option if this dimension is time
- if self.axis.isTime():
- rawIndexAction = axisMenu.addAction(self.axis.id + '_raw')
- rawIndexAction.setCheckable(True)
-
- axisMenu.addSeparator()
-
- # Add axis value options to the menu
- axisOptions = ['Get Axis Values', 'Get Axis Weight Values',
- 'Replace Axis Values']
- getAxisValuesAction = axisMenu.addAction(axisOptions[0])
- getAxisWeightValuesAction = axisMenu.addAction(axisOptions[1])
- replaceAxisValuesAction = axisMenu.addAction(axisOptions[2])
-
- # Add 're-order dimensions' option to menu
- axisMenu.addSeparator()
- reorderAxesMenu = axisMenu.addMenu('Re-Order Dimensions')
- axesNames = self.myParent.getAxesNames()
- for axisID in axesNames:
- reorderAction = reorderAxesMenu.addAction(axisID)
- self.connect(reorderAction, QtCore.SIGNAL('triggered()'),
- self.reorderAxesEvent)
-
- # Create axis button
- axisButton = QtGui.QToolButton()
- axisButton.setMenu(axisMenu)
- axisButton.setPopupMode(QtGui.QToolButton.InstantPopup)
-
- # Connect signals emitted by the axis button menu
- axisButton.connect(axisButton, QtCore.SIGNAL('clicked(bool)'),
- axisButton.showMenu)
- self.connect(indexAction, QtCore.SIGNAL('toggled (bool)'),
- self.setIndexModeEvent)
- self.connect(getAxisValuesAction, QtCore.SIGNAL('triggered ()'),
- self.getAxisValuesEvent)
- self.connect(replaceAxisValuesAction, QtCore.SIGNAL('triggered ()'),
- self.getReplacementAxisValuesEvent)
- self.connect(getAxisWeightValuesAction, QtCore.SIGNAL('triggered ()'),
- self.getAxisWeightValuesEvent)
-
- if self.axis.isTime():
- self.connect(rawIndexAction, QtCore.SIGNAL('toggled (bool)'),
- self.setRawIndexModeEvent)
- # Dont allow _raw and _index to be checked simultaneously
- self.connect(rawIndexAction, QtCore.SIGNAL('toggled (bool)'),
- lambda : indexAction.setChecked(False))
- self.connect(indexAction, QtCore.SIGNAL('toggled (bool)'),
- lambda : rawIndexAction.setChecked(False))
-
- return axisButton
-
- def reorderAxesEvent(self):
- """ reorderAxesEvent is called when the user selects 're-order
- dimensions from the axis button. Swap this axis with the selected axis
- and update the vistrails' Variable module's 'axes' input
- """
- axisB = self.sender().text()
- self.myParent.swapAxes(self.axisName, axisB)
- self.myParent.setVistrailsVariableAxes()
-
- def getReplacementAxisValuesEvent(self):
- """ getReplacementAxisValuesEvent is called when the user selects
- 'Replace Axis Values' Show a dialog box which asks the user to select
- a defined variable for replacement axis values
- """
- definedVars = self.myParent.getParent().getDefinedVars()
- QReplaceAxisValuesDialog(definedVars, self).show()
-
- def replaceAxisValues(self, newValuesVar):
- """ replaceAxisValues(newValuesVar: tvariable)
-
- replaceAxisValues is called after the user selects 'Replace Axis Values'
- and selects a replacement variable from the popup dialog. This method
- replaces the axis' values with 'newValuesVar'
- """
- # TODO doesn't work
- var = self.myParent.getVar()
- axis = var.getAxis(self.axisIndex)
- axis[:] = newValuesVar.astype(axis[:].dtype.char).filled()
- axis.setBounds(None)
- self.myParent.setVar(var)
-
- # Generate teaching command string
- # TODO
-
- def getAxisWeightValuesEvent(self):
- """ getAxisWeightValuesEvent is called when the user selects 'Get Axis
- Weight Values' from the axis button menu. This method will create and
- define a new variable / tab with the axis' weight values
- """
- var = self.myParent.getVar()
- axisVar = genutil.getAxisWeightByName(var, self.axis.id)
- axisVar.id = var.id +'_' + self.axis.id + '_weight'
-
- # Generate teaching command string
- fileID = 'fid2'
- teachingCommand = "\n## Getting axis %s\n" % self.axis.id
- teachingCommand += "%s = genutil.getAxisWeightByName(%s[\"%s\"], \"%s\")\n" % (axisVar.id, fileID, var.id, self.axis.id)
- teachingCommand += "%s.id = \"%s\"\n" % (axisVar.id, axisVar.id)
-
- # Record teaching commands associate 'get axis weight values' and
- # define a new variable/tab with only the axis' weight values
- self.myParent.defineVarAxis(axisVar, teachingCommand)
-
- def getAxisValuesEvent(self):
- """ getAxisValuesEvent is called when the user selects 'Get Axis
- Values' from the axis button menu. This method will create and
- define a new variable / tab with the axis' values
- """
- varID = self.myParent.getVar().id
- axisVar = MV2.array(self.axis)
- axisVar.setAxis(0, self.axis)
- axisVar.id = varID +'_' + self.axis.id + '_axis'
-
- # Generate teaching command string
- fileID = 'fid2'
- teachingCommand = "\n## Getting axis %s\n" % self.axis.id
- teachingCommand += "%s = MV2.array(%s[\"%s\"].getAxisList(axes = \"%s\")[0][:])\n" % (axisVar.id, fileID, varID, self.axis.id)
- teachingCommand += "%s.setAxis(0, %s[\"%s\"].getAxisList(axes = \"%s\")[0])\n" % (axisVar.id, fileID, varID, self.axis.id)
- teachingCommand += "%s.id = \"%s\"\n" % (axisVar.id, axisVar.id)
-
- # Record teaching commands associate 'get axis values' and
- # define a new variable/tab with only the axis' values
- self.myParent.defineVarAxis(axisVar, teachingCommand)
-
- def setIndexModeEvent(self, indexMode):
- """ setIndexModeEvent(indexMode: bool)
-
- If indexMode is True then set the combobox and
- slider values to be indices. If indexMode is False then set the
- combobox and slider values to be the actual axis values.
- """
- axisIndices = self.sliderCombo.getAxisIndices()
- axisValues = self.sliderCombo.getAxisValues()
-
- self.sliderCombo.setIndexMode(indexMode)
- if (indexMode == True):
- self.sliderCombo.setStartIndex(0)
- self.sliderCombo.replaceComboBoxValues(axisIndices)
- else:
- self.sliderCombo.replaceComboBoxValues(axisValues)
-
- self.sliderCombo.updateMax()
- self.sliderCombo.updateMin()
-
- def setRawIndexModeEvent(self, rawIndexMode):
- """ setRawIndexModeEvent(rawIndexMode: bool)
-
- If rawIndexMode is True then set the combobox and
- slider values to be indices since january 1st 1979.
- otherwise set the combobox and slider values to be the actual axis
- values.
- """
- self.sliderCombo.setIndexMode(rawIndexMode)
- axisValues = self.sliderCombo.getAxisValues()
- axisIndices = self.sliderCombo.getAxisIndices()
-
- if (rawIndexMode == True):
- # Calculate months since jan 1st, 1979
- firstTimeEntry = axisValues[0]
- match = re.compile('(\d\d\d\d)(-)(.+)(-)(.*)').match(firstTimeEntry)
-
- if match is None:
- raise NameError("Invalid time string: %s" % firstTimeEntry)
-
- year = int(match.group(1))
- month = int(match.group(3))
- monthsSince1979 = 12 * (year - 1979) + (month - 1)
- self.sliderCombo.setStartIndex(monthsSince1979)
-
- # Add months since jan 1979 to indices
- rawIndices = map(lambda x: x + monthsSince1979, axisIndices)
- self.sliderCombo.replaceComboBoxValues(rawIndices)
- else:
- self.sliderCombo.replaceComboBoxValues(axisValues)
-
- self.sliderCombo.updateMax()
- self.sliderCombo.updateMin()
-
- def sumAxisPoints(self, var):
- """ Update the variable by applying the sum operation to the given
- axis. Note this function is called only when a variable is defined.
- """
- varID = var.id
- var = cdutil.averager(var, axis="(%s)" % self.axis.id, weight='equal',
- action='sum')
- var.id = varID
- return var
-
- def avgAxisPoints(self, var):
- """ Update the variable by applying the avg operation to the given
- axis.
- """
- varID = var.id
- var = cdutil.averager(var, axis="(%s)" % self.axis.id, weight='equal')
- var.id = varID
- return var
-
- def weightedAvgAxisPoints(self, var):
- """ Update the variable by applying the weighted avg operation to the
- the given axis.
- """
- varID = var.id
- var = cdutil.averager(var, axis="(%s)" % self.axis.id)
- var.id = varID
- return var
-
- def geoMeanAxisPoints(self, var):
- """ Update the variable by applying the geometrical mean operation to
- the given axis.
- """
- varID = var.id
- var = genutil.statistics.geometricmean(var, axis="(%s)" % self.axis.id)
- var.id = varID
- return var
-
- def stdAxisPoints(self, var):
- """ Update the variable by applying the standard deviation operation to
- the given axis.
- """
- varID = var.id
- var = genutil.statistics.std(var, axis="(%s)" % self.axis.id)
- var.id = varID
- return var
-
- def alteredWeightedAvgAxisPoints(self, var):
- """ Update the variable by applying the altered weighted avg operation
- to the given axis.
- """
- varID = var.id
- var = cdutil.averager(var, axis="(%s)" % self.axis.id,
- weight=self.alteredWeightsVar.filled())
- var.id = varID
- return var
-
- def setAlteredWeights(self, var):
- self.alteredWeightsVar = var
- self.axisOperationsButton.setText(' awt ')
-
- def setAxisButtonText(self, name):
- self.axisButton.setText(name + ' ')
-
- def getCurrentValues(self):
- return self.sliderCombo.getCurrentValues()
-
- def getCurrentValuesAsStr(self):
- return self.sliderCombo.getCurrentValuesAsStr()
-
- def numValues(self):
- return self.sliderCombo.numValues()
-
- def getIndexes(self):
- return self.sliderCombo.getIndexes()
-
- def getID(self):
- return self.axis.id
-
- def getAxisOperationsButton(self):
- return self.axisOperationsButton
-
- def getAxisButton(self):
- return self.axisButton
-
- def getAlteredWeightsVar(self):
- return self.alteredWeightsVar
-
-class QAxisComboWidget(QtGui.QComboBox):
- """ Specialized ComboBox widget for Axis Values listing / selecting the
- axis' values. """
-
- def __init__(self, parent=None):
- QtGui.QComboBox.__init__(self, parent)
- self.setMin = False
- self.stride = 1 # TODO : Changing the stride does nothing as of now
- self.minValue = 0
- self.maxValue = 0
-
- self.setMouseTracking(True)
- self.setEditable(True)
- self.setMinimumContentsLength(10)
- self.setCurrentIndex(1)
- self.setMaxVisibleItems(10)
- self.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToMinimumContentsLengthWithIcon)
-
- # Set highlighted text color to gray instead of default white
- comboPalette = self.view().palette()
- comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.darkGray)
- self.view().setPalette(comboPalette)
-
- # Connect Signals
- self.connect(self, QtCore.SIGNAL('currentIndexChanged(const QString&)'),
- self.valueChangedEvent)
-
- def initValues(self, axisValues):
- """ initValues(axisValues: list)
-
- Initialize the values in the combo box from a list of axis values.
- """
- for axisValue in axisValues:
- self.addItem(str(axisValue),
- QtCore.QVariant(QtCore.QStringList(['variables', str(axisValue)])))
-
- self.minValue = axisValues[0]
- self.maxValue = axisValues[-1]
- self.setLineEditText() # Set lineedit text to be valueA : valueB by stride
-
- def replaceComboBoxValues(self, axisValues):
- """ replaceComboBoxValues(axisValues: list)
-
- Replace the values in the comboBox with new values: raw indices, indices
- or actual values.
- """
- for i in range(len(axisValues)):
- data = QtCore.QVariant(QtCore.QStringList(['variables', str(axisValues[i])]))
- self.setItemData(i, data)
- self.setItemText(i, str(axisValues[i]))
-
- self.minValue = axisValues[0]
- self.maxValue = axisValues[-1]
- self.setLineEditText()
-
- def setMinValue(self, minValue):
- self.minValue = minValue
- self.setLineEditText()
-
- def setMaxValue(self, maxValue):
- self.maxValue = maxValue
- self.setLineEditText()
-
- def setLineEditText(self):
- """ Set the comboBox's lineEdit to show: minValue : maxValue by stride
- """
- self.setEditText(str(self.minValue) + " : " + str(self.maxValue) + " by "
- + str(self.stride))
- self.lineEdit().setCursorPosition(0)
-
- def valueChangedEvent(self, axisValue):
- """ valueChangedEvent(axisValue: str)
-
- Event handler for when a user changes a combobox value by selecting a
- value or entering a value into the line edit. Update the corresponding
- slider / label with the same value
- """
- index = self.findData(QtCore.QVariant(QtCore.QStringList(['variables', str(axisValue)])))
-
- # If user entered a value into the lineEdit.
- if index == -1:
- self.updateValueFromLineEditText(axisValue)
- return
-
- # If user selected a value from the combo box.
- # Selecting values from the combo box will alternate between setting the
- # min and max values & emit a signal to update corresponding slider
- if (self.setMin == True):
- self.setMin = False
- self.minValue = axisValue
- self.emit(QtCore.SIGNAL('axisComboMinValueChanged (int)'), self.currentIndex())
- else:
- self.setMin = True
- self.maxValue = axisValue
- self.emit(QtCore.SIGNAL('axisComboMaxValueChanged (int)'), self.currentIndex())
-
- self.setLineEditText()
-
- def updateValueFromLineEditText(self, axisValue):
- """ updateValueFromLineEditText(axisValue: str)
-
- Check if the user entered a valid string in the line edit and if the
- values exist. If it is valid & the values exist, set the values in the
- corresponding slidingAxisWidget so the combobox and sliders match.
- """
- # The lineEdit text must have format "ValueA : ValueB by Stride"
- pattern = re.compile("(.*)\s:\s(.*)\sby\s(\w*)")
- result = pattern.match(axisValue)
-
- # If invalid string format, do nothing
- if (result == None):
- return
-
- # Set stride if it is a valid digit
- # Stride functionality not implemented yet
- if (str(result.group(3)).isdigit() == True):
- self.stride = result.group(3)
-
- minValue = result.group(1)
- maxValue = result.group(2)
- minIndex = self.findData(QtCore.QVariant(QtCore.QStringList(['variables', str(minValue)])))
- maxIndex = self.findData(QtCore.QVariant(QtCore.QStringList(['variables', str(maxValue)])))
-
- # If min or max values are not in the list of values do nothing
- if (minIndex == -1 or maxIndex == -1):
- return
-
- # LineEdit string is valid, emit signal to update the corresponding axis sliders
- self.emit(QtCore.SIGNAL('axisComboMinValueChanged (int)'), minIndex)
- self.emit(QtCore.SIGNAL('axisComboMaxValueChanged (int)'), maxIndex)
-
-class QAxisList(QtGui.QWidget):
- """ Widget containing a list of axis widgets for the selected variable """
-
- def __init__(self, file=None, var=[], parent=None):
- QtGui.QWidget.__init__(self, parent)
- self.axisWidgets = [] # List of QAxis widgets
- self.axesNames = [] # List of axis names (including labels)
- self.axisOrder = [] # List of ints to specify axes ordering
- self.file = file # cdms file associated with the variable
- self.var = var # variable associated with the axes
- self.axisList = None # list of axes from the variable
- self.myParent = parent
-
- # Init & set the layout
- vbox = QtGui.QVBoxLayout()
- self.gridLayout = QtGui.QGridLayout()
- self.gridLayout.setMargin(0)
- self.gridLayout.setSpacing(0)
- vbox.addLayout(self.gridLayout)
- vbox.addStretch()
- vbox.setSpacing(0)
- vbox.setMargin(5)
- self.setLayout(vbox)
-
- def clear(self):
- """ Remove the QAxis widgets, empty axisWidgets and axesNames lists from
- the grid layout
- """
- self.gridLayout.setRowStretch(self.gridLayout.rowCount()-1, 0)
- for i in reversed(range(self.gridLayout.count())):
- item = self.gridLayout.itemAt(i)
- axis = item.widget()
- if axis:
- self.gridLayout.removeWidget(axis)
- axis.hide()
- axis.deleteLater()
- else:
- self.gridLayout.removeItem(item)
-
- self.axisWidgets = []
- self.axesNames = []
-
- def setupVariableAxes(self):
- """ Iterate through the variable's axes and create and initialize an Axis
- object for each axis.
- """
- if self.var is None:
- return
-
- if (self.axisList is None):
- self.axisList = self.var.getAxisList()
- self.axisOrder = range(len(self.axisList))
-
- self.clear()
- self.setAxesNames()
-
- # Iterate through the variables axes & init each axis widget
- axisIndex = 0
- for axis, axisName in zip(self.axisList, self.axesNames):
- # Create the axis widget
- axisWidget = QAxis(axis, axisName, axisIndex, self)
- axisWidget.setAxisButtonText(axisName)
- self.axisWidgets.append(axisWidget)
-
- # Setup the layout for each axis
- row = self.gridLayout.rowCount()
- self.gridLayout.addWidget(axisWidget.getAxisButton(), row, 0)
- self.gridLayout.addWidget(axisWidget, row, 1)
- self.gridLayout.addWidget(axisWidget.getAxisOperationsButton(), row, 2)
-
- # Create separator line between each axis widget
- vline = QtGui.QFrame()
- vline.setFrameStyle(QtGui.QFrame.HLine | QtGui.QFrame.Sunken)
- self.gridLayout.addWidget(vline, row+1, 0, 1,
- self.gridLayout.columnCount())
-
- axisIndex += 1
-
- self.gridLayout.setRowStretch(self.gridLayout.rowCount(), 1)
-
- def defineVarAxis(self, var, teachingCommand):
- self.myParent.defineVarAxis(var, teachingCommand)
-
- def swapAxes(self, axisA, axisB):
- """ swapAxes(axisA: QAxis, axisB: QAxis)
-
- swap the axis widgets: axisA and axisB
- """
- if (axisA == axisB):
- return
-
- if axisA in self.axesNames and axisB in self.axesNames:
- i = self.axesNames.index(axisA)
- j = self.axesNames.index(axisB)
- self.axisList[i], self.axisList[j] = self.axisList[j], self.axisList[i]
- self.axisOrder[i], self.axisOrder[j] = self.axisOrder[j], self.axisOrder[i]
- self.setupVariableAxes()
-
- def execAxesOperations(self, var):
- """ Return the updated variable by doing the 'sum', 'avg', 'wgt', 'awt',
- 'gtm' and 'std' operations.
- """
- for axis in self.axisWidgets:
- op = str(axis.getAxisOperationsButton().text()).strip()
- if op == 'sum':
- var = axis.sumAxisPoints(var)
- elif op == 'avg':
- var = axis.avgAxisPoints(var)
- elif op == 'wgt':
- var = axis.weightedAvgAxisPoints(var)
- elif op == 'gtm':
- var = axis.geoMeanAxisPoints(var)
- elif op == 'std':
- var = axis.stdAxisPoints(var)
- elif op == 'awt':
- var = axis.alteredWeightedAvgAxisPoints(var)
- return var
-
- # * At this point in fixing up the code
-
- def getAxesOperationsTeachingCommands(self, varID):
- """ Create and return the teaching commands for the axes operations:
- def, sum, avg, wgt, awt, gtm, std
- """
- commands = ""
- for axis in self.axisWidgets:
- axisID = axis.getID()
- op = str(axis.getAxisOperationsButton().text()).strip()
-
- if op == 'sum':
- commands += "%s=cdutil.averager(%s, axis='(%s)', weight='equal', action='sum')\n" % (varID, varID, axisID)
- commands += "%s.id = '%s'\n" % (varID, varID)
- elif op == 'avg':
- commands += "%s=cdutil.averager(%s, axis='(%s)', weight='equal')\n" % (varID, varID, axisID)
- commands += "%s.id = '%s'\n" % (varID, varID)
- elif op == 'wgt':
- commands += "%s=cdutil.averager(%s, axis='(%s)')\n" % (varID, varID, axisID)
- commands += "%s.id = '%s'\n" % (varID, varID)
- elif op == 'awt':
- alteredWeightsID = axis.getAlteredWeightsVar().id
- commands += "%s=cdutil.averager(%s, axis='(%s)', weight=%s.filled())" % (varID, varID, axisID, alteredWeightsID)
- commands += "\n# Currently, VCDAT cannot record the altered average weight command."
- elif op == 'gtm':
- commands += "%s=genutil.statistics.geometricmean(%s, axis='(%s)')\n" % (varID, varID, axisID)
- commands += "%s.id = '%s'\n" % (varID, varID)
- elif op == 'std':
- commands += "%s=genutil.statistics.std(%s, axis='(%s)')\n" % (varID, varID, axisID)
- commands += "%s.id = '%s'\n" % (varID, varID)
- return commands
-
- def getAxesOperations(self):
- """ Return a dict where keys are axis names, and values are the
- operation to be done on the axis such as: def, sum, avg, etc ... """
-
- axisOpsDict = {}
- for axis in self.axisWidgets:
- op = str(axis.getAxisOperationsButton().text()).strip()
- axisOpsDict[axis.getID()] = op
-
- return axisOpsDict
-
- def getAxesNames(self):
- return self.axesNames
-
- def getAxisWidgets(self):
- return self.axisWidgets
-
- def getFile(self):
- return self.file
-
- def getFileID(self):
- return self.file.id
-
- def getVar(self):
- return self.var
-
- def getVarID(self):
- return self.var.id
-
- def getParent(self):
- return self.myParent
-
- def getAxesOrderString(self):
- """ Return a string with the axes' order """
-
- order = list(self.axisOrder)
- return ''.join(map(str, order))
-
- def setAxesNames(self):
- """ Generate a list with the axis label + axis name and store it in
- self.axesNames """
-
- labels = ['T', 'Z', 'Y', 'X'] + [chr(ord('S')-i) for i in xrange(18)]
- if (len(self.axisList) >= 4):
- i = 0
- else:
- i = 4 - len(self.axisList)
-
- for axis in self.axisList:
- self.axesNames.append(labels[i] + ' - ' + axis.id)
- i += 1
-
- def setFile(self, cdmsFile):
- self.file = cdmsFile
-
- def setVar(self, var):
- self.var = var
-
- def currentTabName(self):
- return self.myParent.currentTabName()
-
- def setVistrailsVariableAxes(self):
- """ Vistrails: Update the vistrails Variable modules 'axes' input. This
- method is called whenever the sliders values are changed.
- """
- axesKwargs = {}
- # Add the each axes' args for example: latitude: (-90, 90)
- for axisWidget in self.axisWidgets:
- axesKwargs[axisWidget.axis.id] = axisWidget.getCurrentValues()
- # Add other args
- axesKwargs['squeeze'] = 0
- axesKwargs['order'] = self.getAxesOrderString()
-
- self.myParent.emit(QtCore.SIGNAL('updateModule'),
- self.myParent.currentTabName(), 'axes', str(axesKwargs))
-
-class QVariableView(QtGui.QWidget):
- """ Main widget containing plotting related information / options. Contains
- a tab widget with a tab for each defined variable, plotting options widget,
- and variable information widget """
-
- def __init__(self, parent=None):
- QtGui.QWidget.__init__(self, parent)
- self.selectedVars = []
-
- # Init layout
- vbox = QtGui.QVBoxLayout()
- vbox.setMargin(0)
- self.setLayout(vbox)
-
- self.plotOptions = QPlotOptionsWidget(self)
- self.tabWidget = QAxisListTabWidget(self)
-
- # Init variable information widget
- self.varInfoWidget = QtGui.QTextEdit()
- self.varInfoWidget.setText('')
- self.varInfoWidget.setReadOnly(True)
-
- # Create splitter for tabWidget and variable information text
- vsplitter = QtGui.QSplitter(QtCore.Qt.Vertical)
- vsplitter.addWidget(self.tabWidget)
- vsplitter.addWidget(self.varInfoWidget)
- vsplitter.setStretchFactor(1,1)
- vsplitter.setSizes([300, 100])
-
- vbox.addWidget(self.plotOptions)
- vbox.addWidget(vsplitter)
-
- def getUpdatedVar(self):
- """ Return a new tvariable object with the updated information from
- evaluating the var with the current user selected args / options
- """
- axisList = self.tabWidget.currentWidget()
- kwargs = self.generateKwArgs()
- updatedVar = axisList.getVar()(**kwargs)
-
- # Get the variable after carrying out the: def, sum, avg... operations
- updatedVar = axisList.execAxesOperations(updatedVar)
-
- return updatedVar
-
- def generateKwArgs(self, axisList=None):
- """ Generate and return the variable axes keyword arguments """
- if axisList is None:
- axisList = self.tabWidget.currentWidget()
-
- kwargs = {}
- for axisWidget in axisList.getAxisWidgets():
- kwargs[axisWidget.axis.id] = axisWidget.getCurrentValues()
-
- # Generate additional args
- kwargs['squeeze'] = 0
- kwargs['order'] = axisList.getAxesOrderString()
-
- return kwargs
-
- def generateKwargsAsString(self):
- """ Generate and return the variable axes keyword arguments as a string
- that is formatted to be used in teaching commands
- """
- args = ""
- axisList = self.tabWidget.currentWidget()
-
- for axisWidget in axisList.getAxisWidgets():
- args += "%s = %s, " % (axisWidget.axis.id,
- axisWidget.getCurrentValuesAsStr())
-
- # Generate additional args
- args += 'squeeze = 0'
- args += ", order = '%s' " % axisList.getAxesOrderString()
- return args
-
- def updateVarInfo(self, axisList):
- """ Update the text box with the variable's information """
- if axisList is None:
- return
-
- var = axisList.getVar()
- varInfo = ''
- for line in var.listall():
- varInfo += line + '\n'
- self.varInfoWidget.setText(varInfo)
-
- def setupDefinedVariableAxes(self, cdmsFile, var, tabName):
- """ Create a new axis list and tab with the specified tab name and setup
- the axis list. Initialize the vistrails Variable module associated with
- the tab and variable.
- """
- if var is None:
- return
-
- # Create and setup the axislist
- axisList = QAxisList(cdmsFile, var, self)
- axisList.setupVariableAxes()
- self.updateVarInfo(axisList)
- self.tabWidget.createNewTab(axisList, tabName)
-
- # Create the vistrails variable module if it doesn't exist, and update
- # the modules input ports' values
- if tabName == 'quickplot':
- self.emit(QtCore.SIGNAL('createModule'), quickplot_name,
- quickplot_name.lower())
- else:
- self.emit(QtCore.SIGNAL('createModule'), variable_name, tabName)
- self.emit(QtCore.SIGNAL('updateModule'), tabName, 'id',
- var.id)
- self.emit(QtCore.SIGNAL('updateModule'), tabName, 'axes',
- str(self.generateKwArgs()))
- self.emit(QtCore.SIGNAL('updateModule'),
- tabName, 'axesOperations',
- str(axisList.getAxesOperations()))
-
- def defineVarAxis(self, var, teachingCommand):
- """ Create a new tab/axisList, store it in defined var list, and record
- the associated teaching commands. This method is called when the user
- clicks on the axisButton -> 'Get Axis Values' """
-
- cdmsFile = self.tabWidget.currentWidget().getFile()
- axisList = QAxisList(cdmsFile, var, self)
- axisList.setupVariableAxes()
- argString = self.generateKwargsAsString()
-
- self.emit(QtCore.SIGNAL('recordTeachingCommand'), teachingCommand)
- self.emit(QtCore.SIGNAL('defineVariable'), cdmsFile, var, argString)
-
- def defineVariableEvent(self):
- """ Get a copy of the updated var and file and pass it to the Defined
- Variables widget """
- if self.tabWidget.currentWidget() is None:
- return
-
- cdmsFile = self.tabWidget.currentWidget().getFile()
- var = self.getUpdatedVar()
- argString = self.generateKwargsAsString()
-
- self.emit(QtCore.SIGNAL('defineVariable'), cdmsFile, var, argString)
-
- def selectDefinedVariableEvent(self, tabName, cdmsFile, selectedVars):
- """ Save the list of selected variables and show the selected variable,
- variables are sorted in least recently selected to most recently selected
- """
- if selectedVars != []:
- self.selectedVars = selectedVars
- self.tabWidget.selectAndUpdateDefinedVarTab(tabName, cdmsFile, selectedVars[-1])
-
- def plot(self):
- """ Create the graphics method and cdatcell modules. Update the input
- port values and setup connections. Then plot.
- """
- if self.tabWidget.count() == 0:
- return
-
- # Error if not enough slabs
- plotType = str(self.plotOptions.getPlotType())
- if len(self.selectedVars) < 2 and self.requiresTwoSlabs(plotType):
- self.showError('Error Message to User', 'Vector, Scatter, Meshfill or XvsY plots \nmust have two data variables. The data \nvariables must be selected in the \n"Defined Variables" window.')
- return
-
- # Create & Update the graphics method / CDATCell vistrails modules
- # *** IMPORTANT ***
- # Everytime plot is pressed, this will create a new Graphics Method and
- # CDATCell Module. Instead it should ONLY create a new graphics method
- # and CDATCell module if the variable isn't already connected to an
- # existing Graphics Method / CDATCell module. This results in plots
- # being plotted multiple times.
- axisList = self.tabWidget.currentWidget()
- self.emit(QtCore.SIGNAL('createModule'), gm_name)
- self.emit(QtCore.SIGNAL('createModule'), cdatcell_name)
- self.setVistrailsGraphicsMethod()
- self.setVistrailsCDATCell()
-
- # Get the names of the 2 slabs so we can connect their modules in vistrails
- if self.requiresTwoSlabs(plotType):
- var1 = self.selectedVars[-1].id
- var2 = self.selectedVars[-2].id
- else:
- var1 = self.currentTabName()
- var2 = None
-
- # Emit signal to GuiController to connect ports and plot
- self.emit(QtCore.SIGNAL('plot'), var1, var2)
-
- # If a quickplot is plotted, define current variable under 'quickplot'
- if (self.currentTabName() == 'quickplot'):
- var = self.getUpdatedVar()
- self.emit(QtCore.SIGNAL('plotPressed'), axisList.getFile(), var)
-
- # Record plot teaching commands
- self.recordPlotTeachingCommand()
-
- def recordPlotTeachingCommand(self):
- axisList = self.tabWidget.currentWidget()
- tabName = self.tabWidget.currentTabName()
- argString = self.generateKwargsAsString()
- var = axisList.getVar()
- fileID = "fid2"
-
- slabCommand = ''
- if tabName == 'quickplot':
- slabCommand += '\n# Get new slab\n'
- slabCommand += "%s = %s('%s', %s)\n" %(tabName, fileID, var.id, argString)
-
- slabCommand += '\n# Get new slab\n'
- slabCommand += "%s = %s(%s)\n" %(tabName, tabName, argString)
-
- slabCommand += axisList.getAxesOperationsTeachingCommands(tabName)
-
- canvasNum = 0 # Change the canvas # with respect to the cell?
- clearCommand = '\n# Clear the VCS Canvas\n'
- clearCommand += "vcs_canvas_list[%d].clear()\n" % canvasNum
-
- plotID = "vcs_display"
- plotType = str(self.plotOptions.getPlotType())
- template = self.getTemplateName(plotType)
- gm = self.getGraphicsMethodName(plotType)
- plotArgs = "%s, '%s', '%s', '%s'" % (tabName, template, plotType, gm)
-
- if self.plotOptions.getContinentType() is not None:
- plotArgs += ", continents = %d" % self.plotOptions.getContinentType()
-
- plotCommand = '\n# Plot slab\n'
- plotCommand += "%s = vcs_canvas_list[%d].plot(%s)\n" %(plotID, canvasNum, plotArgs)
-
- command = slabCommand + clearCommand + plotCommand
- self.emit(QtCore.SIGNAL('recordTeachingCommand'), command)
-
- def requiresTwoSlabs(self, plotType):
- """ Returns true if the plot requires 2 slabs """
- multiVarPlots = ['Vector', 'Scatter', 'XvsY']
- return plotType in multiVarPlots
-
- def getDefinedVars(self):
- """ Get a list of all of the defined tabnames / variables """
- numTabs = self.tabWidget.count()
- varList = []
-
- for i in range(numTabs):
- var = self.tabWidget.widget(i).getVar()
- name = self.tabWidget.tabText(i)
- varList.append([name, var])
-
- return varList
-
- def getAxisList(self, var):
- for i in range(self.tabWidget.count()):
- if self.tabWidget.widget(i).getVar() is var:
- return self.tabWidget.widget(i)
-
- return None
-
- def getTemplateName(self, plotType):
- """ Return the template given the plotType. This is currently hardcoded
- but should change based on the user? """
-
- # TODO ?
- return self.getGraphicsMethodName(plotType)
-
- def getGraphicsMethodName(self, plotType):
- """ Return the graphics method given the plotType. This is currently
- hardcoded but should change based on the user? """
-
- # TODO ?
- hasASD = ['Boxfill', 'Isofill', 'Isoline', 'Scatter', 'Taylordiagram']
- hasquick = ['Vector']
- hasASD1 = ['Xyvsy', 'Yxvsx']
-
- if plotType in hasASD:
- return 'ASD'
- if plotType in hasquick:
- return 'quick'
- if plotType in hasASD1:
- return 'ASD1'
- return 'default'
-
- def setVistrailsCDATCell(self):
- """ Vistrails: Update the vistrails' CDAT Cell modules' input ports: """
-
- visInput = []
- plotType = str(self.plotOptions.getPlotType())
-
- visInput.append(('plotType', plotType))
- visInput.append(('row', str(self.plotOptions.getRow())))
- visInput.append(('col', str(self.plotOptions.getCol())))
- visInput.append(('gmName', self.getGraphicsMethodName(plotType)))
- visInput.append(('template', self.getTemplateName(plotType)))
-
- if self.plotOptions.getContinentType() is not None:
- visInput.append(('continents', self.plotOptions.getContinentType())) # TODO
-
- self.emit(QtCore.SIGNAL('updateModuleOps'), cdatcell_name, visInput)
-
- def setVistrailsGraphicsMethod(self):
- """ Vistrails: Update the vistrails' Graphics Method modules' boxfill
- input ports. Only set the plotType and graphics method (gm) name.
- Setting the input for gm attributes should be handled by the gm
- controller (graphics_method_controller.py)
- """
- visInput = [] # List of tuples where each tuple = (inputPortName, value)
- plotType = str(self.plotOptions.getPlotType())
-
- visInput.append(('plotType', plotType))
- visInput.append(('gmName', self.getGraphicsMethodName(plotType)))
- self.emit(QtCore.SIGNAL('updateModuleOps'), gm_name, visInput)
-
- def showError(self, title, text):
- """ Show an error message in a simple popup message box. Currently there
- is no error icon. """
-
- errorWidget = QtGui.QMessageBox(self)
- errorWidget.setWindowTitle(title)
- errorWidget.setText(text)
- errorWidget.show()
-
- def currentTabName(self):
- return self.tabWidget.currentTabName()
-
-class QSelectVarDialog(QtGui.QDialog):
- """ Popup box that allows user to selected a defined variable to replace an
- axis """
-
- def __init__(self, definedVars, parent):
- QtGui.QDialog.__init__(self, parent)
- self.selectedVariable = None
- self.currentListIndex = None
- self.definedVars = definedVars
- self.myParent = parent
-
- vbox = QtGui.QVBoxLayout()
- hbox = QtGui.QHBoxLayout()
- self.setLayout(vbox)
-
- vbox.addWidget(QtGui.QLabel("Defined Variables:"))
-
- # Add List of defined vars
- self.varList = QtGui.QListWidget()
- self.varList.setAlternatingRowColors(True)
- vbox.addWidget(self.varList)
-
- # Initialize the list of defined vars
- # self.definedVars = parent.getDefinedVars()
- for name, var in self.definedVars:
- label = name + ' ' + str(var.shape)
- item = QtGui.QListWidgetItem()
- item.setData(0, QtCore.QVariant(QtCore.QString(label)))
- self.varList.addItem(item)
-
- # Add OK / Cancel Buttons
- okButton = QtGui.QPushButton('OK')
- cancelButton = QtGui.QPushButton('Cancel')
- hbox.addWidget(okButton)
- hbox.addWidget(cancelButton)
- vbox.addLayout(hbox)
-
- # Connect Signals
- self.connect(self.varList, QtCore.SIGNAL('clicked(const QModelIndex&)'),
- self.selectVariableFromListEvent)
- self.connect(okButton, QtCore.SIGNAL('pressed()'),
- self.selectDefinedVariableEvent)
- self.connect(cancelButton, QtCore.SIGNAL('pressed()'), self.close)
-
- def selectVariableFromListEvent(self, modelIndex):
- self.currentListIndex = modelIndex
-
- def varIsValid(self, var):
- """ Return true if the var has 1 dimension and it has the same # of
- values as the one it is replacing
- """
- if len(var.getAxisList()) != 1:
- return False
- if self.myParent.numValues() != self.myParent.numValues():
- return False
- return True
-
- def showError(self):
- errorMsg = "Invalid shape or size. Axis requiers a 1D \narray that matches in size."
- errorMessageBox = QtGui.QMessageBox(self)
- errorMessageBox.setWindowTitle("Error")
- errorMessageBox.setText(errorMsg)
- errorMessageBox.show()
- # TODO need an icon for the message box
-
- def selectDefinedVariableEvent(self):
- # Implement in child
- return
-
-class QReplaceAxisValuesDialog(QSelectVarDialog):
- """ Popup box that prompts user to select a variable to replace the current
- axis values """
-
- def __init__(self, definedVars, parent):
- QSelectVarDialog.__init__(self, definedVars, parent)
- self.setWindowTitle("Replace Axis Values")
-
- def selectDefinedVariableEvent(self):
- # Do nothing if no variable is selected
- if self.currentListIndex is None:
- return
-
- name, var = self.definedVars[self.currentListIndex.row()]
- if self.varIsValid(var):
- self.myParent.replaceAxisValues(var)
- self.close()
- else:
- self.showError()
-
-class QReplaceAxisWeightsDialog(QSelectVarDialog):
- """ Popup box that prompts user to select a variable to replace the current
- axis weight values """
-
- def __init__(self, definedVars, parent):
- QSelectVarDialog.__init__(self, definedVars, parent)
- self.setWindowTitle("Replace Dimension Weights")
-
- def selectDefinedVariableEvent(self):
- # Do nothing if no variable is selected
- if self.currentListIndex is None:
- return
-
- name, var = self.definedVars[self.currentListIndex.row()]
- if self.varIsValid(var):
- self.myParent.setAlteredWeights(var)
- self.close()
- else:
- self.showError()
-
-class QPlotOptionsWidget(QtGui.QWidget):
- """ Widget containing plot options: plot button, plot type combobox, cell
- col and row selection combo box, and an options button """
-
- def __init__(self, parent=None):
- QtGui.QWidget.__init__(self, parent)
- self.myParent = parent
- self.cellRow = -1 # if row/col = -1, then automatically plot in an open cell
- self.cellCol = -1
- hbox = QtGui.QHBoxLayout()
-
- # Add plot button
- self.plotButton = QtGui.QPushButton('&Plot')
- hbox.addWidget(self.plotButton)
-
- # Add plot type combo box
- self.plotTypeCombo = QtGui.QComboBox()
- comboPalette = self.plotTypeCombo.view().palette()
- comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
- comboPalette.setColor(QtGui.QPalette.Highlight, QtCore.Qt.blue)
- self.plotTypeCombo.view().setPalette(comboPalette)
-
- plotTypes = ['Boxfill', 'Isofill', 'Isoline', 'Meshfill', 'Outfill',
- 'Outline', 'Scatter', 'Taylordiagram', 'Vector', 'XvsY',
- 'Xyvsy', 'Yxvsx','Ext']
- self.plotTypeCombo.addItems(plotTypes)
- hbox.addWidget(self.plotTypeCombo)
-
- # Add cell row / col combo boxes
- rowLabel = QtGui.QLabel('Row')
- colLabel = QtGui.QLabel('Col')
- self.cellRowCombo = QtGui.QComboBox()
- self.cellColCombo = QtGui.QComboBox()
-
- comboPalette = self.cellRowCombo.view().palette()
- comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
- comboPalette.setColor(QtGui.QPalette.Highlight, QtCore.Qt.blue)
- self.cellRowCombo.view().setPalette(comboPalette)
-
- comboPalette = self.cellColCombo.view().palette()
- comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
- self.cellColCombo.view().setPalette(comboPalette)
-
- self.cellRowCombo.addItem('Auto')
- self.cellColCombo.addItem('Auto')
-
- for i in range(1, 9):
- self.cellRowCombo.addItems(str(i))
- self.cellColCombo.addItems(str(i))
-
- hbox.addWidget(rowLabel)
- hbox.addWidget(self.cellRowCombo)
- hbox.addWidget(colLabel)
- hbox.addWidget(self.cellColCombo)
-
- # Create the options menu
- optionsMenu = QtGui.QMenu(self)
- menuVbox = QtGui.QVBoxLayout()
- menuVbox.setMargin(2)
- optionsMenu.setLayout(menuVbox)
-
- # Create the Continents Types Menu
- self.continentTypesMenu = QCheckMenu()
- self.continentTypesMenu.setTitle('Continent Types')
- optionsMenu.addMenu(self.continentTypesMenu)
- self.continentTypes = [('Auto Continents', None),
- ('No Continents', 0),
- ('Coarse Continents', 2),
- ('Fine Continents', 1),
- ('United States Continents', 3),
- ('Political Boundary Continents', 4),
- ('Rivers Continents', 5),
- ('User1 Continents', 6),
- ('User2 Continents', 7),
- ('User3 Continents', 8),
- ('User4 Continents', 9),
- ('User5 Continents', 10),
- ('User6 Continents', 11)]
-
- for continentType in self.continentTypes:
- self.continentTypesMenu.addCheckableAction(continentType[0])
- self.continentTypesMenu.setDefaultAction('Auto Continents')
-
- # Create graphic method attribute option / editor
- canvas = vcs.init()
- self.graphicsMethodController = QGraphicsMethodAttributeWindow(canvas, self)
- graphicMethodAction = optionsMenu.addAction('Se&t Graphics Method Attributes')
-
- # Create Colormap option / widget
- colorMapAction = optionsMenu.addAction("&Colormap Editor")
- self.colorDialog = QtGui.QColorDialog(self)
- self.connect(colorMapAction, QtCore.SIGNAL('triggered ()'),
- self.colorDialog.open)
-
- # Create the options button
- self.optionButton = QtGui.QToolButton()
- self.optionButton.setText(' Options ')
- self.optionButton.setMenu(optionsMenu)
- self.optionButton.setPopupMode(QtGui.QToolButton.InstantPopup)
-
- hbox.addWidget(self.optionButton)
- hbox.addStretch()
- self.setLayout(hbox)
-
- # Connect Signals
- self.connect(self.plotButton, QtCore.SIGNAL('clicked(bool)'),
- parent.plot)
- self.connect(self.optionButton, QtCore.SIGNAL('clicked(bool)'),
- self.optionButton.showMenu)
- self.connect(graphicMethodAction, QtCore.SIGNAL('triggered ()'),
- self.graphicsMethodController.show)
-
- def getRow(self):
- if self.cellRowCombo.currentText() == 'Auto':
- return -1
- return int(self.cellRowCombo.currentText()) - 1
-
- def getCol(self):
- if self.cellColCombo.currentText() == 'Auto':
- return -1
- return int(self.cellColCombo.currentText()) - 1
-
- def getPlotType(self):
- return self.plotTypeCombo.currentText()
-
- def getContinentType(self):
- """ Returns None or a number from 0-11 corresponding to the option
- selected in the continents menu """
-
- selectedText = self.continentTypesMenu.getCheckedText()
- for text, continentType in self.continentTypes:
- if text == selectedText:
- return continentType
-
- return None
-
- def getGraphicsMethodController(self):
- return self.graphicsMethodController
-
- def getParent(self):
- return self.myParent
-
-class QCheckMenu(QtGui.QMenu):
- """ Menu where only a single 'checkable' action can be checked at a time """
-
- def __init__(self, parent=None):
- QtGui.QMenu.__init__(self, parent)
- self.defaultAction = None
- self.currentAction = None
- self.handleCheckEvent = False
- self.actions = {}
-
- def addCheckableAction(self, actionText):
- action = self.addAction(actionText)
- action.setCheckable(True)
- self.actions[actionText] = action
- self.connect(action, QtCore.SIGNAL('toggled (bool)'), self.checkEvent)
-
- def setDefaultAction(self, actionText):
- if actionText in list(self.actions):
- self.currentAction = self.defaultAction = self.actions[actionText]
- self.defaultAction.setChecked(True)
-
- def getCheckedText(self):
- return self.currentAction.text()
-
- def checkEvent(self, isChecked):
- """ Force the menu to have only 1 item checked. If an action is
- unchecked, check the default item """
-
- # handleCheckEvent prevents infinite recursion because this method also
- # generates checkEvents
- if self.handleCheckEvent == False:
- self.handleCheckEvent = True
- return
-
- if isChecked == True:
- self.handleCheckEvent = False
- self.currentAction.setChecked(False)
- self.currentAction = self.sender()
- elif isChecked == False and not self.defaultAction is None:
- self.handleCheckEvent = False
- self.defaultAction.setChecked(True)
-
-class QAxisListTabWidget(QtGui.QTabWidget):
- """ TabWidget where each tab contains a QAxisList """
-
- def __init__(self, parent=None):
- QtGui.QTabWidget.__init__(self, parent)
- self.myParent = parent
-
- self.connect(self, QtCore.SIGNAL('currentChanged(int)'),
- self.tabChangeEvent)
-
- def createNewTab(self, axisList, tabName):
- """ Create a new tab given the axisList widget and tab name. If a
- tab with the same name exists already, replace it. Set the current tab
- to the newly created tab """
-
- if (self.tabExists(tabName)):
- self.removeTab(self.getTabIndexFromName(tabName))
-
- if tabName == 'quickplot':
- self.insertTab(0, axisList, tabName) # quickplot is always first tab
- else:
- self.addTab(axisList, tabName)
-
- self.setTabTip(tabName)
- self.setCurrentIndex(self.getTabIndexFromName(tabName))
-
- def setupQuickplotTab(self, axisList):
- """ Create a new quickplot tab if one doesn't exist otherwise replace
- the existing quickplot tab """
-
- tabName = 'quickplot'
- if (self.tabExists(tabName) == True):
- index = self.getTabIndexFromName(tabName)
- self.removeTab(index)
-
- self.insertTab(0, axisList, tabName)
- self.setTabTip(tabName)
- self.setCurrentIndex(0)
-
- def setTabTip(self, tabName):
- if self.tabExists(tabName):
- index = self.getTabIndexFromName(tabName)
- toolTip = "'%s' axisList tab widget" % tabName
- self.setTabToolTip(index, toolTip)
-
- def tabChangeEvent(self, tabIndex):
- """ Event handler for when a tab is changed. Update the variable info
- text box.
- """
- axisList = self.widget(tabIndex)
- self.myParent.updateVarInfo(axisList)
-
- def selectAndUpdateDefinedVarTab(self, tabName, cdmsFile, var):
- """ This function selects a tab given the tabName and then updates the
- tab's axisList using the passed var's values
- """
- if (not self.tabExists(tabName)):
- raise NameError("Error: tab '%s' was not found" % tabName)
-
- tabIndex = self.getTabIndexFromName(tabName)
- self.setCurrentIndex(tabIndex)
-
- if (tabName == 'quickplot'):
- axisList = QAxisList(cdmsFile, var, self)
- self.setupQuickplotTab(axisList)
- axisList.setupVariableAxes()
- else:
- axisList = self.currentWidget()
- axisList.setupVariableAxes()
-
- self.emit(QtCore.SIGNAL('updateVarInfo'), axisList)
-
- def tabExists(self, name):
- """ Returns True if a tab with the given name exists """
- numTabs = self.count()
- for i in range(numTabs):
- if (name == self.tabText(i)):
- return True
- return False
-
- def getTabIndexFromName(self, name):
- numTabs = self.count()
- for i in range(numTabs):
- if (name == self.tabText(i)):
- return i
- return None
-
- def currentTabName(self):
- currentTab = self.currentIndex()
- return str(self.tabText(currentTab))
-
-class QMenuWidget(QtGui.QMenuBar):
- def __init__(self, parent=None):
- QtGui.QMenuBar.__init__(self, parent)
- self.myParent = parent
-
- self.file = self.addMenu('&File')
- self.pref = self.addMenu('&Preferences')
- self.tools = self.addMenu('&Tools')
- self.pcmdiTools = self.addMenu('&PCMDITools')
- self.help = self.addMenu('&Help')
- self.initToolsMenu()
-
- def initToolsMenu(self):
- recordTeachingAction = self.tools.addAction('Record Commands')
- recordTeachingAction.setCheckable(True)
- recordTeachingAction.setChecked(True)
-
- viewTeachingAction = self.tools.addAction('View Teaching Commands')
- closeTeachingAction = self.tools.addAction('Close Teaching Commands')
-
- self.connect(viewTeachingAction, QtCore.SIGNAL('triggered ()'),
- self.viewTeachingCommands)
- self.connect(closeTeachingAction, QtCore.SIGNAL('triggered ()'),
- self.closeTeachingCommands)
- self.connect(recordTeachingAction, QtCore.SIGNAL('toggled (bool)'),
- self.setRecordCommands)
-
- def setRecordCommands(self, checked):
- self.myParent.emit(QtCore.SIGNAL('setRecordCommands'), checked)
-
- def viewTeachingCommands(self):
- self.myParent.emit(QtCore.SIGNAL('viewTeachingCommands'))
-
- def closeTeachingCommands(self):
- self.myParent.emit(QtCore.SIGNAL('closeTeachingCommands'))
-
diff --git a/contrib/cdat/configure.py b/contrib/cdat/configure.py
deleted file mode 100644
index e36b245..0000000
--- a/contrib/cdat/configure.py
+++ /dev/null
@@ -1,72 +0,0 @@
-import os
-import sipconfig
-from PyQt4 import pyqtconfig
-
-
-from distutils import sysconfig
-
-vcs_so = '%s/vcs/_vcs.so' % sysconfig.get_python_lib()
-vcs_inc = '%s/vcs/Include' % sysconfig.get_python_lib()
-
-## vcs_so = '/Users/hvo/src/uvcdat/cdatBuild/lib/python2.7/site-packages/vcs/_vcs.so'
-## vcs_inc = '/Users/hvo/src/uvcdat/cdat/Packages/vcs/Include'
-
-
-# The name of the SIP build file generated by SIP and used by the build
-# system.
-build_file = "pyqtscripting.sbf"
-
-# Get the PyQt configuration information.
-config = pyqtconfig.Configuration()
-
-# Get the extra SIP flags needed by the imported qt module. Note that
-# this normally only includes those flags (-x and -t) that relate to SIP's
-# versioning system.
-qt_sip_flags = config.pyqt_sip_flags
-
-os.system("rm -rf cdatwrap")
-os.mkdir("cdatwrap")
-os.system("touch cdatwrap/__init__.py")
-
-# Run SIP to generate the code. Note that we tell SIP where to find the qt
-# module's specification files using the -I flag.
-os.system(" ".join([ \
- config.sip_bin, \
- "-c", "cdatwrap", \
- "-b", build_file, \
- "-I", config.pyqt_sip_dir, \
- qt_sip_flags, \
- "cdat.sip" \
-]))
-
-# Create the Makefile. The QtModuleMakefile class provided by the
-# pyqtconfig module takes care of all the extra preprocessor, compiler and
-# linker flags needed by the Qt library.
-makefile = pyqtconfig.QtGuiModuleMakefile(
- dir="cdatwrap",
- configuration=config,
- build_file='../' + build_file
-)
-
-# Add the library we are wrapping. The name doesn't include any platform
-# specific prefixes or extensions (e.g. the "lib" prefix on UNIX, or the
-# ".dll" extension on Windows).
-#makefile.extra_libs = ["vcs"]
-import cdat_info
-makefile.CFLAGS.append("-I%s/include" % cdat_info.externals)
-makefile.CFLAGS.append("-I%s" % vcs_inc)
-makefile.CFLAGS.append("-I%s/.." % sysconfig.get_python_inc())
-
-makefile.CXXFLAGS.append("-I%s/include" % cdat_info.externals)
-makefile.CXXFLAGS.append("-I%s" % vcs_inc)
-makefile.CXXFLAGS.append("-I%s/.." % sysconfig.get_python_inc())
-
-cwd = os.getcwd()
-makefile.LFLAGS.append("-Wl,-rpath,%s/cdatwrap" % cwd)
-
-# Generate the Makefile itself.
-makefile.generate()
-os.chdir("cdatwrap")
-os.system("make clean")
-os.system("MACOSX_DEPLOYMENT_TARGET=10.6 make -j")
-os.system("make install")
diff --git a/contrib/cdat/graphics_method_controller.py b/contrib/cdat/graphics_method_controller.py
deleted file mode 100644
index 1d1ff10..0000000
--- a/contrib/cdat/graphics_method_controller.py
+++ /dev/null
@@ -1,1624 +0,0 @@
-import types
-from PyQt4 import QtCore, QtGui
-from gui_controller import gm_name
-
-indentSpacing = 10
-
-class QGraphicsMethodAttributeWindow(QtGui.QMainWindow):
-
- def __init__(self, canvas=None, parent=None):
- QtGui.QMainWindow.__init__(self, parent)
- initialWidth = 480
- initialHeight = 640
- self.resize(initialWidth, initialHeight)
- self.setWindowTitle('Graphics Methods Attrtibute Settings')
- self.parent = parent
-
- # Create tab widgets
- self.tabWidget = QtGui.QTabWidget()
- if canvas is not None:
- self.boxfillEditor = QBoxfillEditor(gm=canvas.getboxfill('ASD'))
- self.continentsEditor = QContinentsEditor(gm=canvas.getcontinents('ASD'))
- self.meshfillEditor = QMeshfillEditor(gm=canvas.getmeshfill())
- self.outfillEditor = QOutfillEditor(gm=canvas.getoutfill())
- self.scatterEditor = QScatterEditor(gm=canvas.getscatter('ASD'))
- self.taylorEditor = QTaylorDiagramEditor(gm=canvas.gettaylordiagram('ASD'))
- self.vectorEditor = QVectorEditor(gm=canvas.getvector())
- else:
- self.boxfillEditor = QBoxfillEditor()
- self.continentsEditor = QContinentsEditor()
- self.meshfillEditor = QMeshfillEditor()
- self.outfillEditor = QOutfillEditor()
- self.scatterEditor = QScatterEditor()
- self.taylorEditor = QTaylorDiagramEditor()
- self.vectorEditor = QVectorEditor()
-
- self.contourEditor = QContourEditor()
- self.oneDimEditor = Q1DPlotEditor()
- self.outlineEditor = QOutlineEditor()
-
- # Add tabs
- self.tabWidget.addTab(self.boxfillEditor, 'Boxfill')
- self.tabWidget.addTab(self.continentsEditor, 'Continents')
- self.tabWidget.addTab(self.contourEditor, 'Contour')
- self.tabWidget.addTab(self.meshfillEditor, 'Meshfill')
- self.tabWidget.addTab(self.oneDimEditor, '1D Plot')
- self.tabWidget.addTab(self.outfillEditor, 'Outfill')
- self.tabWidget.addTab(self.outlineEditor, 'Outline')
- self.tabWidget.addTab(self.scatterEditor, 'Scatter')
- self.tabWidget.addTab(self.taylorEditor, 'Taylor Diagram')
- self.tabWidget.addTab(self.vectorEditor, 'Vector')
- self.setToolTips()
-
- # Add preview, reset, apply, cancel buttons
- previewButton = self.getButton('Preview')
- resetButton = self.getButton('Reset')
- applyButton = self.getButton('Apply')
- cancelButton = self.getButton('Cancel')
-
- hbox = QtGui.QHBoxLayout()
- hbox.addWidget(previewButton)
- hbox.addWidget(resetButton)
- hbox.addWidget(applyButton)
- hbox.addWidget(cancelButton)
-
- # Setup the layout
- vbox = QtGui.QVBoxLayout()
- vbox.addWidget(self.tabWidget)
- vbox.addLayout(hbox)
- wrapperWidget = QtGui.QWidget()
- wrapperWidget.setLayout(vbox)
- self.setCentralWidget(wrapperWidget)
-
- # Connect Signals
- self.connect(cancelButton, QtCore.SIGNAL('pressed()'), self.close)
- self.connect(resetButton, QtCore.SIGNAL('pressed()'), self.resetPressedEvent)
- self.connect(applyButton, QtCore.SIGNAL('pressed()'), self.applyPressedEvent)
- self.connect(previewButton, QtCore.SIGNAL('pressed()'), self.previewPressedEvent)
-
- def resetPressedEvent(self):
- self.boxfillEditor.initValues()
- self.continentsEditor.initValues()
- self.meshfillEditor.initValues()
- self.outfillEditor.initValues()
- self.scatterEditor.initValues()
- self.taylorEditor.initValues()
- self.vectorEditor.initValues()
-
- self.contourEditor.initValues()
- self.oneDimEditor.initValues()
- self.outlineEditor.initValues()
-
- def applyPressedEvent(self):
- self.boxfillEditor.setVistrailsGraphicsMethod(self.parent.getParent())
-
- # TODO
- # self.continentsEditor.setVistrailsGraphicsMethod()
- # self.meshfillEditor.setVistrailsGraphicsMethod()
- # self.outfillEditor.setVistrailsGraphicsMethod()
- # self.scatterEditor.setVistrailsGraphicsMethod()
- # self.taylorEditor.setVistrailsGraphicsMethod()
- # self.vectorEditor.setVistrailsGraphicsMethod()
- # self.contourEditor.setVistrailsGraphicsMethod()
- # self.oneDimEditor.setVistrailsGraphicsMethod()
- # self.outlineEditor.setVistrailsGraphicsMethod()
-
- def previewPressedEvent(self):
- return # TODO
-
- def setToolTips(self):
- self.tabWidget.setTabToolTip(0, 'The Boxfill graphics method displays a two-dimensional data\narray by surrounding each data value with a colored grid box.')
- self.tabWidget.setTabToolTip(1, "The Continents graphics method draws a predefined,\ngeneric set of continental outlines in a longitude\nby latitude space. (To draw continental outlines,\nno external data set is required.)")
- self.tabWidget.setTabToolTip(2, "This Contour notebook tab represent both the Isofill\nand Isoline graphics methods. The Isofill graphics\nmethod fills the area between selected isolevels\n(levels of constant value) of a two-dimensional\narray; the manner of filling the area is determined\nby the named fill area attributes. The Isoline\ngraphics method draws lines of constant value at\nspecified levels to graphically represent the values\nof a two-dimensional array; labels also c [...]
- self.tabWidget.setTabToolTip(3, "The Meshfill graphics method draws data on irregular grid (or 'mesh')at specified levels to graphically represent\nthe values of a one-dimensional array;\nUnless the irregular grid is supported by cdms2, a mesh array must be passed as well")
- self.tabWidget.setTabToolTip(4, "This 1D Plot notebook tab represent the XvsY, Xyvsy,\nand Yxvsx graphics methods. The XvsY graphics method\ndisplays a line plot from two 1D data arrays, that\nis X(t) and Y(t), where t represents the 1D\ncoordinate values. The Xyvsy graphics method displays\na line plot from a 1D data array, that is X(y),\nwhere y represents the 1D coordinate values. The\nYxvsx graphics method displays a line plot from\na 1D data array, that is Y(x), where y repr [...]
- self.tabWidget.setTabToolTip(5, "The Outfill graphics method fills a set of integer\nvalues in any data array. Its primary purpose is\nto display continents by filling their area as\ndefined by a surface type array that indicates land,\nocean, and sea-ice points. ")
- self.tabWidget.setTabToolTip(6, "The Outline graphics method outlines a set of integer\nvalues in any data array. Its primary purpose is\nto display continental outlines as defined by a\nsurface type array that indicates land, ocean, and\nsea-ice points.")
- self.tabWidget.setTabToolTip(7, "The Scatter graphics method displays a scatter plot\nof two 4-dimensional data arrays, e.g. A(x,y,z,t)\nand B(x,y,z,t). ")
- self.tabWidget.setTabToolTip(8, "The Taylor diagram graphics method provides a statistical\nsummary of pattern correspondence. A single point on\nthe diagram indicates how similar two patterns are in\nterms of their correlation, root-mean-square (RMS)\ndifference, and the ratio of their variances. The\nstandard deviation of a pattern is proportional to the\nradial distance. The correlation is given by the cosine\nof the azimuthal angle. The RMS difference is proportional\nto th [...]
- self.tabWidget.setTabToolTip(9, "The Vector graphics method displays a vector plot\nof a 2D vector field. Vectors are located at the\ncoordinate locations and point in the direction of\nthe data vector field. Vector magnitudes are the\nproduct of data vector field lengths and a scaling\nfactor. ")
-
- def getButton(self, text):
- button = QtGui.QToolButton()
- button.setText(text)
- return button
-
-class QVectorEditor(QtGui.QScrollArea):
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
-
- frame = QFramedWidget()
- self.lineType = frame.addLabeledComboBox('Vector Line Type:',
- ['solid', 'dash', 'dot','dash-dot', 'long-dash'])
- self.colorIndex = frame.addLabeledSpinBox('Vector Line Color Index',
- 0, 255)
- self.scale = frame.addLabeledDoubleSpinBox('Vector Scale', -1e20, 1e20, .1)
- self.alignment = frame.addLabeledComboBox('Vector Alignment:',
- ['head', 'center', 'tail'])
- self.headType = frame.addLabeledComboBox('Vector Head Type:',
- ['arrows', 'barbs', 'solidarrows'])
- self.reference = frame.addLabeledDoubleSpinBox('Vector reference', -1e20, 1e20, .1)
-
- vbox.addWidget(frame)
-
- # Init values & set tool tips
- self.initValues()
- self.lineType.setToolTip("Select the vector line type.")
- self.colorIndex.setToolTip("Select the vector color index.")
- self.scale.setToolTip("Select the vector scale factor.")
- self.alignment.setToolTip("Set the vector alignment.")
- self.headType.setToolTip("Set the vector head type.")
- self.reference.setToolTip("Set the vector reference. Note: if the value is 1e+20,\nthen VCS will determine the vector reference.")
-
- # Set up the scrollbar
- widgetWrapper = QtGui.QWidget()
- widgetWrapper.setLayout(vbox)
- widgetWrapper.setMinimumWidth(580)
- self.setWidget(widgetWrapper)
-
- def initValues(self):
- # TODO: don't init w/ hardcoded values?
- self.colorIndex.setValue(241)
- self.scale.setValue(1)
- self.alignment.setCurrentIndex(1)
- self.headType.setCurrentIndex(0)
- self.reference.setValue(1e20)
-
-class QTaylorDiagramEditor(QtGui.QScrollArea):
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
-
- tabWidget = QtGui.QTabWidget()
- interfaceTab = QTaylorInterfaceTab()
- tickAndLabelTab = QTaylorTicksLabels()
- markersTab = QTaylorMarkers()
- tabWidget.addTab(interfaceTab, 'Interface')
- tabWidget.addTab(markersTab, 'Markers')
- tabWidget.addTab(tickAndLabelTab, 'Ticks and Labels')
- vbox.addWidget(tabWidget)
-
- # Set up the scrollbar / widget size
- widgetWrapper = QtGui.QWidget()
- widgetWrapper.resize(670, 520)
- widgetWrapper.setLayout(vbox)
- self.setWidget(widgetWrapper)
-
- def initValues(self):
- interfaceTab.initValues()
- markersTab.initValues()
- tickAndLabelTab.initValues()
-
-class QTaylorMarkers(QtGui.QScrollArea):
- """ Tabbed Widget for Taylor -> Markers """
-
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- self.row = 1
- self.grid = QtGui.QGridLayout()
- self.markerList = []
- vbox = QtGui.QVBoxLayout()
-
- # Create Column Labels
- self.grid.addWidget(QtGui.QLabel(''), 0, 0)
- self.grid.addWidget(QtGui.QLabel('#'), 0, 1)
- self.grid.addWidget(QtGui.QLabel('Active'), 0, 2)
- self.grid.addWidget(QtGui.QLabel('Symbol'), 0, 3)
- self.grid.addWidget(QtGui.QLabel('Color'), 0, 4)
- self.grid.addWidget(QtGui.QLabel('Size'), 0, 5)
- self.grid.addWidget(QtGui.QLabel('Id'), 0, 6)
- self.grid.addWidget(QtGui.QLabel('Id Size'), 0, 7)
- self.grid.addWidget(QtGui.QLabel('+X'), 0, 8)
- self.grid.addWidget(QtGui.QLabel('+Y'), 0, 9)
- self.grid.addWidget(QtGui.QLabel('Id Color'), 0, 10)
- self.grid.addWidget(QtGui.QLabel('Id Font'), 0, 11)
- self.grid.addWidget(QtGui.QLabel('Line'), 0, 12)
- self.grid.addWidget(QtGui.QLabel('Type'), 0, 13)
- self.grid.addWidget(QtGui.QLabel('Size'), 0, 14)
- self.grid.addWidget(QtGui.QLabel('Color'), 0, 15)
-
- vbox.addLayout(self.grid)
-
- # Create Buttons
- hbox = QtGui.QHBoxLayout()
- addButton = self.createButton('Add')
- delButton = self.createButton('Delete')
- insertButton = self.createButton('Insert')
- hbox.addWidget(addButton)
- hbox.addWidget(delButton)
- hbox.addWidget(insertButton)
- vbox.addLayout(hbox)
- vbox.setAlignment(self.grid, QtCore.Qt.AlignTop)
- vbox.setAlignment(hbox, QtCore.Qt.AlignBottom)
-
- # Set up the scrollbar
- widgetWrapper = QtGui.QWidget()
- widgetWrapper.resize(1200, 440)
- widgetWrapper.setLayout(vbox)
- self.setWidget(widgetWrapper)
-
- # Connect Signals
- self.connect(addButton, QtCore.SIGNAL('pressed()'), self.addMarker)
- self.connect(delButton, QtCore.SIGNAL('pressed()'), self.removeSelectedMarkers)
- self.connect(insertButton, QtCore.SIGNAL('pressed()'), self.insertMarkers)
-
- def initValues(self):
- # Delete all markers
- # TODO
- return
-
- def removeMarker(self, marker):
- widgets = marker.getWidgets()
- for key in list(widgets):
- self.grid.removeWidget(widgets[key])
- widgets[key].hide()
-
- self.row -= 1
-
- def removeSelectedMarkers(self):
- """ Delete all of the selected markers from the grid layout"""
-
- removeList = []
- for marker in self.markerList:
- if marker.isSelected():
- self.removeMarker(marker)
- removeList.append(marker)
-
- # Update each subsequent marker's entry number, and position in the grid
- for i in range(self.markerList.index(marker) + 1, len(self.markerList)):
- row = int(self.markerList[i].getEntryNumber())
- self.markerList[i].setEntryNumber(row - 1)
- self.moveMarkerRow(row, row-1)
-
- for marker in removeList:
- if marker.isSelected():
- self.markerList.remove(marker)
-
- def moveMarkerRow(self, row, newRow):
- """ Move a marker grid item at row to newRow """
- numCols = 16
- for col in range(numCols):
- if self.grid.itemAtPosition(row, col) is not None:
- widget = self.grid.itemAtPosition(row, col).widget()
- self.grid.removeWidget(widget)
- self.grid.addWidget(widget, newRow, col, QtCore.Qt.AlignTop)
-
- def insertMarkers(self):
- """ For each marker that is selected, create and insert a new marker before it """
- selectedMarkerList = []
- for marker in self.markerList:
- if marker.isSelected():
- selectedMarkerList.append(marker)
- # Update the selected and each subsequent marker's entry number, and position in the grid
- for i in range(self.markerList.index(marker), len(self.markerList)):
- row = int(self.markerList[i].getEntryNumber())
- self.markerList[i].setEntryNumber(row + 1)
- self.moveMarkerRow(row, row + 1)
-
- # Insert the new markers in the correct positions
- for marker in selectedMarkerList:
- index = self.markerList.index(marker)
- newMarker = QMarkerEditorEntry(self.grid, index + 1)
- self.markerList.insert(index, newMarker)
- self.row += 1
-
- def addMarker(self):
- self.markerList.append(QMarkerEditorEntry(self.grid, self.row))
- self.row += 1
-
- def createButton(self, text):
- button = QtGui.QToolButton()
- button.setText(text)
- return button
-
-class QMarkerEditorEntry(QtGui.QWidget):
- def __init__(self, grid, row, parent=None):
- QtGui.QWidget.__init__(self, parent)
- self.widgets = {}
-
- symbolList = ["dot", "plus", "star", "circle", "cross", "diamond", "triangle_up", "triangle_down", "triangle_left", "triangle_right", "square", "diamond_fill", "triangle_up_fill", "triangle_down_fill", "triangle_left_fill", "triangle_right_fill", "square_fill"]
- lineList = ['None', 'Tail', 'Head', 'Line']
- typeList = ['solid', 'dash', 'dot', 'dash-dot', 'long-dash']
-
- self.widgets['selectedBox'] = QtGui.QCheckBox()
- self.widgets['entryNumber'] = QtGui.QLabel(str(row))
- self.widgets['activeBox'] = QtGui.QCheckBox()
- self.widgets['symbolCombo'] = self.createCombo(symbolList)
- self.widgets['colorCombo1'] = self.createCombo(['TODO'])
- self.widgets['size'] = QtGui.QLineEdit()
- self.widgets['id'] = QtGui.QLineEdit()
- self.widgets['idSize'] = QtGui.QLineEdit()
- self.widgets['x'] = QtGui.QLineEdit()
- self.widgets['y'] = QtGui.QLineEdit()
- self.widgets['idColorCombo'] = self.createCombo(['TODO'])
- self.widgets['idFontCombo'] = self.createCombo(map(str, range(1,10)))
- self.widgets['lineCombo'] = self.createCombo(lineList)
- self.widgets['typeCombo'] = self.createCombo(typeList)
- self.widgets['size2'] = QtGui.QLineEdit()
- self.widgets['colorCombo2'] = self.createCombo(['TODO'])
-
- grid.addWidget(self.widgets['selectedBox'], row, 0, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['entryNumber'], row, 1, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['activeBox'], row, 2, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['symbolCombo'], row, 3, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['colorCombo1'], row, 4, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['size'], row, 5, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['id'], row, 6, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['idSize'], row, 7, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['x'], row, 8, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['y'], row, 9, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['idColorCombo'], row, 10, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['idFontCombo'], row, 11, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['lineCombo'], row, 12, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['typeCombo'], row, 13, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['size2'], row, 14, QtCore.Qt.AlignTop)
- grid.addWidget(self.widgets['colorCombo2'], row, 15, QtCore.Qt.AlignTop)
-
- # TODO initialize the values
-
- def getWidgets(self):
- return self.widgets
-
- def getColor2(self):
- return self.widgets['colorCombo2'].currentText()
-
- def getSize2(self):
- return self.widgets['size2'].currentText()
-
- def getType(self):
- return self.widgets['typeCombo'].currentText()
-
- def getLine(self):
- return self.widgets['lineCombo'].currentText()
-
- def getIdFont(self):
- return self.widgets['idFontCombo'].currentText()
-
- def getIdColor(self):
- return self.widgets['idColorCombo'].currentText()
-
- def getSize(self):
- return self.widgets['size'].currentText()
-
- def getID(self):
- return self.widgets['id'].currentText()
-
- def getIdSize(self):
- return self.widgets['idSize'].currentText()
-
- def getX(self):
- return self.widgets['x'].currentText()
-
- def gety(self):
- return self.widgets['y'].currentText()
-
- def getColor(self):
- return self.widgets['colorCombo1'].currentText()
-
- def getSymbol(self):
- return self.widgets['symbolCombo'].currentText()
-
- def getEntryNumber(self):
- return int(self.widgets['entryNumber'].text())
-
- def setEntryNumber(self, num):
- self.widgets['entryNumber'].setText(str(num))
-
- def isActive(self):
- return self.widgets['activeBox'].isChecked()
-
- def isSelected(self):
- return self.widgets['selectedBox'].isChecked()
-
- def createCombo(self, entries):
- comboBox = QtGui.QComboBox()
- comboBox.setMaximumWidth(120)
- comboPalette = comboBox.view().palette()
- comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
- comboPalette.setColor(QtGui.QPalette.Highlight, QtCore.Qt.blue)
- comboBox.view().setPalette(comboPalette)
-
- for entry in entries:
- comboBox.addItem(entry)
-
- return comboBox
-
-class QTaylorTicksLabels(QtGui.QScrollArea):
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
-
- vbox = QtGui.QVBoxLayout()
- xFrame = QFramedWidget('X axis')
- self.xlabels = xFrame.addLabeledLineEdit('Labels:')
- self.xticks = xFrame.addLabeledLineEdit('Ticks:')
- vbox.addWidget(xFrame)
-
- yFrame = QFramedWidget('Y axis')
- self.ylabels = yFrame.addLabeledLineEdit('Labels:')
- self.yticks = yFrame.addLabeledLineEdit('Ticks:')
- vbox.addWidget(yFrame)
-
- corArcFrame = QFramedWidget('Correlation arc')
- self.corLabels = corArcFrame.addLabeledLineEdit('Labels:')
- self.corTicks = corArcFrame.addLabeledLineEdit('Ticks:')
- vbox.addWidget(corArcFrame)
-
- # Init line edits
- self.initValues()
-
- # Set up the scrollbar
- wrapperWidget = QtGui.QWidget()
- wrapperWidget.setLayout(vbox)
- wrapperWidget.setMinimumWidth(580)
- self.setWidget(wrapperWidget)
-
- def initValues(self):
- self.xlabels.setText('*')
- self.xticks.setText('*')
- self.ylabels.setText('*')
- self.yticks.setText('*')
- self.corLabels.setText('*')
- self.corTicks.setText('*')
-
-class QTaylorInterfaceTab(QtGui.QScrollArea):
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
-
- # General Aspect
- genFrame = QFramedWidget('General Aspect')
- self.detailSlider = genFrame.addLabeledSlider('Detail:', newRow=False)
- self.maxValue = genFrame.addLabeledLineEdit('Maximum Value:')
- self.quadran = genFrame.addRadioFrame('Quadran', ['1', '2'])
- self.refValue = genFrame.addLabeledLineEdit('Reference Value:')
- vbox.addWidget(genFrame)
-
- # Skill
- skillFrame = QFramedWidget('Skill')
- self.skillValues = skillFrame.addLabeledLineEdit('Skill Values:')
- self.skillLineColor = skillFrame.addLabeledComboBox('Skill Lines Color:',
- ['TODO'])
- self.drawLabels = skillFrame.addCheckBox('Draw Skill Contour Labels')
- self.skillCoefficients = skillFrame.addLabeledLineEdit('Skill Coefficients:')
- vbox.addWidget(skillFrame)
-
- # Arrows
- arrowFrame = QFramedWidget('Arrows')
- self.lengthSlider = arrowFrame.addLabeledSlider('Length:', newRow=False)
- self.angleSlider = arrowFrame.addLabeledSlider('Angle:')
- self.baseSlider = arrowFrame.addLabeledSlider('Base:')
- # TODO - Create a widget to draw the arrow
-
- vbox.addWidget(arrowFrame)
- vbox.setAlignment(arrowFrame, QtCore.Qt.AlignTop)
-
- # Set up the scrollbar
- wrapperWidget = QtGui.QWidget()
- wrapperWidget.setLayout(vbox)
- wrapperWidget.setMinimumWidth(580)
- self.setWidget(wrapperWidget)
-
- # Init Values
- self.initValues()
-
- # Connect Signals
- self.connect(self.lengthSlider, QtCore.SIGNAL('valueChanged(int)'), self.lengthChangedEvent)
- self.connect(self.angleSlider, QtCore.SIGNAL('valueChanged(int)'), self.angleChangedEvent)
- self.connect(self.baseSlider, QtCore.SIGNAL('valueChanged(int)'), self.baseChangedEvent)
-
- def initValues(self):
- # TODO Init w/ non hardcoded values?
-
- # General Aspect
- self.detailSlider.setTickPosition(QtGui.QSlider.TicksBelow)
- self.detailSlider.setMinimum(0)
- self.detailSlider.setMaximum(100)
- self.detailSlider.setSingleStep(5)
- self.detailSlider.setTickInterval(10)
-
- self.maxValue.setText('None')
- self.refValue.setText('1.0')
- self.quadran.setChecked('1')
-
- # Arrows
- self.lengthSlider.setTickPosition(QtGui.QSlider.TicksBelow)
- self.angleSlider.setTickPosition(QtGui.QSlider.TicksBelow)
- self.baseSlider.setTickPosition(QtGui.QSlider.TicksBelow)
-
- def lengthChangedEvent(self, int):
- return # TODO
-
- def angleChangedEvent(self, int):
- return # TODO
-
- def baseChangedEvent(self, int):
- return # TODO
-
-class QScatterEditor(QtGui.QScrollArea):
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
-
- # Create Widgets
- frame = QFramedWidget()
- markerTypes = ["dot", "plus", "star", "circle", "cross", "diamond", "triangle_up",
- "triangle_down", "triangle_left", "triangle_right", "square",
- "diamond_fill", "triangle_up_fill", "triangle_down_fill",
- "triangle_left_fill", "triangle_right_fill", "square_fill"]
- self.markerType = frame.addLabeledComboBox('Scatter Marker Type:',
- markerTypes, indent=False)
- self.colorIndex = frame.addLabeledSpinBox('Scatter Marker Color Index',
- 0, 255, indent=False)
- self.markerSize = frame.addLabeledSpinBox('Scatter Marker Size',
- 1, 300, indent=False)
-
- self.initValues()
-
- # Set toolTips
- self.markerType.setToolTip("Select the scatter marker type. ")
- self.colorIndex.setToolTip("Select the scatter marker color index. ")
- self.markerSize.setToolTip("Select the scatter marker size. ")
-
- vbox.addWidget(frame)
- vbox.setAlignment(frame, QtCore.Qt.AlignTop)
-
- # Set up the scrollbar
- widgetWrapper = QtGui.QWidget()
- widgetWrapper.setMinimumWidth(580)
- widgetWrapper.setLayout(vbox)
- self.setWidget(widgetWrapper)
-
- def initValues(self):
- # TODO: init w/ non-hardcoded values?
- self.colorIndex.setValue(241)
- self.markerSize.setValue(3)
-
-class QOutlineEditor(QtGui.QScrollArea):
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
-
- # Create Widgets
- frame = QFramedWidget()
- self.lineType = frame.addLabeledComboBox('Outfill Fill Area Style:',
- ['solid', 'dash', 'dot', 'dash-dot', 'long-dash'],
- indent=False)
- self.lineColorIndex = frame.addLabeledSpinBox('Outfill Line Color Index:',
- 0, 255, indent=False)
- self.indexValues = frame.addLabeledLineEdit('Outfill Index Values:',
- indent=False)
-
- # Init Values - TODO: init w/ non-hardcoded values?
- self.lineColorIndex.setValue(241)
- self.indexValues.setText('1')
-
- # Set tool tips
- self.lineType.setToolTip("Select the outline line type. ")
- self.lineColorIndex.setToolTip("Enter the line color index value. There can only\nbe one color index value (ranging from 0 to 255).\nIf an error in the color index value occurs, then the\ndefault color value index (i.e., 241) will be used.")
- self.indexValues.setToolTip("Outlines are drawn to enclose the specified values\nin the data array. As few as one, or\nas many as\nten values, can be specified:\noutline=([n1,[n2,[n3,...[n10]...]]]).")
-
- vbox.addWidget(frame)
- vbox.setAlignment(frame, QtCore.Qt.AlignTop)
-
- # Set up the scrollbar
- widgetWrapper = QtGui.QWidget()
- widgetWrapper.setMinimumWidth(580)
- widgetWrapper.setLayout(vbox)
- self.setWidget(widgetWrapper)
-
-class QOutfillEditor(QtGui.QScrollArea):
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
-
- # Create Widgets
- frame = QFramedWidget()
- self.fillArea = frame.addLabeledComboBox('Outfill Fill Area Style:',
- ['Solid', 'Hatch', 'Pattern', 'Hallow'],
- indent=False)
- self.fillAreaIndex = frame.addLabeledSpinBox('Outfill Fill Area Index:',
- 1, 20, indent=False)
- self.fillColorIndex = frame.addLabeledSpinBox('Outfill Fill Area Color Index:',
- 0, 255, indent=False)
- self.indexValues = frame.addLabeledLineEdit('Outfill Index Values:',
- indent=False)
- vbox.addWidget(frame)
- vbox.setAlignment(frame, QtCore.Qt.AlignTop)
-
- self.initValues()
-
- # Set ToolTips
- self.fillArea.setToolTip("Select the outfill fill area style type. ")
- self.fillAreaIndex.setToolTip("Select the outfill fill area index value. ")
- self.fillColorIndex.setToolTip("Enter the fillarea color index value. There can only\nbe one color index value (ranging from 0 to 255).\nIf an error in the color index value occurs, then the\ndefault color value index (i.e., 241) will be used.")
- self.indexValues.setToolTip("Outlines are filled to enclose the selected values\nthat appear in the data array. As few as one, or\nas many as ten values, can be specified:\noutline=([n1,[n2,[n3,...[n10]...]]]).")
-
- # Set up the scrollbar
- widgetWrapper = QtGui.QWidget()
- widgetWrapper.setMinimumWidth(580)
- widgetWrapper.setLayout(vbox)
- self.setWidget(widgetWrapper)
-
- def initValues(self):
- # TODO - init w/ non hardcoded values?
- self.fillAreaIndex.setValue(1)
- self.fillColorIndex.setValue(241)
- self.indexValues.setText('1')
-
-class Q1DPlotEditor(QtGui.QScrollArea):
-
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
-
- frame = QFramedWidget()
- frame.addWidget(QtGui.QLabel('Define up to 15 values:'), QtCore.Qt.AlignTop)
- self.lineTypes = frame.addLabeledLineEdit('Line Types: ')
- self.lineColors = frame.addLabeledLineEdit('Line Colors: ')
- self.lineWidths = frame.addLabeledLineEdit('Line Widths: ')
- self.markerTypes = frame.addLabeledLineEdit('Marker Types: ')
- self.markerColors = frame.addLabeledLineEdit('Marker Colors: ')
- self.markerSizes = frame.addLabeledLineEdit('Marker Sizes: ')
-
- self.initValues()
- self.lineTypes.setToolTip("Set the line types. The line values can either be\n('solid', 'dash', 'dot', 'dash-dot', 'long-dash')\nor (0, 1, 2, 3, 4) or None")
- self.lineColors.setToolTip("Set the line colors. The line color attribute\n values must be integers ranging from 0 to 255.\n(e.g., 16, 32, 48, 64) ")
- self.lineWidths.setToolTip("Set the line width. The line width is an integer\nor float value in the range (1 to 100)")
- self.markerTypes.setToolTip("Set the marker types. The marker values can either\nbe (None, 'dot', 'plus', 'star', 'circle', 'cross', 'diamond',\n'triangle_up', 'triangle_down', 'triangle_left',\n'triangle_right', 'square', 'diamond_fill',\n'triangle_up_fill', 'triangle_down_fill',\n'triangle_left_fill', 'triangle_right_fill',\n'square_fill') or (0, 1, 2, 3, 4, 5, 6, 7, 8, 9,\n10, 11, 12, 13, 14, 15, 16, 17) or None. ")
- self.markerColors.setToolTip("Set the marker colors. The marker color attribute\nvalues must be integers ranging from 0 to 255.")
- self.markerSizes.setToolTip("Set the marker sizes. The marker size attribute\nvalues must be integers or floats ranging from\n1 to 300. " )
-
- vbox.addWidget(frame)
- vbox.setAlignment(frame, QtCore.Qt.AlignTop)
-
- # Set up the scrollbar
- widgetWrapper = QtGui.QWidget()
- widgetWrapper.setMinimumWidth(580)
- widgetWrapper.setLayout(vbox)
- self.setWidget(widgetWrapper)
-
- def initValues(self):
- # TODO ?
- self.lineTypes.setText('None')
- self.lineColors.setText('None')
- self.lineWidths.setText('None')
- self.markerTypes.setText('None')
- self.markerColors.setText('None')
- self.markerSizes.setText('None')
-
-class QMeshfillEditor(QtGui.QScrollArea):
-
- def __init__(self, parent=None, gm=None):
- QtGui.QWidget.__init__(self, parent)
-
- if type(gm) in [types.ListType, types.TupleType, types.NoneType]:
- self.gm = gm
- else:
- self.gm=[gm,]
-
- vbox = QtGui.QVBoxLayout()
-
- # General Settings
- genSettings = QFramedWidget('General Settings')
- self.missing = genSettings.addLabeledLineEdit('Missing:')
- self.xWrap = genSettings.addLabeledLineEdit('X Wrap:')
- self.yWrap = genSettings.addLabeledLineEdit('Y Wrap:', newRow = False)
- self.genLegend = genSettings.addLabeledLineEdit('Legend Labels')
- self.showMesh = genSettings.addRadioFrame('Show Mesh:', ['No', 'Yes'])
- self.ext1 = genSettings.addRadioFrame('Ext 1:', ['No', 'Yes'], newRow=False)
- self.ext2 = genSettings.addRadioFrame('Ext 2:', ['No', 'Yes'], newRow=False)
- vbox.addWidget(genSettings)
-
- # Custom Settings
- custSettings = QFramedWidget('Custom Settings')
- custSettings.addLabel('Define iso level range values')
- self.incZero = custSettings.addRadioFrame('Include Zero:', ['Off', 'On'],
- newRow=False)
- self.ranges = custSettings.addLabeledLineEdit('Ranges:')
- self.colors = custSettings.addLabeledLineEdit('Colors:')
- self.lineTypes = custSettings.addLabeledLineEdit('Line Types:')
- self.lineWidths = custSettings.addLabeledLineEdit('Line Widths:')
- self.orientation = custSettings.addLabeledLineEdit('Orientation:')
- self.arrowScale = custSettings.addLabeledLineEdit('Contour Arrows Scale:')
- self.arrowSpacing = custSettings.addLabeledLineEdit('Contour Arrows Spacing:')
- self.arrowAngle = custSettings.addLabeledLineEdit('Contour Arrows Angle:')
- self.custLegend = custSettings.addLabeledLineEdit('Legend Labels:')
- self.isolineLabels = custSettings.addRadioFrame('Isoline Labels:',
- ['Off', 'On'])
- custSettings.newRow()
- custSettings.addLabel('Define iso level parameters:')
- self.spacing = custSettings.addRadioFrame('Spacing:',
- ['Linear', 'Log'],
- newRow=False)
- self.minVal = custSettings.addLabeledLineEdit('Minimum Value:')
- self.maxVal = custSettings.addLabeledLineEdit('Maximum Value:')
- self.nIntervals = custSettings.addLabeledSpinBox('Number of Intervals:',
- 2, 223)
- self.smallestExpLabel, self.smallestExp = custSettings.addLabelAndLineEdit('Smallest Exponent for Negative Values:')
- self.numNegDecLabel, self.numNegDec = custSettings.addLabelAndLineEdit('Number of Negative Decades:')
- genRangesButton = custSettings.addButton('Generate Ranges')
- clearButton = custSettings.addButton('Clear All', newRow=False)
- vbox.addWidget(custSettings)
-
- # Init values / tool tips
- self.initValues()
- self.setToolTips()
-
- # Set up the scrollbar
- widgetWrapper = QtGui.QWidget()
- widgetWrapper.setLayout(vbox)
- self.setWidget(widgetWrapper)
-
- # Connect Signals
- self.connect(clearButton, QtCore.SIGNAL('pressed()'),
- custSettings.clearAllLineEdits)
- self.connect(self.spacing.getButton('Linear'),
- QtCore.SIGNAL('pressed()'),
- lambda : self.setEnabledLogLineEdits(False))
- self.connect(self.spacing.getButton('Log'),
- QtCore.SIGNAL('pressed()'),
- lambda : self.setEnabledLogLineEdits(True))
- self.connect(genRangesButton, QtCore.SIGNAL('pressed()'),
- self.generateRanges)
-
- def initValues(self):
- # TODO : init missing, x wrap, y wrap, legend labels
-
- self.showMesh.setChecked('No')
- self.ext1.setChecked('No')
- self.ext2.setChecked('No')
- self.incZero.setChecked('Off')
- self.spacing.setChecked('Linear')
- self.setEnabledLogLineEdits(False)
-
- def generateRanges(self):
- try:
- minValue = float(self.minVal.text())
- maxValue = float(self.maxVal.text())
- numIntervals = int(self.nIntervals.text())
- except:
- QSimpleMessageBox('Values must be a number', self).show()
- return
-
- if numIntervals < 2 or numIntervals > 223:
- QSimpleMessageBox("The 'number of intervals' value must be between 2 and 223.",
- self).show()
- return
-
- colors = []
- values = []
- value = minValue
- color = 16
-
- # Generate ranges and colors (Linear)
- if self.spacing.isChecked('Linear'):
- delta = float((maxValue - minValue) / numIntervals)
- d = int(222 / (numIntervals - 1))
-
- for a in range(numIntervals + 1):
- if color <= 238:
- colors.append(color)
- values.append(value)
- color += d
- value += delta
- # Generate ranges (Log)
- else:
- A = float(self.minVal.text())
- B = float(self.maxVal.text())
- C = float(self.nIntervals.text())
- try:
- D = float(self.smallestExp.text())
- except:
- D = 0
- try:
- E = float(self.numNegDec.text())
- except:
- E = 0
-
- if C > 0:
- if E > 0: # Generate negative contours
- for i in range(int(E * C), 0, -1):
- values.append(round_number(-10.0 ** (D+(i-1)/C)))
- if B > 0: # Generate positive contours
- for i in range(1, int((B * C) + 1)):
- values.append(round_number(10.0 ** (A+(i-1)/C)))
- else:
- QSimpleMessageBox("The 'Levels per Decade' must be a positive number.").show()
-
- # Gen colors (Log)
- numIntervals = len(values) - 1
- d = int(222 / (numIntervals - 1))
- for a in range(numIntervals):
- colors.append(16 + a * d)
-
- if self.incZero.isChecked('On'):
- values.insert(0, 0.0)
-
- self.ranges.setText(str(values))
- self.colors.setText(str(colors))
-
- def setEnabledLogLineEdits(self, enable):
- """ Disable or Enable the 'Num neg decades' and 'smallest exp for neg
- values' lineEdits """
- self.smallestExp.setEnabled(enable)
- self.numNegDec.setEnabled(enable)
- self.smallestExpLabel.setEnabled(enable)
- self.numNegDecLabel.setEnabled(enable)
-
- if enable == True:
- self.smallestExp.setToolTip("Smallest exponent for negative values")
- self.numNegDec.setToolTip("Number of negative decades.")
- else:
- self.smallestExp.setToolTip("Disabled. Not in use for linear spacing.")
- self.numNegDec.setToolTip("Disabled. Not in use for linear spacing.")
-
- def setToolTips(self):
- # General Setting Tips
- self.missing.setToolTip("Set the missing color index value. The colormap\nranges from 0 to 255, enter the desired color index value 0\nthrough 255.")
- self.xWrap.setToolTip("Set the wrapping along X axis, 0 means no wrapping")
- self.yWrap.setToolTip("Set the wrapping along Y axis, 0 means no wrapping")
- self.genLegend.setToolTip("Specify the desired legend labels.\nFor example:\nNone -- Allow VCS to generate legend labels\n( ), or [ ], or { } -- No legend labels\n[ 0, 10, 20 ] or { 0:'0', 10:'10', 20:'20' }\n[ 0, 10 ] or { 0:'text', 10:'more text' }")
-
- # Custom Setting Tips
- self.ranges.setToolTip("The iso level range values. (e.g., 10, 20, 30, 40, 50).")
- self.colors.setToolTip("The iso level color index values. The index colors range\nfrom 0 to 255. For example:\n Use explicit indices: 16, 32, 48, 64, 80;\n Use two values to generate index range: 16, 32")
- self.lineTypes.setToolTip("The line type for the isolines. (e.g., 4, 1, 3, 2, 0).")
- self.lineWidths.setToolTip("The width values for the isolines. (e.g., 1, 3, 5, 2, 7).")
- self.orientation.setToolTip("Drawing orientation arrows:\n none (0)\n clokwise (1)\n clockwise where y axis is positive (2)\n clockwise where x axis is positive(3)\n Negative values indicate counter-clockwise.")
- self.arrowScale.setToolTip("Scale factor for arrows length")
- self.arrowSpacing.setToolTip("Spacing factor for arrows")
- self.arrowAngle.setToolTip("Angle of Arrows heads")
- self.isolineLabels.setToolTip("Toggle 'Isoline Labels' on or off.")
- self.custLegend.setToolTip("Specify the desired legend labels.\nFor example:\nNone -- Allow VCS to generate legend labels\n( ), or [ ], or { } -- No legend labels\n[ 0, 10, 20 ] or { 0:'0', 10:'10', 20:'20' }\n[ 0, 10 ] or { 0:'text', 10:'more text' }")
- self.minVal.setToolTip("The minimum contour level.")
- self.maxVal.setToolTip("The maximum contour level.")
- self.nIntervals.setToolTip("The number of intervals between each contour level. Maximum number range [2 to 223].")
- self.smallestExp.setToolTip("Disabled. Not in use for linear spacing.")
- self.numNegDec.setToolTip("Disabled. Not in use for linear spacing.")
-
-class QContourEditor(QtGui.QScrollArea):
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
-
- #### TODO gm stuff
-
- frame = QFramedWidget()
-
- frame.addWidget(QtGui.QLabel('Define iso level range values:'))
- self.includeZeroButtonGroup = frame.addRadioFrame('Include Zero:',
- ['Off', 'On'],
- newRow=False)
- self.ranges = frame.addLabeledLineEdit('Ranges:')
- self.colors = frame.addLabeledLineEdit('Colors:')
- self.lineTypes = frame.addLabeledLineEdit('Line Types:', )
- self.lineWidths = frame.addLabeledLineEdit('Line Widths:')
- self.orientation = frame.addLabeledLineEdit('Orientation:')
- self.arrowScale = frame.addLabeledLineEdit('Contour Arrows Scale:')
- self.arrowSpacing = frame.addLabeledLineEdit('Contour Arrows Spacing:')
- self.angle = frame.addLabeledLineEdit('Contour Arrows Angle:')
- self.labelButtonGroup = frame.addRadioFrame('Isoline Labels:',
- ['Off', 'On'])
- self.legendLabels = frame.addLabeledLineEdit('Legend Labels')
- frame.newRow()
- frame.addWidget(QtGui.QLabel('Define iso level parameters:'))
- self.spacingButtonGroup = frame.addRadioFrame('Spacing:',
- ['Linear', 'Log'],
- newRow=False)
- self.minVal = frame.addLabeledLineEdit('Minimum Value:')
- self.maxVal = frame.addLabeledLineEdit('Maximum Value:')
- self.nIntervals = frame.addLabeledSpinBox('Number of Intervals:',
- 2, 223,)
- self.smallestExpLabel, self.smallestExp = frame.addLabelAndLineEdit('Smallest Exponent for Negative Values:')
- self.numNegDecLabel, self.numNegDec = frame.addLabelAndLineEdit('Number of Negative Decades:')
- genRangesButton = frame.addButton('Generate Ranges')
- clearButton = frame.addButton('Clear All', newRow=False)
-
- vbox.addWidget(frame)
- self.frame = frame
-
- # Init values / tool tips
- self.initValues()
- self.setToolTips()
-
- # Set up the scrollbar
- widgetWrapper = QtGui.QWidget()
- widgetWrapper.setLayout(vbox)
- widgetWrapper.setMinimumWidth(630)
- self.setWidget(widgetWrapper)
-
- # Connect Signals
- self.connect(clearButton, QtCore.SIGNAL('pressed()'),
- self.frame.clearAllLineEdits)
- self.connect(genRangesButton, QtCore.SIGNAL('pressed()'),
- self.generateRanges)
- self.connect(self.spacingButtonGroup.getButton('Linear'),
- QtCore.SIGNAL('pressed()'),
- lambda : self.setEnabledLogLineEdits(False))
- self.connect(self.spacingButtonGroup.getButton('Log'),
- QtCore.SIGNAL('pressed()'),
- lambda : self.setEnabledLogLineEdits(True))
-
- def initValues(self):
- self.includeZeroButtonGroup.setChecked('Off')
- self.spacingButtonGroup.setChecked('Linear')
- self.setEnabledLogLineEdits(False)
-
- self.minVal.setText('1.0')
- self.maxVal.setText('2.0')
- self.nIntervals.setValue(2)
-
- def generateRanges(self):
- try:
- minValue = float(self.minVal.text())
- maxValue = float(self.maxVal.text())
- numIntervals = int(self.nIntervals.text())
- except:
- QSimpleMessageBox('Values must be a number', self).show()
- return
-
- if numIntervals < 2 or numIntervals > 223:
- QSimpleMessageBox("The 'number of intervals' value must be between 2 and 223.",
- self).show()
- return
-
- colors = []
- values = []
- value = minValue
- color = 16
-
- # Generate ranges and colors (Linear)
- if self.spacingButtonGroup.isChecked('Linear'):
- delta = float((maxValue - minValue) / numIntervals)
- d = int(222 / (numIntervals - 1))
-
- for a in range(numIntervals + 1):
- if color <= 238:
- colors.append(color)
- values.append(value)
- color += d
- value += delta
- # Generate ranges (Log)
- else:
- A = float(self.minVal.text())
- B = float(self.maxVal.text())
- C = float(self.nIntervals.text())
- try:
- D = float(self.smallestExp.text())
- except:
- D = 0
- try:
- E = float(self.numNegDec.text())
- except:
- E = 0
-
- if C > 0:
- if E > 0: # Generate negative contours
- for i in range(int(E * C), 0, -1):
- values.append(round_number(-10.0 ** (D+(i-1)/C)))
- if B > 0: # Generate positive contours
- for i in range(1, int((B * C) + 1)):
- values.append(round_number(10.0 ** (A+(i-1)/C)))
- else:
- QSimpleMessageBox("The 'Levels per Decade' must be a positive number.").show()
-
- # Gen colors (Log)
- numIntervals = len(values) - 1
- d = int(222 / (numIntervals - 1))
- for a in range(numIntervals):
- colors.append(16 + a * d)
-
- if self.includeZeroButtonGroup.isChecked('On'):
- values.insert(0, 0.0)
-
- self.ranges.setText(str(values))
- self.colors.setText(str(colors))
-
- def setEnabledLogLineEdits(self, enable):
- """ Disable or Enable the 'Num neg decades' and 'smallest exp for neg
- values' lineEdits """
- self.smallestExp.setEnabled(enable)
- self.numNegDec.setEnabled(enable)
- self.smallestExpLabel.setEnabled(enable)
- self.numNegDecLabel.setEnabled(enable)
-
- if enable == True:
- self.smallestExp.setToolTip("Smallest exponent for negative values")
- self.numNegDec.setToolTip("Number of negative decades.")
- else:
- self.smallestExp.setToolTip("Disabled. Not in use for linear spacing.")
- self.numNegDec.setToolTip("Disabled. Not in use for linear spacing.")
-
- def setToolTips(self):
- self.ranges.setToolTip("The iso level range values. (e.g., 10, 20, 30, 40, 50).")
- self.colors.setToolTip("The iso level color index values. The index colors range\nfrom 0 to 255. For example:\n Use explicit indices: 16, 32, 48, 64, 80;\n Use two values to generate index range: 16, 32")
- self.lineTypes.setToolTip("The line type for the isolines. (e.g., 4, 1, 3, 2, 0).")
- self.lineWidths.setToolTip("The width values for the isolines. (e.g., 1, 3, 5, 2, 7).")
- self.orientation.setToolTip("Drawing orientation arrows:\n none (0)\n clokwise (1)\n clockwise where y axis is positive (2)\n clockwise where x axis is positive(3)\n Negative values indicate counter-clockwise.")
- self.arrowScale.setToolTip("Scale factor for arrows length")
- self.arrowSpacing.setToolTip("Spacing factor for arrows")
- self.angle.setToolTip("Angle of Arrows heads")
- self.labelButtonGroup.setToolTip("Toggle 'Isoline Labels' on or off.")
- self.legendLabels.setToolTip("Specify the desired legend labels.\nFor example:\nNone -- Allow VCS to generate legend labels\n( ), or [ ], or { } -- No legend labels\n[ 0, 10, 20 ] or { 0:'0', 10:'10', 20:'20' }\n[ 0, 10 ] or { 0:'text', 10:'more text' }")
- self.minVal.setToolTip("The minimum contour level.")
- self.maxVal.setToolTip("The maximum contour level.")
- self.nIntervals.setToolTip("The number of intervals between each contour level. Maximum number range [2 to 223].")
- self.smallestExp.setToolTip("Disabled. Not in use for linear spacing.")
- self.numNegDec.setToolTip("Disabled. Not in use for linear spacing.")
-
-class QContinentsEditor(QtGui.QScrollArea):
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
- frame = QFramedWidget()
-
- self.lineTypeComboBox = frame.addLabeledComboBox('Continents Line Type:',
- ['solid', 'dash', 'dot', 'dash-dot', 'long-dash'])
- self.lineColorIndex = frame.addLabeledSpinBox('Continents Line Color Index:',
- 0, 255)
- self.lineWidth = frame.addLabeledSpinBox('Continents Line Width:', 1, 300)
- self.typeIndex = frame.addLabeledSpinBox('Continents Type Index:', -1, 11)
- vbox.addWidget(frame)
-
- # Init values / tool tips
- self.initValues()
- self.setToolTips()
-
- # Set up the scrollbar
- widgetWrapper = QtGui.QWidget()
- widgetWrapper.setMinimumWidth(580)
- widgetWrapper.setLayout(vbox)
- self.setWidget(widgetWrapper)
-
- def initValues(self):
- self.lineColorIndex.setValue(0)
- self.lineWidth.setValue(1)
- self.typeIndex.setValue(-1)
-
- def setToolTips(self):
- self.lineTypeComboBox.setToolTip('Select the continents line type.')
- self.lineColorIndex.setToolTip('Select the continents color index.')
- self.lineWidth.setToolTip('Set the continents line width.')
- self.typeIndex.setToolTip("Select the continents type index.Where\n-1 = 'Auto Continents';\n0 = 'No Continents';\n1 = 'Fine Continents';\n2 = 'Coarse Continents';\n3 = 'United States Continents';\n4 = 'Political Borders Continents';\n5 = 'Rivers Continents';\n6 - 11 = 'User defined Continents'")
-
- def getLineType(self):
- return self.lineTypeComboBox.currentText()
-
- def getTypeIndex(self):
- try:
- return int(self.typeIndex.text())
- except:
- return None
-
- def getLineWidth(self):
- try:
- return int(self.lineWidth.text())
- except:
- return None
-
- def getLineColorIndex(self):
- try:
- return int(self.lineColorIndex.text())
- except:
- return None
-
-class QBoxfillEditor(QtGui.QScrollArea):
-
- def __init__(self, parent=None, gm=None):
- QtGui.QScrollArea.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
-
- if type(gm) in [types.ListType, types.TupleType, types.NoneType]:
- self.gm = gm
- elif type(gm) is not None:
- self.gm=[gm,]
-
- # 'define boxfill attributes + boxfill type radio buttons'
- hbox1 = QtGui.QHBoxLayout()
- hbox1.addWidget(QtGui.QLabel('Define boxfill attribute values'))
-
- self.boxfillTypeButtonGroup = QRadioButtonFrame('Boxfill type:')
- self.boxfillTypeButtonGroup.addButtonList(['linear', 'log10', 'custom'])
- hbox1.addWidget(self.boxfillTypeButtonGroup)
-
- vbox.addLayout(hbox1)
-
- # General Settings
- generalSettings = QFramedWidget('General Settings')
- self.missingLineEdit = generalSettings.addLabeledLineEdit('Missing:')
- self.ext1ButtonGroup = generalSettings.addRadioFrame('Ext1:',
- ['No', 'Yes'],
- newRow = False)
- self.ext2ButtonGroup = generalSettings.addRadioFrame('Ext2:',
- ['No', 'Yes'],
- newRow = False)
- self.legendLineEdit = generalSettings.addLabeledLineEdit('Legend Labels:')
- vbox.addWidget(generalSettings)
-
- # Linear & Log Settings
- linLogSettings = QFramedWidget('Linear and Log Settings')
-
- self.level1LineEdit = linLogSettings.addLabeledLineEdit('Level 1:')
- self.level2LineEdit = linLogSettings.addLabeledLineEdit('Level 2:',
- newRow = False)
- self.color1LineEdit = linLogSettings.addLabeledLineEdit('Color 1:')
- self.color2LineEdit = linLogSettings.addLabeledLineEdit('Color 2:',
- newRow = False)
- vbox.addWidget(linLogSettings)
-
- # Custom Settings
- customSettings = QFramedWidget('Custom Settings')
-
- customSettings.addWidget(QtGui.QLabel('Define iso level range values:'))
- self.includeZeroButtonGroup = customSettings.addRadioFrame('Include Zero:',
- ['Off', 'On'],
- newRow=False)
- self.rangeLineEdit = customSettings.addLabeledLineEdit('Ranges:')
- self.colorsLineEdit = customSettings.addLabeledLineEdit('Colors:')
-
- customSettings.newRow()
- customSettings.addWidget(QtGui.QLabel('Define iso level parameters:'))
- self.spacingButtonGroup = customSettings.addRadioFrame('spacing:',
- ['Linear', 'Log'],
- newRow=False)
-
- self.minValLineEdit = customSettings.addLabeledLineEdit('Minimum Value:')
- self.maxValLineEdit = customSettings.addLabeledLineEdit('Maximum Value:')
- self.nIntervals = customSettings.addLabeledSpinBox('Number of Intervals:',
- 2, 223)
- self.smallestExpLabel, self.expLineEdit = customSettings.addLabelAndLineEdit('Smallest Exponent for Negative Values:')
- self.numNegDecLabel, self.negDecadesLineEdit = customSettings.addLabelAndLineEdit('Number of Negative Decades:')
- genRangesButton = customSettings.addButton('Generate Ranges')
- clearButton = customSettings.addButton('Clear All', newRow=False)
- vbox.addWidget(customSettings)
-
- # Init values
- self.initValues()
- self.setToolTips()
-
- # Set up the scrollbar
- widgetWrapper = QtGui.QWidget()
- widgetWrapper.setLayout(vbox)
- self.setWidget(widgetWrapper)
-
- # Connect Signals
- self.connect(clearButton, QtCore.SIGNAL('pressed()'), self.clearCustomSettings)
- self.connect(genRangesButton, QtCore.SIGNAL('pressed()'), self.generateRanges)
- self.connect(self.spacingButtonGroup.getButton('Linear'),
- QtCore.SIGNAL('pressed()'),
- lambda : self.setEnabledLogLineEdits(False))
- self.connect(self.spacingButtonGroup.getButton('Log'),
- QtCore.SIGNAL('pressed()'),
- lambda : self.setEnabledLogLineEdits(True))
-
- def initValues(self):
- if self.gm is None:
- return
-
- # Init Line Edit Text
- self.missingLineEdit.setText(str(self.gm[0].missing))
- self.legendLineEdit.setText('None')
- self.level1LineEdit.setText(str(self.gm[0].level_1))
- self.level2LineEdit.setText(str(self.gm[0].level_2))
- self.color1LineEdit.setText(str(self.gm[0].color_1))
- self.color2LineEdit.setText(str(self.gm[0].color_2))
- self.rangeLineEdit.setText(str(self.gm[0].levels))
- self.colorsLineEdit.setText('None')
- self.minValLineEdit.setText('')
- self.maxValLineEdit.setText('')
- self.expLineEdit.setText('')
- self.negDecadesLineEdit.setText('')
- self.nIntervals.setValue(2)
- self.setEnabledLogLineEdits(False)
-
- # Init selected radio buttons
- self.boxfillTypeButtonGroup.setChecked('linear')
- self.ext1ButtonGroup.setChecked('No')
- self.ext2ButtonGroup.setChecked('No')
- self.includeZeroButtonGroup.setChecked('Off')
- self.spacingButtonGroup.setChecked('Linear')
-
- def generateRanges(self):
- try:
- minValue = float(self.minValLineEdit.text())
- maxValue = float(self.maxValLineEdit.text())
- numIntervals = int(self.nIntervals.text())
- except:
- QSimpleMessageBox('Values must be a number', self).show()
- return
-
- if numIntervals < 2 or numIntervals > 223:
- QSimpleMessageBox("The 'number of intervals' value must be between 2 and 223.",
- self).show()
- return
-
- colors = []
- values = []
- value = minValue
- color = 16
-
- # Generate ranges and colors (Linear)
- if self.spacingButtonGroup.isChecked('Linear'):
- delta = float((maxValue - minValue) / numIntervals)
- d = int(222 / (numIntervals - 1))
-
- for a in range(numIntervals + 1):
- if color <= 238:
- colors.append(color)
- values.append(value)
- color += d
- value += delta
- # Generate ranges (Log)
- else:
- A = float(self.minValLineEdit.text())
- B = float(self.maxValLineEdit.text())
- C = float(self.nIntervals.text())
-
- try:
- D = float(self.expLineEdit.text())
- except:
- D = 0
- try:
- E = float(self.negDecadesLineEdit.text())
- except:
- E = 0
-
- if C > 0:
- if E > 0: # Generate negative contours
- for i in range(int(E * C), 0, -1):
- values.append(round_number(-10.0 ** (D+(i-1)/C)))
- if B > 0: # Generate positive contours
- for i in range(1, int((B * C) + 1)):
- values.append(round_number(10.0 ** (A+(i-1)/C)))
- else:
- QSimpleMessageBox("The 'Levels per Decade' must be a positive number.").show()
-
- # Gen colors (Log)
- numIntervals = len(values) - 1
- d = int(222 / (numIntervals - 1))
- for a in range(numIntervals):
- colors.append(16 + a * d)
-
- if self.includeZeroButtonGroup.isChecked('On'):
- values.insert(0, 0.0)
-
- self.rangeLineEdit.setText(str(values))
-
- self.colorsLineEdit.setText(str(colors))
-
- def setEnabledLogLineEdits(self, enable):
- """ Disable or Enable the 'Num neg decades' and 'smallest exp for neg
- values' lineEdits """
- self.expLineEdit.setEnabled(enable)
- self.negDecadesLineEdit.setEnabled(enable)
- self.smallestExpLabel.setEnabled(enable)
- self.numNegDecLabel.setEnabled(enable)
-
- if enable == True:
- self.expLineEdit.setToolTip("Smallest exponent for negative values")
- self.negDecadesLineEdit.setToolTip("Number of negative decades.")
- else:
- self.expLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
- self.negDecadesLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
-
- def setToolTips(self):
- self.missingLineEdit.setToolTip("Set the missing color index value. The colormap\nranges from 0 to 255, enter the desired color index value 0\nthrough 255.")
- self.legendLineEdit.setToolTip("Specify the desired legend labels.\nFor example:\n None -- Allow VCS to generate legend labels\n(), or [ ], or { } -- No legend labels\n [0, 10, 20] or { 0:'0', 10:'10', 20:'20' }\n[ 0, 10 ] or { 0:'text', 10:'more text'}")
- self.level1LineEdit.setToolTip("The minimum data value. If level 1 is set to '1e+20',\nthen VCS will select the level.")
- self.level2LineEdit.setToolTip("The maximum data value. If level 2 is set to '1e+20',\nthen VCS will select the level.")
- self.color1LineEdit.setToolTip("The minimum color range index value. The colormap\nranges from 0 to 255, but only color indices 0\nthrough 239 can be changed.")
- self.color2LineEdit.setToolTip("The maximum color range index value. The colormap\nranges from 0 to 255, but only color indices 0\nthrough 239 can be changed.")
- self.rangeLineEdit.setToolTip("The iso level range values. (e.g., 10, 20, 30, 40, 50).")
- self.colorsLineEdit.setToolTip("The iso level color index values. The index colors range\nfrom 0 to 255. For example:\n Use explicit indices: 16, 32, 48, 64, 80;\n Use two values to generate index range: 16, 32")
- self.minValLineEdit.setToolTip("The minimum contour level.")
- self.maxValLineEdit.setToolTip("The maximum contour level.")
- self.nIntervals.setToolTip("The number of intervals between each contour level. Maximum number range [2 to 223].")
- self.expLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
- self.negDecadesLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
-
- def clearCustomSettings(self):
- self.rangeLineEdit.setText('')
- self.colorsLineEdit.setText('')
- self.minValLineEdit.setText('')
- self.maxValLineEdit.setText('')
- self.nIntervals.setValue(2)
- self.expLineEdit.setText('')
- self.negDecadesLineEdit.setText('')
-
- def linearButtonPressEvent(self):
- """ Disable the 'Num neg decades' and 'smallest exp for neg values'
- lineEdits """
-
- self.expLineEdit.setReadOnly(True)
- self.negDecadesLineEdit.setReadOnly(True)
- self.expLineEdit.setText('')
- self.negDecadesLineEdit.setText('')
- self.expLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
- self.negDecadesLineEdit.setToolTip("Disabled. Not in use for linear spacing.")
-
- def logButtonPressEvent(self):
- """ Enable the 'Num neg decades' and 'smallest exp for neg values'
- lineEdits """
-
- self.expLineEdit.setReadOnly(False)
- self.negDecadesLineEdit.setReadOnly(False)
- self.expLineEdit.setText('')
- self.negDecadesLineEdit.setText('')
- self.expLineEdit.setToolTip("Smallest exponent for negative values")
- self.negDecadesLineEdit.setToolTip("Number of negative decades.")
-
- def setVistrailsGraphicsMethod(self, varViewWidget):
- """ Vistrails: Update the vistrails' Graphics Method modules' boxfill
- input ports """
-
- # Generate a list of tuples where each tuple is: (Input Port Name, value)
- # and update the vistrails' graphics method input ports
- visInput = []
- visInput.append(('color_1', self.getValue(self.color1LineEdit, int)))
- visInput.append(('color_2', self.getValue(self.color2LineEdit, int)))
- visInput.append(('level_1', self.getValue(self.level1LineEdit, float)))
- visInput.append(('level_2', self.getValue(self.level2LineEdit, float)))
-
- varViewWidget.emit(QtCore.SIGNAL('createModule'), gm_name)
- varViewWidget.emit(QtCore.SIGNAL('updateModuleOps'), gm_name, visInput)
-
- def getValue(self, lineEdit, convertType, default=None):
- try:
- return convertType(lineEdit.text())
- except:
- return default
-
-class QSimpleMessageBox(QtGui.QMessageBox):
-
- def __init__(self, text, parent):
- QtGui.QMessageBox.__init__(self, parent)
- self.setText(text)
-
-class QFramedWidget(QtGui.QFrame):
-
- def __init__(self, titleText=None, parent=None):
- QtGui.QFrame.__init__(self, parent)
- self.setFrameStyle(QtGui.QFrame.Raised)
- self.setFrameShape(QtGui.QFrame.Box)
- self.lineEditList = []
- self.vbox = QtGui.QVBoxLayout()
- self.setLayout(self.vbox)
- self.indent = 10
-
- if titleText is not None:
- title = QtGui.QLabel(titleText)
- title.setFont(QtGui.QFont("Times", 14, QtGui.QFont.Bold))
- self.vbox.addWidget(title)
-
- self.newRow()
-
- def setSpacing(self, spacing):
- self.vbox.setSpacing(spacing)
-
- def newRow(self):
- self.hbox = QtGui.QHBoxLayout()
- self.vbox.addLayout(self.hbox)
-
- def addCheckBox(self, text, indent=True, newRow=True):
- if newRow == True:
- self.newRow()
- if indent == True:
- self.hbox.addSpacing(indentSpacing)
-
- checkbox = QtGui.QCheckBox(text)
- self.addWidget(checkbox)
- return checkbox
-
- def addLabeledComboBox(self, text, comboStringList, indent=True, newRow=True):
- if newRow == True:
- self.newRow()
- if indent == True:
- self.hbox.addSpacing(indentSpacing)
-
- # Init combo box & set text to white on blue
- comboBox = QtGui.QComboBox()
- comboPalette = comboBox.view().palette()
- comboPalette.setColor(QtGui.QPalette.HighlightedText, QtCore.Qt.white)
- comboPalette.setColor(QtGui.QPalette.Highlight, QtCore.Qt.blue)
- comboBox.view().setPalette(comboPalette)
-
- for string in comboStringList:
- comboBox.addItem(string)
-
- self.addLabel(text)
- self.addWidget(comboBox)
- return comboBox
-
- def addLabeledSpinBox(self, text, minValue=None, maxValue=None,
- indent=True, newRow=True):
- if newRow == True:
- self.newRow()
- if indent == True:
- self.hbox.addSpacing(indentSpacing)
-
- spinbox = QtGui.QSpinBox()
- if maxValue is not None:
- spinbox.setMaximum(maxValue)
- if minValue is not None:
- spinbox.setMinimum(minValue)
- self.addWidget(QtGui.QLabel(text))
- self.addWidget(spinbox)
-
- return spinbox
-
- def addLabeledDoubleSpinBox(self, text, minValue=None, maxValue=None,
- step=None, indent=True, newRow=True):
- if newRow == True:
- self.newRow()
- if indent == True:
- self.hbox.addSpacing(indentSpacing)
-
- spinbox = QtGui.QDoubleSpinBox()
- if maxValue is not None:
- spinbox.setMaximum(maxValue)
- if minValue is not None:
- spinbox.setMinimum(minValue)
- if step is not None:
- spinbox.setSingleStep(step)
-
- self.addWidget(QtGui.QLabel(text))
- self.addWidget(spinbox)
- return spinbox
-
- def addButton(self, text, newRow=True):
- if newRow == True:
- self.newRow()
-
- button = QtGui.QToolButton()
- button.setText(text)
- self.addWidget(button)
- return button
-
- def addRadioFrame(self, text, buttonList, newRow=True):
- if newRow == True:
- self.newRow()
-
- buttonGroup = QRadioButtonFrame(text, buttonList)
- self.addWidget(buttonGroup)
- return buttonGroup
-
- def clearAllLineEdits(self):
- for lineEdit in self.lineEditList:
- lineEdit.setText('')
-
- def addLabeledLineEdit(self, text, indent=True, newRow=True, align=None):
- if newRow == True:
- self.newRow()
- if indent == True:
- self.hbox.addSpacing(indentSpacing)
-
- lineEdit = QtGui.QLineEdit()
- self.lineEditList.append(lineEdit)
- self.addWidget(QtGui.QLabel(text))
- self.addWidget(lineEdit, align)
-
- if align is not None:
- self.vbox.setAlignment(self.hbox, align)
-
- return lineEdit
-
- def addLabelAndLineEdit(self, text, indent=True, newRow=True):
- if newRow == True:
- self.newRow()
- if indent == True:
- self.hbox.addSpacing(indentSpacing)
-
- lineEdit = QtGui.QLineEdit()
- self.lineEditList.append(lineEdit)
- label = QtGui.QLabel(text)
-
- self.addWidget(label)
- self.addWidget(lineEdit)
- return label, lineEdit
-
- def addWidget(self, widget, align=None):
- if align is None:
- self.hbox.addWidget(widget)
- else:
- self.hbox.addWidget(widget, alignment=align)
-
- def addLabel(self, text):
- label = QtGui.QLabel(text)
- self.addWidget(label)
- return label
-
- def addSlider(self):
- slider = QtGui.QSlider(QtCore.Qt.Horizontal)
- self.addWidget(slider)
- return slider
-
- def addLabeledSlider(self, text, newRow=True):
- if newRow == True:
- self.newRow()
-
- labeledSlider = QLabeledSlider(text)
- self.addWidget(labeledSlider)
- return labeledSlider.getSlider()
-
-class QLabeledSlider(QtGui.QWidget):
- def __init__(self, text, parent=None):
- QtGui.QWidget.__init__(self, parent)
- vbox = QtGui.QVBoxLayout()
- vbox.setSpacing(10)
- self.setLayout(vbox)
- self.text = text
- self.label = QtGui.QLabel(text)
- self.slider = QtGui.QSlider(QtCore.Qt.Horizontal)
-
- vbox.addWidget(self.label)
- vbox.addWidget(self.slider)
-
- self.connect(self.slider, QtCore.SIGNAL('valueChanged(int)'),
- self.updateLabel)
-
- def getSlider(self):
- return self.slider
-
- def updateLabel(self, value):
- self.label.setText("%s %d" %(self.text, value))
-
-class QRadioButtonFrame(QtGui.QFrame):
- """ Framed widget containing a label and list of radiobuttons """
- def __init__(self, labelText=None, buttonList=None, parent=None):
- QtGui.QFrame.__init__(self, parent)
- self.setFrameStyle(QtGui.QFrame.Raised)
- self.setFrameShape(QtGui.QFrame.Box)
-
- self.hbox = QtGui.QHBoxLayout()
- self.setLayout(self.hbox)
- self.buttonGroup = QtGui.QButtonGroup()
- self.buttons = {}
-
- if labelText is not None:
- self.addLabel(QtGui.QLabel(labelText))
- if buttonList is not None:
- self.addButtonList(buttonList)
-
- def addLabel(self, label):
- self.hbox.addWidget(label)
-
- def addButton(self, button):
- self.buttonGroup.addButton(button)
- self.hbox.addWidget(button)
- self.buttons[str(button.text())] = button
-
- def setChecked(self, buttonText):
- if buttonText in list(self.buttons):
- self.buttons[buttonText].setChecked(True)
-
- def isChecked(self, buttonText):
- if buttonText in list(self.buttons):
- return self.buttons[buttonText].isChecked()
-
- return False
-
- def getButton(self, buttonText):
- if buttonText in list(self.buttons):
- return self.buttons[buttonText]
-
- return None
-
- def addButtonList(self, buttonList):
- """ Create and add buttons from a list of strings """
- for buttonText in buttonList:
- button = QtGui.QRadioButton(buttonText)
- self.buttons[buttonText] = button
- self.addButton(button)
-
-def round_number( N ):
- import numpy
- P = 10.0 ** ( numpy.floor(numpy.log10(abs(N) ) ) )
- return( sign(N) * int( abs(N)/P + 0.5) * P )
-
-def sign ( N ):
- if (N < 0): return -1
- else: return 1
-
-
diff --git a/contrib/cdat/gui_controller.py b/contrib/cdat/gui_controller.py
deleted file mode 100644
index c6a9546..0000000
--- a/contrib/cdat/gui_controller.py
+++ /dev/null
@@ -1,350 +0,0 @@
-import core.modules.module_registry
-import core.modules.vistrails_module
-from logging import debug, warn
-from core.vistrail.connection import Connection
-from core.vistrail.port import Port
-from PyQt4 import QtGui, QtCore
-import api
-import vcs
-import os
-
-cdat_id = "edu.utah.sci.vistrails.cdat"
-
-# Module names
-# Note: open_name, quickplot_name, etc... are used in cdat_window.py
-# and graphics_method_controller.py
-open_name = 'open'
-quickplot_name = 'Quickplot'
-variable_name = 'Variable'
-cdatcell_name = 'CDATCell'
-gm_name = 'GraphicsMethod'
-
-# Port names
-
-
-# Module Namespaces
-namespace = {}
-namespace[open_name] = 'cdms2'
-namespace[quickplot_name] = 'cdat'
-namespace[variable_name] = 'cdat'
-namespace[cdatcell_name] = 'cdat'
-namespace[gm_name] = 'cdat'
-
-# MAJOR TODO: Support for multiple workflows
-
-class Workflow():
- """ A Workflow contains a dict of modules belonging to the workflow. Workflow
- manages the updating of its modules connections / values """
-
- def __init__(self):
- """ Workflow contains a dictionary of modules in the workflow.
- * Key - if module is a variable then the key is the name of the variable
- otherwise the key is the name of the module. ***** IMPORTANT *****
- * Value - module object
- """
- self.modules = {}
- self.variableNames = [] # Names of the variables in this workflow
- self.filename = None # Name of the cdms file associated with this workflow
-
- def moduleExists(self, key):
- return key in list(self.modules)
-
- def addModule(self, name, module, isVariable=False):
- self.modules[name] = module
-
- # If the module is a variable save the name and connect the variable
- # module to the open module
- if isVariable:
- self.variableNames.append(name)
- self.connectPorts(self.modules[open_name], 'dataset', module,
- 'cdmsfile')
-
- def updatePorts(self, var1, var2):
- """ updatePorts(var1: str, var2: str)
-
- updatePorts connects the output ports of Variable modules with vars
- var1 and var2 to the input ports of Graphics Method and then connects
- the output of Graphics Method to the input of CDATCell.
- """
- m_open = self.modules[open_name]
- m_variable1 = self.modules[var1]
- m_gm = self.modules[gm_name]
- m_cdatcell = self.modules[cdatcell_name]
-
- # Connect the variable module being plotted to the graphics method
- # module and store the connection
- self.connectPorts(m_variable1, 'variable', m_gm, 'slab1')
-
- # Connect graphics method module & cdatcell module
- self.connectPorts(m_gm, 'canvas', m_cdatcell, 'canvas')
- self.connectPorts(m_gm, 'slab1', m_cdatcell, 'slab1')
-
- # Connect the second variable module (if given) to graphics method
- # and Graphics Method to CDATCell
- if var2 is not None:
- m_var2 = self.modules[var2]
- self.connectPorts(m_var2, 'variable', m_gm, 'slab2')
- self.connectPorts(m_gm, 'slab2', m_cdatcell, 'slab2')
-
- def connectPorts(self, moduleA, outputPortName, moduleB, inputPortName):
- """ connectPorts(moduleA: Module, outputPortName: str, moduleB: Module,
- inputPortName: str) -> Connection
-
- connectPorts connects moduleA's outputPort to moduleB's inputPort.
- """
- reg = api.get_module_registry()
- in_port = moduleA.get_port_spec(outputPortName, 'output')
- out_port = moduleB.get_port_spec(inputPortName, 'input')
-
- return api.add_connection(moduleA.id, outputPortName, moduleB.id,
- inputPortName)
-
- def updateModule(self, name, portName, value):
- """ updateModule(name: str, portName: str, value: *)
-
- updateModule updates the vistrail module given the module name, input
- port name, and value
- """
- if name not in list(self.modules):
- return
-
- # Set the filename associated w/ this workflow
- if name == open_name:
- self.filename = value
-
- module = self.modules[name]
- api.get_current_controller().update_function(module, portName, [value])
-
- def updateModuleOps(self, name, args):
- """ updateModule(name: str, args: list)
-
- updateModule updates the vistrail module given the module name and a
- list of tuples where each tuple = (input port name, value)
- """
- if name not in list(self.modules):
- return
-
- module = self.modules[name]
- for portName, value in args:
- api.get_current_controller().update_function(module, portName,
- [value])
-
-class GuiController(QtCore.QObject):
- """ GuiController calls vistrails functions and handles recording and
- displaying teaching commands.
-
- The two most important functions that GuiController provides are:
- 'createModule' and 'updateModule'. 'createModule' creates a new box.
- 'updateModule' updates the input of a box. Widgets interact with
- GuiController by sending signals (which is why GuiController inherits
- from QObject).
- """
-
- def __init__(self, fileWidget, defVarWidget, varWidget):
- """ __init__(fileWidget: QCDATFileWidget, defVarWidget:QDefinedVariable,
- varWidget: QVariableView)
- """
- QtCore.QObject.__init__(self)
- self.teachingCommands = ''
- self.editorPid = 0
- self.recordCommands = True
-
- self.workflows = [] # List of workflows
-
- # X coordinates of open, variable, and plot related modules
- self.openX = -300
- self.variableX = -300
- self.plotX = -320
-
- self.m_open = None
- self.m_variable = None
- self.m_graphics_method = None
- self.m_cdat_cell = None
-
- # Connect the 3 main widgets to the primary GuiController
- # functionality. If a childwidget of the 3 main widgets wants to
- # send signals to GuiController, then it must send it through one of the
- # main widgets to try to keep things less messy
- self.connect(fileWidget, QtCore.SIGNAL('createModule'),
- self.createModule)
- self.connect(fileWidget, QtCore.SIGNAL('updateModule'),
- self.updateModule)
- self.connect(fileWidget, QtCore.SIGNAL('recordTeachingCommand'),
- self.recordTeachingCommand)
-
- self.connect(defVarWidget, QtCore.SIGNAL('createModule'),
- self.createModule)
- self.connect(defVarWidget, QtCore.SIGNAL('updateModule'),
- self.updateModule)
- self.connect(defVarWidget, QtCore.SIGNAL('recordTeachingCommand'),
- self.recordTeachingCommand)
-
- self.connect(varWidget, QtCore.SIGNAL('recordTeachingCommand'),
- self.recordTeachingCommand)
- self.connect(varWidget, QtCore.SIGNAL('createModule'),
- self.createModule)
- self.connect(varWidget, QtCore.SIGNAL('updateModule'),
- self.updateModule)
- self.connect(varWidget, QtCore.SIGNAL('updateModuleOps'),
- self.updateModuleOps)
- self.connect(varWidget, QtCore.SIGNAL('plot'),
- self.plot)
-
- def createNewWorkflow(self):
- """ createnewWorkflow(filename: str)
-
- createNewWorkflow is called when the user selects a new file. It makes
- a new workflow and appends it to the workflow list.
- """
- if self.workflows == []:
- api.get_current_controller().change_selected_version(0)
-
- self.currentWorkflow = Workflow()
- self.workflows.append(self.currentWorkflow)
-
- def getCoordinates(self, name):
- """ getCoordinates(name: str) -> x: int, y: int
-
- Return the x, y coordinate of where to place the new module given the
- name.
- """
- if name == open_name:
- self.openX += 100
- return self.openX, 170
- elif name == variable_name or name == quickplot_name:
- self.variableX += 120
- return self.variableX, 70
- elif name == gm_name:
- self.plotX += 160
- return self.plotX, -70
- elif name == cdatcell_name:
- return self.plotX, -170
-
- def createModule(self, name, key=None):
- """ createModule(name: str, key: str)
-
- createModule creates a new module given the name and adds it to the
- current workflow. If key is specified, use the key instead of the name
- as the key into the workflow's module dictionary.
-
- Note: For Variable modules I pass key = variabe name (the tabName)
- """
- # If module is the 'open' module, create a new workflow
- if name == open_name:
- self.createNewWorkflow()
-
- # If module is 'quickplot' module, and it already exists, do nothing
- if name == quickplot_name:
- if self.currentWorkflow.moduleExists(quickplot_name.lower()):
- return
-
- # Create & add the module
- x, y = self.getCoordinates(name)
- module = api.add_module(x, y, cdat_id, name, namespace[name])
-
- if key is not None:
- self.currentWorkflow.addModule(key, module, isVariable=True)
- else:
- self.currentWorkflow.addModule(name, module)
-
- def updateModule(self, name, portName, value):
- """ updateModule(name: str, portName: str, value: *)
-
- updateModule updates the vistrail module given the module name, input
- port name, and value
- """
- self.currentWorkflow.updateModule(name, portName, value)
-
- def updateModuleOps(self, name, args):
- """ updateModule(name: str, args: list)
-
- updateModule updates the vistrail module given the module name and a
- list of tuples where each tuple = (input port name, value)
- """
- self.currentWorkflow.updateModuleOps(name, args)
-
- def plot(self, var1, var2):
- """ Connect / disconnect the necessary ports and exec workflow -> plot
- into the cell
- """
- self.currentWorkflow.updatePorts(var1, var2)
- api.get_current_controller().execute_current_workflow()
-
- def initTeachingCommands(self):
- """ The initial teaching commands still have 4 canvases like the old
- vcdat. This allows you to run the teaching commands independently
- of vistrails' spreadsheets.
- """
- self.teachingCommands += 'import cdms2, vcs, cdutil, genutil, os, sys\n'
- self.teachingCommands += 'import MV2\n'
-
- self.teachingCommands += '\n# Initialize the four VCS Canvases by creating\n'
- self.teachingCommands += '# a list to hold the 4 VCS Canvas\n'
- self.teachingCommands += 'vcs_canvas_list = []\n'
-
- self.teachingCommands += '\n# Loop (from 0 to 3) to create VCS Canvas 1, 2, 3, and 4\n'
- self.teachingCommands += 'for i in range(4):\n'
- self.teachingCommands += ' vcs_canvas_list.append(vcs.init())\n'
-
- self.teachingCommands += '\n# Set the Command Line VCS Canvas hooks\n'
- self.teachingCommands += 'vcs_hook1 = vcs_canvas_list[0]\n'
- self.teachingCommands += 'vcs_hook2 = vcs_canvas_list[1]\n'
- self.teachingCommands += 'vcs_hook3 = vcs_canvas_list[2]\n'
- self.teachingCommands += 'vcs_hook4 = vcs_canvas_list[3]\n'
-
- self.writeTeachingCommands()
-
- def recordTeachingCommand(self, command):
- if (self.recordCommands == True):
- self.teachingCommands += command
- self.writeTeachingCommands()
-
- def setRecordCommands(self, recordCommands):
- self.recordCommands = recordCommands
-
- def writeTeachingCommands(self):
- try:
- fn = '%s/PCMDI_GRAPHICS' % os.environ['HOME']
- except:
- print "Could not find the $HOME directory. Set your environment variable 'HOME'"
- print "to your home directory. (e.g., 'setenv HOME /home/user')."
- sys.exit()
-
- # Create PCMDI_GRAPHICS directory if it does not exist
- if (os.access(fn, os.X_OK) == 0):
- try:
- os.mkdir(fn)
- except:
- print 'Do not have write permission for home directory. Must have write permissions.'
- sys.exit()
-
- # Write teaching commands to vcdat_recording_script_file.py
- self.teachingScript = fn + '/vcdat_recording_script_file.py'
- file = open(self.teachingScript, 'w')
- file.write(self.teachingCommands)
- file.flush()
-
- def viewTeachingCommands(self):
- """ Open the teaching commands script in a child process """
- self.editorPid = os.fork()
-
- if (self.editorPid == 0):
- editor = 'idle'
-
- # If idle editor is found, view teaching commands with idle
- for path in os.environ["PATH"].split(os.pathsep):
- file = os.path.join(path, editor)
- if (os.path.exists(file)):
- args = (editor, self.teachingScript)
- os.execvp(editor, args)
- return
-
- # If idle editor is not found, use default editor
- secondaryEditor = os.environ['EDITOR']
- args = (secondaryEditor, self.teachingScript)
- os.execvp(secondaryEditor, args)
-
- def closeTeachingCommands(self):
- if (self.editorPid != 0):
- os.kill(self.editorPid, 9)
- self.editorPid = 0
diff --git a/contrib/cdat/pyqtscripting.sbf b/contrib/cdat/pyqtscripting.sbf
deleted file mode 100644
index ccee4f3..0000000
--- a/contrib/cdat/pyqtscripting.sbf
+++ /dev/null
@@ -1,3 +0,0 @@
-target = coreappwrap
-sources = sipcoreappwrapcmodule.cpp sipcoreappwrapVCSQtManager.cpp sipcoreappwrapMainWindow.cpp
-headers = sipAPIcoreappwrap.h
diff --git a/contrib/cdat/quickplot.py b/contrib/cdat/quickplot.py
deleted file mode 100644
index f38e54a..0000000
--- a/contrib/cdat/quickplot.py
+++ /dev/null
@@ -1,50 +0,0 @@
-from cdat_cell import QCDATWidget, CDATCell
-from core.modules.vistrails_module import (Module, ModuleError, NotCacheable)
-from packages.spreadsheet.spreadsheet_controller import spreadsheetController
-from packages.spreadsheet.spreadsheet_event import DisplayCellEvent
-from PyQt4 import QtCore, QtGui
-
-class quickplot(Module, NotCacheable):
- """hackiness to push a cdat plot to our spreadsheet.
- needs: QCDATWidget ref
- cdms2.open()d dataset
- blah this is out of date variable name"""
-
- def compute(self):
- args = []
- if not self.hasInputFromPort('dataset'):
- raise ModuleError(self, "'dataset' is mandatory.")
- if not self.hasInputFromPort('plot'):
- raise ModuleError(self, "'plot' is mandatory.")
-
- dataset = self.getInputFromPort('dataset')
- plotType = self.getInputFromPort('plot')
- axes = self.forceGetInputFromPort('axes')
- inCanvas = self.forceGetInputFromPort('canvas')
-
- if axes!=None:
- try:
- kwargs = eval(axes)
- except:
- raise ModuleError(self, "Invalid 'axes' specification", axes)
- dataset = dataset(**kwargs)
-
- outCanvas = None
- if inCanvas!=None:
- inCanvas.plot(dataset, 'ASD', plotType)
- outCanvas = inCanvas
- else:
- ev = DisplayCellEvent()
- ev.vistrail = {'locator': None, 'version': -1, 'actions': []}
- ev.cellType = QCDATWidget
- ev.inputPorts = (dataset, 'ASD', plotType)
-
- QtCore.QCoreApplication.processEvents()
- spreadsheetWindow = spreadsheetController.findSpreadsheetWindow()
-
- cdatWidget = spreadsheetWindow.displayCellEvent(ev)
- if cdatWidget!=None:
- outCanvas = cdatWidget.canvas
-
- self.setResult('dataset', dataset)
- self.setResult('canvas', outCanvas)
diff --git a/contrib/cdat/scripts/cdat_domain.py b/contrib/cdat/scripts/cdat_domain.py
deleted file mode 100755
index 1c29e44..0000000
--- a/contrib/cdat/scripts/cdat_domain.py
+++ /dev/null
@@ -1,289 +0,0 @@
-#!/usr/bin/env python
-############################################################################
-##
-## Copyright (C) 2006-2008 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-def convert_to_vt_type(t):
- vt_type_dict = {'str':'core.modules.basic_modules.String',
- 'float': 'core.modules.basic_modules.Float',
- 'int':'core.modules.basic_modules.Integer',
- 'bool':'core.modules.basic_modules.Boolean',
- #'numpy.ndarray':'reg.get_module_by_name("edu.utah.sci.vistrails.numpyscipy", "Numpy Array", namespace="numpy|array")',
- }
- if vt_type_dict.has_key(t):
- return vt_type_dict[t]
- else:
- print "Type %s not found!" % t
- return None
-
-do_not_cache_me = ['png','plot','isofill','isoline','boxfill']
-class CDATModule:
- _extra_modules = []
- _extra_vistrails_modules = {}
- def __init__(self, author=None, language=None, type=None, url=None,
- codepath=None, version=None, actions=None):
- self._author = author
- self._language = language
- self._type = type
- self._url = url
- self._codepath = codepath
- self._version = version
- self._actions = actions
- (self._namespace, self._name) = self.split(codepath)
-
- @staticmethod
- def split(codepath):
- dot = codepath.rfind('.')
- if dot != -1:
- name = codepath[dot+1:]
- data = codepath[:dot]
- namespace = data.replace('.','|')
- else:
- name = codepath
- namespace = codepath
- return (namespace,name)
-
- def write_extra_module_definition(self, lines, name):
- lines.append("%s = new_module(Module,'%s')\n"%(name,name))
-
- @staticmethod
- def write_extra_module_definitions_init(lines):
- lines.append("vt_type_dict = {}\n")
- lines.append("def get_late_type(type):\n")
- lines.append(" return vt_type_dict[type]\n\n")
-
- @staticmethod
- def write_extra_module_definitions(lines):
- for t in CDATModule._extra_modules:
- namespace,name = CDATModule.split(t)
- lines.append("%s = new_module(Module,'%s')\n"%(name,name))
- lines.append("vt_type_dict['%s'] = %s\n"%(t,name))
- CDATModule._extra_vistrails_modules[name] = namespace
- lines.append("\n\n")
-
- @staticmethod
- def register_extra_vistrails_modules(lines, ident=''):
- for (name,namespace) in CDATModule._extra_vistrails_modules.iteritems():
- lines.append(ident + " reg.add_module(%s,namespace='%s')\n"%(name,
- namespace))
-
- def register_extra_vistrails_module(self, lines, name, ident=''):
- lines.append(ident + " reg.add_module(%s,namespace='%s')\n"%(name,
- self._namespace))
-
- def write_module_definitions(self, lines):
- for a in self._actions:
- a.write_module_definition(lines)
-
- def register_vistrails_modules(self, lines):
- for a in self._actions:
- a.register_itself(lines,self._namespace)
-
- def build_vistrails_modules_dict(self):
- for a in self._actions:
- types = a.check_output_types()
- for t in types:
- if t not in CDATModule._extra_modules:
- CDATModule._extra_modules.append(t)
-
- def add_extra_input_port_to_all_modules(self, lines, port_name, port_type,
- doc, optional = False):
- lines.append("\n #extra input ports not available in the xml file\n")
- for a in self._actions:
- a.register_extra_input_port(port_name, port_type, lines, doc,
- optional)
-
- def add_extra_output_port_to_all_modules(self, lines, port_name, port_type,
- doc, optional = False):
- lines.append("\n #extra output ports not available in the xml file\n")
- for a in self._actions:
- a.register_extra_output_port(port_name, port_type, lines, doc,
- optional)
-class CDATAction:
- def __init__(self, name=None, type=None, options=None, inputs=None,
- outputs=None, doc=None):
- self._name = name
- self._type = type
- self._options = options
- self._inputs = inputs
- self._outputs = outputs
- self._doc = doc
-
- def write_module_definition(self, lines, ident='', compute_method=None):
- def write_compute_method(self,lines, ident):
- lines.append(ident + "def compute(self):\n")
- lines.append(ident + " if self.hasInputFromPort('canvas'):\n")
- lines.append(ident + " canvas = self.getInputFromPort('canvas')\n")
- lines.append(ident + " else:\n")
- lines.append(ident + " canvas = vcs.init()\n")
- lines.append(ident + " args = []\n")
- for inp in self._inputs:
- lines.append(ident + " %s = None\n"%inp._name)
- for inst in inp._valid_instances:
- if inp._valid_instances.index(inst) == 0:
- lines.append(ident + " if self.hasInputFromPort('%s'):\n" % inst)
- lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
- lines.append(ident + " args.append(%s)\n"%inp._name)
- else:
- lines.append(ident + " elif self.hasInputFromPort('%s'):\n" % inst)
- lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
- lines.append(ident + " args.append(%s)\n"%inp._name)
- if inp._required:
- lines.append("\n"+ ident +" # %s is a required port\n" % inp._name)
- lines.append(ident + " if %s == None:\n" % inp._name)
- lines.append(ident + " raise ModuleError(self, \"'%s' is a mandatory port\")\n" % inp._name)
-
- lines.append("\n"+ident +" # build up the keyword arguments from the optional inputs.\n")
- lines.append(ident +" kwargs = {}\n")
-
- for opt in self._options:
- for inst in opt._valid_instances:
- if opt._valid_instances.index(inst) == 0:
- lines.append(ident +" if self.hasInputFromPort('%s'):\n" % inst)
- lines.append(ident +" kwargs['%s'] = self.getInputFromPort('%s')\n" % (opt._name, inst))
- else:
- lines.append(ident +" elif self.hasInputFromPort('%s'):\n" % inst)
- lines.append(ident +" kwargs['%s'] = self.getInputFromPort('%s')\n" % (opt._name, inst))
-
- lines.append(ident + " #force images to be created in the background\n")
- lines.append(ident + " kwargs['bg'] = 1\n")
- lines.append(ident + " res = canvas.%s(*args,**kwargs)\n"%self._name)
- lines.append(ident + " self.setResult('%s',res)\n"%(self._outputs[0]._name))
- lines.append(ident + " self.setResult('canvas',canvas)\n")
- lines.append("\n")
- if self._name in do_not_cache_me:
- lines.append(ident + "class %s(Module,NotCacheable):\n" % self._name)
- else:
- lines.append(ident + "class %s(Module):\n" % self._name)
- lines.append(ident + ' """%s\n'%self._doc)
- lines.append(ident + ' """\n')
- if not compute_method:
- write_compute_method(self,lines,ident=" ")
- else:
- lines.extend(compute_method)
-
- def register_itself(self,lines, namespace):
- lines.append("\n #Module %s\n" % self._name)
- lines.append(" reg.add_module(%s,namespace='%s')\n" % (self._name,namespace))
- for inp in self._inputs:
- inp.write_input_ports(self._name, lines)
- for opt in self._options:
- opt.write_input_ports(self._name, lines, True, force=False)
- for out in self._outputs:
- out.write_output_ports(self._name, lines, force=True)
-
- def check_output_types(self):
- types = []
- for out in self._outputs:
- if out._instance[0] not in types:
- types.append(out._instance[0])
- return types
-
- def register_extra_input_port(self, port_name, port_type, lines, doc,
- optional=False):
- self._write_port('input', port_name, port_type, lines, doc, optional)
-
- def register_extra_output_port(self, port_name, port_type, lines, doc,
- optional=False):
- self._write_port('output', port_name, port_type, lines, doc, optional)
-
- #private methods
- def _write_port(self, io_type, port_name, port_type,
- lines, doc, optional=False):
- lines.append(" reg.add_%s_port(%s, '%s', \n" % (io_type,
- self._name,
- port_name))
- lines.append(" ")
- lines.append("(%s,\n" % port_type)
- lines.append(" ")
- if not optional:
- lines.append("\"%s\"))\n" % doc)
- else:
- lines.append("\"%s\"), True)\n" % doc)
-
-class CDATItem:
- def __init__(self, tag=None, doc=None, instance=None, required=False):
- self._name = tag
- self._doc = doc
- self._instance = [i.strip(" \t\n") for i in instance.split('/')]
- self._valid_instances = []
- if required == None:
- self._required = False
- else:
- self._required = required
-
- def write_input_ports(self, module_name, lines, optional=False, force=False):
- self._write_ports('input',module_name, lines, optional, force)
-
- def write_output_ports(self, module_name, lines, optional=False, force=False):
- self._write_ports('output',module_name, lines, optional, force)
-
- def _write_ports(self, port_type, module_name, lines, optional=False,
- force=False):
- if len(self._instance) == 1:
- type = convert_to_vt_type(self._instance[0])
- if type == None and self._instance[0] in CDATModule._extra_modules:
- force = True
- if force and type == None:
- type = "get_late_type('%s')"%self._instance[0]
- if type != None:
- self._valid_instances.append(self._name)
- lines.append(" reg.add_%s_port(%s, '%s', \n" % (port_type,
- module_name,
- self._name))
- lines.append(" ")
- lines.append("(%s,\n" % type)
- lines.append(" ")
- if not optional:
- lines.append("\"%s\"))\n" % self._doc)
- else:
- lines.append("\"%s\"), True)\n" % self._doc)
- else:
- count = 0
- for i in xrange(len(self._instance)):
- type = convert_to_vt_type(self._instance[i])
- new_force = force
- if type == None and self._instance[i] in CDATModule._extra_modules:
- new_force = True
- if new_force and type == None:
- type = "get_late_type('%s')"%self._instance[i]
- if type != None:
- name = "%s_%s"%(self._name,count)
- self._valid_instances.append(name)
- count += 1
- lines.append(" reg.add_input_port(%s, '%s', \n" % (module_name,
- name))
- lines.append(" ")
- lines.append("(%s,\n" % type)
- lines.append(" ")
- if not optional:
- lines.append("\"%s\"))\n" % self._doc)
- else:
- lines.append("\"%s\"), True)\n" % self._doc)
-
-class CDATOption(CDATItem):
- def __init__(self, tag=None, default=None, doc=None, instance=None):
- CDATItem.__init__(self, tag, doc, instance, False)
- self._default = default
-
-class CDATPort(CDATItem):
- def __init__(self, tag=None, doc=None, instance=None, position=None, required=False):
- CDATItem.__init__(self, tag, doc, instance, required)
- self._position = position
\ No newline at end of file
diff --git a/contrib/cdat/scripts/cdatwindow_init_inc.py b/contrib/cdat/scripts/cdatwindow_init_inc.py
deleted file mode 100644
index 0122627..0000000
--- a/contrib/cdat/scripts/cdatwindow_init_inc.py
+++ /dev/null
@@ -1,85 +0,0 @@
-
- ##########################################################################
- # included from cdatwindow_init_inc.py
- #display = sip.unwrapinstance(QtGui.QX11Info.display())
- #vcs._vcs.setdisplay(display)
-
- #cdat GUI modules
- global cdatWindow
- cdatWindow = QCDATWindow()
- cdatWindow.show()
-
- reg.add_module(CDATCell,namespace='cdat')
- reg.add_input_port(CDATCell, 'slab1',
- (TransientVariable, "variable to be plotted"))
- reg.add_input_port(CDATCell, 'slab2',
- (TransientVariable, "variable to be plotted"))
- reg.add_input_port(CDATCell, 'plotType',
- (core.modules.basic_modules.String, "Plot type"))
- reg.add_input_port(CDATCell, 'template',
- (core.modules.basic_modules.String, "template name"))
- reg.add_input_port(CDATCell, 'gmName',
- (core.modules.basic_modules.String, "graphics method name"))
- reg.add_input_port(CDATCell, 'canvas',
- (Canvas, "Canvas object"))
- reg.add_input_port(CDATCell, 'col',
- (core.modules.basic_modules.Integer, "Cell Col"))
- reg.add_input_port(CDATCell, 'row',
- (core.modules.basic_modules.Integer, "Cell Row"))
- reg.add_input_port(CDATCell, 'continents',
- (core.modules.basic_modules.Integer,
- "continents type number"), True)
-
- reg.add_module(Variable, namespace='cdat')
- reg.add_module(Quickplot, namespace='cdat')
- reg.add_input_port(Variable, 'id',
- (core.modules.basic_modules.String,
- ""))
- reg.add_input_port(Variable, 'type',
- (core.modules.basic_modules.String,
- "variable, axis, or weighted-axis"))
- reg.add_input_port(Variable, 'inputVariable',
- (core.modules.basic_modules.List,
- ""))
- reg.add_output_port(Variable, 'variable',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- ""))
- reg.add_input_port(Variable, 'axes',
- (core.modules.basic_modules.String, "Axes of variables"))
- reg.add_input_port(Variable, 'axesOperations',
- (core.modules.basic_modules.String, "Axes Operations"))
- reg.add_input_port(Variable, 'cdmsfile',
- (CdmsFile, "cdmsfile"))
-
- reg.add_module(GraphicsMethod, namespace='cdat')
- reg.add_input_port(GraphicsMethod, 'gmName',
- (core.modules.basic_modules.String,
- "Get the graphics method object of the given name."))
- reg.add_input_port(GraphicsMethod, 'plotType',
- (core.modules.basic_modules.String, "Plot type"))
- reg.add_input_port(GraphicsMethod, 'slab1',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "slab1"))
- reg.add_input_port(GraphicsMethod, 'slab2',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "slab2"))
- reg.add_input_port(GraphicsMethod, 'color_1',
- (core.modules.basic_modules.Integer, "color_1"), True)
- reg.add_input_port(GraphicsMethod, 'color_2',
- (core.modules.basic_modules.Integer, "color_2"), True)
- reg.add_input_port(GraphicsMethod, 'level_1',
- (core.modules.basic_modules.Float, "level_1"), True)
- reg.add_input_port(GraphicsMethod, 'level_2',
- (core.modules.basic_modules.Float, "level_2"), True)
- reg.add_output_port(GraphicsMethod, 'slab1',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "slab1"))
- reg.add_output_port(GraphicsMethod, 'slab2',
- (get_late_type('cdms2.tvariable.TransientVariable'),
- "slab2"))
- reg.add_output_port(GraphicsMethod, 'canvas', (Canvas, "Canvas object"))
-
- # end of cdatwindow_init_inc.py
- ##########################################################################
-
-
diff --git a/contrib/cdat/scripts/gen_init.py b/contrib/cdat/scripts/gen_init.py
deleted file mode 100755
index c622bbe..0000000
--- a/contrib/cdat/scripts/gen_init.py
+++ /dev/null
@@ -1,267 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2008 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-import os, sys
-sys.path.append('../../../vistrails')
-from parse_cdat_xml_file import parse_cdat_xml_file
-from cdat_domain import CDATModule
-
-
-
-#cdat package identifiers
-cp_version = '0.2'
-cp_identifier = 'edu.utah.sci.vistrails.cdat'
-cp_name = 'CDAT'
-
-def write_init(output_file, classes_lines, init_lines):
- """write_init(output_file: str, classes_lines: list, init_lines: list)
- -> None
- Writes the necessary contents for the package init file"""
-
- # cdat dependencies
- init_lines.append("\n\n")
- init_lines.append("def package_dependencies():\n")
- #init_lines.append(" return ['edu.utah.sci.vistrails.numpyscipy']\n")
- init_lines.append(" return []\n")
- init_lines.append("\n\n")
- init_lines.append("def package_requirements():\n")
- init_lines.append(" import core.requirements\n")
- init_lines.append(" if not core.requirements.python_module_exists('vcs'):\n")
- init_lines.append(" raise core.requirements.MissingRequirements('vcs')\n")
- init_lines.append(" if not core.requirements.python_module_exists('cdms2'):\n")
- init_lines.append(" raise core.requirements.MissingRequirements('cdms2')\n")
- init_lines.append(" if not core.requirements.python_module_exists('cdutil'):\n")
- init_lines.append(" raise core.requirements.MissingRequirements('cdutil')\n")
- init_lines.append(" import vcs, cdms2, cdutil\n")
- init_lines.append("\n\n")
-
- header = open("init_inc.py").readlines()
- header.append("\n\n")
- header.append('version = "' + cp_version + '"\n')
- header.append('identifier = "' + cp_identifier + '"\n')
- header.append('name = "' + cp_name + '"\n\n')
-
- outfile = open(output_file, "w")
- outfile.writelines(header)
- outfile.writelines(classes_lines)
- outfile.writelines(init_lines)
- outfile.close()
-
-def parse_files(input_files):
- modules = []
- for f in input_files:
- modules.append(parse_cdat_xml_file(f))
- return modules
-
-def add_canvas_ports_to_canvas_modules(canvas, lines):
- canvas.add_extra_input_port_to_all_modules(lines,
- port_name='canvas',
- port_type='Canvas',
- doc='Canvas object',
- optional=False
- )
- canvas.add_extra_output_port_to_all_modules(lines,
- port_name='canvas',
- port_type='Canvas',
- doc='Canvas object',
- optional=False
- )
-
-def add_canvas_module(canvas,init_lines,class_lines):
- canvas.write_extra_module_definition(class_lines,'Canvas')
- canvas.register_extra_vistrails_module(init_lines,'Canvas')
-
-def get_image_compute_method(action, ident=''):
- lines = []
- lines.append(ident + "def compute(self):\n")
- lines.append(ident + " if self.hasInputFromPort('canvas'):\n")
- lines.append(ident + " canvas = self.getInputFromPort('canvas')\n")
- lines.append(ident + " else:\n")
- lines.append(ident + " canvas = vcs.init()\n")
- lines.append(ident + " args = []\n")
- for inp in action._inputs:
- lines.append(ident + " %s = None\n"%inp._name)
- for inst in inp._valid_instances:
- if inp._valid_instances.index(inst) == 0:
- lines.append(ident + " if self.hasInputFromPort('%s'):\n" % inst)
- lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
- lines.append(ident + " args.append(%s)\n"%inp._name)
- else:
- lines.append(ident + " elif self.hasInputFromPort('%s'):\n" % inst)
- lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
- lines.append(ident + " args.append(%s)\n"%inp._name)
- if inp._required:
- lines.append("\n"+ ident +" # %s is a required port\n" % inp._name)
- lines.append(ident + " if %s is None:\n" % inp._name)
- lines.append(ident + " raise ModuleError(self, \"'%s' is a mandatory port\")\n" % inp._name)
-
- lines.append(ident + " ofile = core.modules.basic_modules.File()\n")
- lines.append(ident + " ofile.name = %s\n"%action._inputs[0]._name)
-
- lines.append(ident + " canvas.%s(*args)\n"%action._name)
- lines.append(ident + " self.setResult('file',ofile)\n")
- lines.append("\n")
- return lines
-
-def get_cdms2_compute_method(action, ident=''):
- lines = []
- lines.append(ident + "def compute(self):\n")
- lines.append(ident + " args = []\n")
- for inp in action._inputs:
- lines.append(ident + " %s = None\n"%inp._name)
- for inst in inp._valid_instances:
- if inp._valid_instances.index(inst) == 0:
- lines.append(ident + " if self.hasInputFromPort('%s'):\n" % inst)
- lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
- lines.append(ident + " args.append(%s)\n"%inp._name)
- else:
- lines.append(ident + " elif self.hasInputFromPort('%s'):\n" % inst)
- lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
- lines.append(ident + " args.append(%s)\n"%inp._name)
- if inp._required:
- lines.append("\n"+ ident +" # %s is a required port\n" % inp._name)
- lines.append(ident + " if %s is None:\n" % inp._name)
- lines.append(ident + " raise ModuleError(self, \"'%s' is a mandatory port\")\n" % inp._name)
-
- lines.append(ident + " res = cdms2.%s(*args)\n"%action._name)
- lines.append(ident + " self.setResult('%s',res)\n"%action._outputs[0]._name)
- lines.append("\n")
- return lines
-
-def get_CdmsFile_compute_method(action, ident=''):
- lines = []
- lines.append(ident + "def compute(self):\n")
- lines.append(ident + " self.checkInputPort('cdmsfile')\n")
- lines.append(ident + " cdmsfile = self.getInputFromPort('cdmsfile')\n")
- lines.append(ident + " args = []\n")
- for inp in action._inputs:
- lines.append(ident + " %s = None\n"%inp._name)
- for inst in inp._valid_instances:
- if inp._valid_instances.index(inst) == 0:
- lines.append(ident + " if self.hasInputFromPort('%s'):\n" % inst)
- lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
- lines.append(ident + " args.append(%s)\n"%inp._name)
- else:
- lines.append(ident + " elif self.hasInputFromPort('%s'):\n" % inst)
- lines.append(ident + " %s = self.getInputFromPort('%s')\n" % (inp._name, inst))
- lines.append(ident + " args.append(%s)\n"%inp._name)
- if inp._required:
- lines.append("\n"+ ident +" # %s is a required port\n" % inp._name)
- lines.append(ident + " if %s is None:\n" % inp._name)
- lines.append(ident + " raise ModuleError(self, \"'%s' is a mandatory port\")\n" % inp._name)
-
- lines.append(ident + " res = cdmsfile.%s(*args)\n"%action._name)
- lines.append(ident + " self.setResult('%s',res)\n"%action._outputs[0]._name)
- lines.append("\n")
- return lines
-
-if __name__ == '__main__':
- # usage:
- args = sys.argv
- if len(args) > 2:
- root_dir = args[1]
- output_file = args[2]
- else:
- print "Usage: %s root_dir output_file" % args[0]
- sys.exit(0)
-
- xmlfiles = []
- input_files = os.walk(root_dir)
- for (d, tree, files) in input_files:
- for f in files:
- if os.path.isfile(os.path.join(d,f)) and f.endswith(".xml"):
- xmlfiles.append(os.path.join(d,f))
-
- modules = parse_files(xmlfiles)
-
- extra_init_lines = []
- init_lines = []
- extra_init_lines.append("\ndef initialize(*args, **keywords):\n")
- extra_init_lines.append(" reg = core.modules.module_registry.get_module_registry()\n\n")
-
- class_lines = []
- extra_class_lines = []
-
- print "%s xml file(s) found."% len(modules)
-
- CDATModule.write_extra_module_definitions_init(extra_class_lines)
-
- for m in modules:
- print "codepath: %s has %s Vistrails Modules."%(m._codepath, len(m._actions))
- m.build_vistrails_modules_dict()
-
- for m in modules:
- m.register_vistrails_modules(init_lines)
- if m._codepath == 'vcs.Canvas.Canvas':
- for a in m._actions:
- if a._name == 'png':
- a.write_module_definition(class_lines,
- ident='',
- compute_method=get_image_compute_method(a,ident=" "))
- a.register_extra_output_port('file',
- 'core.modules.basic_modules.File',
- init_lines,
- "File output",
- False)
- else:
- a.write_module_definition(class_lines)
-
- add_canvas_ports_to_canvas_modules(m,init_lines)
- add_canvas_module(m,extra_init_lines, extra_class_lines)
-
- elif m._codepath == "cdms2.dataset.CdmsFile":
- for a in m._actions:
- if a._name == "__call__":
- a.write_module_definition(class_lines,
- ident='',
- compute_method=get_CdmsFile_compute_method(a,
- ident=" "))
- else:
- a.write_module_definition(class_lines)
-
- m.add_extra_input_port_to_all_modules(init_lines,
- port_name='cdmsfile',
- port_type='CdmsFile',
- doc='cdmsfile',
- optional=False
- )
- elif m._codepath == 'cdms2':
- for a in m._actions:
- if a._name == "open":
- a.write_module_definition(class_lines,
- ident='',
- compute_method=get_cdms2_compute_method(a,
- ident=" "))
- else:
- a.write_module_definition(class_lines)
- else:
- m.write_module_definitions(class_lines)
-
- CDATModule.write_extra_module_definitions(extra_class_lines)
- CDATModule.register_extra_vistrails_modules(extra_init_lines)
-
- cdatwindow_init_lines = open("cdatwindow_init_inc.py").readlines()
- extra_init_lines.extend(cdatwindow_init_lines)
-
- extra_init_lines.extend(init_lines)
- extra_class_lines.extend(class_lines)
- write_init(output_file, extra_class_lines, extra_init_lines)
\ No newline at end of file
diff --git a/contrib/cdat/scripts/init_inc.py b/contrib/cdat/scripts/init_inc.py
deleted file mode 100644
index b4b7d89..0000000
--- a/contrib/cdat/scripts/init_inc.py
+++ /dev/null
@@ -1,49 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2008 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-""" Do not edit this file!
-
-File automatically generated by scripts/gen_init.py
-Change History:
-version : description
- 0.2 : Integrated quickplot module that displays the CDAT plot
- widget inside the spreadsheet
- 0.1 : First automatically generated package based on xml descriptions
-
-"""
-from PyQt4 import QtCore, QtGui
-import sip
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import (Module, NotCacheable,
- ModuleError, new_module)
-from core.bundles import py_import
-import os, sys
-
-#cdat specific packages
-vcs = py_import('vcs',{})
-cdms2 = py_import('cdms2', {})
-cdutil = py_import('cdutil', {})
-
-#local python modules
-from cdat_window import QCDATWindow
-from cdat_cell import QCDATWidget
-from quickplot import quickplot
\ No newline at end of file
diff --git a/contrib/cdat/scripts/old_cdat_init.py b/contrib/cdat/scripts/old_cdat_init.py
deleted file mode 100644
index 39f6cef..0000000
--- a/contrib/cdat/scripts/old_cdat_init.py
+++ /dev/null
@@ -1,447 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-import vcs, cdms, cdutil
-import inspect
-import os, sys
-
-class cdms_dataarray(Module) :
- def __init__(self, arr) :
- self.arr = arr
-
-class cdms_dataset(Module) :
- def __init__(self, dataset) :
- self.dataset = dataset
- def slice(self, id, kwargs) :
- dummy = []
- return self.dataset(id, *dummy, **kwargs)
-
-class cdms_get_data(Module) :
- def compute(self) :
- if not self.hasInputFromPort('id') :
- print "Error: must have id input"
- return
-
- if not self.hasInputFromPort('dataset') :
- print "Error: must have dataset input"
- return
- id = self.getInputFromPort('id')
- dataset = self.getInputFromPort('dataset')
- kwargs = {}
-
- if (self.hasInputFromPort('arg_key_1') and
- self.hasInputFromPort('arg_val_1')) :
-
- k = self.getInputFromPort('arg_key_1')
- t = self.getInputFromPort('arg_val_1')
- kwargs[k] = t
-
-
- if (self.hasInputFromPort('arg_key_2') and
- self.hasInputFromPort('arg_val_2')) :
-
- k = self.getInputFromPort('arg_key_2')
- t = self.getInputFromPort('arg_val_2')
- kwargs[k] = t
-
-
- if (self.hasInputFromPort('arg_key_3') and
- self.hasInputFromPort('arg_val_3')) :
-
- k = self.getInputFromPort('arg_key_3')
- t = self.getInputFromPort('arg_val_3')
- kwargs[k] = t
-
- dummy = []
- arr = dataset.slice(id, kwargs)
- darr = cdms_dataarray(arr)
- self.setResult("cdms_dataarray", darr)
-
-class cdms_open(Module) :
- def compute(self) :
- args = inspect.getargspec(cdms.open)
- def_args = args[3]
- uri = None
- mode = def_args[0]
- template = def_args[1]
- dods = def_args[2]
-
- if not self.hasInputFromPort('uri') :
- print "Error: must have uri input"
- return
-
- if self.hasInputFromPort('uri') :
- inuri = self.getInputFromPort('uri')
- uri = os.path.join(sys.prefix, inuri)
- if self.hasInputFromPort('mode') :
- mode = self.getInputFromPort('mode')
- if self.hasInputFromPort('template') :
- template = self.getInputFromPort('template')
- if self.hasInputFromPort('dods') :
- dods = self.getInputFromPort('dods')
-
- # output the cdmsfile object.
- cdmsfile = cdms.open(uri,mode,template,dods)
- output = cdms_dataset(cdmsfile)
- self.setResult("cdms_dataset", output)
-
-# just wrap whatever so it can be sent downstream
-class generic_port(Module) :
- def __init__(self, data) :
- self.data = data
-
-class vcs_canvas(Module) :
- def __init__(self) :
- Module.__init__(self)
- self.canvas = None
-
- def compute(self):
- if self.canvas == None :
- print "calling vcs.init()"
- self.canvas = vcs.init()
- self.setResult("vcs_canvas", self)
-
-
-class vcs_canvas_getboxfill(Module) :
- def compute(self) :
- if not self.hasInputFromPort('canvas') :
- print "ERROR: Must have canvas input port"
- return
-
- bname = None
- if self.hasInputFromPort('boxfill name') :
- bname = self.getInputFromPort('boxfill name')
- vcs_c = self.getInputFromPort('canvas')
-
- if bname == None :
- bfm = vcs_c.canvas.getboxfill()
- else :
- bfm = vcs_c.canvas.getboxfill(bname)
-
- out = generic_port(bfm)
- self.setResult("boxfill graphics method", out)
-
-class vcs_canvas_gettemplate(Module) :
- def compute(self) :
- if not self.hasInputFromPort('canvas') :
- print "ERROR: Must have canvas input port"
- return
-
- tname = None
- if self.hasInputFromPort('template name') :
- tname = self.getInputFromPort('template name')
- vcs_c = self.getInputFromPort('canvas')
-
- if tname == None :
- t = vcs_c.canvas.gettemplate()
- else :
- t = vcs_c.canvas.gettemplate(tname)
-
- out = generic_port(t)
- self.setResult("template", out)
-
-class vcs_canvas_plot(Module) :
- def compute(self) :
-
- canvas = self.getInputFromPort('vcs_canvas').canvas
- data1 = self.getInputFromPort('array1').arr
- data2 = None
- if self.hasInputFromPort('array2') :
- data2 = self.getInputFromPort('array2').arr
-
- gm = self.getInputFromPort('graphics_method').data
- t = self.getInputFromPort('template_name').data
-
-
- # build up the kewword arguments from the optional inputs.
- kwargs = {}
- kwargs['bg'] = 1
- if self.hasInputFromPort('ratio') :
- kwargs['ratio'] = self.getInputFromPort('ratio')
-
- #variable attribute keys
- if self.hasInputFromPort('comment1') :
- kwargs['comment1'] = self.getInputFromPort('comment1')
- if self.hasInputFromPort('comment2') :
- kwargs['comment2'] = self.getInputFromPort('comment2')
- if self.hasInputFromPort('comment3') :
- kwargs['comment3'] = self.getInputFromPort('comment3')
- if self.hasInputFromPort('comment4') :
- kwargs['comment4'] = self.getInputFromPort('comment4')
- if self.hasInputFromPort('file_comment') :
- kwargs['file_comment'] = self.getInputFromPort('file_comment')
- if self.hasInputFromPort('hms') :
- kwargs['hms'] = self.getInputFromPort('hms')
- if self.hasInputFromPort('long_name') :
- kwargs['long_name'] = self.getInputFromPort('long_name')
- if self.hasInputFromPort('name') :
- kwargs['name'] = self.getInputFromPort('name')
- if self.hasInputFromPort('time') :
- kwargs['time'] = self.getInputFromPort('time')
- if self.hasInputFromPort('units') :
- kwargs['units'] = self.getInputFromPort('units')
- if self.hasInputFromPort('ymd') :
- kwargs['ymd'] = self.getInputFromPort('ymd')
-
- # dimension attribute keys
- if self.hasInputFromPort('xarray1') :
- kwargs['xarray1'] = self.getInputFromPort('xarray1')
- if self.hasInputFromPort('yarray1') :
- kwargs['yarray1'] = self.getInputFromPort('yarray1')
- if self.hasInputFromPort('zarray1') :
- kwargs['zarray1'] = self.getInputFromPort('zarray1')
- if self.hasInputFromPort('tarray1') :
- kwargs['tarray1'] = self.getInputFromPort('tarray1')
- if self.hasInputFromPort('warray1') :
- kwargs['warray1'] = self.getInputFromPort('warray1')
- if self.hasInputFromPort('xarray2') :
- kwargs['xarray2'] = self.getInputFromPort('xarray2')
- if self.hasInputFromPort('yarray2') :
- kwargs['yarray2'] = self.getInputFromPort('yarray2')
- if self.hasInputFromPort('zarray2') :
- kwargs['zarray2'] = self.getInputFromPort('zarray2')
- if self.hasInputFromPort('tarray2') :
- kwargs['tarray2'] = self.getInputFromPort('tarray2')
- if self.hasInputFromPort('warray2') :
- kwargs['warray2'] = self.getInputFromPort('warray2')
- if self.hasInputFromPort('xbounds') :
- kwargs['xbounds'] = self.getInputFromPort('xbounds')
- if self.hasInputFromPort('ybounds') :
- kwargs['ybounds'] = self.getInputFromPort('ybounds')
- if self.hasInputFromPort('xname') :
- kwargs['xname'] = self.getInputFromPort('xname')
- if self.hasInputFromPort('yname') :
- kwargs['yname'] = self.getInputFromPort('yname')
- if self.hasInputFromPort('zname') :
- kwargs['zname'] = self.getInputFromPort('zname')
- if self.hasInputFromPort('tname') :
- kwargs['tname'] = self.getInputFromPort('tname')
- if self.hasInputFromPort('wname') :
- kwargs['wname'] = self.getInputFromPort('wname')
- if self.hasInputFromPort('xunits') :
- kwargs['xunits'] = self.getInputFromPort('xunits')
- if self.hasInputFromPort('yunits') :
- kwargs['yunits'] = self.getInputFromPort('yunits')
- if self.hasInputFromPort('zunits') :
- kwargs['zunits'] = self.getInputFromPort('zunits')
- if self.hasInputFromPort('tunits') :
- kwargs['tunits'] = self.getInputFromPort('tunits')
- if self.hasInputFromPort('wunits') :
- kwargs['wunits'] = self.getInputFromPort('wunits')
- if self.hasInputFromPort('xweights') :
- kwargs['xweights'] = self.getInputFromPort('xweights')
- if self.hasInputFromPort('yweights') :
- kwargs['yweights'] = self.getInputFromPort('yweights')
-
- if data2 == None :
- canvas.plot(data1, gm, t, **kwargs)
- else :
- canvas.plot(data1, data2, gm, t, **kwargs)
- o = self.interpreter.filePool.create_file(suffix='.cdat.gif')
- canvas.gif(o.name)
- self.setResult("image", o)
-
-
-def initialize(*args, **keywords):
- reg = core.modules.module_registry
-
-
- reg.addModule(cdms_open)
- reg.addInputPort(cdms_open, 'dods',
- (core.modules.basic_modules.String, 'tip'))
- reg.addInputPort(cdms_open, 'template',
- (core.modules.basic_modules.String, 'tip'))
- reg.addInputPort(cdms_open, 'mode',
- (core.modules.basic_modules.String, 'tip'))
- reg.addInputPort(cdms_open, 'uri',
- (core.modules.basic_modules.String, 'tip'))
-
- # output dataset.
- reg.addOutputPort(cdms_open, "cdms_dataset",
- (cdms_dataset, 'cdms.dataset'))
- #holds the tetgenio class, and acts as a port.
- reg.addModule(cdms_dataset)
-
- reg.addModule(cdms_get_data)
- reg.addInputPort(cdms_get_data, 'dataset',
- (cdms_dataset, 'dataset'))
- reg.addInputPort(cdms_get_data, 'id',
- (core.modules.basic_modules.String, 'dataset id'))
-
- reg.addInputPort(cdms_get_data, 'arg_key_1',
- (core.modules.basic_modules.String, 'argument 1 key'))
- reg.addInputPort(cdms_get_data, 'arg_val_1',
- ([core.modules.basic_modules.Float,
- core.modules.basic_modules.Float]))
-
- reg.addInputPort(cdms_get_data, 'arg_key_2',
- (core.modules.basic_modules.String, 'argument 2 key'))
- reg.addInputPort(cdms_get_data, 'arg_val_2',
- ([core.modules.basic_modules.Float,
- core.modules.basic_modules.Float]))
-
- reg.addInputPort(cdms_get_data, 'arg_key_3',
- (core.modules.basic_modules.String, 'argument 3 key'))
- reg.addInputPort(cdms_get_data, 'arg_val_3',
- ([core.modules.basic_modules.Float,
- core.modules.basic_modules.Float]))
- # output data array.
- reg.addOutputPort(cdms_get_data, "cdms_dataarray",
- (cdms_dataarray, 'data'))
-
-
- # port for passing data arrays
- reg.addModule(cdms_dataarray)
- # port for passing anything
- reg.addModule(generic_port)
- #canvas module
- reg.addModule(vcs_canvas)
- reg.addOutputPort(vcs_canvas, "vcs_canvas",
- (vcs_canvas, 'the canvas'))
-
- #canvas module methods...
- reg.addModule(vcs_canvas_getboxfill)
- reg.addInputPort(vcs_canvas_getboxfill, 'canvas',
- (vcs_canvas, 'the canvas'))
- reg.addInputPort(vcs_canvas_getboxfill, 'boxfill name',
- (core.modules.basic_modules.String, 'boxfill method name'))
-
- reg.addOutputPort(vcs_canvas_getboxfill, "boxfill graphics method",
- (generic_port, 'graphics method'))
-
- reg.addModule(vcs_canvas_gettemplate)
- reg.addInputPort(vcs_canvas_gettemplate, 'canvas',
- (vcs_canvas, 'the canvas'))
- reg.addInputPort(vcs_canvas_gettemplate, 'template name',
- (core.modules.basic_modules.String, 'template name'))
-
- reg.addOutputPort(vcs_canvas_gettemplate, "template",
- (generic_port, 'template'))
-
-
- reg.addModule(vcs_canvas_plot)
- reg.addInputPort(vcs_canvas_plot, 'vcs_canvas',
- vcs_canvas)
- reg.addInputPort(vcs_canvas_plot, 'array1',
- cdms_dataarray)
- reg.addInputPort(vcs_canvas_plot, 'array2',
- cdms_dataarray)
- reg.addInputPort(vcs_canvas_plot, 'template_name',
- generic_port)
- reg.addInputPort(vcs_canvas_plot, 'graphics_method',
- generic_port)
- reg.addInputPort(vcs_canvas_plot, 'graphics_name',
- generic_port)
-
- # keyword args
- reg.addInputPort(vcs_canvas_plot, 'ratio',
- core.modules.basic_modules.String, True)
-
- # Variable attribute keys
- reg.addInputPort(vcs_canvas_plot, 'comment1',
- core.modules.basic_modules.String, True)
-
- reg.addInputPort(vcs_canvas_plot, 'comment2',
- core.modules.basic_modules.String, True)
-
- reg.addInputPort(vcs_canvas_plot, 'comment3',
- core.modules.basic_modules.String, True)
-
- reg.addInputPort(vcs_canvas_plot, 'comment4',
- core.modules.basic_modules.String, True)
-
- reg.addInputPort(vcs_canvas_plot, 'file_comment',
- core.modules.basic_modules.String, True)
-
- reg.addInputPort(vcs_canvas_plot, 'hms',
- core.modules.basic_modules.String, True)
-
- reg.addInputPort(vcs_canvas_plot, 'long_name',
- core.modules.basic_modules.String, True)
-
- reg.addInputPort(vcs_canvas_plot, 'name',
- core.modules.basic_modules.String, True)
-
- reg.addInputPort(vcs_canvas_plot, 'time',
- core.modules.basic_modules.String, True)
-
- reg.addInputPort(vcs_canvas_plot, 'units',
- core.modules.basic_modules.String, True)
-
- reg.addInputPort(vcs_canvas_plot, 'ymd',
- core.modules.basic_modules.String, True)
-
- # Dimension attribuge keys
- reg.addInputPort(vcs_canvas_plot, 'xarray1',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'yarray1',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'zarray1',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'tarray1',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'warray1',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'xarray2',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'yarray2',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'zarray2',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'tarray2',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'warray2',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'xbounds',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'ybounds',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'xname',
- core.modules.basic_modules.String, True)
- reg.addInputPort(vcs_canvas_plot, 'yname',
- core.modules.basic_modules.String, True)
- reg.addInputPort(vcs_canvas_plot, 'zname',
- core.modules.basic_modules.String, True)
- reg.addInputPort(vcs_canvas_plot, 'tname',
- core.modules.basic_modules.String, True)
- reg.addInputPort(vcs_canvas_plot, 'wname',
- core.modules.basic_modules.String, True)
- reg.addInputPort(vcs_canvas_plot, 'xunits',
- core.modules.basic_modules.String, True)
- reg.addInputPort(vcs_canvas_plot, 'yunits',
- core.modules.basic_modules.String, True)
- reg.addInputPort(vcs_canvas_plot, 'zunits',
- core.modules.basic_modules.String, True)
- reg.addInputPort(vcs_canvas_plot, 'tunits',
- core.modules.basic_modules.String, True)
- reg.addInputPort(vcs_canvas_plot, 'wunits',
- core.modules.basic_modules.String, True)
- reg.addInputPort(vcs_canvas_plot, 'xweights',
- cdms_dataarray, True)
- reg.addInputPort(vcs_canvas_plot, 'yweights',
- cdms_dataarray, True)
-
- reg.addOutputPort(vcs_canvas_plot, "image",
- (core.modules.basic_modules.File, 'rendered image'))
diff --git a/contrib/cdat/scripts/parse_cdat_xml_file.py b/contrib/cdat/scripts/parse_cdat_xml_file.py
deleted file mode 100755
index 6a6ffe5..0000000
--- a/contrib/cdat/scripts/parse_cdat_xml_file.py
+++ /dev/null
@@ -1,165 +0,0 @@
-#!/usr/bin/env python
-############################################################################
-##
-## Copyright (C) 2006-2008 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-from core.system import get_elementtree_library
-ElementTree = get_elementtree_library()
-from cdat_domain import CDATAction, CDATModule, CDATOption, CDATPort
-
-class XMLNode:
- def __init__(self):
- pass
-
- def has_attribute(self, node, attr):
- return node.hasAttribute(attr)
-
- def get_attribute(self, node, attr):
- try:
- attribute = node.attributes.get(attr)
- if attribute is not None:
- return attribute.value
- except KeyError:
- pass
- return None
-
- @staticmethod
- def convert_from_str(value, type):
- def bool_conv(x):
- s = str(x).upper()
- if s == 'TRUE':
- return True
- if s == 'FALSE':
- return False
-
- if value is not None:
- if type == 'str':
- return str(value)
- elif value.strip() != '':
- if type == 'long':
- return long(value)
- elif type == 'float':
- return float(value)
- elif type == 'int':
- return int(value)
- elif type == 'bool':
- return bool_conv(value)
- elif type == 'date':
- return date(*strptime(value, '%Y-%m-%d')[0:3])
- elif type == 'datetime':
- return datetime(*strptime(value, '%Y-%m-%d %H:%M:%S')[0:6])
- return None
-
-class CDATOptionNode(XMLNode):
- @staticmethod
- def from_xml(node):
- tag = node.tag
- data = node.get('default', None)
- default = CDATOptionNode.convert_from_str(data, 'str')
- data = node.get('doc', None)
- doc = CDATOptionNode.convert_from_str(data, 'str')
- data = node.get('instance', None)
- instance = CDATOptionNode.convert_from_str(data, 'str')
- return CDATOption(tag=tag, default=default,doc=doc,instance=instance)
-
-class CDATPortNode(XMLNode):
- """Represents Input or Output nodes"""
- @staticmethod
- def from_xml(node):
- tag = node.tag
- data = node.get('doc', None)
- doc = CDATPortNode.convert_from_str(data, 'str')
- data = node.get('instance', None)
- instance = CDATPortNode.convert_from_str(data, 'str')
- data = node.get('position', None)
- position = CDATPortNode.convert_from_str(data, 'int')
- data = node.get('required', None)
- required = CDATPortNode.convert_from_str(data, 'bool')
- return CDATPort(tag=tag, doc=doc, instance=instance,
- position=position, required=required)
-
-class CDATActionNode(XMLNode):
- @staticmethod
- def from_xml(node):
- data = node.get('name', None)
- name = CDATActionNode.convert_from_str(data,'str')
- data = node.get('type', None)
- type = CDATActionNode.convert_from_str(data,'str')
-
- options = []
- inputs = []
- outputs = []
-
- #read children
- for child in node.getchildren():
- if child.tag == 'options':
- for optnode in child.getchildren():
- option = CDATOptionNode.from_xml(optnode)
- options.append(option)
- elif child.tag == 'input':
- for inode in child.getchildren():
- port = CDATPortNode.from_xml(inode)
- inputs.insert(port._position,port)
- elif child.tag == 'output':
- for onode in child.getchildren():
- port = CDATPortNode.from_xml(onode)
- outputs.insert(port._position,port)
- elif child.tag == 'doc':
- doc = child.text
- return CDATAction(name=name, type=type, options=options, inputs=inputs,
- outputs=outputs, doc=doc)
-
-class CDATModuleNode(XMLNode):
- @staticmethod
- def from_xml(node):
- data = node.get('author',None)
- author = CDATModuleNode.convert_from_str(data,'str')
- data = node.get('programminglanguage', None)
- language = CDATModuleNode.convert_from_str(data,'str')
- data = node.get('type', None)
- type = CDATModuleNode.convert_from_str(data, 'str')
- data = node.get('url', None)
- url = CDATModuleNode.convert_from_str(data, 'str')
- data = node.get('version', None)
- version = CDATModuleNode.convert_from_str(data, 'str')
- data = node.get('codepath', None)
- codepath = CDATModuleNode.convert_from_str(data, 'str')
-
- actions = []
- #read actions
- for child in node.getchildren():
- if child.tag == 'action':
- action = CDATActionNode.from_xml(child)
- actions.append(action)
-
- return CDATModule(author=author,
- language=language,
- type=type,
- url=url,
- codepath=codepath,
- version=version,
- actions=actions)
-
-def parse_cdat_xml_file(filename):
- """ parse_cdat_xml_file(filename:str) -> CDATDiagnostic
- """
- tree = ElementTree.parse(filename)
- module = CDATModuleNode.from_xml(tree.getroot())
- return module
\ No newline at end of file
diff --git a/contrib/cdat/scripts/xml/canvas.xml b/contrib/cdat/scripts/xml/canvas.xml
deleted file mode 100644
index 5d99a75..0000000
--- a/contrib/cdat/scripts/xml/canvas.xml
+++ /dev/null
@@ -1,2747 +0,0 @@
-<diagnostic author="PCMDI's software team" programminglanguage="Python" type="class" url="http://cdat.sf.net" version="5.0.0.alpha7" codepath="vcs.Canvas.Canvas">
- <action name="boxfill" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <slab doc="Data at least 2D, last 2 dimensions will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0" required="True"/>
- </input>
- <output>
- <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
- </output>
- <doc>
- Function: boxfill # Generate a boxfill plot
-
- Description of Function:
- Generate a boxfill plot given the data, boxfill graphics method, and
- template. If no boxfill class object is given, then the 'default' boxfill
- graphics method is used. Similarly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('boxfill') # Show all the existing boxfill graphics methods
- box=a.getboxfill('quick') # Create instance of 'quick'
- a.boxfill(array,box) # Plot array using specified box and default
- # template
- templt=a.gettemplate('AMIP') # Create an instance of template 'AMIP'
- a.clear() # Clear VCS canvas
- a.boxfill(array,box,template) # Plot array using specified box and template
- a.boxfill(box,array,template) # Plot array using specified box and template
- a.boxfill(template,array,box) # Plot array using specified box and template
- a.boxfill(template,array,box) # Plot array using specified box and template
- a.boxfill(array,'AMIP','quick') # Use 'AMIP' template and 'quick' boxfill
- a.boxfill('AMIP',array,'quick') # Use 'AMIP' template and 'quick' boxfill
- a.boxfill('AMIP','quick',array) # Use 'AMIP' template and 'quick' boxfill
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End boxfill Description ################################################
-######################################### #################################################
-###################################################################################################################
- </doc>
- </action>
- <action name="createboxfill" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
- <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
- </input>
- <output>
- <boxfill doc="no default" instance="vcs.boxfill.Gfb" position="0"/>
- </output>
- <doc>
- Function: createboxfill # Construct a new boxfill graphics method
-
- Description of Function:
- Create a new boxfill graphics method given the the name and the existing
- boxfill graphics method to copy the attributes from. If no existing
- boxfill graphics method name is given, then the default boxfill graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
- a=vcs.init()
- a.show('boxfill')
- box=a.createboxfill('example1',)
- a.show('boxfill')
- box=a.createboxfill('example2','quick')
- a.show('boxfill')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createboxfill Description ################################################
-######################################### #################################################
-#########################################################################################################################
- </doc>
- </action>
- <action name="createisofill" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
- <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False" />
- </input>
- <output>
- <isofill doc="no default" instance="vcs.isofill.Gfi" position="0"/>
- </output>
- <doc>
- Function: createisofill # Construct a new isofill graphics method
-
- Description of Function:
- Create a new isofill graphics method given the the name and the existing
- isofill graphics method to copy the attributes from. If no existing
- isofill graphics method name is given, then the default isofill graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
- a=vcs.init()
- a.show('isofill')
- iso=a.createisofill('example1',)
- a.show('isofill')
- iso=a.createisofill('example2','quick')
- a.show('isofill')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createisofill Description ################################################
-######################################### #################################################
-#########################################################################################################################
- </doc>
- </action>
- <action name="createisoline" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
- <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
- </input>
- <output>
- <isoline doc="no default" instance="vcs.isoline.Gi" position="0"/>
- </output>
- <doc>
- Function: createisoline # Construct a new isoline graphics method
-
- Description of Function:
- Create a new isoline graphics method given the the name and the existing
- isoline graphics method to copy the attributes from. If no existing
- isoline graphics method name is given, then the default isoline graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
-
- a=vcs.init()
- a.show('isoline')
- iso=a.createisoline('example1',)
- a.show('isoline')
- iso=a.createisoline('example2','quick')
- a.show('isoline')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createisoline Description ################################################
-######################################### #################################################
-#########################################################################################################################
- </doc>
- </action>
- <action name="createoutfill" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
- <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
- </input>
- <output>
- <outfill doc="no default" instance="vcs.outfill.Gfo" position="0"/>
- </output>
- <doc>
- Function: createoutfill # Construct a new outfill graphics method
-
- Description of Function:
- Create a new outfill graphics method given the the name and the existing
- outfill graphics method to copy the attributes from. If no existing
- outfill graphics method name is given, then the default outfill graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
-
- a=vcs.init()
- a.show('outfill')
- out=a.createoutfill('example1',)
- a.show('outfill')
- out=a.createoutfill('example2','quick')
- a.show('outfill')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createoutfill Description ################################################
-######################################### #################################################
-#########################################################################################################################
- </doc>
- </action>
- <action name="createoutline" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
- <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
- </input>
- <output>
- <outline doc="no default" instance="vcs.outline.Go" position="0"/>
- </output>
- <doc>
- Function: createoutline # Construct a new outline graphics method
-
- Description of Function:
- Create a new outline graphics method given the the name and the existing
- outline graphics method to copy the attributes from. If no existing
- outline graphics method name is given, then the default outline graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
-
- a=vcs.init()
- a.show('outline')
- out=a.createoutline('example1',)
- a.show('outline')
- out=a.createoutline('example2','quick')
- a.show('outline')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createoutline Description ################################################
-######################################### #################################################
-#########################################################################################################################
- </doc>
- </action>
- <action name="createscatter" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
- <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
- </input>
- <output>
- <scatter doc="no default" instance="vcs.scatter.GSp" position="0"/>
- </output>
- <doc>
- Function: createscatter # Construct a new scatter graphics method
-
- Description of Function:
- Create a new scatter graphics method given the the name and the existing
- scatter graphics method to copy the attributes from. If no existing
- scatter graphics method name is given, then the default scatter graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
- a=vcs.init()
- a.show('scatter')
- sct=a.createscatter('example1',)
- a.show('scatter')
- sct=a.createscatter('example2','quick')
- a.show('scatter')
-
-#########################################################################################################################
-########################################### ###############################################
-########################################## End createscatter Description ################################################
-######################################### #################################################
-#########################################################################################################################
- </doc>
- </action>
- <action name="createxvsy" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
- <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
- </input>
- <output>
- <xvsy doc="no default" instance="vcs.xvsy.GXY" position="0"/>
- </output>
- <doc>
- Function: createxvsy # Construct a new XvsY graphics method
-
- Description of Function:
- Create a new XvsY graphics method given the the name and the existing
- XvsY graphics method to copy the attributes from. If no existing
- XvsY graphics method name is given, then the default XvsY graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
- a=vcs.init()
- a.show('xvsy')
- xy=a.createxvsy('example1',)
- a.show('xvsy')
- xy=a.createxvsy('example2','quick')
- a.show('xvsy')
-
-######################################################################################################################
-########################################### ###############################################
-########################################## End createxvsy Description ################################################
-######################################### #################################################
-######################################################################################################################
- </doc>
- </action>
- <action name="createxyvsy" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
- <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
- </input>
- <output>
- <xyvsy doc="no default" instance="vcs.xyvsy.GXy" position="0"/>
- </output>
- <doc>
- Function: createxyvsy # Construct a new Xyvsy graphics method
-
- Description of Function:
- Create a new Xyvsy graphics method given the the name and the existing
- Xyvsy graphics method to copy the attributes from. If no existing
- Xyvsy graphics method name is given, then the default Xyvsy graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
-
- a=vcs.init()
- a.show('xyvsy')
- xyy=a.createxyvsy('example1',)
- a.show('xyvsy')
- xyy=a.createxyvsy('example2','quick')
- a.show('xyvsy')
-
-#######################################################################################################################
-########################################### ###############################################
-########################################## End createxyvsy Description ################################################
-######################################### #################################################
-#######################################################################################################################
- </doc>
- </action>
- <action name="createyxvsx" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <source_GM_name doc="copy the contents of the source object to the newly created one. If no name is given, then the 'default' graphics methond contents is copied over to the new object." instance="str" position="1" required="False"/>
- <new_GM_name doc="name of the new graphics method object. If no name is given, then one will be created for use." instance="str" position="0" required="False"/>
- </input>
- <output>
- <yxvsx doc="no default" instance="vcs.yxvsx.GYx" position="0"/>
- </output>
- <doc>
- Function: createyxvsx # Construct a new Yxvsx graphics method
-
- Description of Function:
- Create a new Yxvsx graphics method given the the name and the existing
- Yxvsx graphics method to copy the attributes from. If no existing
- Yxvsx graphics method name is given, then the default Yxvsx graphics
- method will be used as the graphics method to which the attributes will
- be copied from.
-
- If the name provided already exists, then a error will be returned. Graphics
- method names must be unique.
-
- Example of Use:
-
- a=vcs.init()
- a.show('yxvsx')
- yxx=a.createyxvsx('example1',)
- a.show('yxvsx')
- yxx=a.createyxvsx('example2','quick')
- a.show('yxvsx')
-
-#######################################################################################################################
-########################################### ###############################################
-########################################## End createyxvsx Description ################################################
-######################################### #################################################
-#######################################################################################################################
- </doc>
- </action>
- <action name="getboxfill" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0" required="False"/>
- </input>
- <output>
- <boxfill doc="no default" instance="vcs.boxfill.Gfb" position="0"/>
- </output>
- <doc>
- Function: getboxfill # Construct a new boxfill graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- boxfill class object from an existing VCS boxfill graphics method. If
- no boxfill name is given, then boxfill 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createboxfill function.)
-
- Example of Use:
- a=vcs.init()
- a.show('boxfill') # Show all the existing boxfill graphics methods
- box=a.getboxfill() # box instance of 'default' boxfill graphics
- # method
- box2=a.getboxfill('quick') # box2 instance of existing 'quick' boxfill
- # graphics method
-######################################################################################################################
-########################################### ###############################################
-########################################## End getboxfill Description ################################################
-######################################### #################################################
-######################################################################################################################
- </doc>
- </action>
- <action name="getisofill" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0" required="False"/>
- </input>
- <output>
- <isofill doc="no default" instance="vcs.isofill.Gfi" position="0"/>
- </output>
- <doc>
- Function: getisofill Construct a new isofill graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- isofill class object from an existing VCS isofill graphics method. If
- no isofill name is given, then isofill 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createisofill function.)
-
- Example of Use:
- a=vcs.init()
- a.show('isofill') # Show all the existing isofill graphics methods
- iso=a.getisofill() # iso instance of 'default' isofill graphics
- # method
- iso2=a.getisofill('quick') # iso2 instance of existing 'quick' isofill
- # graphics method
-######################################################################################################################
-########################################### ###############################################
-########################################## End getisofill Description ################################################
-######################################### #################################################
-######################################################################################################################
- </doc>
- </action>
- <action name="getisoline" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0" required="False"/>
- </input>
- <output>
- <isoline doc="no default" instance="vcs.isoline.Gi" position="0"/>
- </output>
- <doc>
- Function: getisoline # Construct a new isoline graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- isoline class object from an existing VCS isoline graphics method. If
- no isoline name is given, then isoline 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createisoline function.)
-
- Example of Use:
- a=vcs.init()
- a.show('isoline') # Show all the existing isoline graphics methods
- iso=a.getisoline() # iso instance of 'default' isoline graphics
- # method
- iso2=a.getisoline('quick') # iso2 instance of existing 'quick' isoline
- # graphics method
-######################################################################################################################
-########################################### ###############################################
-########################################## End getisoline Description ################################################
-######################################### #################################################
-######################################################################################################################
- </doc>
- </action>
- <action name="getoutfill" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0" required="False"/>
- </input>
- <output>
- <outfill doc="no default" instance="vcs.outfill.Gfo" position="0"/>
- </output>
- <doc>
- Function: getoutfill # Construct a new outfill graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- outfill class object from an existing VCS outfill graphics method. If
- no outfill name is given, then outfill 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createoutfill function.)
-
- Example of Use:
- a=vcs.init()
- a.show('outfill') # Show all the existing outfill graphics methods
- out=a.getoutfill() # out instance of 'default' outfill graphics
- # method
- out2=a.getoutfill('quick') # out2 instance of existing 'quick' outfill
- # graphics method
-
-######################################################################################################################
-########################################### ###############################################
-########################################## End getoutfill Description ################################################
-######################################### #################################################
-######################################################################################################################
- </doc>
- </action>
- <action name="getoutline" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0" required="False"/>
- </input>
- <output>
- <outline doc="no default" instance="vcs.outline.Go" position="0"/>
- </output>
- <doc>
- Function: getoutline # Construct a new outline graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- outline class object from an existing VCS outline graphics method. If
- no outline name is given, then outline 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createoutline function.)
-
- Example of Use:
- a=vcs.init()
- a.show('outline') # Show all the existing outline graphics methods
- out=a.getoutline() # out instance of 'default' outline graphics
- # method
- out2=a.getoutline('quick') # out2 instance of existing 'quick' outline
- # graphics method
-
-######################################################################################################################
-########################################### ###############################################
-########################################## End getoutline Description ################################################
-######################################### #################################################
-######################################################################################################################
- </doc>
- </action>
- <action name="getscatter" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0"/>
- </input>
- <output>
- <scatter doc="no default" instance="vcs.scatter.GSp" position="0"/>
- </output>
- <doc>
- Function: getscatter # Construct a new scatter graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- scatter class object from an existing VCS scatter graphics method. If
- no scatter name is given, then scatter 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createscatter function.)
-
- Example of Use:
- a=vcs.init()
- a.show('scatter') # Show all the existing scatter graphics methods
- sct=a.getscatter() # sct instance of 'default' scatter graphics
- # method
- sct2=a.getscatter('quick') # sct2 instance of existing 'quick' scatter
- # graphics method
-
-######################################################################################################################
-########################################### ###############################################
-########################################## End getscatter Description ################################################
-######################################### #################################################
-######################################################################################################################
- </doc>
- </action>
- <action name="getxvsy" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0"/>
- </input>
- <output>
- <xvsy doc="no default" instance="vcs.xvsy.GXY" position="0"/>
- </output>
- <doc>
- Function: getxvsy # Construct a new XvsY graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- XvsY class object from an existing VCS XvsY graphics method. If
- no XvsY name is given, then XvsY 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createxvsy function.)
-
- Example of Use:
- a=vcs.init()
- a.show('xvsy') # Show all the existing XvsY graphics methods
- xy=a.getxvsy() # xy instance of 'default' XvsY graphics
- # method
- xy2=a.getxvsy('quick') # xy2 instance of existing 'quick' XvsY
- # graphics method
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End getxvsy Description ################################################
-######################################### #################################################
-###################################################################################################################
- </doc>
- </action>
- <action name="getxyvsy" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0"/>
- </input>
- <output>
- <xyvsy doc="no default" instance="vcs.xyvsy.GXy" position="0"/>
- </output>
- <doc>
- Function: getxyvsy # Construct a new Xyvsy graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- Xyvsy class object from an existing VCS Xyvsy graphics method. If
- no Xyvsy name is given, then Xyvsy 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createxyvsy function.)
-
- Example of Use:
- a=vcs.init()
- a.show('xyvsy') # Show all the existing Xyvsy graphics methods
- xyy=a.getxyvsy() # xyy instance of 'default' Xyvsy graphics
- # method
- xyy2=a.getxyvsy('quick') # xyy2 instance of existing 'quick' Xyvsy
- # graphics method
-####################################################################################################################
-########################################### ###############################################
-########################################## End getxyvsy Description ################################################
-######################################### #################################################
-####################################################################################################################
- </doc>
- </action>
- <action name="getyxvsx" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <GM_name doc="retrieve the graphics method object of the given name. If no name is given, then retrieve the 'default' graphics method." instance="str" position="0"/>
- </input>
- <output>
- <yxvsx doc="no default" instance="vcs.yxvsx.GYx" position="0"/>
- </output>
- <doc>
- Function: getyxvsx # Construct a new Yxvsx graphics method
-
- Description of Function:
- VCS contains a list of graphics methods. This function will create a
- Yxvsx class object from an existing VCS Yxvsx graphics method. If
- no Yxvsx name is given, then Yxvsx 'default' will be used.
-
- Note, VCS does not allow the modification of `default' attribute
- sets. However, a `default' attribute set that has been copied under a
- different name can be modified. (See the createyxvsx function.)
-
- Example of Use:
- a=vcs.init()
- a.show('yxvsx') # Show all the existing Yxvsx graphics methods
- yxx=a.getyxvsx() # yxx instance of 'default' Yxvsx graphics
- # method
- yxx2=a.getyxvsx('quick') # yxx2 instance of existing 'quick' Yxvsx
- # graphics method
-####################################################################################################################
-########################################### ###############################################
-########################################## End getyxvsx Description ################################################
-######################################### #################################################
-####################################################################################################################
- </doc>
- </action>
- <action name="isofill" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <slab doc="Data at least 2D, last 2 dimensions will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
- </input>
- <output>
- <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
- </output>
- <doc>
- Function: isofill # Generate an isofill plot
-
- Description of Function:
- Generate a isofill plot given the data, isofill graphics method, and
- template. If no isofill class object is given, then the 'default' isofill
- graphics method is used. Similarly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('isofill') # Show all the existing isofill graphics methods
- iso=a.getisofill('quick') # Create instance of 'quick'
- a.isofill(array,iso) # Plot array using specified iso and default
- # template
- a.clear() # Clear VCS canvas
- a.isofill(array,iso,template) # Plot array using specified iso and template
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End isofill Description ################################################
-######################################### #################################################
-###################################################################################################################
- </doc>
- </action>
- <action name="isoline" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <slab doc="Data at least 2D, last 2 dimensions will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
- </input>
- <output>
- <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
- </output>
- <doc>
- Function: isoline # Generate an isoline plot
-
- Description of Function:
- Generate a isoline plot given the data, isoline graphics method, and
- template. If no isoline class object is given, then the 'default' isoline
- graphics method is used. Similarly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('isoline') # Show all the existing isoline graphics methods
- iso=a.getisoline('quick') # Create instance of 'quick'
- a.isoline(array,iso) # Plot array using specified iso and default
- # template
- a.clear() # Clear VCS canvas
- a.isoline(array,iso,template) # Plot array using specified iso and template
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End isoline Description ################################################
-######################################### #################################################
-###################################################################################################################
- </doc>
- </action>
- <action name="outfill" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <slab doc="Data at least 2D, last 2 dimensions will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
- </input>
- <output>
- <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
- </output>
- <doc>
- Function: outfill # Generate an outfill plot
-
- Description of Function:
- Generate a outfill plot given the data, outfill graphics method, and
- template. If no outfill class object is given, then the 'default' outfill
- graphics method is used. Simerly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('outfill') # Show all the existing outfill graphics methods
- out=a.getoutfill('quick') # Create instance of 'quick'
- a.outfill(array,out) # Plot array using specified out and default
- # template
- a.clear() # Clear VCS canvas
- a.outfill(array,out,template) # Plot array using specified out and template
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End outfill Description ################################################
-######################################### #################################################
-###################################################################################################################
- </doc>
- </action>
- <action name="outline" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <slab doc="Data at least 2D, last 2 dimensions will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
- </input>
- <output>
- <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
- </output>
- <doc>
- Function: outline # Generate an outline plot
-
- Description of Function:
- Generate a outline plot given the data, outline graphics method, and
- template. If no outline class object is given, then the 'default' outline
- graphics method is used. Simerly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('outline') # Show all the existing outline graphics methods
- out=a.getoutline('quick') # Create instance of 'quick'
- a.outline(array,out) # Plot array using specified out and default
- # template
- a.clear() # Clear VCS canvas
- a.outline(array,out,template) # Plot array using specified out and template
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End outline Description ################################################
-######################################### #################################################
-###################################################################################################################
- </doc>
- </action>
- <action name="plot" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <slab1 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0" required="True"/>
- <slab2 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0" required="False"/>
- </input>
- <output>
- <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
- </output>
- <doc>
- Function: plot
-
- Description of plot:
- Plot an array(s) of data given a template and graphics method. The VCS template is
- used to define where the data and variable attributes will be displayed on the VCS
- Canvas. The VCS graphics method is used to define how the array(s) will be shown
- on the VCS Canvas.
-
- The form of the call is:
- plot(array1=None, array2=None, template_name=None, graphics_method=None,
- graphics_name=None, [key=value [, key=value [, ...]]])
-
- where array1 and array2 are NumPy arrays.
-
- Plot keywords:
- ratio [default is none]
- None: let the self.ratio attribute decide
- 0,'off': overwritte self.ratio and do nothing about the ratio
- 'auto': computes an automatic ratio
- '3',3: y dim will be 3 times bigger than x dim (restricted to original tempalte.data area
- Adding a 't' at the end of the ratio, makes the tickmarks and boxes move along.
-
- Variable attribute keys:
- comment1 = string #Comment plotted above file_comment
- comment2 = string #Comment plotted above comment1
- comment3 = string #Comment plotted above comment2
- comment4 = string #Comment plotted above comment4
- file_comment = string #Comment (defaults to file.comment)
- hms = string (hh:mm:ss) #Hour, minute, second
- long_name = string #Descriptive variable name
- name = string #Variable name (defaults to var.id)
- time = cdtime #instance (relative or absolute),
- cdtime, reltime or abstime value
- units = string #Variable units
- ymd = string (yy/mm/dd) #Year, month, day
-
- Dimension attribute keys (dimension length=n):
- [x|y|z|t|w]array = NumPy array of length n # x or y Dimension values
- [x|y|z|t|w]array = NumPy array of length n # x or y Dimension values
- [x|y]bounds = NumPy array of shape (n,2) # x or y Dimension boundaries
- [x|y|z|t|w]name = string # x or y Dimension name
- [x|y|z|t|w]units = string # x or y Dimension units
- [x|y]weights = NumPy array of length n # x or y Dimension weights (used to
- calculate area-weighted mean)
-
- CDMS object:
- [x|y|z|t|w]axis = CDMS axis object # x or y Axis
- grid = CDMS grid object # Grid object (e.g. grid=var.getGrid()
- variable = CDMS variable object # Variable object
-
- Other:
- [x|y]rev = 0|1 # if ==1, reverse the direction of the x
- or y axis
- continents = 0,1,2,3,4,5,6,7,8,9,10,11 # if >=1, plot continental outlines
- (default: plot if xaxis is
- longitude, yaxis is latitude -or-
- xname is 'longitude' and yname is
- 'latitude'
- # The continents-type values are integers
- # ranging from 0 to 11, where:
- # 0 signifies "No Continents"
- # 1 signifies "Fine Continents"
- # 2 signifies "Coarse Continents"
- # 3 signifies "United States"
- # 4 signifies "Political Borders"
- # 5 signifies "Rivers"
-
- # Values 6 through 11 signify the line type
- # defined by the files data_continent_other7
- # through data_continent_other12.
-
- Graphics Output in Background Mode:
- bg = 0|1 # if ==1, create images in the background
- (Don't display the VCS Canvas)
-
- Note:
- More specific attributes take precedence over general attributes. In particular,
- specifie attributes override variable object attributes, dimension attributes and
- arrays override axis objects, which override grid objects, which override variable
- objects.
-
- For example, if both 'file_comment' and 'variable' keywords are specified, the value of
- 'file_comment' is used instead of the file comment in the parent of variable. Similarly,
- if both 'xaxis' and 'grid' keywords are specified, the value of 'xaxis' takes precedence
- over the x-axis of grid.
-
- Example of Use:
- x=vcs.init() # x is an instance of the VCS class object (constructor)
- x.plot(array) # this call will use default settings for template and boxfill
- x.plot(array, 'AMIP', 'isofill','AMIP_psl') # this is specifying the template and
- graphics method
- t=x.gettemplate('AMIP') # get a predefined the template 'AMIP'
- vec=x.getvector('quick') # get a predefined the vector graphics method 'quick'
- x.plot(array1, array2, t, vec) # plot the data as a vector using the 'AMIP' template
- x.clear() # clear the VCS Canvas of all plots
- box=x.createboxfill('new') # create boxfill graphics method 'new'
- x.plot(box,t,array) # plot array data using box 'new' and template 't'
-
-###############################################################################################################
-########################################### ##############################################
-########################################## End plot Description ###############################################
-######################################### ################################################
-###############################################################################################################
- </doc>
- </action>
- <action name="scatter" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <slab1 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
- <slab2 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
- </input>
- <output>
- <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
- </output>
- <doc>
- Function: scatter # Generate a scatter plot
-
- Description of Function:
- Generate a scatter plot given the data, scatter graphics method, and
- template. If no scatter class object is given, then the 'default' scatter
- graphics method is used. Similarly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('scatter') # Show all the existing scatter graphics methods
- sct=a.getscatter('quick') # Create instance of 'quick'
- a.scatter(array,sct) # Plot array using specified sct and default
- # template
- a.clear() # Clear VCS canvas
- a.scatter(array,sct,template) # Plot array using specified sct and template
-
-###################################################################################################################
-########################################### ###############################################
-########################################## End scatter Description ################################################
-######################################### #################################################
-###################################################################################################################
- </doc>
- </action>
- <action name="xvsy" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <yaxisconvert default="'linear'" doc="converting yaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <slab1 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
- <slab2 doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
- </input>
- <output>
- <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
- </output>
- <doc>
- Function: xvsy # Generate a XvsY plot
-
- Description of Function:
- Generate a XvsY plot given the data, XvsY graphics method, and
- template. If no XvsY class object is given, then the 'default' XvsY
- graphics method is used. Similarly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('xvsy') # Show all the existing XvsY graphics methods
- xy=a.getxvsy('quick') # Create instance of 'quick'
- a.xvsy(array,xy) # Plot array using specified xy and default
- # template
- a.clear() # Clear VCS canvas
- a.xvsy(array,xy,template) # Plot array using specified xy and template
-
-#################################################################################################################
-########################################### ###############################################
-########################################## End xvsy Description ################################################
-######################################### #################################################
-#################################################################################################################
- </doc>
- </action>
- <action name="xyvsy" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <slab doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
- </input>
- <output>
- <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
- </output>
- <doc>
- Function: xyvsy # Generate a Xyvsy plot
-
- Description of Function:
- Generate a Xyvsy plot given the data, Xyvsy graphics method, and
- template. If no Xyvsy class object is given, then the 'default' Xyvsy
- graphics method is used. Simerly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('xyvsy') # Show all the existing Xyvsy graphics methods
- xyy=a.getxyvsy('quick') # Create instance of 'quick'
- a.xyvsy(array,xyy) # Plot array using specified xyy and default
- # template
- a.clear() # Clear VCS canvas
- a.xyvsy(array,xyy,template) # Plot array using specified xyy and template
-
-#################################################################################################################
-########################################### ###############################################
-########################################## End xyvsy Description ################################################
-######################################### #################################################
-#################################################################################################################
- </doc>
- </action>
- <action name="yxvsx" type="function">
- <options>
- <datawc_timeunits default="'days since 2000'" doc="units to use when disaplaying time dimension auto tick" instance="str"/>
- <long_name doc="replaces long_name on plot" instance="str"/>
- <projection default="'default'" doc="projection to use, name or object" instance="str/vcs.projection.Proj"/>
- <xticlabels2 default="'*'" doc="values for labels on 2nd side of x axis" instance="str/{float:str}"/>
- <xarray doc="Values to use instead of x axis" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <yweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xweights doc="replace xaxis weights used for computing mean" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <warray doc="Values to use instead of w axis, only if var has more than 4D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <tunits doc="replace taxis units on plot (if exists)" instance="str"/>
- <ymtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <ymtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <datawc_x1 default="1.E20" doc="first value of xaxis on plot" instance="float"/>
- <datawc_x2 default="1.E20" doc="second value of xaxis on plot" instance="float"/>
- <continents doc="continents type number" instance="int"/>
- <xmtics1 default="''" doc="dictionary with location of intermediate tics as keys for 1st side of y axis" instance="str/{float:str}"/>
- <xmtics2 default="''" doc="dictionary with location of intermediate tics as keys for 2nd side of y axis" instance="str/{float:str}"/>
- <xbounds doc="Values to use instead of x axis bounds values" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <ybounds doc="Values to use instead of y axis bounds values (if exist)" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <datawc_y2 default="1.E20" doc="second value of yaxis on plot" instance="float"/>
- <wname doc="replace waxis name on plot (if exists)" instance="str"/>
- <file_comment doc="replaces file_comment on plot" instance="str"/>
- <datawc_calendar default="135441" doc="calendar to use when displaying time dimension auto tick, default is proleptic gregorian calendar" instance="int"/>
- <wunits doc="replace waxis units on plot (if exists)" instance="str"/>
- <xrev doc="reverse x axis" instance="bool"/>
- <zaxis doc="Axis object to replace the slab -3 dim axis, only if slab has more than 2D" instance="cdms2.axis.TransientAxis"/>
- <ymd doc="replaces year/month/day on plot" instance="str"/>
- <yarray doc="Values to use instead of y axis, only if var has more than 1D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <units doc="replaces units value on plot" instance="str"/>
- <yunits doc="replace yaxis units on plot (if exists)" instance="str"/>
- <zarray doc="Values to use instead of z axis, only if var has more than 2D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <xname doc="replace xaxis name on plot" instance="str"/>
- <tarray doc="Values to use instead of t axis, only if var has more than 3D" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list"/>
- <bg doc="plots in background mode" instance="bool/int"/>
- <xaxis doc="Axis object to replace the slab -1 dim axis" instance="cdms2.axis.TransientAxis"/>
- <xaxisconvert default="'linear'" doc="converting xaxis linear/log/log10/ln/exp/area_wt" instance="str"/>
- <zname doc="replace zaxis name on plot (if exists)" instance="str"/>
- <hms doc="replaces hh/mm/ss on plot" instance="str"/>
- <tname doc="replace taxis name on plot (if exists)" instance="str"/>
- <grid doc="replaces array grid (if exists)" instance="cdms2.grid.TransientRectGrid"/>
- <yname doc="replace yaxis name on plot (if exists)" instance="str"/>
- <ratio doc="sets the y/x ratio ,if passed as a string with 't' at the end, will aslo moves the ticks" instance="int/str"/>
- <datawc_y1 default="1.E20" doc="first value of yaxis on plot" instance="float"/>
- <xunits doc="replace xaxis units on plot" instance="str"/>
- <name doc="replaces variable name on plot
-time "" (cdtime.comptime/cdtime.reltime/cdtime.abstime) () replaces time name on plot" instance="str"/>
- <yaxis doc="Axis object to replace the slab -2 dim axis, only if slab has more than 1D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels1 default="'*'" doc="values for labels on 1st side of y axis" instance="str/{float:str}"/>
- <waxis doc="Axis object to replace the slab -5 dim axis, only if slab has more than 4D" instance="cdms2.axis.TransientAxis"/>
- <yticlabels2 default="'*'" doc="values for labels on 2nd side of y axis" instance="str/{float:str}"/>
- <comment1 doc="replaces comment1 on plot" instance="str"/>
- <zunits doc="replace zaxis units on plot (if exists)" instance="str"/>
- <comment3 doc="replaces comment3 on plot" instance="str"/>
- <comment2 doc="replaces comment2 on plot" instance="str"/>
- <xticlabels1 default="'*'" doc="values for labels on 1st side of x axis" instance="str/{float:str}"/>
- <comment4 doc="replaces comment4 on plot" instance="str"/>
- <yrev doc="reverse y axis, only if slab has more than 1D" instance="bool"/>
- <taxis doc="Axis object to replace the slab -4 dim axis, only if slab has more than 3D" instance="cdms2.axis.TransientAxis"/>
- </options>
- <input>
- <slab doc="Data at least 1D, last dimension will be plotted" instance="cdms2.tvariable.TransientVariable/numpy.core.ma.MaskedArray/numpy.ndarray/list" position="0"/>
- </input>
- <output>
- <display doc="no default" instance="vcs.displayplot.Dp" position="0"/>
- </output>
- <doc>
- Function: yxvsx # Generate a Yxvsx plot
-
- Description of Function:
- Generate a Yxvsx plot given the data, Yxvsx graphics method, and
- template. If no Yxvsx class object is given, then the 'default' Yxvsx
- graphics method is used. Simerly, if no template class object is given,
- then the 'default' template is used.
-
- Example of Use:
- a=vcs.init()
- a.show('yxvsx') # Show all the existing Yxvsx graphics methods
- yxx=a.getyxvsx('quick') # Create instance of 'quick'
- a.yxvsx(array,yxx) # Plot array using specified yxx and default
- # template
- a.clear() # Clear VCS canvas
- a.yxvsx(array,yxx,template) # Plot array using specified yxx and template
-
-#################################################################################################################
-########################################### ###############################################
-########################################## End yxvsx Description ################################################
-######################################### #################################################
-#################################################################################################################
- </doc>
- </action>
- <action name="png" type="function">
- <input>
- <file doc="" instance="str" position="0" required="True"/>
- <width doc="" instance="float" position="1" required="False"/>
- <height doc="" instance="float" position="2" required="False"/>
- <units doc="" instance="str" position="3" required="False"/>
- </input>
- <doc>
- Function: png
-
- Description of Function:
- Png output is another form of raster graphics.
-
- Example of Use:
- a=vcs.init()
- a.plot(array)
- a.png('example') # Overwrite a png file
- a.png('example', width=11.5, height= 8.5) # US Legal
- a.png('example', width=21, height=29.7, units='cm') # A4
-#################################################################################################################
-########################################### ###############################################
-########################################## End png Description ################################################
-######################################### #################################################
-#################################################################################################################
- </doc>
- </action>
-</diagnostic>
diff --git a/contrib/cdat/scripts/xml/cdms2.xml b/contrib/cdat/scripts/xml/cdms2.xml
deleted file mode 100644
index 1d384fc..0000000
--- a/contrib/cdat/scripts/xml/cdms2.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<diagnostic author="PCMDI's software team" programminglanguage="Python" type="class" url="http://cdat.sf.net" version="5.0.0.alpha7" codepath="cdms2">
- <action name="open" type="function">
- <input>
- <uri doc="" instance="str" position="0" required="True"/>
- <mode doc="" instance="str" position="1" required="False"/>
- <template doc="" instance="str" position="2" required="False"/>
- <dods doc="" instance="int" position="3" required="False"/>
- </input>
- <output>
- <dataset doc="" instance="cdms2.dataset.CdmsFile" position="0"/>
- </output>
- <doc>
- Function: open # Open an existing dataset
-
-Description of Function:
- 'uri' is a Uniform Resource Identifier, referring to a cdunif file, XML file,
- or LDAP URL of a catalog dataset entry.
- 'mode' is 'r', 'r+', 'a', or 'w'
-###################################################################################################################
-########################################### ###############################################
-########################################## End open Description ################################################
-######################################### #################################################
-###################################################################################################################
- </doc>
-</action>
-</diagnostic>
\ No newline at end of file
diff --git a/contrib/cdat/scripts/xml/cdmsFile.xml b/contrib/cdat/scripts/xml/cdmsFile.xml
deleted file mode 100644
index fe2727a..0000000
--- a/contrib/cdat/scripts/xml/cdmsFile.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<diagnostic author="PCMDI's software team" programminglanguage="Python" type="class" url="http://cdat.sf.net" version="5.0.0.alpha7" codepath="cdms2.dataset.CdmsFile">
- <action name="__call__" type="function">
- <input>
- <id doc="" instance="str" position="0" required="True"/>
- </input>
- <output>
- <variable doc="" instance="cdms2.tvariable.TransientVariable" position="0"/>
- </output>
- <doc>
- Function: __call__ # Call a variable object with the given id
-
-Description of Function:
- Call a variable object with the given id
- Exception if not found.
- Call the variable with the other arguments.
-###################################################################################################################
-########################################### ###############################################
-########################################## End _call_ Description ################################################
-######################################### #################################################
-###################################################################################################################
- </doc>
-</action>
-</diagnostic>
\ No newline at end of file
diff --git a/contrib/edu_utah_sci_cscheid_macet/MANIFEST b/contrib/edu_utah_sci_cscheid_macet/MANIFEST
deleted file mode 100644
index 61b0205..0000000
--- a/contrib/edu_utah_sci_cscheid_macet/MANIFEST
+++ /dev/null
@@ -1 +0,0 @@
-F __init__.py
diff --git a/contrib/edu_utah_sci_cscheid_macet/__init__.py b/contrib/edu_utah_sci_cscheid_macet/__init__.py
deleted file mode 100644
index 6a86374..0000000
--- a/contrib/edu_utah_sci_cscheid_macet/__init__.py
+++ /dev/null
@@ -1,125 +0,0 @@
-# VisTrails Macet package
-
-# Macet is an isosurface triangle mesh generator that consistently
-# generates good-triangle quality.
-
-# Macet is described in
-
-# Carlos Dietrich, Joao Comba, Luciana Nedel, Carlos Scheidegger, John
-# Schreiner, Claudio Silva. Edge Transformations for Improving Mesh
-# Quality of Marching Cubes. 2007, submitted.
-
-# This package was created by Carlos Eduardo Scheidegger, 2007
-# cscheid at sci.utah.edu. This is GPL v2 or later, your choice.
-
-##############################################################################
-
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from core.system import list2cmdline
-
-# This accomodates two different VisTrails versions: the released one,
-# and the one in development
-
-
-try:
- from core.configuration import ConfigurationObject
- global configuration
- configuration = ConfigurationObject(executable_path=(None, str))
- old_vistrails = False
-except ImportError:
- old_vistrails = True
-
-import os
-
-identifier = 'edu.utah.sci.cscheid.macet'
-version = '0.1.0'
-name = 'Macet'
-
-##############################################################################
-
-def get_path():
- global _macet_path
- if old_vistrails:
- return _macet_path
- if configuration.has('executable_path'):
- p = configuration.executable_path + '/'
- else:
- p = ''
- p += 'macet'
- return p
-
-class Macet(Module):
-
- def compute(self):
- self.checkInputPort('input_file')
- self.checkInputPort('iso_value')
-
- input_file = self.getInputFromPort('input_file')
- output_file = self.interpreter.filePool.create_file(suffix='.off')
-
- iso_value = self.getInputFromPort('iso_value')
-
- values = [get_path(), input_file.name,
- str(iso_value), output_file.name, '-isCombined']
- cmdline = list2cmdline(values)
- print cmdline
- result = os.system(cmdline)
- if result != 0:
- raise ModuleError(self, 'Execution failed')
-
- self.setResult('output_file', output_file)
-
-class MarchingCubes(Module):
-
- def compute(self):
- self.checkInputPort('input_file')
- self.checkInputPort('iso_value')
-
- input_file = self.getInputFromPort('input_file')
- output_file = self.interpreter.filePool.create_file(suffix='.off')
-
- iso_value = self.getInputFromPort('iso_value')
-
- values = [get_path(), input_file.name,
- str(iso_value), output_file.name]
- cmdline = list2cmdline(values)
- print cmdline
- result = os.system(cmdline)
- if result != 0:
- raise ModuleError(self, 'Execution failed')
-
- self.setResult('output_file', output_file)
-
-##############################################################################
-
-def initialize(executable_path=None):
-
- if old_vistrails:
- global _macet_path
- if executable_path:
- _macet_path = executable_path + '/macet'
- else:
- _macet_path = 'macet'
-
- reg = core.modules.module_registry
-
- reg.add_module(Macet)
-
- reg.add_input_port(Macet, 'input_file',
- core.modules.basic_modules.File)
- reg.add_input_port(Macet, 'iso_value',
- core.modules.basic_modules.Float)
- reg.add_output_port(Macet, 'output_file',
- core.modules.basic_modules.File)
-
- reg.add_module(MarchingCubes)
-
- reg.add_input_port(MarchingCubes, 'input_file',
- core.modules.basic_modules.File)
- reg.add_input_port(MarchingCubes, 'iso_value',
- core.modules.basic_modules.Float)
- reg.add_output_port(MarchingCubes, 'output_file',
- core.modules.basic_modules.File)
-
diff --git a/contrib/edu_utah_sci_cscheid_metro/MANIFEST b/contrib/edu_utah_sci_cscheid_metro/MANIFEST
deleted file mode 100644
index 4273023..0000000
--- a/contrib/edu_utah_sci_cscheid_metro/MANIFEST
+++ /dev/null
@@ -1,2 +0,0 @@
-F __init__.py
-
diff --git a/contrib/edu_utah_sci_cscheid_metro/__init__.py b/contrib/edu_utah_sci_cscheid_metro/__init__.py
deleted file mode 100644
index bf3b9a6..0000000
--- a/contrib/edu_utah_sci_cscheid_metro/__init__.py
+++ /dev/null
@@ -1,158 +0,0 @@
-# VisTrails package for metro support
-# Copyright Carlos Eduardo Scheidegger, 2007
-# Get metro at http://vcg.sourceforge.net/
-
-# License: GPLv2 or later
-
-# ChangeLog:
-
-# 2007-03-13 Carlos Scheidegger <cscheid at juggernaut>
-# * First release
-##############################################################################
-
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-import core.bundles
-from core.system import list2cmdline
-import core.requirements
-import os
-import re
-
-try:
- from core.configuration import ConfigurationObject
- global configuration
- configuration = ConfigurationObject(executable_path=(None, str))
- old_vistrails = False
-except ImportError:
- old_vistrails = True
-
-identifier = 'edu.utah.sci.cscheid.metro'
-version = '0.1'
-name = 'metro'
-
-################################################################################
-
-def get_path():
- global _metro_path
- if old_vistrails:
- return _metro_path
- if configuration.has('executable_path'):
- p = configuration.executable_path + '/'
- else:
- p = ''
- p += 'metro'
- return p
-
-class Metro(Module):
-
- def __init__(self):
- Module.__init__(self)
- self.need_error_meshes = False
- self.need_histograms = False
-
- def is_cacheable(self):
- return self.need_error_meshes and self.need_histograms
-
- def compute(self):
- self.checkInputPort('mesh1')
- self.checkInputPort('mesh2')
- f1 = self.getInputFromPort('mesh1')
- f2 = self.getInputFromPort('mesh2')
-
- make_file = self.interpreter.filePool.create_file
-
- metro_output = make_file(suffix='.txt')
-
- values = [get_path(), f1.name, f2.name, '-q']
-
- need_error_meshes = False
- if (self.outputPorts.has_key('error_mesh_1') or
- self.outputPorts.has_key('error_mesh_2')):
- need_error_meshes = True
- error_mesh_output = (make_file(suffix='.ply'),
- make_file(suffix='.ply'))
- values.append('-c')
- values.append(error_mesh_output[0].name)
- values.append(error_mesh_output[1].name)
-
- need_histograms = False
- if (self.outputPorts.has_key('error_hist_1') or
- self.outputPorts.has_key('error_hist_2')):
- need_histograms = True
- error_hist_output = (make_file(suffix='.csv'),
- make_file(suffix='.csv'))
- values.append('-h')
- values.append(error_hist_output[0].name)
- values.append(error_hist_output[1].name)
-
- values.append('>')
- values.append(metro_output.name)
-
- cmdline = list2cmdline(values)
-
-# cmdline = ('%s ' * len(values)) % tuple(values)
-# cmdline += '> '
-# cmdline += metro_output.name
- print cmdline
-
- result = os.system(cmdline)
- if result != 0:
- raise ModuleError(self, "Execution failed")
- l = [x for x in file(metro_output.name).readlines()
- if x.startswith('Hausdorff')][0]
- regexp = re.compile(r'Hausdorff distance: ([0123456789.]+) \(([0123456789.]+) wrt bounding box diagonal\)')
- results = regexp.match(l).groups()
-
- if need_error_meshes:
- self.setResult('error_mesh_1', error_mesh_output[0])
- self.setResult('error_mesh_2', error_mesh_output[1])
-
- if need_histograms:
- self.setResult('error_hist_1', error_hist_output[0])
- self.setResult('error_hist_2', error_hist_output[1])
-
- self.need_error_meshes = need_error_meshes
- self.need_histograms = need_histograms
-
- self.setResult('hausdorff_error', float(results[0]))
- self.setResult('normalized_hausdorff_error', float(results[1]))
-
-################################################################################
-
-def initialize(executable_path=None):
- if old_vistrails:
- global _metro_path
- if (core.requirements.executable_file_exists('metro') or
- core.bundles.install({'linux-ubuntu': 'vcg-metro'})):
- _metro_path = 'metro'
- elif executable_path:
- _metro_path = executable_path + '/metro'
- print "Will assume metro is in ",executable_path
- else:
- raise core.requirements.MissingRequirement("VCG's Metro")
- else:
- if (not core.requirements.executable_file_exists('metro') and
- not core.bundles.install({'linux-ubuntu': 'vcg-metro'})):
- raise core.requirements.MissingRequirement("VCG's Metro")
-
- reg = core.modules.module_registry
-
- reg.add_module(Metro)
- reg.add_input_port(Metro, 'mesh1',
- core.modules.basic_modules.File)
- reg.add_input_port(Metro, 'mesh2',
- core.modules.basic_modules.File)
-
- reg.add_output_port(Metro, 'hausdorff_error',
- core.modules.basic_modules.Float)
- reg.add_output_port(Metro, 'normalized_hausdorff_error',
- core.modules.basic_modules.Float)
- reg.add_output_port(Metro, 'error_mesh_1',
- core.modules.basic_modules.File)
- reg.add_output_port(Metro, 'error_mesh_2',
- core.modules.basic_modules.File)
- reg.add_output_port(Metro, 'error_hist_1',
- core.modules.basic_modules.File)
- reg.add_output_port(Metro, 'error_hist_2',
- core.modules.basic_modules.File)
diff --git a/contrib/edu_utah_sci_cscheid_teem/__init__.py b/contrib/edu_utah_sci_cscheid_teem/__init__.py
deleted file mode 100644
index 1be4c00..0000000
--- a/contrib/edu_utah_sci_cscheid_teem/__init__.py
+++ /dev/null
@@ -1,909 +0,0 @@
-"""Teem package for VisTrails.
-"""
-
-##############################################################################
-# Changes
-#
-# 20081002: Added UnuSlice
-
-import core.modules
-import core.modules.module_registry
-import core.modules.basic_modules as basic
-from core.modules.vistrails_module import Module, ModuleError, \
- new_module, IncompleteImplementation
-
-import os
-import subprocess
-
-_teemPath = None
-_teemLimnTestPath = None
-_teemTenTestPath = None
-
-identifier = 'edu.utah.sci.cscheid.teem'
-version = '0.2'
-name = 'teem'
-
-###############################################################################
-
-FileType = [(basic.File, '')]
-FloatType = [(basic.Float, '')]
-IntegerType = [(basic.Integer, '')]
-StringType = [(basic.String, '')]
-Vec3Type = [(basic.Float, 'x'),
- (basic.Float, 'y'),
- (basic.Float, 'z')]
-
-class Teem(Module):
-
- def run_at_path(self, cmdline, path):
- cmdline = path + cmdline
- print cmdline
- result = os.system(cmdline)
- if result != 0:
- raise ModuleError(self, '"%s" failed' % cmdline)
-
- def run_path(self, *cmds):
- cmdline = " ".join([str(cmd) for cmd in cmds])
- self.run_at_path(cmdline, '')
-
- def run_teem(self, *cmds):
- cmdline = " ".join([str(cmd) for cmd in cmds])
- self.run_at_path(cmdline, _teemPath)
-
- def run_limn_test(self, *cmds):
- cmdline = " ".join([str(cmd) for cmd in cmds])
- self.run_at_path(cmdline, _teemLimnTestPath)
-
- def run_ten_test(self, *cmds):
- cmdline = " ".join([str(cmd) for cmd in cmds])
- self.run_at_path(cmdline, _teemTenTestPath)
-
- def opt_command_line_val(self, option_name, port_name):
- if self.hasInputFromPort(port_name):
- return [option_name, self.getInputFromPort(port_name)]
- else:
- return []
-
- def opt_command_line_vec(self, option_name, port_name):
- if self.hasInputFromPort(port_name):
- t = self.getInputFromPort(port_name)
- return [option_name] + list(t)
- else:
- return []
-
- def opt_command_line_file(self, option_name, port_name):
- if self.hasInputFromPort(port_name):
- t = self.getInputFromPort(port_name)
- return [option_name, t.name]
- else:
- return []
-
- def opt_command_line_noopt(self, option_name, port_name):
- if self.hasInputFromPort(port_name):
- return [option_name]
- else:
- return []
-
- ##########################################################################
- # Default compute for (hopefully) most classes
-
- _opt_dict = {'v': opt_command_line_val,
- 'V': opt_command_line_vec,
- 'f': opt_command_line_file,
- 'n': opt_command_line_noopt}
-
- def process_command_line_input(self):
- cmdline = [self._cmdline_base]
- for (opt_type, port_name, option_name) in self._cmdline_inputs:
- call = self._opt_dict[opt_type]
- cmdline += call(self, option_name=option_name,
- port_name=port_name)
- return cmdline
-
- def process_command_line_output(self):
- (port_name, opt_name, format) = self._cmdline_output
- if callable(format):
- format = format(self)
- output_file = self.interpreter.filePool.create_file(suffix='.'+format)
- self.setResult(port_name, output_file)
- return [opt_name, output_file.name]
-
- def compute(self):
- cmdline_input = self.process_command_line_input()
- cmdline_output = self.process_command_line_output()
- self._cmdline_callable(*(cmdline_input + cmdline_output))
-
-class Emap(Teem):
-
- def compute(self):
- cmdline = ['emap']
- cmdline += self.opt_command_line_vec(port_name='from',
- option_name='-fr')
- cmdline += self.opt_command_line_vec(port_name='ambient',
- option_name='-amb')
- cmdline += self.opt_command_line_vec(port_name='up',
- option_name='-up')
- cmdline += self.opt_command_line_noopt(port_name='right_hand',
- option_name='-rh')
- self.checkInputPort('input_file')
- cmdline += self.opt_command_line_file(port_name='input_file',
- option_name='-i')
-
- output_file = self.interpreter.filePool.create_file(suffix='.nrrd')
- cmdline += ['-o', output_file.name]
-
- self.run_teem(*cmdline)
-
- self.setResult("output_file", output_file)
-
- _input_ports = [('right_hand', []),
- ('input_file', [(basic.File, 'the lights input file')]),
- ('from', Vec3Type),
- ('ambient', Vec3Type),
- ('up', Vec3Type)]
- _output_ports = [('output_file', [(basic.File, 'the resulting nrrd')])]
-
-class Soid(Teem):
-
- def compute(self):
- cmdline = ['soid']
- cmdline += self.opt_command_line_val(port_name='resolution',
- option_name='-res')
- cmdline += self.opt_command_line_val(port_name='radius',
- option_name='-r')
- cmdline += self.opt_command_line_vec(port_name='scalings',
- option_name='-sc')
- cmdline += self.opt_command_line_noopt(port_name='sphere',
- option_name='-sphere')
-
- if self.hasInputFromPort('AB'):
- cmdline += self.opt_command_line_vec(port_name='AB',
- option_name='-AB')
- elif self.hasInputFromPort('A') and self.hasInputFromPort('B'):
- cmdline += ['-AB',
- self.getInputFromPort('A'),
- self.getInputFromPort('B')]
-
- output_file = self.interpreter.filePool.create_file(suffix='.nrrd')
- cmdline += ['-o', output_file.name]
-
- self.run_limn_test(*cmdline)
- self.setResult("output_file", output_file)
-
- _input_ports = [('resolution', [(basic.Float, 'The ellipsoid resolution')]),
- ('radius', [(basic.Float, 'The radius')]),
- ('sphere', []),
- ('scalings', Vec3Type),
- ('AB', [(basic.Float, 'A exponent'),
- (basic.Float, 'B exponent')]),
- ('A', [(basic.Float, 'A exponent')]),
- ('B', [(basic.Float, 'B exponent')]),
- ]
- _output_ports = [('output_file', [(basic.File, 'the resulting OFF file')])]
-
-
-class OffToEps(Teem):
-
- def compute(self):
- cmdline = ['off2eps']
- cmdline += self.opt_command_line_vec(port_name='from_point',
- option_name='-fr')
- cmdline += self.opt_command_line_vec(port_name='u_range',
- option_name='-ur')
- cmdline += self.opt_command_line_vec(port_name='v_range',
- option_name='-vr')
- cmdline += self.opt_command_line_vec(port_name='edge_widths',
- option_name='-wd')
- cmdline += self.opt_command_line_file(port_name='environment_map',
- option_name='-e')
- cmdline += self.opt_command_line_noopt(port_name='orthogonal',
- option_name='-or')
- cmdline += self.opt_command_line_noopt(port_name='right_hand',
- option_name='-rh')
- cmdline += self.opt_command_line_noopt(port_name='concave',
- option_name='-concave')
- cmdline += self.opt_command_line_noopt(port_name='no_background',
- option_name='-nobg')
- cmdline += self.opt_command_line_val(port_name='world_to_points_scale',
- option_name='-ws')
-
-
- self.checkInputPort('input_file')
- input_file = self.getInputFromPort('input_file')
- cmdline += ['-i', input_file.name]
-
- output_file = self.interpreter.filePool.create_file(suffix='.eps')
- cmdline += ['-o', output_file.name]
-
- self.run_limn_test(*cmdline)
- self.setResult("output_file", output_file)
-
-
- _input_ports = [
- ("right_hand", []),
- ("input_file", [(basic.File, 'the input OFF file')]),
- ("environment_map", [(basic.File, 'the nrrd storing the environment map')]),
- ("from_point", [(basic.Float, '')] * 3),
- ("u_range", [(basic.Float, '')] * 2),
- ("v_range", [(basic.Float, '')] * 2),
- ("edge_widths", [(basic.Float, '')] * 5),
- ("orthogonal", []),
- ("no_background", []),
- ("concave", []),
- ("world_to_points_scale", [(basic.Float, '')]),
- ]
-
- _output_ports = [
- ("output_file", [(basic.File, '')]),
- ]
-
-class EpsToPpm(Teem):
-
- def compute(self):
- cmdline = ['eps2ppm']
- self.checkInputPort('input_file')
- self.checkInputPort('resolution')
- cmdline += [self.getInputFromPort('input_file').name]
- cmdline += [self.getInputFromPort('resolution')]
- cmdline += ['>']
- output_file = self.interpreter.filePool.create_file(suffix='.ppm')
- cmdline += [output_file.name]
- self.run_path(*cmdline)
- self.setResult("output_file", output_file)
-
- _input_ports = [
- ("input_file", [(basic.File, 'the input EPS')]),
- ("resolution", [(basic.Float, 'the resolution to rasterize the EPS')]),
- ]
-
- _output_ports = [
- ("output_file", [(basic.File, 'the resulting PPM file')]),
- ]
-
-class Unu(Teem):
-
- def do_output(self):
- if self.hasInputFromPort('format'):
- suffix = '.'+self.getInputFromPort('format')
- else:
- suffix = '.nrrd'
- output_file = self.interpreter.filePool.create_file(suffix=suffix)
- return (['-o', output_file.name], output_file)
-
- def do_input(self):
- self.checkInputPort('input_file')
- return ['-i', self.getInputFromPort('input_file').name]
-
- _input_ports = [
- ("format", [(basic.String, 'file format for output')]),
- ]
- _output_ports = [
- ("output_file", [(basic.File, 'the output file')]),
- ]
-
-class UnuSave(Unu):
-
- def compute(self):
- cmdline = ['unu save']
- cmdline += self.do_input()
- (ocmd, output_file) = self.do_output()
- self.setResult("output_file", output_file)
- self.setResult("output_name", output_file.name)
- cmdline += ocmd
- cmdline += self.opt_command_line_val(port_name='output_format', option_name='-f')
- self.run_teem(*cmdline)
-
- _input_ports = [
- ("input_file", [(basic.File, 'Input File')]),
- ("output_format", [(basic.String, 'Output Format')]),
- ]
- _output_ports = [
- ("output_name", [(basic.String, 'Output Filename')]),
- ]
-
-class UnuSwap(Unu):
-
- def compute(self):
- cmdline = ['unu swap']
- cmdline += self.do_input()
- (ocmd, output_file) = self.do_output()
- self.setResult("output_file", output_file)
- v1, v2 = self.getInputFromPort('axes')
- cmdline += ['-a', str(v1), str(v2)]
- cmdline += ocmd
- self.run_teem(*cmdline)
-
- _input_ports = [
- ("input_file", [(basic.File, 'Input File')]),
- ("axes", [(basic.Integer, '')]*2),
- ]
-
-class UnuProject(Unu):
-
- def compute(self):
- cmdline = ['unu project']
- cmdline += self.do_input()
- (ocmd, output_file) = self.do_output()
- self.setResult("output_file", output_file)
- cmdline += ocmd
- cmdline += self.opt_command_line_val(port_name='axis',
- option_name='-a')
- cmdline += self.opt_command_line_val(port_name='measure',
- option_name='-m')
- self.run_teem(*cmdline)
-
- _input_ports = [
- ("input_file", [(basic.File, 'the input file')]),
- ("measure", [(basic.String, 'the measure to use')]),
- ("axis", (basic.Integer, 'the axis to project')),
- ]
-
-class UnuMinmax(Teem):
-
- def do_input(self):
- self.checkInputPort('input_file')
- return [self.getInputFromPort('input_file').name]
-
- def compute(self):
- cmdline = ['unu minmax']
- cmdline += self.do_input()
- if self.hasInputFromPort('blind8'):
- cmdline += '-blind8 true'
- output_file = self.interpreter.filePool.create_file()
- # FIXME use popen*
- cmdline += ['>%s'%output_file.name]
- self.run_teem(*cmdline)
- f = file(output_file.name)
- try:
- mn = float(f.readline().split()[-1])
- mx = float(f.readline().split()[-1])
- except:
- raise ModuleError(self, 'Could not read result')
- self.setResult('range', (mn, mx))
-
- _input_ports = [('input_file', [(basic.File, 'the input file')]),
- ('blind8', [])]
- _output_ports = [('range', [(basic.Float,'')] * 2)]
-
-class UnuReshape(Unu):
-
- def compute(self):
- cmdline = ['unu reshape']
- cmdline += self.do_input()
- cmdline += self.opt_command_line_val(port_name='axes',
- option_name='-s')
- (ocmd, output_file) = self.do_output()
- self.setResult("output_file", output_file)
- cmdline += ocmd
- self.run_teem(*cmdline)
-
- _input_ports = [
- ("input_file", [(basic.File, 'the input file')]),
- ("axes", [(basic.String, 'axes to split')]),
- ]
-
-
-class UnuResample(Unu):
-
- def compute(self):
- cmdline = ['unu resample']
- cmdline += self.do_input()
- (ocmd, output_file) = self.do_output()
- cmdline += ocmd
- self.setResult("output_file", output_file)
- cmdline += self.opt_command_line_val(port_name='sampling_spec',
- option_name='-s')
- cmdline += self.opt_command_line_val(port_name='centering',
- option_name='-c')
- cmdline += self.opt_command_line_val(port_name='kernel',
- option_name='-k')
- self.run_teem(*cmdline)
-
- _input_ports = [
- ("input_file", [(basic.File, 'the input file')]),
- ("sampling_spec", [(basic.String, 'the sampling spec')]),
- ("centering", [(basic.String, 'centering (node/cell)')]),
- ("kernel", [(basic.String, 'the resampling kernel')]),
- ]
-
-class UnuJoin(Unu):
-
- def do_input(self):
- self.checkInputPort('input_list')
- return ['-i'] + [x.name
- for x in self.getInputFromPort('input_list')]
-
- def compute(self):
- cmdline = ['unu join']
- cmdline += self.do_input()
- cmdline += self.opt_command_line_val(port_name='axis',
- option_name='-a')
- (ocmd, output_file) = self.do_output()
- cmdline += ocmd
- self.setResult("output_file", output_file)
- self.run_teem(*cmdline)
-
- _input_ports = [
- ("input_list", [(basic.List, 'list of input files')]),
- ("axis", [(basic.Integer, 'the axis to join')]),
- ]
-
-class UnuQuantize(Unu):
-
- def do_input(self):
- current = Unu.do_input(self)
- self.checkInputPort('bits')
- return current + ['-b', self.getInputFromPort('bits')]
-
- def compute(self):
- cmdline = ['unu quantize']
- cmdline += self.do_input()
- cmdline += self.opt_command_line_val(port_name='min',
- option_name='-min')
- cmdline += self.opt_command_line_val(port_name='max',
- option_name='-max')
- (ocmd, output_file) = self.do_output()
- cmdline += ocmd
- self.setResult("output_file", output_file)
- self.run_teem(*cmdline)
-
- _input_ports = [
- ("input_file", [(basic.File, 'the input file')]),
- ('bits', [(basic.Integer, 'bits to quantize down to')]),
- ('min', [(basic.Float, 'min value')]),
- ('max', [(basic.Float, 'max value')]),
- ]
-
-class Unu1op(Unu):
-
- def do_input(self):
- r = []
- if self.hasInputFromPort('in1_file'):
- r += ['-i', self.getInputFromPort('in1_file').name]
- return r
-
- def is_cacheable(self):
- return not self.getInputFromPort('op') in ['rand', 'nrand']
-
- def compute(self):
- allowed_ops = ['-', 'r', 'sin',
- 'cos', 'tan', 'asin', 'acos', 'atan',
- 'exp', 'log', 'log10', 'log1p', 'log2', 'sqrt'
- 'cbrt', 'ceil', 'floor', 'erf', 'rup',
- 'abs', 'sgn', 'exists', 'rand', 'nrand',
- 'if', '0', '1']
- self.checkInputPort('op')
- if not self.getInputFromPort('op') in allowed_ops:
- raise ModuleError(self, ("Operation %s is not allowed." %
- self.getInputFromPort('op')))
- cmdline = ['unu 1op']
- cmdline += [self.getInputFromPort('op')]
- cmdline += self.do_input()
- (ocmd, output_file) = self.do_output()
- cmdline += ocmd
- self.setResult('output_file', output_file)
- self.run_teem(*cmdline)
-
- _input_ports = [
- ("in1_file", [(basic.File, 'input file 1')]),
- ("op", [(basic.String, 'the operation')]),
- ]
-
-class Unu2op(Unu):
-
- def do_input(self):
- r = []
- if self.hasInputFromPort('in1_file'):
- r += [self.getInputFromPort('in1_file').name]
- elif self.hasInputFromPort('in1_value'):
- r += [self.getInputFromPort('in1_value')]
- else:
- raise ModuleError(self, "Needs either in1_file or in1_value")
- if self.hasInputFromPort('in2_file'):
- r += [self.getInputFromPort('in2_file').name]
- elif self.hasInputFromPort('in2_value'):
- r += [self.getInputFromPort('in2_value')]
- else:
- raise ModuleError(self, "Needs either in2_file or in2_value")
- return r
-
- def compute(self):
- allowed_ops = ['+', '-', 'x', '/',
- '^', 'pow', 'spow', '%', 'fmod', 'atan2',
- 'min', 'max', 'lt', 'lte', 'gt', 'gte'
- 'eq', 'neq', 'comp', 'if', 'exists']
- self.checkInputPort('op')
- if not self.getInputFromPort('op') in allowed_ops:
- raise ModuleError(self, ("Operation %s is not allowed." %
- self.getInputFromPort('op')))
- cmdline = ['unu 2op']
- cmdline += [self.getInputFromPort('op')]
- cmdline += self.do_input()
- (ocmd, output_file) = self.do_output()
- cmdline += ocmd
- self.setResult('output_file', output_file)
- self.run_teem(*cmdline)
-
- _input_ports = [
- ("in1_file", [(basic.File, 'input file 1')]),
- ("in1_value", [(basic.String, 'input value 1')]),
- ("in2_file", [(basic.File, 'input file 2')]),
- ("in2_value", [(basic.String, 'input value 2')]),
- ("op", [(basic.String, 'the operation')]),
- ]
-
-
-class Unu3op(Unu):
-
- def do_input(self):
- r = []
- if self.hasInputFromPort('in1_file'):
- r += [self.getInputFromPort('in1_file').name]
- elif self.hasInputFromPort('in1_value'):
- r += [self.getInputFromPort('in1_value')]
- else:
- raise ModuleError(self, "Needs either in1_file or in1_value")
- if self.hasInputFromPort('in2_file'):
- r += [self.getInputFromPort('in2_file').name]
- elif self.hasInputFromPort('in2_value'):
- r += [self.getInputFromPort('in2_value')]
- else:
- raise ModuleError(self, "Needs either in2_file or in2_value")
- if self.hasInputFromPort('in3_file'):
- r += [self.getInputFromPort('in3_file').name]
- elif self.hasInputFromPort('in3_value'):
- r += [self.getInputFromPort('in3_value')]
- else:
- raise ModuleError(self, "Needs either in3_file or in3_value")
- return r
-
- def compute(self):
- allowed_ops = ['+', 'x',
- 'min', 'max',
- 'clamp', 'ifelse',
- 'lerp', 'exists',
- 'in_op', 'in_cl']
- self.checkInputPort('op')
- if not self.getInputFromPort('op') in allowed_ops:
- raise ModuleError(self, ("Operation %s is not allowed." %
- self.getInputFromPort('op')))
- cmdline = ['unu 3op']
- cmdline += [self.getInputFromPort('op')]
- cmdline += self.do_input()
- (ocmd, output_file) = self.do_output()
- cmdline += ocmd
- self.setResult('output_file', output_file)
- self.run_teem(*cmdline)
-
- _input_ports = [
- ("in1_file", [(basic.File, 'input file 1')]),
- ("in1_value", [(basic.String, 'input value 1')]),
- ("in2_file", [(basic.File, 'input file 2')]),
- ("in2_value", [(basic.String, 'input value 2')]),
- ("in3_file", [(basic.File, 'input file 3')]),
- ("in3_value", [(basic.String, 'input value 3')]),
- ("op", [(basic.String, 'the operation')]),
- ]
-
-class Teem_TT(Teem):
- _cmdline_base = 'tt'
- _cmdline_inputs = [('v', 'num_samples', '-n'),
- ('V', 'location', '-p'),
- ('v', 'max_ca', '-ca'),
- ('n', 'right_triangle', '-r'),
- ('n', 'whole', '-w'),
- ('v', 'westin_metric', '-v'),
- ('v', 'hack', '-hack')]
- _cmdline_output = ('output_file', '-o', '.nrrd')
- _cmdline_callable = Teem.run_ten_test
-
- _input_ports = [
- ("num_samples", [(basic.String, 'number of samples')]),
- ("location", Vec3Type),
- ("max_ca", [(basic.Float, 'max CA')]),
- ("westin_metric", [(basic.Float, 'Metric to use')]),
- ("hack", [(basic.Float, '"this is a hack"')]),
- ("right_triangle", []),
- ("whole", []),
- ]
- _output_ports = [
- ("output_file", [(basic.File, "the output file")]),
- ]
-
-class Tend_norm(Teem):
- _cmdline_base = 'tend norm'
- _cmdline_inputs = [('V', 'weights', '-w'),
- ('v', 'amount', '-a'),
- ('v', 'target', '-t'),
- ('f', 'input_file', '-i')]
- _cmdline_output = ('output_file', '-o', 'nrrd')
- _cmdline_callable = Teem.run_teem
-
- _input_ports = [
- ("weights", Vec3Type),
- ("amount", [(basic.Float, "amount of normalization")]),
- ("target", [(basic.Float, "target size post normalization")]),
- ("input_file", [(basic.File, "input DT volume")]),
- ]
-
- _output_ports = [
- ("output_file", [(basic.File, "output file")]),
- ]
-
-class Tend_glyph(Teem):
- _cmdline_base = 'tend glyph'
- _cmdline_inputs = [('v', 'sat', '-sat'),
- ('f', 'emap', '-emap'),
- ('f', 'input_file', '-i'),
- ('V', 'from_point', '-fr'),
- ('V', 'up', '-up'),
- ('v', 'psc', '-psc'),
- ('V', 'u_range', '-ur'),
- ('V', 'v_range', '-vr'),
- ('n', 'orthogonal', '-or'),
- ('v', 'atr', '-atr'),
- ('n', 'no_background', '-nobg'),
- ('n', 'right_hand', '-rh'),
- ('v', 'glyph_shape', '-g'),
- ('v', 'glyph_size', '-gsc'),
- ('v', 'glyph_resolution', '-gr'),
- ('V', 'widths', '-wd')]
- _cmdline_output = ('output_file', '-o', 'eps')
- _cmdline_callable = Teem.run_teem
-
- _input_ports = [
- ("sat", [(basic.Float, "max saturation")]),
- ("from_point", [(basic.Float, '')] * 3),
- ("up", [(basic.Float, '')] * 3),
- ("psc", [(basic.Float, 'ps scale')]),
- ("u_range", [(basic.Float, '')] * 2),
- ("v_range", [(basic.Float, '')] * 2),
- ("orthogonal", []),
- ("atr", [(basic.Float, 'anisotropy threshold')]),
- ("emap", [(basic.File, 'environment map nrrd')]),
- ("input_file", [(basic.File, 'the input file')]),
- ("no_background", []),
- ("glyph_shape", [(basic.String, 'glyph shape')]),
- ("glyph_size", [(basic.Float, 'glyph size in world space')]),
- ("glyph_resolution", [(basic.Integer, 'glyph resolution of polygonization')]),
- ("widths", [(basic.Float, '')] * 3),
- ("right_hand", []),
- ]
- _output_ports = [
- ("output_file", [(basic.File, 'output EPS file')])
- ]
-
-class UnuSlice(Unu):
-
- def do_input(self):
- r = []
- self.checkInputPort('in_file')
- self.checkInputPort('axis')
- self.checkInputPort('position')
- r += ['-i', self.getInputFromPort('in_file').name]
- r += ['-a', str(self.getInputFromPort('axis'))]
- r += ['-p', str(self.getInputFromPort('position'))]
- return r
-
- def compute(self):
- cmdline = ['unu slice']
- cmdline += self.do_input()
- (ocmd, output_file) = self.do_output()
- cmdline += ocmd
- self.setResult('output_file', output_file)
- self.run_teem(*cmdline)
-
- _input_ports = [
- ('in_file', basic.File),
- ('axis', basic.Integer),
- ('position', basic.Integer),
- ]
-
-
-###############################################################################
-
-class TeemScaledTransferFunction(Teem):
- _input_ports = [('range', [(basic.Float, '')] * 2),
- ('steps', [basic.Integer])]
- _output_ports = [('nrrd', [(basic.File, 'the output TF')])]
-
- def compute(self):
- ramp = self.interpreter.filePool.create_file(suffix='.txt')
- tf_vals = self.interpreter.filePool.create_file(suffix='.txt')
- output = self.interpreter.filePool.create_file(suffix='.nrrd')
- steps = self.getInputFromPort('steps')
- rng = self.getInputFromPort('range')
- self.run_teem('echo "0 1"',
- '| unu reshape -s 1 2',
- '| unu resample -s = %d -k tent -c node' % steps,
- '| unu save -f text -o %s' % ramp.name)
- tf_file = file(tf_vals.name, 'w')
- tf = self.getInputFromPort('transfer_function')
- for (scalar, op, (r, g, b)) in tf._pts:
- tf_file.write('%f %f %f %f %f\n' % (scalar, r, g, b, op))
-# tf_file.write('%f %f\n' % (scalar, op))
- tf_file.close()
- self.run_teem('cat %s' % tf_vals.name,
- '| unu reshape -s 5 %d' % len(tf._pts),
- '| unu imap -i %s -r -m -' % ramp.name,
- '| unu reshape -s 4 %d' % steps,
- '| unu axinfo -a 0 -l "RGBA"',
- '| unu axinfo -a 1 -l "gage(scalar:v)" -mm %f %f -o %s' % (rng[0],
- rng[1],
- output.name))
- self.setResult('nrrd', output)
-
-##############################################################################
-
-class Miter(Teem):
-
- _input_ports = [
- # Input data
- ('input_file', FileType),
- ('transfer_function', FileType),
- # Camera
- ('from_point', Vec3Type),
- ('at_point', Vec3Type),
- ('up_vec', Vec3Type),
- ('right_handed', []),
- ('relative_to_at_point', []),
- ('near_dist', FloatType),
- ('far_dist', FloatType),
- ('image_plane_dist', FloatType),
- ('urange', FloatType * 2),
- ('vrange', FloatType * 2),
- ('image_size', IntegerType * 2),
- # Lighting
- ('light_pos', Vec3Type),
- ('ambient_light', FloatType * 3),
- ('phong_components', FloatType * 3),
- ('shininess', FloatType),
- ('value_kernel', StringType),
- ('d_kernel', StringType),
- ('dd_kernel', StringType),
- ('step_size', FloatType),
- ('ref_step_size', FloatType),
- ('thread_count', IntegerType),
- ('opacity_termination', FloatType),
- ]
-
- _output_ports = [('output_file', FileType)]
-
- def compute(self):
- cmdline = ['miter']
- self.checkInputPort('input_file')
- self.checkInputPort('transfer_function')
- cmdline += self.opt_command_line_file('-i', 'input_file')
- f = self.interpreter.filePool.create_file(suffix='.nrrd')
- cmdline += ['-o', f.name]
- cmdline += self.opt_command_line_vec('-fr', 'from_point')
- cmdline += self.opt_command_line_vec('-at', 'at_point')
- cmdline += self.opt_command_line_vec('-up', 'up_vec')
- cmdline += self.opt_command_line_noopt('-rh', 'right_handed')
- cmdline += self.opt_command_line_noopt('-ar', 'relative_to_at_point')
- cmdline += self.opt_command_line_val('-dn', 'near_dist')
- cmdline += self.opt_command_line_val('-di', 'image_plane_dist')
- cmdline += self.opt_command_line_val('-df', 'far_dist')
- cmdline += self.opt_command_line_vec('-ur', 'urange')
- cmdline += self.opt_command_line_vec('-vr', 'vrange')
- cmdline += self.opt_command_line_vec('-is', 'image_size')
- cmdline += self.opt_command_line_vec('-ld', 'light_pos')
- cmdline += self.opt_command_line_vec('-am', 'ambient_light')
- cmdline += self.opt_command_line_vec('-ads', 'phong_components')
- cmdline += self.opt_command_line_val('-sp', 'shininess')
- cmdline += self.opt_command_line_val('-k00', 'value_kernel')
- cmdline += self.opt_command_line_val('-k11', 'd_kernel')
- cmdline += self.opt_command_line_val('-k22', 'dd_kernel')
- cmdline += self.opt_command_line_val('-step', 'step_size')
- cmdline += self.opt_command_line_val('-ref', 'ref_step_size')
- cmdline += self.opt_command_line_val('-nt', 'thread_count')
- cmdline += self.opt_command_line_val('-n1', 'opacity_termination')
- cmdline += self.opt_command_line_file('-txf', 'transfer_function')
- self.setResult('output_file', f)
- self.run_teem(*cmdline)
-
-###############################################################################
-
-class OverRGB(Teem):
-
- _input_ports = [
- ('input_file', FileType),
- ('contrast', FloatType),
- ('component_fixed_point', FloatType),
- ('gamma', FloatType),
- ('background', Vec3Type),
- ('background_image', FileType),]
-
- _output_ports = [
- ('output_image', FileType),
- ]
-
- def compute(self):
- cmdline = ['overrgb']
- self.checkInputPort('input_file')
- cmdline += self.opt_command_line_file('-i', 'input_file')
- f = self.interpreter.filePool.create_file(suffix='.png')
- cmdline += ['-o', f.name]
- self.setResult('output_image', f)
- cmdline += self.opt_command_line_val('-c', 'contrast')
- cmdline += self.opt_command_line_val('-cfp', 'component_fixed_point')
- cmdline += self.opt_command_line_val('-g', 'gamma')
- cmdline += self.opt_command_line_vec('-b', 'background')
- cmdline += self.opt_command_line_file('-bi', 'background_image')
- self.run_teem(*cmdline)
-
-###############################################################################
-
-_modules = [Teem, Emap, Soid, Miter, OverRGB,
- OffToEps,
- EpsToPpm,
- Unu,
- UnuMinmax,
- UnuSave,
- UnuSwap,
- UnuProject,
- UnuReshape,
- UnuResample,
- UnuJoin,
- UnuQuantize,
- Unu1op,
- Unu2op,
- Unu3op,
- UnuSlice,
- Teem_TT,
- Tend_norm,
- Tend_glyph]
-
-##############################################################################
-
-def package_dependencies():
- import core.packagemanager
- manager = core.packagemanager.get_package_manager()
- if manager.has_package('edu.utah.sci.vistrails.vtk'):
- return ['edu.utah.sci.vistrails.vtk']
- else:
- return []
-
-###############################################################################
-
-def initialize(path=None, limnTestPath=None, tenTestPath=None,
- *args, **keywords):
- global _teemPath
- if not path:
- print "path not specified or incorrect: Will assume teem is on path"
- _teemPath = ""
- else:
- print "will use teem from ", path
- _teemPath = path + '/'
-
- global _teemLimnTestPath
- if not limnTestPath:
- print "limnTestPath not specified or incorrect: Will not install",
- print "limnTest modules"
- _teemLimnTestPath = ""
- else:
- print "will use limnTest tools from ", limnTestPath
- _teemLimnTestPath = limnTestPath + '/'
-
- global _teemTenTestPath
- if not tenTestPath:
- print "tenTestPath not specified or incorrect: Will not install",
- print "tenTestPath modules"
- _teemTenTestPath = ""
- else:
- print "will use tenTest tools from ", tenTestPath
- _teemTenTestPath = tenTestPath + '/'
-
- reg = core.modules.module_registry.registry
-
- # Register the TF widget interaction modules if they're available
- if reg.has_module('edu.utah.sci.vistrails.vtk',
- 'TransferFunction'):
- # Update the auto-add _modules list
- _modules.append(TeemScaledTransferFunction)
- TF = reg.get_descriptor_by_name('edu.utah.sci.vistrails.vtk',
- 'TransferFunction').module
- # Update the input ports for TeemScaledTransferFunction now that we
- # know TF is present
- TeemScaledTransferFunction._input_ports.append(('transfer_function', [(TF,
- "the transfer function")]))
diff --git a/contrib/edu_utah_sci_cscheid_teem/examples.vt b/contrib/edu_utah_sci_cscheid_teem/examples.vt
deleted file mode 100644
index a79507f..0000000
Binary files a/contrib/edu_utah_sci_cscheid_teem/examples.vt and /dev/null differ
diff --git a/contrib/edu_utah_sci_eranders_proteindatabank/PDB.py b/contrib/edu_utah_sci_eranders_proteindatabank/PDB.py
deleted file mode 100644
index 39e4e92..0000000
--- a/contrib/edu_utah_sci_eranders_proteindatabank/PDB.py
+++ /dev/null
@@ -1,144 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-
-class ProteinDataBank(Module):
- pass
-
-class Protein(ProteinDataBank):
-
- def __init__(self):
- ProteinDataBank.__init__(self)
- self.atoms = {}
- self.sequence = {}
- self.hatoms = {}
- self.author = ''
- self.title = ''
-
- def compute(self):
- pass
-
- def getAtomOfType(self, type):
- if self.atoms.has_key(type):
- return self.atoms[type]
- else:
- return 0
-
- def getHetAtomOfType(self, type):
- if self.hatoms.has_key(type):
- return self.hatoms[type]
- else:
- return 0
-
- def getSequence(self, seqID):
- if self.sequence.has_key(seqID):
- return self.sequence[seqID].__str__()
- else:
- k = self.sequence.keys().__str__()
- str = 'Invalid Sequence ID ' + k
-
-class PDBParser(ProteinDataBank):
-
- ############################################################################
- # line parsers
-
- def is_continuation(self, line):
- try:
- int(line[0])
- return True
- except:
- return False
-
- def parse_ATOM(self, line, protein):
- type = line[-1]
- if protein.atoms.has_key(type):
- protein.atoms[type] = protein.atoms[type] + 1
- else:
- protein.atoms[type] = 1
-
- def parse_SEQRES(self, line, protein):
- els = len(line)
- seqID = line[2]
- if not protein.sequence.has_key(seqID):
- protein.sequence[seqID] = []
-
- s = protein.sequence[seqID]
-
- i = 4
- while i < len(line):
- s.append(line[i])
- i = i + 1
-
- protein.sequence[seqID] = s
-
- def parse_HETATM(self, line, protein):
- type = line[-1]
- if protein.hatoms.has_key(type):
- protein.hatoms[type] = protein.hatoms[type] + 1
- else:
- protein.hatoms[type] = 1
-
- def parse_AUTHOR(self, line, protein):
- if self.is_continuation(line):
- protein.author += ' ' + ' '.join(line[1:])
- else:
- protein.author = ' '.join(line)
-
- def parse_TITLE(self, line, protein):
- if self.is_continuation(line):
- protein.title += ' ' + ' '.join(line[1:])
- else:
- protein.title = ' '.join(line)
-
- def parse_HEADER(self, line, protein):
- protein.pdb_name = line[-1]
- protein.date = line[-2]
- protein.short_title = ' '.join(line[:-2])
-
- ############################################################################
-
- def compute(self):
- f = self.getInputFromPort("File")
-
- p = Protein()
-
- for l in file(f.name):
- l = l.strip()
- toks = l.split()
- if hasattr(self, 'parse_' + toks[0]):
- getattr(self, 'parse_' + toks[0])(toks[1:], p)
-
- self.setResult("Protein", p)
-
-class GetAtoms(ProteinDataBank):
- def compute(self):
- prot = self.getInputFromPort("Protein")
- aType = self.getInputFromPort("Atom Type")
- self.setResult("NumAtoms", prot.getAtomOfType(aType))
-
-class GetHetAtoms(ProteinDataBank):
- def compute(self):
- prot = self.getInputFromPort("Protein")
- aType = self.getInputFromPort("Atom Type")
- self.setResult("NumAtoms", prot.getHetAtomOfType(aType))
-
-class GetSequence(ProteinDataBank):
- def compute(self):
- prot = self.getInputFromPort("Protein")
- sID = self.getInputFromPort("SequenceID")
- self.setResult("Sequence", prot.getSequence(sID))
-
-class GetTitle(ProteinDataBank):
- def compute(self):
- prot = self.getInputFromPort("Protein")
- self.setResult("Title", prot.title)
-
-class GetAuthor(ProteinDataBank):
- def compute(self):
- prot = self.getInputFromPort("Protein")
- self.setResult("Title", prot.author)
-
-class GetPDBName(ProteinDataBank):
- def compute(self):
- prot = self.getInputFromPort("Protein")
- self.setResult("name", prot.pdb_name)
diff --git a/contrib/edu_utah_sci_eranders_proteindatabank/__init__.py b/contrib/edu_utah_sci_eranders_proteindatabank/__init__.py
deleted file mode 100644
index 7c18d70..0000000
--- a/contrib/edu_utah_sci_eranders_proteindatabank/__init__.py
+++ /dev/null
@@ -1,68 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-
-from PDB import *
-
-identifier = 'edu.utah.sci.eranders.proteindatabank'
-version = '0.1.0'
-name = 'Protein Data Bank'
-
-def initialize(*args, **keywords):
- reg = core.modules.module_registry
- basic = core.modules.basic_modules
-
- reg.add_module(ProteinDataBank, abstract=True)
- reg.add_module(Protein, abstract=True)
-
- reg.add_module(PDBParser)
- reg.add_input_port(PDBParser, "File", (basic.File, 'File'))
- reg.add_output_port(PDBParser, "Protein", (Protein, 'Protein'))
-
- reg.add_module(GetAtoms)
- reg.add_input_port(GetAtoms, "Protein", (Protein, 'Protein'))
- reg.add_input_port(GetAtoms, "Atom Type", (basic.String, 'AtomType'))
- reg.add_output_port(GetAtoms, "NumAtoms", (basic.Integer, 'NumAtoms'))
-
- reg.add_module(GetHetAtoms)
- reg.add_input_port(GetHetAtoms, "Protein", (Protein, 'Protein'))
- reg.add_input_port(GetHetAtoms, "Atom Type", (basic.String, 'AtomType'))
- reg.add_output_port(GetHetAtoms, "NumAtoms", (basic.Integer, 'NumAtoms'))
-
- reg.add_module(GetSequence)
- reg.add_input_port(GetSequence, "Protein", (Protein, 'Protein'))
- reg.add_input_port(GetSequence, "SequenceID", (basic.String, 'SequenceID'))
- reg.add_output_port(GetSequence, "Sequence", (basic.String, 'Sequence'))
-
- reg.add_module(GetTitle)
- reg.add_input_port(GetTitle, "Protein", (Protein, 'Protein'))
- reg.add_output_port(GetTitle, "Title", (basic.String, 'Title'))
-
- reg.add_module(GetAuthor)
- reg.add_input_port(GetAuthor, "Protein", (Protein, 'Protein'))
- reg.add_output_port(GetAuthor, "Author", (basic.String, 'Author'))
-
- reg.add_module(GetPDBName)
- reg.add_input_port(GetPDBName, "Protein", (Protein, 'Protein'))
- reg.add_output_port(GetPDBName, "Name", (basic.String, 'Name'))
diff --git a/contrib/edu_utah_sci_vgc_afront/MANIFEST b/contrib/edu_utah_sci_vgc_afront/MANIFEST
deleted file mode 100644
index 61b0205..0000000
--- a/contrib/edu_utah_sci_vgc_afront/MANIFEST
+++ /dev/null
@@ -1 +0,0 @@
-F __init__.py
diff --git a/contrib/edu_utah_sci_vgc_afront/__init__.py b/contrib/edu_utah_sci_vgc_afront/__init__.py
deleted file mode 100644
index 7a71995..0000000
--- a/contrib/edu_utah_sci_vgc_afront/__init__.py
+++ /dev/null
@@ -1,143 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-"""The package afront defines three modules, Afront, AfrontIso and
-MeshQualityHistogram. These run the meshing code described in
-
-Schreiner et al, Vis 2006
-Schreiner et al, Eurographics 2006
-Scheidegger et al, SGP 2005
-
-"""
-
-from core.configuration import ConfigurationObject
-from core.modules.vistrails_module import Module, ModuleError
-from core.system import list2cmdline
-import core.bundles
-import core.modules.basic_modules
-import core.modules.module_registry
-import core.requirements
-import os
-
-configuration = ConfigurationObject(path=(None, str),
- debug=False)
-version = '0.1.0'
-identifier = 'edu.utah.sci.vgc.afront'
-name = 'Afront'
-
-################################################################################
-
-class AfrontRun(object):
-
- def run(self, args):
- cmd = ['afront', '-nogui'] + args
- cmdline = list2cmdline(cmd)
- print cmdline
- os.system(cmdline)
-# if result != 0:
-# raise ModuleError(self, "Execution failed")
-
-
-class Afront(Module, AfrontRun):
-
- def compute(self):
- o = self.interpreter.filePool.create_file(suffix='.m')
- args = []
- if not self.hasInputFromPort("file"):
- raise ModuleError(self, "Needs input file")
- args.append(self.getInputFromPort("file").name)
- if self.hasInputFromPort("rho"):
- args.append("-rho")
- args.append(str(self.getInputFromPort("rho")))
- if self.hasInputFromPort("eta"):
- args.append("-reduction")
- args.append(str(self.getInputFromPort("eta")))
- args.append("-outname")
- args.append(o.name)
- args.append("-tri")
- self.run(args)
- self.setResult("output", o)
-
-
-class MeshQualityHistogram(Module, AfrontRun):
-
- def compute(self):
- o = self.interpreter.filePool.create_file(suffix='.csv')
- args = []
- self.checkInputPort("file")
- args.append(self.getInputFromPort("file").name)
- args.append('-histname')
- args.append(o.name)
- args.append('-histogram')
- self.run(args)
- self.setResult("output", o)
-
-class AfrontIso(Afront):
-
- def compute(self):
- o = self.interpreter.filePool.create_file(suffix='.m')
- args = []
- if not self.hasInputFromPort("file"):
- raise ModuleError(self, "Needs input file")
- args.append(self.getInputFromPort("file").name)
- if self.hasInputFromPort("rho"):
- args.append("-rho")
- args.append(str(self.getInputFromPort("rho")))
- if self.hasInputFromPort("eta"):
- args.append("-eta")
- args.append(str(self.getInputFromPort("eta")))
- self.checkInputPort("iso")
- args.append("-outname")
- args.append(o.name)
- args.append("-tri")
- args.append(str(self.getInputFromPort("iso")))
- self.run(args)
- self.setResult("output", o)
-
-
-################################################################################
-
-def initialize():
-
- print "Afront VisTrails package"
- print "------------------------"
- print "Testing afront presence..."
-
-# if (not core.requirements.executable_file_exists('afront') and
-# not core.bundles.install({'linux-ubuntu': 'afront'})):
-# raise core.requirements.MissingRequirement("Afront")
-
- print "Ok, found afront"
- __version__ = 0.1
-
- reg = core.modules.module_registry
- reg.add_module(Afront)
- reg.add_input_port(Afront, "rho", (core.modules.basic_modules.Float, 'rho'))
- reg.add_input_port(Afront, "eta", (core.modules.basic_modules.Float, 'eta'))
- reg.add_input_port(Afront, "file", (core.modules.basic_modules.File, 'the file to process'))
- reg.add_output_port(Afront, "output", (core.modules.basic_modules.File, 'the result'))
-
- reg.add_module(MeshQualityHistogram)
- reg.add_input_port(MeshQualityHistogram, "file", core.modules.basic_modules.File)
- reg.add_output_port(MeshQualityHistogram, "output", core.modules.basic_modules.File)
-
- reg.add_module(AfrontIso)
- reg.add_input_port(AfrontIso, "iso", (core.modules.basic_modules.Float, 'iso'))
diff --git a/contrib/itk/FeatureExtractionFilters.py b/contrib/itk/FeatureExtractionFilters.py
deleted file mode 100644
index 6cb8cc7..0000000
--- a/contrib/itk/FeatureExtractionFilters.py
+++ /dev/null
@@ -1,208 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import itk
-import core.modules
-from core.modules.vistrails_module import Module, ModuleError
-
-from ITK import *
-from Image import Image
-
-class GradientMagnitudeRecursiveGaussianImageFilter(Module):
- my_namespace = "Filter|Feature"
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- sigma_ = self.getInputFromPort("Sigma")
-
- self.filter_ = itk.GradientMagnitudeRecursiveGaussianImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.SetSigma(sigma_)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Gradient Magnitude Recursive Gaussian Image Filter", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Sigma", (basic.Float, 'Sigma'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-#TODO this filter doesn't produce any results
-class DanielssonDistanceMapImageFilter(Module):
- my_namespace = 'Filter|Feature'
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- squared_distance = self.getInputFromPort("Squared Distance")
-
- image_spaceing = self.getInputFromPort("Image Spaceing")
-
- self.filter_ = itk.DanielssonDistanceMapImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.SetSquaredDistance(squared_distance)
- self.filter_.SetUseImageSpacing(image_spaceing)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="DanielssonDistance Map Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
- reg.add_input_port(cls, "Squared Distance", (basic.Float, 'Squared Distance'))
- reg.add_input_port(cls, "Image Spaceing", (basic.Float, 'Image Spaceing'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-class SobelEdgeDetectionImageFilter(Module):
- my_namespace = 'Filter|Feature'
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- self.filter_ = itk.SobelEdgeDetectionImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Sobel Edge Detection Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
diff --git a/contrib/itk/GradientFilters.py b/contrib/itk/GradientFilters.py
deleted file mode 100644
index 931d4e5..0000000
--- a/contrib/itk/GradientFilters.py
+++ /dev/null
@@ -1,84 +0,0 @@
-#############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import itk
-import core.modules
-from core.modules.vistrails_module import Module, ModuleError
-
-from ITK import *
-from Image import Image
-
-class GradientMagnitudeImageFilter(Module):
- my_namespace = 'Filter|Gradient'
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- self.filter_ = itk.GradientMagnitudeImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Gradient Magnitude Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
diff --git a/contrib/itk/ITK.py b/contrib/itk/ITK.py
deleted file mode 100644
index 2834326..0000000
--- a/contrib/itk/ITK.py
+++ /dev/null
@@ -1,166 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import core.modules
-from core.modules.vistrails_module import Module, ModuleError
-
-import itk
-
-class ITK(object):
- my_namespace="itk"
-
-class PixelType(Module, ITK):
- my_namespace = "disregard"
-
- def compute(self):
- pass
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Pixel Type", namespace=cls.my_namespace)
-
-class Filter(Module, ITK):
- my_namespace="disregard"
-
- def compute(self):
- pass
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Filter", namespace=cls.my_namespace)
-
-
-class Index2D(Module, ITK):
- my_namespace = "index"
-
- def compute(self):
- self.ind_ = itk.Index[2]()
- self.x_ = self.getInputFromPort("X Index")
- self.y_ = self.getInputFromPort("Y Index")
-
- self.ind_.SetElement(0,self.x_)
- self.ind_.SetElement(1,self.y_)
-
- self.setResult("Index", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Index2D", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "X Index", (basic.Integer, 'X Index'))
- reg.add_input_port(cls, "Y Index", (basic.Integer, 'Y Index'))
-
- reg.add_output_port(cls, "Index", (Index2D, 'Index'))
-
-class Index3D(Module, ITK):
- my_namespace = "index"
- def compute(self):
- self.ind_ = itk.Index[3]()
- self.x_ = self.getInputFromPort("X Index")
- self.y_ = self.getInputFromPort("Y Index")
- self.z_ = self.getInputFromPort("Z Index")
-
- self.ind_.SetElement(0,self.x_)
- self.ind_.SetElement(1,self.y_)
- self.ind_.SetElement(2,self.z_)
-
- self.setResult("Index", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Index3D", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "X Index", (basic.Integer, 'X Index'))
- reg.add_input_port(cls, "Y Index", (basic.Integer, 'Y Index'))
- reg.add_input_port(cls, "Z Index", (basic.Integer, 'Z Index'))
-
- reg.add_output_port(cls, "Index", (Index3D, 'Index'))
-
-class Size(Module, ITK):
- my_namespace = "size"
- def compute(self):
- dim = self.getInputFromPort("Dimension")
- self.size_ = itk.Size[dim]()
- self.x = self.getInputFromPort("Element 1")
- self.y = self.getInputFromPort("Element 2")
- if dim > 2:
- self.z = self.getInputFromPort("Element 3")
-
- self.size_.SetElement(0,self.x)
- self.size_.SetElement(1,self.y)
-
- if dim > 2:
- self.size_.SetElement(2,self.z)
-
- self.setResult("Size",self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Size", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
- reg.add_input_port(cls, "Element 1", (basic.Integer, 'Element 1'))
- reg.add_input_port(cls, "Element 2", (basic.Integer, 'Element 2'))
- reg.add_input_port(cls, "Element 3", (basic.Integer, 'Element 3'))
-
- reg.add_output_port(cls, "Size", (Size, 'Size'))
-
-class Region(Module, ITK):
- my_namespace = "region"
- def compute(self):
- dim = self.getInputFromPort("Dimension")
- self.region_ = itk.ImageRegion[dim]()
- self.region_.SetSize(self.getInputFromPort("Size").size_)
- if dim > 2:
- self.region_.SetIndex(self.getInputFromPort("Input 3D Index").ind_)
- else:
- self.region_.SetIndex(self.getInputFromPort("Input 2D Index").ind_)
-
- self.setResult("Region", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Region", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
- reg.add_input_port(cls, "Size", (Size, 'Size'))
- reg.add_input_port(cls, "Input 2D Index", (Index2D, 'Input 2D Index'))
- reg.add_input_port(cls, "Input 3D Index", (Index3D, 'Input 3D Index'), True)
-
- reg.add_output_port(cls, "Region", (Region, 'Region'))
-
-class Kernel(Module, ITK):
- my_namespace = "kernel"
- def compute(self):
- dim = self.getInputFromPort("Dimension")
- radius = self.getInputFromPort("Radius")
- self.kernel = itk.strel(dim,radius)
-
- self.setResult("Kernel", self.kernel)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Kernel", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
- reg.add_input_port(cls, "Radius", (basic.Integer, 'Radius'))
-
- reg.add_output_port(cls, "Kernel", (Kernel, 'Kernel'))
diff --git a/contrib/itk/Image.py b/contrib/itk/Image.py
deleted file mode 100644
index c4facc4..0000000
--- a/contrib/itk/Image.py
+++ /dev/null
@@ -1,64 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import itk
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from ITK import *
-from PixelType import *
-
-class Image(Module, ITK):
- my_namespace="disregard"
-
- def getPixelType(self):
- return self._type
-
- def getDim(self):
- return self.dim
-
- def getImg(self):
- return self.inIm
-
- def setImg(self, img):
- self.inIm = img
-
- def setDim(self, dim):
- self.dim = dim
-
- def setPixelType(self, pt):
- self._type = pt
-
- def compute(self):
- self.inIm = self.getInputFromPort("Image")
- self.dim = self.getInputFromPort("Dimension")
- self._type = self.getInputFromPort("Pixel Type")
-
- self.setResult("Output Image", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Image", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
- reg.add_input_port(cls, "Image", (Image, 'Image'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
diff --git a/contrib/itk/ImageReader.py b/contrib/itk/ImageReader.py
deleted file mode 100644
index c186ff7..0000000
--- a/contrib/itk/ImageReader.py
+++ /dev/null
@@ -1,169 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import itk
-import core.modules
-
-from ITK import *
-from Image import Image
-
-class ImageReader(Module):
- my_namespace = "ImageReader"
- def compute(self):
- dim = self.getInputFromPort("Dimension")
- outPixelType = self.getInputFromPort("Pixel Type")
- fn = self.getInputFromPort("Filename")
- self.reader = itk.ImageFileReader[itk.Image[outPixelType._type, dim]].New()
- self.reader.SetFileName(fn)
- self.reader.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.reader.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- self.setResult("Image", outIm)
- self.setResult("Reader", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="ImageReader", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
- reg.add_input_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
-
- reg.add_output_port(cls, "Image", (Image, 'Image'))
- reg.add_output_port(cls, "Reader", (ImageReader, 'Reader'))
-
-class ImageToFile(Module):
- my_namespace = "ImageReader"
- def compute(self):
- im = self.getInputFromPort("Image")
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")._type
- else:
- inPixelType = im.getPixelType()
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- suf = self.getInputFromPort("Suffix")
- f = self.createOutputFile(suf)
- writeType = itk.Image[inPixelType._type, dim]
- writer = itk.ImageFileWriter[writeType].New(im.getImg(), FileName=f.name)
- writer.Update()
- self.setResult("File", f)
-
- def createOutputFile(self, s):
- return self.interpreter.filePool.create_file(suffix=s)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="ImageToFile", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Suffix", (basic.String, 'Suffix'))
- reg.add_input_port(cls, "Pixel Type", (PixelType, 'Pixel Type'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Image", (Image, 'Image'))
-
- reg.add_output_port(cls, "File", (basic.File, 'File'))
-
-class GDCMReader(Module):
- my_namespace = "ImageReader"
- def compute(self):
- dir = self.getInputFromPort("Directory")
- dim = self.getInputFromPort("Dimension")
- self.dicomNames_ = itk.GDCMSeriesFileNames.New()
-
- self.dicomNames_.SetDirectory(dir)
- self.dicomNames_.SetUseSeriesDetails(True)
- self.dicomNames_.SetRecursive(True)
- self.dicomNames_.LoadSequencesOn()
-
- self.iType_ = itk.Image[itk.US,dim]
- self.reader_ = itk.ImageSeriesReader[self.iType_].New()
- self.reader_.SetFileNames(self.dicomNames_.GetInputFileNames())
- self.io_ = itk.GDCMImageIO.New()
- self.reader_.SetImageIO(self.io_.GetPointer())
- self.reader_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.reader_.GetOutput())
- outIm.setPixelType(itk.US)
- outIm.setDim(dim)
-
- self.setResult("Image Series", outIm)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="GDCMReader", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Directory", (basic.String, 'Directory'))
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
- reg.add_output_port(cls, "Image Series", (Image, 'Image Series'))
-
-class DICOMReader(Module):
- my_namespace = "ImageReader"
- def compute(self):
- dir = self.getInputFromPort("Directory")
- dim = self.getInputFromPort("Dimension")
- self.dicomNames_ = itk.DICOMSeriesFileNames.New()
-
- self.dicomNames_.SetFileNameSortingOrderToSortByImagePositionPatient()
- self.dicomNames_.SetDirectory(dir)
-
- self.iType_ = itk.Image[itk.US,dim]
- self.reader_ = itk.ImageSeriesReader[self.iType_].New()
- self.reader_.SetFileNames(self.dicomNames_.GetFileNames(False))
- self.reader_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.reader_.GetOutput())
- outIm.setPixelType(itk.US)
- outIm.setDim(dim)
-
- self.setResult("Image Series", outIm)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="DICOMReader", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Directory", (basic.String, 'Directory'))
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
- reg.add_output_port(cls, "Image Series", (Image, 'Image Series'))
-
-class ITKImageToVTKData(Module):
- my_namespace = "ImageReader"
- def compute(self):
- dim = self.getInputFromPort("Dimension")
- pType = self.getInputFromPort("Input PixelType")
- iType = itk.Image[itk.pType,dim]
- self.vtkExport_ = itk.VTKImageExport[iType].New()
- im = self.getInputFromPort("Input Image")
- self.vtkExport_.SetInput(im)
- self.vtkExport_.Update()
- self.setResult("VTK Output", self.vtkExport_.GetOutput())
-
- #TODO add register method
diff --git a/contrib/itk/IntensityFilters.py b/contrib/itk/IntensityFilters.py
deleted file mode 100644
index 987dfa9..0000000
--- a/contrib/itk/IntensityFilters.py
+++ /dev/null
@@ -1,343 +0,0 @@
-#############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import itk
-import core.modules
-from core.modules.vistrails_module import Module, ModuleError
-
-from ITK import *
-from Image import Image
-
-class RescaleIntensityImageFilter(Module):
- my_namespace = "Filter|Intensity"
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- minimum = self.getInputFromPort("Minimum")
- maximum = self.getInputFromPort("Maximum")
-
- self.filter_ = itk.RescaleIntensityImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.SetOutputMaximum(maximum)
- self.filter_.SetOutputMinimum(minimum)
-
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Rescale Intensity Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Minimum", (basic.Integer, 'Minimum'))
- reg.add_input_port(cls, "Maximum", (basic.Integer, 'Maximum'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-class SigmoidImageFilter(Module):
- my_namespace = "Filter|Intensity"
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- #default values are those that are recommended
- if self.hasInputFromPort("Minimum"):
- min = self.getInputFromPort("Minimum")
- else:
- min = 10
-
- if self.hasInputFromPort("Maximum"):
- max = self.getInputFromPort("Maximum")
- else:
- max = 240
-
- if self.hasInputFromPort("Alpha"):
- alpha = self.getInputFromPort("Alpha")
- else:
- alpha = 10
-
- if self.hasInputFromPort("Beta"):
- beta = self.getInputFromPort("Beta")
- else:
- beta = 170
-
- self.filter_ = itk.SigmoidImageFilter[inImgType,outImgType].New(im.getImg())
- self.filter_.SetOutputMinimum(min)
- self.filter_.SetOutputMaximum(max)
- self.filter_.SetAlpha(alpha)
- self.filter_.SetBeta(beta)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Sigmoid Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Minimum", (basic.Integer, 'Minimum'), True)
- reg.add_input_port(cls, "Maximum", (basic.Integer, 'Maximum'), True)
- reg.add_input_port(cls, "Alpha", (basic.Float, 'Alpha'), True)
- reg.add_input_port(cls, "Beta", (basic.Float, 'Beta'), True)
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Output Filter'),True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-class ThresholdImageFilter(Module):
- my_namespace = "Filter|Intensity"
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #setup filter
- inImgType = itk.Image[inPixelType._type, dim]
- up = self.getInputFromPort("Upper Value")
- lo = self.getInputFromPort("Lower Value")
-
- self.filter_ = itk.ThresholdImageFilter[inImgType].New(im.getImg())
-
- self.filter_.SetUpper(up)
- self.filter_.SetLower(lo)
-# self.filter_.ThresholdAbove(up)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(inPixelType)
- outIm.setDim(dim)
-
- self.setResult("Output Image", outIm)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Threshold Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Upper Value", (basic.Integer, 'Upper Value'))
- reg.add_input_port(cls, "Lower Value", (basic.Integer, 'Lower Value'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
-
-class ShiftScaleImageFilter(Module):
- my_namespace = "Filter|Intensity"
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- shift_value = self.getInputFromPort("Shift Value")
-
- scale_value = self.getInputFromPort("Scale Value")
-
- self.filter_ = itk.ShiftScaleImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.SetShift(shift_value)
- self.filter_.SetScale(scale_value)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Shift Scale Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
- reg.add_input_port(cls, "Shift Value", (basic.Float, 'Shift Value'))
- reg.add_input_port(cls, "Scale Value", (basic.Integer, 'Scale Value'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-class NormalizeImageFilter(Module):
- my_namespace = 'Filter|Intensity'
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- self.filter_ = itk.NormalizeImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Normalize Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
diff --git a/contrib/itk/NeighborhoodFilters.py b/contrib/itk/NeighborhoodFilters.py
deleted file mode 100644
index 0dbcaf2..0000000
--- a/contrib/itk/NeighborhoodFilters.py
+++ /dev/null
@@ -1,210 +0,0 @@
-#############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-import itk
-import core.modules
-from core.modules.vistrails_module import Module, ModuleError
-
-from ITK import *
-from Image import Image
-
-class MeanImageFilter(Module):
- my_namespace = 'Filter|Neighborhood'
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- self.filter_ = itk.MeanImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Mean Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-
-class MedianImageFilter(Module):
- my_namespace = 'Filter|Neighborhood'
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- self.filter_ = itk.MedianImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Median Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-#TODO does this filter even modify the image?
-class BinaryErodeImageFilter(Module):
- my_namespace = 'Filter|Neighborhood'
-
- def compute(self):
- print "comput"
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- kernel = self.getInputFromPort("Kernel")
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- erode_value = self.getInputFromPort("Erode Value")
-
- self.filter_ = itk.BinaryErodeImageFilter[inImgType, outImgType, kernel].New(im.getImg())
- self.filter_.SetKernel(kernel)
- self.filter_.SetErodeValue(erode_value)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Binary Erode Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Kernel", (Kernel, 'Kernel'))
-
- reg.add_input_port(cls, "Erode Value", (basic.Integer, 'Erode Value'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
diff --git a/contrib/itk/PixelType.py b/contrib/itk/PixelType.py
deleted file mode 100644
index 2f2beb4..0000000
--- a/contrib/itk/PixelType.py
+++ /dev/null
@@ -1,71 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import itk
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-
-from ITK import PixelType
-
-class PixelTypeFloat(Module):
- my_namespace = "pixeltype"
- def compute(self):
- self._type = itk.F
- self.setResult("Pixel Type", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Pixel Type Float", namespace=cls.my_namespace)
- reg.add_output_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
-
-class PixelTypeUnsignedChar(Module):
- my_namespace = "pixeltype"
- def compute(self):
- self._type = itk.UC
- self.setResult("Pixel Type", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Pixel Type Unsigned Char", namespace=cls.my_namespace)
- reg.add_output_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
-
-class PixelTypeUnsignedShort(Module):
- my_namespace = "pixeltype"
- def compute(self):
- self._type = itk.US
- self.setResult("Pixel Type", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Pixel Type Unsigned Short", namespace=cls.my_namespace)
- reg.add_output_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
-
-class PixelTypeRGB(Module):
- my_namespace = "pixeltype"
- def compute(self):
- self._type = itk.RGBPixel[itk.US]
- self.setResult("Pixel Type", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Pixel Type RGB", namespace=cls.my_namespace)
- reg.add_output_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
diff --git a/contrib/itk/SegmentationFilters.py b/contrib/itk/SegmentationFilters.py
deleted file mode 100644
index 77c5ad7..0000000
--- a/contrib/itk/SegmentationFilters.py
+++ /dev/null
@@ -1,319 +0,0 @@
-#############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import itk
-import core.modules
-from core.modules.vistrails_module import Module, ModuleError
-
-from ITK import *
-from Image import Image
-
-class IsolatedWatershedImageFilter(Module):
- my_namespace="Filter|Segmentation"
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- self.filter_ = itk.IsolatedWatershedImageFilter[inImgType, outImgType].New(im.getImg())
-
- if self.hasInputFromPort("Seed1"):
- self.filter_.SetSeed1(self.getInputFromPort("Seed1").ind_)
-
- if self.hasInputFromPort("Seed2"):
- self.filter_.SetSeed2(self.getInputFromPort("Seed2").ind_)
-
- if self.hasInputFromPort("ReplaceValue1"):
- self.filter_.SetReplaceValue1(self.getInputFromPort("ReplaceValue1"))
-
- if self.hasInputFromPort("ReplaceValue2"):
- self.filter_.SetReplaceValue2(self.getInputFromPort("ReplaceValue2"))
-
- if self.hasInputFromPort("Threshold"):
- self.filter_.SetThreshold(self.getInputFromPort("Threshold"))
-
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- self.setResult("Output Image", outIm)
- self.setResult("Output PixelType", outPixelType)
- self.setResult("Filter", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Isolated Watershed Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Seed1", (Index2D, 'Seed 1 Location'))
-
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
- reg.add_input_port(cls, "Threshold", (basic.Float, 'Threshold'), True)
- reg.add_input_port(cls, "Seed2", (Index2D, 'Seed 2 Location'))
- reg.add_input_port(cls, "ReplaceValue1", (basic.Float, 'Replacement Value 1'), True);
- reg.add_input_port(cls, "ReplaceValue2", (basic.Float, 'Replacement Value 2'), True);
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
-
-class ConnectedThresholdImageFilter(Module):
- my_namespace="Filter|Segmentation"
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- if self.hasInputFromPort("Seed2D"):
- seed = self.getInputFromPort("Seed2D")
- else:
- seed = self.getInputFromPort("Seed3D")
-
- replace = self.getInputFromPort("Replace Value")
- t_lower = self.getInputFromPort("Lower Value")
- t_upper = self.getInputFromPort("Upper Value")
-
- #setup filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- self.filter_ = itk.ConnectedThresholdImageFilter[inImgType,outImgType].New(im.getImg())
-
- self.filter_.SetSeed(seed.ind_)
- self.filter_.SetReplaceValue(replace)
- self.filter_.SetLower(t_lower)
- self.filter_.SetUpper(t_upper)
-
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- self.setResult("Output Image", outIm)
- self.setResult("Output PixelType", outPixelType)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Connected Threshold Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Seed2D", (Index2D, 'Seed Point'))
- reg.add_input_port(cls, "Seed3D", (Index3D, 'Seed Point'))
- reg.add_input_port(cls, "Replace Value", (basic.Float, 'Replacement Value'))
- reg.add_input_port(cls, "Upper Value", (basic.Float, 'Upper Threshold Value'))
- reg.add_input_port(cls, "Lower Value", (basic.Float, 'Lower Threshold Value'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
-
-class ConfidenceConnectedImageFilter(Module):
- my_namespace="Filter|Segmentation"
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- if self.hasInputFromPort("Seed2D"):
- seed = self.getInputFromPort("Seed2D")
- else:
- seed = self.getInputFromPort("Seed3D")
-
- replace = self.getInputFromPort("Replace Value")
- multiplier = self.getInputFromPort("Multiplier")
- iterations = self.getInputFromPort("Iterations")
- radius = self.getInputFromPort("Neighborhood Radius")
-
- #setup filter
- inImgType = itk.Image[inPixelType._type,dim]
- outImgType = itk.Image[outPixelType._type,dim]
-
- self.filter_ = itk.ConfidenceConnectedImageFilter[inImgType,outImgType].New(im.getImg())
-
- self.filter_.SetReplaceValue(replace)
- self.filter_.SetMultiplier(multiplier)
- self.filter_.SetNumberOfIterations(iterations)
- self.filter_.SetInitialNeighborhoodRadius(radius)
-
- self.filter_.SetSeed(seed.ind_)
-
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- self.setResult("Output Image", outIm)
- self.setResult("Output PixelType", outPixelType)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Confidence Connected Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Seed2D", (Index2D, 'Seed Point'))
- reg.add_input_port(cls, "Seed3D", (Index3D, 'Seed Point'))
- reg.add_input_port(cls, "Replace Value", (basic.Float, 'Replacement Value'))
- reg.add_input_port(cls, "Multiplier", (basic.Float, 'Multiplier'))
- reg.add_input_port(cls, "Iterations", (basic.Float, 'Iterations'))
- reg.add_input_port(cls, "Neighborhood Radius", (basic.Float, 'Neighborhood Radius'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
-
-class IsolatedConnectedImageFilter(Module):
- my_namespace="Filter|Segmentation"
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- seed1 = self.getInputFromPort("Seed1")
- seed2 = self.getInputFromPort("Seed2")
-
- replace = self.getInputFromPort("Replace Value")
- t_lower = self.getInputFromPort("Lower Value")
- t_upper = self.getInputFromPort("Upper Value")
-
- inImgType = itk.Image[inPixelType._type,dim]
- outImgType = itk.Image[outPixelType._type,dim]
-
- self.filter_ = itk.IsolatedConnectedImageFilter[inImgType,outImgType].New(im.getImg())
-
- self.filter_.SetReplaceValue(replace)
- self.filter_.SetLower(t_lower)
- self.filter_.SetUpperValueLimit(t_upper)
- self.filter_.SetSeed1(seed1.ind_)
- self.filter_.SetSeed2(seed2.ind_)
-
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- self.setResult("Output Image", outIm)
- self.setResult("Output PixelType", outPixelType)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Isolated Connected Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Seed1", (Index2D, 'Seed Point'))
- reg.add_input_port(cls, "Seed2", (Index2D, 'Seed Point'))
- reg.add_input_port(cls, "Replace Value", (basic.Integer, 'Replacement Value'))
- reg.add_input_port(cls, "Upper Value", (basic.Integer, 'Upper Threshold Value'))
- reg.add_input_port(cls, "Lower Value", (basic.Integer, 'Lower Threshold Value'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
diff --git a/contrib/itk/SelectionFilters.py b/contrib/itk/SelectionFilters.py
deleted file mode 100644
index 61b5302..0000000
--- a/contrib/itk/SelectionFilters.py
+++ /dev/null
@@ -1,231 +0,0 @@
-#############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import itk
-import core.modules
-from core.modules.vistrails_module import Module, ModuleError
-from ITK import *
-from Image import Image
-
-class RegionOfInterestImageFilter(Module):
- my_namespace="Filter|Selection"
-
- def setStart(self, start):
- if start == 2:
- self.index = self.getInputFromPort("Input 2D Index").ind_
- else:
- self.index = self.getInputFromPort("Input 3D Index").ind_
-
- self.region_.SetIndex(self.index)
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Input Dimension"):
- dim = self.getInputFromPort("Input Dimension")
- else:
- dim = im.getDim()
-
- if self.hasInputFromPort("Output Dimension"):
- outDim = self.getInputFromPort("Output Dimension")
- else:
- outDim = dim
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, outDim]
-
- self.filter_ = itk.RegionOfInterestImageFilter[inImgType, outImgType].New()
-
- #TODO this is not correct, needs fixing
- if self.hasInputFromPort("Input Region"):
- self.region_ = self.getInputFromPort("Input Region").region_
- else:
- self.region_ = itk.ImageRegion[indim]()
- self.setStart(indim)
- self.region_.SetSize(self.getInputFromPort("Region Size").size_)
-
- self.filter_.SetRegionOfInterest(self.region_)
- self.filter_.SetInput(im.getImg())
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(outDim)
-
- self.setResult("Output Image", outIm)
- self.setResult("Output PixelType", outPixelType)
- self.setResult("Output Dimension", outDim)
- self.setResult("Filter", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Region of Interest Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Output Dimension", (basic.Integer, 'Dimension'),True)
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Input Region", (Region, 'Input Region'))
- reg.add_input_port(cls, "Region Size", (Size, 'Region Size'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_output_port(cls, "Output Dimension", (basic.Integer, 'Dimension'),True)
-
-class CastImageFilter(Module):
- my_namespace="Filter|Selection"
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for in dimension
- if self.hasInputFromPort("Input Dimension"):
- dim = self.getInputFromPort("Input Dimension")
- else:
- dim = im.getDim()
-
- #check for out dimension
- if self.hasInputFromPort("Output Dimension"):
- outDim = self.getInputFromPort("Output Dimension")
- else:
- outDim = dim
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, outDim]
-
- self.filter_ = itk.CastImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(outDim)
-
- self.setResult("Output Image", outIm)
- self.setResult("Output PixelType", outPixelType)
- self.setResult("Output Dimension", outDim)
- self.setResult("Filter", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Cast Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Input Dimension'),True)
- reg.add_input_port(cls, "Output Dimension", (basic.Integer, 'Output Dimension'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'),True)
- reg.add_output_port(cls, "Output Dimension", (basic.Integer, 'Output Dimension'),True)
-
-
-class ExtractImageFilter(Module):
- my_namespace="Filter|Selection"
- def compute(self):
- #TODO should this be Input Volume?
- im = self.getInputFromPort("Input Volume")
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #set outPixelType
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #check for out dimension
- if self.hasInputFromPort("Output Dimension"):
- outDim = self.getInputFromPort("Output Dimension")
- else:
- outDim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, outDim]
-
- self.filter_ = itk.ExtractImageFilter[inImgType,outImgType].New(im.getImg())
-
- region = self.getInputFromPort("Extraction Region")
- self.filter_.SetExtractionRegion(region.region_)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(outDim)
-
- self.setResult("Output Image", outIm)
- self.setResult("Output PixelType", outPixelType)
- self.setResult("Dimension", outDim)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Extract Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Volume", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Input Dimension'),True)
- reg.add_input_port(cls, "Output Dimension", (basic.Integer, 'Output Dimension'),True)
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Extraction Region", (Region, 'Extraction Region'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_output_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
diff --git a/contrib/itk/SmoothingFilters.py b/contrib/itk/SmoothingFilters.py
deleted file mode 100644
index dd9e764..0000000
--- a/contrib/itk/SmoothingFilters.py
+++ /dev/null
@@ -1,558 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import itk
-import core.modules
-from core.modules.vistrails_module import Module, ModuleError
-from ITK import *
-from Image import Image
-
-class CurvatureAnisotropicDiffusionFilter(Module):
- my_namespace="Filter|Smoothing"
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
-
- try:
- self.filter_ = itk.CurvatureAnisotropicDiffusionImageFilter[inImgType, inImgType].New(im.getImg())
- except:
- raise ModuleError(self, "Filter requires a decimal PixelType")
-
- #default values are recommended
- if self.hasInputFromPort("Iterations"):
- iterations = self.getInputFromPort("Iterations")
- else:
- iterations = 5
-
- if self.hasInputFromPort("TimeStep"):
- timestep = self.getInputFromPort("TimeStep")
- else:
- if dim == 2:
- timestep = 0.125
- else:
- timestep = 0.0625
-
- if self.hasInputFromPort("Conductance"):
- conductance = self.getInputFromPort("Conductance")
- else:
- conductance = 3.0
-
- self.filter_.SetNumberOfIterations(iterations)
- self.filter_.SetTimeStep(timestep)
- self.filter_.SetConductanceParameter(conductance)
-
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(inPixelType)
- outIm.setDim(dim)
-
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Curvature Anisotropic Diffusion Filter", namespace=cls.my_namespace)
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Input Dimension'),True)
- reg.add_input_port(cls, "Input PixelType Float", (PixelType, 'Input PixelType Float'),True)
- reg.add_input_port(cls, "Iterations", (basic.Integer, 'Iterations'), True)
- reg.add_input_port(cls, "TimeStep", (basic.Float, 'TimeStep'), True)
- reg.add_input_port(cls, "Conductance", (basic.Float, 'Conductance'), True)
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
-
-
-class RecursiveGaussianImageFilter(Module):
- my_namespace="Filter|Smoothing"
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- outdim = dim
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- self.filter_ = itk.RecursiveGaussianImageFilter[inImgType, outImgType].New(im.getImg())
-
- sigma = self.getInputFromPort("Sigma")
- self.filter_.SetSigma(sigma)
-
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- self.setResult("Output Image", outIm)
- self.setResult("Output PixelType", outPixelType)
- self.setResult("Output Dimension", outdim)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Recursive Gaussian Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Input Dimension'),True)
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Sigma", (basic.Float, 'Sigma'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Output Dimension", (basic.Integer, 'Output Dimension'),True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-class CurvatureFlowImageFilter(Module):
- my_namespace="Filter|Smoothing"
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
-
- try:
- self.filter_ = itk.CurvatureFlowImageFilter[inImgType, inImgType].New(im.getImg())
- except:
- raise ModuleError(self, "Filter requires a decimal PixelType")
-
- #default values recommended
- if self.hasInputFromPort("TimeStep"):
- self.ts = self.getInputFromPort("TimeStep")
- else:
- self.ts = 0.125
-
- if self.hasInputFromPort("Iterations"):
- self.iterations = self.getInputFromPort("Iterations")
- else:
- self.iterations = 5
-
- self.filter_.SetTimeStep(self.ts)
- self.filter_.SetNumberOfIterations(self.iterations)
-
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(inPixelType)
- outIm.setDim(dim)
-
- self.setResult("Output Image", outIm)
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Curvature Flow Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input Dimension", (basic.Integer, 'Input Dimension'),True)
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "TimeStep", (basic.Float, 'TimeStep'), True)
- reg.add_input_port(cls, "Iterations", (basic.Integer, 'Iterations'), True)
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
-
-class DiscreteGaussianImageFilter(Module):
- my_namespace = 'Filter|Smoothing'
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- gaussian_variance = self.getInputFromPort("Gaussian Variance")
-
- max_kernel_width = self.getInputFromPort("Max Kernel Width")
-
- try:
- self.filter_ = itk.DiscreteGaussianImageFilter[inImgType, outImgType].New(im.getImg())
- except:
- raise ModuleError(self, "Requires Signed PixelType")
-
- self.filter_.SetVariance(gaussian_variance)
- self.filter_.SetMaximumKernelWidth(max_kernel_width)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Discrete Gaussian Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
- reg.add_input_port(cls, "Gaussian Variance", (basic.Float, 'Gaussian Variance'))
- reg.add_input_port(cls, "Max Kernel Width", (basic.Integer, 'Max Kernel Width'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-class BinomialBlurImageFilter(Module):
- my_namespace = 'Filter|Smoothing'
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- repetitions = self.getInputFromPort("Repetitions")
-
- self.filter_ = itk.BinomialBlurImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.SetRepetitions(repetitions)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="BinomialBlur Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
- reg.add_input_port(cls, "Repetitions", (basic.Integer, 'Repetitions'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-class GradientAnisotropicDiffusionImageFilter(Module):
- my_namespace = 'Filter|Smoothing'
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- timestep = self.getInputFromPort("Timestep")
-
- conductance = self.getInputFromPort("Conductance")
-
- iterations = self.getInputFromPort("Iterations")
-
- try:
- self.filter_ = itk.GradientAnisotropicDiffusionImageFilter[inImgType, outImgType].New(im.getImg())
- except:
- raise ModuleError(self, "Requires Decimal PixelType")
-
- self.filter_.SetTimeStep(timestep)
- self.filter_.SetConductanceParameter(conductance)
- self.filter_.SetNumberOfIterations(iterations)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Gradient Anisotropic Diffusion Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
- reg.add_input_port(cls, "Timestep", (basic.Float, 'Timestep'))
- reg.add_input_port(cls, "Conductance", (basic.Float, 'Conductance'))
- reg.add_input_port(cls, "Iterations", (basic.Integer, 'Iterations'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-
-class MinMaxCurvatureFlowImageFilter(Module):
- my_namespace = 'Filter|Smoothing'
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- timestep = self.getInputFromPort("Timestep")
-
- radius = self.getInputFromPort("Radius")
-
- iterations = self.getInputFromPort("Iterations")
-
- self.filter_ = itk.MinMaxCurvatureFlowImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.SetTimeStep(timestep)
- self.filter_.SetStencilRadius(radius)
- self.filter_.SetNumberOfIterations(iterations)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="MinMax Curvature Flow Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
- reg.add_input_port(cls, "Timestep", (basic.Float, 'Timestep'))
- reg.add_input_port(cls, "Radius", (basic.Float, 'Radius'))
- reg.add_input_port(cls, "Iterations", (basic.Integer, 'Iterations'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
-class BilateralImageFilter(Module):
- my_namespace = 'Filter|Smoothing'
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- range_sigma = self.getInputFromPort("Range Sigma")
-
- domain_sigma = self.getInputFromPort("Domain Sigma")
-
- self.filter_ = itk.BilateralImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.SetRangeSigma(range_sigma)
- self.filter_.SetDomainSigma(domain_sigma)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="Bilateral Image Filter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
- reg.add_input_port(cls, "Range Sigma", (basic.Float, 'Range Sigma'))
- reg.add_input_port(cls, "Domain Sigma", (basic.Float, 'Domain Sigma'))
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
diff --git a/contrib/itk/ThresholdFilters.py b/contrib/itk/ThresholdFilters.py
deleted file mode 100644
index bab496a..0000000
--- a/contrib/itk/ThresholdFilters.py
+++ /dev/null
@@ -1,110 +0,0 @@
-#############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-import itk
-import core.modules
-from core.modules.vistrails_module import Module, ModuleError
-
-from ITK import *
-from Image import Image
-
-class BinaryThresholdImageFilter(Module):
- my_namespace = "Filter|Threshold"
-
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
-
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-
- if self.hasInputFromPort("Upper Threshold"):
- upper_threshold = self.getInputFromPort("Upper Threshold")
- else:
- upper_threshold = 255
-
- lower_threshold = self.getInputFromPort("Lower Threshold")
-
- if self.hasInputFromPort("Outside Value"):
- outside_value = self.getInputFromPort("Outside Value")
- else:
- outside_value = 0
-
- if self.hasInputFromPort("Inside Value"):
- inside_value = self.getInputFromPort("Inside Value")
- else:
- inside_value = 255
-
- self.filter_ = itk.BinaryThresholdImageFilter[inImgType, outImgType].New(im.getImg())
- self.filter_.SetUpperThreshold(upper_threshold)
- self.filter_.SetLowerThreshold(lower_threshold)
- self.filter_.SetOutsideValue(outside_value)
- self.filter_.SetInsideValue(inside_value)
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-
-
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="BinaryThresholdImageFilter", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-
- reg.add_input_port(cls, "Upper Threshold", (basic.Integer, 'Upper Threshold'),True)
- reg.add_input_port(cls, "Lower Threshold", (basic.Integer, 'Lower Threshold'))
- reg.add_input_port(cls, "Outside Value", (basic.Integer, 'Outside Value'),True)
- reg.add_input_port(cls, "Inside Value", (basic.Integer, 'Inside Value'),True)
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-
diff --git a/contrib/itk/__init__.py b/contrib/itk/__init__.py
deleted file mode 100644
index 65c2952..0000000
--- a/contrib/itk/__init__.py
+++ /dev/null
@@ -1,179 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-# ITK package for VisTrails
-############################################################################
-
-"""ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. www.itk.org
-
-For info on installing itk and python-itk on ubuntu see: http://paulnovo.org/node/2
-
-For info on generating wrapper modules for more itk filters see itk/filter_generator.py"""
-
-version = '0.2'
-identifier = 'edu.utah.sci.vistrails.itk'
-name = 'ITK'
-
-import core.bundles.utils
-import core.requirements
-from core.modules.vistrails_module import Module, ModuleError
-
-# Ugly, but Carlos doesnt know any better
-if core.bundles.utils.guess_system() == 'linux-ubuntu':
- import sys
- sys.path.append('/usr/local/lib/VisTrailsITK')
-
-try:
- from core.bundles import py_import
- itk = py_import('itk', {'linux-ubuntu': 'vistrails-itk'})
-except ImportError:
- raise core.requirements.MissingRequirement("ITK and WrapITK")
-
-import core.modules
-import core.modules.module_registry
-
-# ITK Package imports
-from PixelType import *
-from FeatureExtractionFilters import *
-from ITK import *
-from Image import Image
-from IntensityFilters import *
-from SegmentationFilters import *
-from SelectionFilters import *
-from SmoothingFilters import *
-from ThresholdFilters import *
-from GradientFilters import *
-from NeighborhoodFilters import *
-from ImageReader import *
-
-def initialize(*args, **keywords):
- reg = core.modules.module_registry
- basic = core.modules.basic_modules
-
-########################################################################################
-# Misc.
- Index2D.register(reg,basic)
- Index3D.register(reg,basic)
- Size.register(reg,basic)
- Region.register(reg,basic)
- PixelType.register(reg,basic)
- Filter.register(reg,basic)
- Kernel.register(reg,basic)
-
- Image.register(reg,basic)
-
-########################################################################################
-# Pixel Types
- pixeltypes = [PixelTypeFloat,
- PixelTypeUnsignedChar,
- PixelTypeUnsignedShort,
- PixelTypeRGB]
-
- for cls in pixeltypes:
- cls.register(reg,basic)
-
-
-########################################################################################
-# Feature Extraction Filters
- featurefilters = [GradientMagnitudeRecursiveGaussianImageFilter,
- DanielssonDistanceMapImageFilter,
- SobelEdgeDetectionImageFilter]
-
- for cls in featurefilters:
- cls.register(reg,basic)
-
-########################################################################################
-# Intensity Filters
- intensityfilters = [RescaleIntensityImageFilter,
- SigmoidImageFilter,
- ThresholdImageFilter,
- ShiftScaleImageFilter,
- NormalizeImageFilter]
-
- for cls in intensityfilters:
- cls.register(reg,basic)
-
-########################################################################################
-# Segmentation Filters
- segmentationfilters = [IsolatedWatershedImageFilter,
- ConnectedThresholdImageFilter,
- ConfidenceConnectedImageFilter,
- IsolatedConnectedImageFilter]
-
- for cls in segmentationfilters:
- cls.register(reg,basic)
-
-########################################################################################
-# Selection Filters
- selectionfilters = [RegionOfInterestImageFilter,
- CastImageFilter,
- ExtractImageFilter]
-
- for cls in selectionfilters:
- cls.register(reg,basic)
-
-########################################################################################
-# Smoothing Filters
- smoothingfilters = [CurvatureAnisotropicDiffusionFilter,
- RecursiveGaussianImageFilter,
- DiscreteGaussianImageFilter,
- GradientAnisotropicDiffusionImageFilter,
- MinMaxCurvatureFlowImageFilter,
- BinomialBlurImageFilter,
- BilateralImageFilter,
- CurvatureFlowImageFilter]
-
- for cls in smoothingfilters:
- cls.register(reg,basic)
-
-########################################################################################
-# Threshold Filters
- thresholdfilters = [BinaryThresholdImageFilter]
-
- for cls in thresholdfilters:
- cls.register(reg,basic)
-
-########################################################################################
-# Gradient Filters
- gradientfilters = [GradientMagnitudeImageFilter]
-
- for cls in gradientfilters:
- cls.register(reg,basic)
-
-########################################################################################
-# Neighborhood Filters
- neighborhoodfilters = [MeanImageFilter,
- MedianImageFilter,
- BinaryErodeImageFilter]
-
- for cls in neighborhoodfilters:
- cls.register(reg,basic)
-
-########################################################################################
-# Image Reader
- imagereader = [ImageReader,
- ImageToFile,
- GDCMReader,
- DICOMReader]
-
-
- for cls in imagereader:
- cls.register(reg,basic)
diff --git a/contrib/itk/filter_generator.py b/contrib/itk/filter_generator.py
deleted file mode 100644
index 352cd6a..0000000
--- a/contrib/itk/filter_generator.py
+++ /dev/null
@@ -1,170 +0,0 @@
-# This is a rough code generation tool that works to generate code used to wrap itk functions for Vistrails
-# In order to use this one must:
-# -set generation variables
-# -run script
-# -paste output into desired *Filters.py file
-# -add new filter name to __init__.py file
-#
-#NOTE: some filters require special calls, params, etc. that are not generated with this code
-# for example, many filters only accept decimal PixelTypes meaning that the
-# filter initialization should be wrapped in a try/except raising a ModuleError
-#
-# For example filter implementation, check out:
-# http://math.nist.gov/mcsd/savg/software/filters/
-# http://voxel.jouy.inra.fr/darcs/contrib-itk/WrapITK/Python/Tests/
-
-##########################################################
-#String Manipulation Methods
-##########################################################
-def AddSpaces(word):
- output = ""
- for char in word:
- if char.isupper() and word.index(char)!=0:
- output += " %s"%char
- else:
- output += char
- return output
-
-def SplitCap(word):
- temp = word.split("_")
- output = ""
- for elem in temp:
- output += "%s "%elem.capitalize()
- return output.strip()
-
-##########################################################
-#SETUP generation variables
-##########################################################
-#filter_name should be equal to itk.filter_name
-filter_name = "BinaryErodeImageFilter"
-
-#designate namespace
-namespace = "Filter|Neighborhood"
-
-#some filters require kernel inputs, usually they don't though
-has_kernel = True
-
-#usage: {variable name:[variable type, default value, itk filter set method]}
-#NOTE: you must look up the itk filter set method (dir(itk.filter_name))
-filter_values = {"level":["basic.Float",None, "SetSquaredDistance"],
- "lower_threshold":["basic.Float",None, "SetUseImageSpacing"]}
-
-##########################################################
-#code generation
-##########################################################
-out_class = """class %s(Module):
- my_namespace = '%s'"""%(filter_name, namespace)
-
-compute = """
- def compute(self):
- im = self.getInputFromPort("Input Image")
-
- #check for input PixelType
- if self.hasInputFromPort("Input PixelType"):
- inPixelType = self.getInputFromPort("Input PixelType")
- else:
- inPixelType = im.getPixelType()
-
- #check for output PixelType
- if self.hasInputFromPort("Output PixelType"):
- outPixelType = self.getInputFromPort("Output PixelType")
- else:
- outPixelType = inPixelType
-
- #check for dimension
- if self.hasInputFromPort("Dimension"):
- dim = self.getInputFromPort("Dimension")
- else:
- dim = im.getDim()
- """
-if has_kernel:
- compute += """
- kernel = self.getInputFromPort("Kernel")
- """
-
-compute += """
- #set up filter
- inImgType = itk.Image[inPixelType._type, dim]
- outImgType = itk.Image[outPixelType._type, dim]
-"""
-for param in filter_values:
- #check if default value is set
- if type(filter_values[param][1]).__name__ != "NoneType":
- compute += """
- if self.hasInputFromPort("%s"):
- %s = self.getInputFromPort("%s")
- else:
- %s = %d\n"""%(SplitCap(param), param, SplitCap(param), param, filter_values[param][1])
- else:
- compute += """
- %s = self.getInputFromPort("%s")\n"""%(param, SplitCap(param))
-
-if has_kernel:
- compute += """
- self.filter_ = itk.%s[inImgType, outImgType, kernel].New(im.getImg())
- self.filter_.SetKernel(kernel)"""%filter_name
-
-else:
- compute += """
- self.filter_ = itk.%s[inImgType, outImgType].New(im.getImg())"""%filter_name
-
-#set filter values
-for param in filter_values:
- compute += """
- self.filter_.%s(%s)"""%(filter_values[param][2], param)
-
-compute += """
- self.filter_.Update()
-
- #setup output image
- outIm = Image()
- outIm.setImg(self.filter_.GetOutput())
- outIm.setPixelType(outPixelType)
- outIm.setDim(dim)
-
- #set results
- self.setResult("Output Image", outIm)
- self.setResult("Filter", self)
- self.setResult("Output PixelType", outPixelType)
-"""
-register = """
- @classmethod
- def register(cls, reg, basic):
- reg.add_module(cls, name="%s", namespace=cls.my_namespace)
-
- reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
- reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
- reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
- reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
-"""%AddSpaces(filter_name)
-if has_kernel:
- register += """
- reg.add_input_port(cls, "Kernel", (Kernel, 'Kernel'))
- """
-
-for param in filter_values:
- #check if default value is set
- if type(filter_values[param][1]).__name__ != "NoneType":
- register += """
- reg.add_input_port(cls, "%s", (%s, '%s'),True)"""%(SplitCap(param),\
- filter_values[param][0],\
- SplitCap(param))
- else:
- register += """
- reg.add_input_port(cls, "%s", (%s, '%s'))"""%(SplitCap(param),\
- filter_values[param][0],\
- SplitCap(param))
-
-register += """
-
- reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
- reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
- reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
-"""
-
-##########################################################
-#Output
-##########################################################
-print out_class
-print compute
-print register
diff --git a/contrib/itk/itk_test_example.py b/contrib/itk/itk_test_example.py
deleted file mode 100644
index 4786ae7..0000000
--- a/contrib/itk/itk_test_example.py
+++ /dev/null
@@ -1,42 +0,0 @@
-#example code to be pasted into a python terminal to test itk filters
-#generally used to instaniate filters inorder lookup variable set methods
-
-import itk
-#image setup
-dim = 2
-pixeltype = itk.UC
-kernel = itk.stle(dim, 5)
-filename = "/home/mates/Desktop/brains.jpg"
-reader = itk.ImageFileReader[itk.Image[pixeltype, dim]].New()
-reader.SetFileName(filename)
-reader.Update()
-
-im = reader.GetOutput()
-inImg = itk.Image[pixeltype, dim]
-outImg = inImg
-
-size_ = itk.Size[dim]()
-size_.SetElement(0,150)
-size_.SetElement(1,150)
-region_ = itk.ImageRegion[dim]()
-region_.SetSize(size_)
-
-#filter
-filt = itk.IsolatedConnectedImageFilter[inImg, outImg].New(im)
-filt.SetReplaceValue(120)
-filt.SetLower(155)
-filt.SetUpperValueLimit(235)
-filt.SetSeed1([120,120])
-filt.SetSeed2([140,140])
-filt.Update()
-
-filt2 = itk.ConnectedThresholdImageFilter[itk.Image[pixeltype, dim], itk.Image[pixeltype, dim]].New(im)
-filt2.SetSeed([100,100])
-filt2.SetReplaceValue(100)
-filt2.SetLower(150)
-filt2.SetUpper(250)
-filt2.Update()
-
-#write to file
-writer = itk.ImageFileWriter[itk.Image[pixeltype, dim]].New(filt.GetOutput(), FileName="/home/mates/Desktop/output.jpg")
-writer.Update()
diff --git a/contrib/meshutils.py b/contrib/meshutils.py
deleted file mode 100644
index af0f8f1..0000000
--- a/contrib/meshutils.py
+++ /dev/null
@@ -1,104 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-import core.bundles
-import core.requirements
-import os
-import re
-
-identifier = 'edu.utah.sci.cscheid.meshutils'
-version = '0.1'
-name = 'Mesh utility'
-
-class MeshArea(Module):
-
- def compute(self):
- self.checkInputPort('input_file')
- f1 = self.getInputFromPort('input_file')
- text_output = self.interpreter.filePool.create_file()
-
- cmdline = []
- cmdline.append(meshareapath)
- cmdline.append(f1.name)
- cmdline.append('>' + text_output.name)
- cmdline = ('%s ' * len(cmdline)) % tuple(cmdline)
- print cmdline
- result = os.system(cmdline)
- if result != 0:
- raise ModuleError(self, "execution failed")
- try:
- l = file(text_output.name).readlines()[-1]
- v = float(l)
- except:
- raise ModuleError(self, "Expected a float, got '%s'" % l)
- self.setResult('area', v)
-
-class MeshChoose(Module):
-
- def guess_input_format(self, input_file_name):
- i = input_file_name.rfind('.')
- if i == -1:
- return None
- else:
- return input_file_name[i:]
-
- def compute(self):
- self.checkInputPort('input_file_1')
- self.checkInputPort('input_file_2')
-
- input_file_1 = self.getInputFromPort('input_file_1')
- input_file_2 = self.getInputFromPort('input_file_2')
-
- if self.hasInputFromPort('output_format'):
- output_suffix = self.getInputFromPort('output_format')
- else:
- output_suffix = self.guess_input_format(input_file_2.name)
-
- output_file = self.interpreter.filePool.create_file(output_suffix)
-
- cmdline = [meshchoosepath,
- input_file_1.name,
- input_file_2.name,
- output_file.name]
- cmdline = ('%s ' * len(cmdline)) % tuple(cmdline)
- print cmdline
- result = os.system(cmdline)
- if result != 0:
- raise ModuleError(self, "execution failed")
- self.setResult('output_file', output_file)
-
-def setpath(prefix):
- global meshareapath
- meshareapath = prefix + 'mesh_area'
- global meshchoosepath
- meshchoosepath = prefix + 'mesh_choose'
-
-def initialize(meshutilspath=None):
- global _mesh_utils_path
- if not meshutilspath:
- print "Assuming mesh_utils are on path"
- setpath('')
- else:
- print "Assuming mesh_utils are in '%s/'" % meshutilspath
- setpath(meshutilspath+'/')
- reg = core.modules.module_registry
- reg.add_module(MeshArea)
- reg.add_input_port(MeshArea, 'input_file',
- core.modules.basic_modules.File)
- reg.add_output_port(MeshArea, 'area',
- core.modules.basic_modules.Float)
-
- reg.add_module(MeshChoose)
- reg.add_input_port(MeshChoose, 'input_file_1',
- core.modules.basic_modules.File)
- reg.add_input_port(MeshChoose, 'input_file_2',
- core.modules.basic_modules.File)
- reg.add_input_port(MeshChoose, 'output_format',
- core.modules.basic_modules.String)
-
- reg.add_output_port(MeshChoose, 'output_file',
- core.modules.basic_modules.File)
-
-
-
-
diff --git a/contrib/mobile/__init__.py b/contrib/mobile/__init__.py
deleted file mode 100644
index 4d191e2..0000000
--- a/contrib/mobile/__init__.py
+++ /dev/null
@@ -1,365 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-"""This package provides interaction with mobile devices.
-It contains modules to represent a geolocation, to get an image and a sound memo.
-Executing on a desktop will do nothing for now.
-
-"""
-import base64
-from datetime import datetime
-
-from core.configuration import ConfigurationObject
-from core.modules.vistrails_module import Module, ModuleError
-from core.modules.basic_modules import Constant, Float, File, String
-from core.system import get_elementtree_library
-
-from time import strptime
-from datetime import datetime
-
-ElementTree = get_elementtree_library()
-
-name = "Mobile"
-identifier = "edu.utah.sci.vistrails.mobile"
-version = '0.0.1'
-
-class LocationCoordinate2D(Constant):
- """A structure that contains a geographical coordinate using the
- WGS 84 reference frame."""
- def __init__(self):
- Constant.__init__(self)
- self.latitude = None
- self.longitude = None
- LocationCoordinate2D.default_value = self
-
- @staticmethod
- def from_xml_string(xml_string):
- node = ElementTree.fromstring(xml_string)
- if node.tag != 'coordinate':
- return None
- #read attributes
- data = node.get('latitude', None)
- lati = float(data)
-
- data = node.get('longitude', None)
- longi = float(data)
-
- coord = LocationCoordinate2D()
- coord.latitude = lati
- coord.longitude = longi
- return coord
-
- @staticmethod
- def to_xml_string(x):
- node = ElementTree.Element('coordinate')
- node.set('latitude', str(x.latitude))
- node.set('longitude', str(x.longitude))
- return ElementTree.tostring(node)
-
- @staticmethod
- def translate_to_python(x):
- result = LocationCoordinate2D.from_xml_string(x)
- result.setResult("value", result)
- return result
-
- @staticmethod
- def translate_to_string(x):
- return LocationCoordinate2D.to_xml_string(x)
-
- def compute(self):
- if self.hasInputFromPort("value"):
- data = self.getInputFromPort("value")
- self.latitude = data.latitude
- self.longitude = data.longitude
-
- if self.latitude is None or self.longitude is None:
- self.checkInputPort("latitude")
- self.checkInputPort("longitude")
- self.latitude = self.getInputFromPort("latitude")
- self.longitude = self.getInputFromPort("longitude")
- self.setResult("value", self)
- self.setResult("value_as_string", self.translate_to_string(self))
-
- @classmethod
- def provide_input_port_documentation(cls, port_name):
- if port_name == "latitude":
- return """The latitude in degrees.
-Positive values indicate latitudes north of the equator.
-Negative values indicate latitudes south of the equator."""
- elif port_name == "longitude":
- return """The longitude in degrees.
-Measurements are relative to the zero meridian with positive values extending
-east of the meridian and negative values extending west of the meridian."""
-
-LocationCoordinate2D._input_ports = [('value', LocationCoordinate2D),
- ('latitude', Float, True),
- ('longitude', Float, True)]
-
-LocationCoordinate2D._output_ports = [('value', LocationCoordinate2D)]
-
-class Location(Constant):
- """This class represents the geographical coordinates and altitude of the
- device's location along with values indicating the accuracy of the
- measurements and when those measurements were made. In devices with a GPS,
- this class also reports information about the speed and heading in which
- the device is moving."""
- def __init__(self):
- Constant.__init__(self)
- self.coordinate = None
- self.altitude = None
- self.horizontal_accuracy = None
- self.vertical_accuracy = None
- self.timestamp = None
- self.speed = None
- self.course = None
- Location.default_value = self
-
- @staticmethod
- def from_xml_string(xml_string):
- node = ElementTree.fromstring(xml_string)
- if node.tag != 'location':
- return None
- #read attributes
- data = node.get('altitude', None)
- alti = float(data)
-
- data = node.get('horizontalAccuracy', None)
- hAcc = float(data)
-
- data = node.get('verticalAccuracy', None)
- vAcc = float(data)
-
- data = node.get('timestamp', None)
- timestamp = datetime(*strptime(data, '%Y-%m-%d %H:%M:%S')[0:6])
-
- data = node.get('speed', None)
- speed = float(data)
-
- data = node.get('course', None)
- course = float(data)
-
- coord = None
- for child in node.getchildren():
- if child.tag == "coordinate":
- text = ElementTree.tostring(child)
- coord = LocationCoordinate2D.from_xml_string(text)
-
- loc = Location()
- loc.coordinate = coord
- loc.altitude = alti
- loc.horizontal_accuracy = hAcc
- loc.vertical_accuracy = vAcc
- loc.timestamp = timestamp
- loc.speed = speed
- loc.course = course
-
- return loc
-
- @staticmethod
- def to_xml_string(x):
- node = ElementTree.Element('location')
- node.set('altitude', str(x.altitude))
- node.set('horizontalAccuracy',str(x.horizontal_accuracy))
- node.set('verticalAccuracy',str(x.vertical_accuracy))
- node.set('timestamp', x.timestamp.strftime('%Y-%m-%d %H:%M:%S'))
- node.set('speed', str(x.speed))
- node.set('course', str(x.course))
-
- child_str = LocationCoordinate2D.to_xml_string(x.coordinate)
- child = ElementTree.fromstring(child_str)
- node.append(child)
-
- return ElementTree.tostring(node)
-
- @staticmethod
- def translate_to_python(x):
- result = Location.from_xml_string(x)
- result.setResult("value", result)
- return result
-
- @staticmethod
- def translate_to_string(x):
- return Location.to_xml_string(x)
-
- def compute(self):
- if self.hasInputFromPort("value"):
- data = self.getInputFromPort("value")
- self.coordinate = data.coordinate
- self.altitude = data.altitude
- self.horizontal_accuracy = data.horizontal_accuracy
- self.vertical_accuracy = data.vertical_accuracy
- self.timestamp = data.timestamp
- self.speed = data.speed
- self.course = data.course
-
- if self.coordinate is None or self.altitude is None:
- self.checkInputPort("coordinate")
- self.checkInputPort("altitude")
- self.coordinate = self.getInputFromPort("coordinate")
- self.altitude = self.getInputFromPort("altitude")
-
- #check optional ports
- if self.hasInputFromPort("horizontalAccuracy"):
- self.horizontal_accuracy = \
- self.getInputFromPort("horizontalAccuracy")
-
- if self.hasInputFromPort("verticalAccuracy"):
- self.vertical_accuracy = \
- self.getInputFromPort("verticalAccuracy")
-
- if self.hasInputFromPort("timestamp"):
- data = self.getInputFromPort("timestamp")
- self.timestamp = \
- datetime(*strptime(data, '%Y-%m-%d %H:%M:%S')[0:6])
- if self.hasInputFromPort("speed"):
- self.speed = self.getInputFromPort("speed")
-
- if self.hasInputFromPort("course"):
- self.course = self.getInputFromPort("course")
-
- self.setResult("value", self)
- self.setResult("value_as_string", self.translate_to_string(self))
-
- @classmethod
- def provide_input_port_documentation(cls, port_name):
- if port_name == "coordinate":
- return """The geographical coordinate information
-(latitude and longitude)."""
- elif port_name == "altitude":
- return """The altitude in meters.
-Positive values indicate altitudes above sea level.
-Negative values indicate altitudes below sea level."""
- elif port_name == "horizontalAccuracy":
- return """The radius of uncertainty for the location,
-measured in meters.
-The coordinate's latitude and longitude identify the center of the circle and
-this value indicates the radius of that circle. A negative value indicates
-that the coordinate's latitude and longitude are invalid."""
- elif port_name == "verticalAccuracy":
- return """The accuracy of the altitude value in meters.
-The value in the altitude port could be plus or minus the value indicated
-by this port. A negative value indicates that the altitude value is invalid.
-
-Determining the vertical accuracy requires a device with GPS capabilities.
-Thus, on some earlier iPhone OS-based devices, this property always contains a
-negative value."""
- elif port_name == "timestamp":
- return """The time at which this location was determined.
-Format: '%Y-%m-%d %H:%M:%S' """
- elif port_name == "speed":
- return """The instantaneous speed of the device in meters per second.
-This value reflects the instantaneous speed of the device in the direction of
-its current heading. A negative value indicates an invalid speed.
-Because the actual speed can change many times between the delivery of
-subsequent location events, you should use this property for informational
-purposes only."""
- elif port_name == "course":
- return """The direction in which the device is travelling.
-Course values are measured in degrees starting at due north and continuing
-clockwise around the compass. Thus, north is 0 degrees, east is 90 degrees,
-south is 180 degrees, and so on. Course values may not be available on all
-devices. A negative value indicates that the direction is invalid."""
-
-Location._input_ports = [('value', Location),
- ('coordinate', LocationCoordinate2D, True),
- ('altitude', Float, True),
- ('horizontalAccuracy', Float, True),
- ('verticalAccuracy', Float, True),
- ('timestamp', String, True),
- ('speed', Float, True),
- ('course', Float, True)]
-
-Location._output_ports = [('value', Location)]
-
-class B64EncodedContents(Constant):
- def __init__(self):
- Constant.__init__(self)
- self.contents = None
- B64EncodedContents.default_value = self
-
- @staticmethod
- def translate_to_python(x):
- result = B64EncodedContents()
- result.contents = str(x)
- result.setResult("value", result)
- return result
-
- @staticmethod
- def translate_to_string(x):
- return x.contents
-
- def compute(self):
- if self.hasInputFromPort("value"):
- data = self.getInputFromPort("value")
- self.contents = data.contents
-
- if self.contents is None:
- if self.hasInputFromPort("file"):
- file_ = self.getInputFromPort("file")
- c = open(file_.name)
- self.contents = base64.b64encode(c.read())
-
- self.setResult("value", self)
- self.setResult("value_as_string", self.translate_to_string(self))
-
-B64EncodedContents._input_ports = [('value', B64EncodedContents),
- ('contents', String, True),
- ('file', File, True)]
-
-B64EncodedContents._output_ports = [('value', B64EncodedContents)]
-
-class Image(B64EncodedContents):
- def __init__(self):
- B64EncodedContents.__init__(self)
- Image.default_value = self
-
- @staticmethod
- def translate_to_python(x):
- result = Image()
- result.contents = str(x)
- result.setResult("value", result)
- return result
-
-Image._input_ports = [('value', Image)]
-
-Image._output_ports = [('value', Image)]
-
-class Audio(B64EncodedContents):
- def __init__(self):
- B64EncodedContents.__init__(self)
- Audio.default_value = self
-
- @staticmethod
- def translate_to_python(x):
- result = Audio()
- result.contents = str(x)
- result.setResult("value", result)
- return result
-
-Audio._input_ports = [('value', Audio)]
-
-Audio._output_ports = [('value', Audio)]
-
-_modules = [LocationCoordinate2D,
- Location,
- B64EncodedContents,
- Image,
- Audio]
diff --git a/contrib/pc3/__init__.py b/contrib/pc3/__init__.py
deleted file mode 100644
index cad7b78..0000000
--- a/contrib/pc3/__init__.py
+++ /dev/null
@@ -1,420 +0,0 @@
-from core.modules.basic_modules import String, Boolean, File, Integer
-from core.modules.module_registry import get_module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from core.upgradeworkflow import UpgradeWorkflowHandler
-
-from info.ipaw.pc3.LoadAppLogic import LoadAppLogic
-
-import os
-
-name = "Provenance Challenge 3"
-identifier = "edu.utah.sci.dakoop.pc3"
-version = '1.0.1'
-
-# class Module(object):
-# pass
-
-# class String(Module):
-# pass
-
-# class Boolean(Module):
-# pass
-
-# class Integer(Module):
-# pass
-
-class Collection(Module):
- def __init__(self, lst, klass=None):
- Module.__init__(self)
- self.lst = lst
- self.klass = klass
-
- def compute(self):
- self.lst = self.forceGetInputListFromPort('elements')
- self.setResult('collection', self.list)
-
- _input_ports = [('elements', Module)]
- _output_ports = []
- # _output_ports = [('self', Collection)]
-Collection._output_ports.append(('self', Collection))
-
-class CSVFileEntry(Module):
- def __init__(self, file_entry=None):
- Module.__init__(self)
- if file_entry is not None:
- self.file_entry = file_entry
- else:
- self.file_entry = LoadAppLogic.CSVFileEntry()
-
- def compute(self):
- self.checkInputPort('filePath')
- self.checkInputPort('headerPath')
- self.checkInputPort('rowCount')
- self.checkInputPort('targetTable')
- self.checkInputPort('checksum')
- self.checkInputPort('columnNames')
- self.file_entry.FilePath = self.getInputFromPort('filePath')
- self.file_entry.HeaderPath = self.getInputFromPort('headerPath')
- self.file_entry.RowCount = self.getInputFromPort('rowCount')
- self.file_entry.TargetTable = self.getInputFromPort('targetTable')
- self.file_entry.Checksum = self.getInputFromPort('checksum')
- self.file_entry.ColumnNames = self.getInputFromPort('columnNames').lst
- self.setResult('self', self)
-
- _input_ports = [('filePath', String),
- ('headerPath', String),
- ('rowCount', Integer),
- ('targetTable', String),
- ('checksum', String),
- ('columnNames', Collection)]
- _output_ports = []
- # _output_ports = [('self', CSVFileEntry)]
-CSVFileEntry._output_ports.append(('self', CSVFileEntry))
-
-class DatabaseEntry(Module):
- def __init__(self, db_entry=None):
- Module.__init__(self)
- if db_entry is not None:
- self.db_entry = db_entry
- else:
- self.db_entry = LoadAppLogic.DatabaseEntry()
-
- def compute(self):
- self.checkInputPort('dbGuid')
- self.checkInputPort('dbName')
- self.checkInputPort('connectionString')
- self.db_entry.DBGuid = self.getInputFromPort('dbGuid')
- self.db_entry.DBName = self.getInputFromPort('dbName')
- self.db_entry.ConnectionString = \
- self.getInputFromPort('connectionString')
- self.setResult('self', self)
-
- _input_ports = [('dbGuid', String),
- ('dbName', String),
- ('connectionString', String)]
- _output_ports = []
- # _output_ports = [('self', DatabaseEntry)]
-DatabaseEntry._output_ports.append(('self', DatabaseEntry))
-
-class IsCSVReadyFileExists(Module):
- def compute(self):
- self.checkInputPort('csvRootPath')
- path = self.getInputFromPort('csvRootPath')
- res = LoadAppLogic.IsCSVReadyFileExists(path)
- self.setResult('fileExists', res)
-
- _input_ports = [('csvRootPath', String)]
- _output_ports = [('fileExists', Boolean)]
-
-class ReadCSVReadyFile(Module):
- def compute(self):
- self.checkInputPort('csvRootPath')
- path = self.getInputFromPort('csvRootPath')
- self.annotate({'used_files':
- str([os.path.join(path, "csv_ready.csv")])})
- csv_files = LoadAppLogic.ReadCSVReadyFile(path)
- # wrapped_res = Collection([CSVFileEntry(e) for e in res], CSVFileEntry)
- list_of_elts = [CSVFileEntry(f) for f in csv_files]
- for elt in list_of_elts:
- elt.upToDate = True
- self.setResult('csvFiles', list_of_elts)
-
- _input_ports = [('csvRootPath', String)]
- # _output_ports = [('csvFiles', [Collection, CSVFileEntry])]
- _output_ports = [('csvFiles',
- '(edu.utah.sci.vistrails.basic:List)')]
-
-class IsMatchCSVFileTables(Module):
- def compute(self):
- self.checkInputPort('csvFiles')
- csv_files = self.getInputFromPort('csvFiles')
- res = LoadAppLogic.IsMatchCSVFileTables([f.file_entry
- for f in csv_files])
- self.setResult('tablesMatch', res)
-
- # _input_ports = [('csvFiles', [Collection, CSVFileEntry])]
- _input_ports = [('csvFiles',
- '(edu.utah.sci.vistrails.basic:List)')]
- _output_ports = [('tablesMatch', Boolean)]
-
-class IsExistsCSVFile(Module):
- def compute(self):
- self.checkInputPort('csvFile')
- csv_file = self.getInputFromPort('csvFile')
- res = LoadAppLogic.IsExistsCSVFile(csv_file.file_entry)
- self.setResult('fileExists', res)
-
- _input_ports = [('csvFile', CSVFileEntry)]
- _output_ports = [('fileExists', Boolean)]
-
-class ReadCSVFileColumnNames(Module):
- def compute(self):
- self.checkInputPort('csvFile')
- csv_file = self.getInputFromPort('csvFile')
- self.annotate({'used_files':
- str([csv_file.file_entry.HeaderPath])})
- res = LoadAppLogic.ReadCSVFileColumnNames(csv_file.file_entry)
- self.setResult('csvFile', CSVFileEntry(res))
-
- _input_ports = [('csvFile', CSVFileEntry)]
- _output_ports = [('csvFile', CSVFileEntry)]
-
-class IsMatchCSVFileColumnNames(Module):
- def compute(self):
- self.checkInputPort('csvFile')
- csv_file = self.getInputFromPort('csvFile')
- res = LoadAppLogic.IsMatchCSVFileColumnNames(csv_file.file_entry)
- self.setResult('columnsMatch', res)
-
- _input_ports = [('csvFile', CSVFileEntry)]
- _output_ports = [('columnsMatch', Boolean)]
-
-class CreateEmptyLoadDB(Module):
- def compute(self):
- self.checkInputPort('jobID')
- job_id = self.getInputFromPort('jobID')
- res = LoadAppLogic.CreateEmptyLoadDB(job_id)
- self.setResult('dbEntry', DatabaseEntry(res))
-
- _input_ports = [('jobID', String)]
- _output_ports = [('dbEntry', DatabaseEntry)]
-
-class LoadCSVFileIntoTable(Module):
- def compute(self):
- self.checkInputPort('csvFile')
- self.checkInputPort('dbEntry')
- csv_file = self.getInputFromPort('csvFile')
- db_entry = self.getInputFromPort('dbEntry')
- self.annotate({'used_files':
- str([csv_file.file_entry.FilePath]),
- 'generated_tables':
- str([(db_entry.db_entry.ConnectionString,
- db_entry.db_entry.DBName,
- csv_file.file_entry.TargetTable)])})
- res = LoadAppLogic.LoadCSVFileIntoTable(db_entry.db_entry,
- csv_file.file_entry)
- self.setResult('success', res)
-
- _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
- _output_ports = [('success', Boolean)]
-
-class UpdateComputedColumns(Module):
- def compute(self):
- self.checkInputPort('csvFile')
- self.checkInputPort('dbEntry')
- csv_file = self.getInputFromPort('csvFile')
- db_entry = self.getInputFromPort('dbEntry')
- if csv_file.file_entry.TargetTable.upper() == 'P2DETECTION':
- self.annotate({'used_tables':
- str([(db_entry.db_entry.ConnectionString,
- db_entry.db_entry.DBName,
- csv_file.file_entry.TargetTable)])})
- res = LoadAppLogic.UpdateComputedColumns(db_entry.db_entry,
- csv_file.file_entry)
- self.setResult('success', res)
-
- _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
- _output_ports = [('success', Boolean)]
-
-class IsMatchTableRowCount(Module):
- def compute(self):
- self.checkInputPort('csvFile')
- self.checkInputPort('dbEntry')
- csv_file = self.getInputFromPort('csvFile')
- db_entry = self.getInputFromPort('dbEntry')
- self.annotate({'used_tables':
- str([(db_entry.db_entry.ConnectionString,
- db_entry.db_entry.DBName,
- csv_file.file_entry.TargetTable)])})
- res = LoadAppLogic.IsMatchTableRowCount(db_entry.db_entry,
- csv_file.file_entry)
- self.setResult('countsMatch', res)
-
- _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
- _output_ports = [('countsMatch', Boolean)]
-
-class IsMatchTableColumnRanges(Module):
- def compute(self):
- self.checkInputPort('csvFile')
- self.checkInputPort('dbEntry')
- csv_file = self.getInputFromPort('csvFile')
- db_entry = self.getInputFromPort('dbEntry')
- if csv_file.file_entry.TargetTable.upper() == 'P2DETECTION':
- self.annotate({'used_tables':
- str([(db_entry.db_entry.ConnectionString,
- db_entry.db_entry.DBName,
- csv_file.file_entry.TargetTable)])})
- res = LoadAppLogic.IsMatchTableColumnRanges(db_entry.db_entry,
- csv_file.file_entry)
- self.setResult('rangesMatch', res)
-
- _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
- _output_ports = [('rangesMatch', Boolean)]
-
-class CompactDatabase(Module):
- def compute(self):
- self.checkInputPort('dbEntry')
- db_entry = self.getInputFromPort('dbEntry')
- self.annotate({'used_tables':
- str([(db_entry.db_entry.ConnectionString,
- db_entry.db_entry.DBName,
- "P2Detection"),
- (db_entry.db_entry.ConnectionString,
- db_entry.db_entry.DBName,
- "P2FrameMeta"),
- (db_entry.db_entry.ConnectionString,
- db_entry.db_entry.DBName,
- "P2ImageMeta")])})
- LoadAppLogic.CompactDatabase(db_entry.db_entry)
- self.setResult('dbEntry', db_entry)
-
-
- _input_ports = [('dbEntry', DatabaseEntry)]
- _output_ports = [('dbEntry', DatabaseEntry)]
-
-class GetCSVFiles(Module):
- def compute(self):
- self.checkInputPort('csvRootPath')
- path = self.getInputFromPort('csvRootPath')
- if not LoadAppLogic.IsCSVReadyFileExists(path):
- raise ModuleError(self, "IsCSVReadyFileExists failed")
- self.annotate({'used_files':
- str([os.path.join(path, "csv_ready.csv")])})
- csv_files = LoadAppLogic.ReadCSVReadyFile(path)
- if not LoadAppLogic.IsMatchCSVFileTables(csv_files):
- raise ModuleError(self, "IsMatchCSVFileTables failed")
-# getter = get_module_registry().get_descriptor_by_name
-# descriptor = getter('edu.utah.sci.vistrails.basic',
-# 'List')
-# list_of_elts = descriptor.module()
-# list_of_elts.value = [CSVFileEntry(f) for f in csv_files]
-# self.setResult('csvFiles', list_of_elts)
- list_of_elts = [CSVFileEntry(f) for f in csv_files]
- for elt in list_of_elts:
- elt.upToDate = True
- print 'list_of_elts:', list_of_elts
- self.setResult('csvFiles', list_of_elts)
-# wrapped_res = Collection([CSVFileEntry(f) for f in csv_files],
-# CSVFileEntry)
-# self.setResult('csvFiles', wrapped_res)
-
- _input_ports = [('csvRootPath', String)]
- _output_ports = [('csvFiles',
- '(edu.utah.sci.vistrails.basic:List)')]
- # _output_ports = [('csvFiles', [Collection, CSVFileEntry])]
-
-class ReadCSVFile(Module):
- def compute(self):
- self.checkInputPort('csvFile')
- csv_file = self.getInputFromPort('csvFile')
- if not LoadAppLogic.IsExistsCSVFile(csv_file.file_entry):
- raise ModuleError(self, "IsExistsCSVFile failed")
- self.annotate({'used_files':
- str([csv_file.file_entry.HeaderPath])})
- csv_file.file_entry = \
- LoadAppLogic.ReadCSVFileColumnNames(csv_file.file_entry)
- if not LoadAppLogic.IsMatchCSVFileColumnNames(csv_file.file_entry):
- raise ModuleError(self, "IsMatchCSVFileColumnNames failed")
- self.setResult('csvFile', csv_file)
-
- _input_ports = [('csvFile', CSVFileEntry)]
- _output_ports = [('csvFile', CSVFileEntry)]
-
-class LoadCSVFileIntoDB(Module):
- def compute(self):
- self.checkInputPort('csvFile')
- self.checkInputPort('dbEntry')
- csv_file = self.getInputFromPort('csvFile')
- print 'csv_file:', csv_file
- db_entry = self.getInputFromPort('dbEntry')
- self.annotate({'used_files':
- str([csv_file.file_entry.FilePath])})
- self.annotate({'generated_tables':
- str([(db_entry.db_entry.ConnectionString,
- db_entry.db_entry.DBName,
- csv_file.file_entry.TargetTable)])})
- if not LoadAppLogic.LoadCSVFileIntoTable(db_entry.db_entry,
- csv_file.file_entry):
- raise ModuleError(self, "LoadCSVFileIntoTable failed")
- self.setResult('dbEntry', db_entry)
-
- _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
- _output_ports = [('dbEntry', DatabaseEntry)]
-
-class ComputeColumns(Module):
- def compute(self):
- self.checkInputPort('csvFile')
- self.checkInputPort('dbEntry')
- csv_file = self.getInputFromPort('csvFile')
- db_entry = self.getInputFromPort('dbEntry')
- self.annotate({'used_tables':
- str([(db_entry.db_entry.ConnectionString,
- db_entry.db_entry.DBName,
- csv_file.file_entry.TargetTable)])})
- if not LoadAppLogic.UpdateComputedColumns(db_entry.db_entry,
- csv_file.file_entry):
- raise ModuleError(self, "UpdateComputedColumns failed")
- if not LoadAppLogic.IsMatchTableRowCount(db_entry.db_entry,
- csv_file.file_entry):
- raise ModuleError(self, "IsMatchTableRowCount failed")
- if not LoadAppLogic.IsMatchTableColumnRanges(db_entry.db_entry,
- csv_file.file_entry):
- raise ModuleError(self, "IsMatchTableColumnRanges failed")
- self.setResult('dbEntry', db_entry)
-
- _input_ports = [('csvFile', CSVFileEntry), ('dbEntry', DatabaseEntry)]
- _output_ports = [('dbEntry', DatabaseEntry)]
-
-class DetectionsHistogram(Module):
- def compute(self):
- self.checkInputPort('dbEntry')
- db_entry = self.getInputFromPort('dbEntry')
- high_quality = False
- if self.hasInputFromPort('highQuality'):
- high_quality = self.getInputFromPort('highQuality')
- self.annotate({'used_tables':
- str([(db_entry.db_entry.ConnectionString,
- db_entry.db_entry.DBName,
- "P2Detection")])})
- histogram = LoadAppLogic.DetectionsHistogram(db_entry.db_entry,
- high_quality)
- self.setResult('histogram', histogram)
-
- _input_ports = [('dbEntry', DatabaseEntry), ('highQuality', Boolean, True)]
- _output_ports = [('histogram',
- '(edu.utah.sci.vistrails.basic:List)')]
-
-_modules = [Collection,
- CSVFileEntry,
- DatabaseEntry,
- IsCSVReadyFileExists,
- ReadCSVReadyFile,
- IsMatchCSVFileTables,
- IsExistsCSVFile,
- ReadCSVFileColumnNames,
- IsMatchCSVFileColumnNames,
- CreateEmptyLoadDB,
- LoadCSVFileIntoTable,
- UpdateComputedColumns,
- IsMatchTableRowCount,
- IsMatchTableColumnRanges,
- CompactDatabase,
- GetCSVFiles,
- ReadCSVFile,
- LoadCSVFileIntoDB,
- ComputeColumns,
- DetectionsHistogram,
- ]
-
-def package_dependencies():
- return ['edu.utah.sci.vistrails.control_flow']
-
-def handle_module_upgrade_request(controller, module_id, pipeline):
- module_remap = {'ReadCSVReadyFile': [(None, '1.0.1', None, {})],
- 'IsMatchCSVFileTables': [(None, '1.0.1', None, {})],
- 'GetCSVFiles': [(None, '1.0.1', None, {})],
- 'DetectionsHistogram': [(None, '1.0.1', None, {})],
- }
-
- return UpgradeWorkflowHandler.remap_module(controller, module_id, pipeline,
- module_remap)
diff --git a/contrib/pc3/info/__init__.py b/contrib/pc3/info/__init__.py
deleted file mode 100644
index 2ae2839..0000000
--- a/contrib/pc3/info/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-pass
diff --git a/contrib/pc3/info/ipaw/__init__.py b/contrib/pc3/info/ipaw/__init__.py
deleted file mode 100644
index 2ae2839..0000000
--- a/contrib/pc3/info/ipaw/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-pass
diff --git a/contrib/pc3/info/ipaw/pc3/LoadAppLogic.py b/contrib/pc3/info/ipaw/pc3/LoadAppLogic.py
deleted file mode 100644
index a85a563..0000000
--- a/contrib/pc3/info/ipaw/pc3/LoadAppLogic.py
+++ /dev/null
@@ -1,441 +0,0 @@
-import MySQLdb
-import os
-import uuid
-
-from LoadConstants import LoadConstants
-from LoadSql import LoadSql
-
-class LoadAppLogic(object):
-
- #region Database Constants
- SQL_SERVER = "localhost"
- SQL_USER = "ipaw"
- SQL_PASSWORD = "pc3_load-2009"
- #endregion
-
- #region Helper data structures
- class CSVFileEntry(object):
- def __init__(self):
- self.FilePath = None
- self.HeaderPath = None
- self.RowCount = None
- self.TargetTable = None
- self.Checksum = None
- self.ColumnNames = []
-
- class DatabaseEntry(object):
- def __init__(self):
- self.DBGuid = None
- self.DBName = None
- self.ConnectionString = None
- #endregion
-
- #region Pre-Load Sanity Checks
-
- @staticmethod
- def IsCSVReadyFileExists(CSVRootPath):
- """<summary>
- Checks if the CSV Ready File exists in the given rooth path to the
- CSV Batch
- </summary>
- <param name="CSVRootPath">Path to the root directory for the batch
- </param>
- <returns>true if the csv_ready.csv file exists in the CSVRoothPath.
- False otherwise.</returns>
- """
-
- # 1. Check if parent directory exists.
- if not os.path.exists(CSVRootPath):
- return False
-
- # 2. Check if CSV Ready file exists. We assume a static name for the ready file.
- CSVReadyFilePath = os.path.join(CSVRootPath, "csv_ready.csv")
- return os.path.exists(CSVReadyFilePath)
-
- @staticmethod
- def ReadCSVReadyFile(CSVRootPath):
- """<summary>
-
- </summary>
- <param name="CSVRootPath"></param>
- <returns></returns>
- """
-
- # 1. Initialize output list of file entries
- CSVFileEntryList = []
-
- # 2. Open input stream to read from CSV Ready File
- CSVReadyFilePath = os.path.join(CSVRootPath, "csv_ready.csv")
- ReadyFileStream = open(CSVReadyFilePath);
-
- # 3. Read each line in CSV Ready file and split the lines into
- # individual columns separated by commas
- for ReadyFileLine in ReadyFileStream:
-
- # 3.a. Expect each line in the CSV ready file to be of the format:
- # <FileName>,<NumRows>,<TargetTable>,<MD5Checksum>
- ReadyFileLineTokens = ReadyFileLine.split(',')
-
- # 3.b. Create an empty FileEntry and populate it with the columns
- FilePath = os.path.join(CSVRootPath,
- ReadyFileLineTokens[0].strip())
-
- # CSVFileEntry FileEntry = new CSVFileEntry();
- FileEntry = LoadAppLogic.CSVFileEntry()
- FileEntry.FilePath = FilePath
- FileEntry.HeaderPath = FilePath + ".hdr"
- FileEntry.RowCount = int(ReadyFileLineTokens[1].strip())
- FileEntry.TargetTable = ReadyFileLineTokens[2].strip()
- FileEntry.Checksum = ReadyFileLineTokens[3].strip()
-
- # 3.c. Add file entry to output list
- CSVFileEntryList.append(FileEntry);
-
- # 4. Close input stream and return output file entry list
- ReadyFileStream.close();
-
- return CSVFileEntryList;
-
- @staticmethod
- def IsMatchCSVFileTables(FileEntries):
- """<summary>
- Check if the correct list of files/table names are present in this batch
- </summary>
- <param name="FileEntries"></param>
- <returns></returns>
- """
-
- # check if the file count and the expected number of tables match
- if (len(LoadConstants.EXPECTED_TABLES) != len(FileEntries)):
- return false;
-
- # for each expected table name, check if it is present
- # in the list of file entries
- for TableName in LoadConstants.EXPECTED_TABLES:
- TableExists = False
- for FileEntry in FileEntries:
- if TableName == FileEntry.TargetTable:
- TableExists = True
- break
-
- # if the table name did not exist in list of CSV files,
- # this check fails.
- if not TableExists:
- return False
-
- return True
-
- @staticmethod
- def IsExistsCSVFile(FileEntry):
- """<summary>
- Test if a CSV File defined in the CSV Ready list actually exists on disk.
- </summary>
- <param name="FileEntry">FileEntry for CSVFile to test</param>
- <returns>True if the FilePath in the given FileEntry exists on disk. False otherwise.</returns>
- """
- if not os.path.exists(FileEntry.FilePath):
- return False
-
- return os.path.exists(FileEntry.HeaderPath)
-
- @staticmethod
- def ReadCSVFileColumnNames (FileEntry):
- """<summary>
-
- </summary>
- <param name="FileEntry"></param>
- <param name="FileEntry"></param>
- <returns></returns>
- """
-
- # 2. Read the header line of the CSV File.
- CSVFileReader = open(FileEntry.HeaderPath)
- HeaderRow = CSVFileReader.readline()
-
- # 3. Extract the comma-separated columns names of the CSV File from its header line.
- # Strip empty spaces around column names.
- ColumnNames = HeaderRow.split(',')
- FileEntry.ColumnNames = []
- for ColumnName in ColumnNames:
- FileEntry.ColumnNames.append(ColumnName.strip())
-
- CSVFileReader.close()
-
- return FileEntry
-
- @staticmethod
- def IsMatchCSVFileColumnNames(FileEntry):
- """<summary>
- Checks if the correct list of column headers is present for the CSV file
- to match the table
- </summary>
- <param name="FileEntry">FileEntry for CSV File whose column headers to test</param>
- <returns>True if the column headers present in the CSV File are the same as the
- expected table columns. False otherwise.</returns>
- """
-
- # determine expected columns
- ExpectedColumns = None
-
- ExpectedColumnsLookup = {"P2DETECTION": \
- LoadConstants.EXPECTED_DETECTION_COLS,
- "P2FRAMEMETA": \
- LoadConstants.EXPECTED_FRAME_META_COLS,
- "P2IMAGEMETA": \
- LoadConstants.EXPECTED_IMAGE_META_COLS,
- }
- if FileEntry.TargetTable.upper() in ExpectedColumnsLookup:
- ExpectedColumns = \
- ExpectedColumnsLookup[FileEntry.TargetTable.upper()]
- else:
- return False
-
- # test if the expected and present column name counts are the same
- if len(ExpectedColumns) != len(FileEntry.ColumnNames):
- return False
-
- # test of all expected names exist in the columns present
- for ColumnName in ExpectedColumns:
- if ColumnName not in FileEntry.ColumnNames:
- return False
-
- # all columns match
- return True;
- #endregion
-
- #region Loading Section
- @staticmethod
- def CreateEmptyLoadDB(JobID):
- """<summary>
-
- </summary>
- <param name="JobID"></param>
- <returns></returns>
- """
-
- # initialize database entry for storing database properties
- DBEntry = LoadAppLogic.DatabaseEntry()
- DBEntry.DBName = JobID + "_LoadDB"
- DBEntry.DBGuid = str(uuid.uuid4())
- DBEntry.ConnectionString = {'host': LoadAppLogic.SQL_SERVER,
- 'user': LoadAppLogic.SQL_USER,
- 'passwd': LoadAppLogic.SQL_PASSWORD,
- }
-
- # initialize Sql Connection String to sql server
- SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
-
- # Create empty database instance
- SqlCur = SqlConn.cursor()
- SqlCur.execute("CREATE DATABASE " + DBEntry.DBName)
- DBEntry.ConnectionString['db'] = DBEntry.DBName
-
- # update Sql Connection String to new create tables
- SqlCur = SqlConn.cursor()
- SqlCur.execute("use %s" % DBEntry.DBName)
- SqlCur.execute(LoadSql.CREATE_DETECTION_TABLE)
- SqlCur.execute(LoadSql.CREATE_FRAME_META_TABLE)
- SqlCur.execute(LoadSql.CREATE_IMAGE_META_TABLE)
- SqlCur.close()
- SqlConn.close()
-
- return DBEntry
-
- # derby bulk load: SYSCS_UTIL.SYSCS_IMPORT_TABLE
- @staticmethod
- def LoadCSVFileIntoTable(DBEntry, FileEntry):
- """<summary>
- Loads a CSV File into an existing table using Sql BULK INSERT command
- </summary>
- <param name="DBEntry">Database into which to load the CSV file</param>
- <param name="FileEntry">File to be bulk loaded into database table</param>
- <returns>True if the bulk load ran without exceptions. False otherwise.</returns>
- """
- try:
- # connect to database instance
- SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
- SqlCur = SqlConn.cursor()
- # execute bulk insert command
- SqlCur.execute(("LOAD DATA INFILE %%s INTO TABLE %s "
- "FIELDS TERMINATED BY ','") % \
- FileEntry.TargetTable,
- (FileEntry.FilePath,))
- SqlCur.close()
- SqlConn.close()
- except Exception, e:
- # print e
- # bulk insert failed
- SqlCur.close()
- SqlConn.close()
- return False
- # bulk insert success
- return True
-
- @staticmethod
- def UpdateComputedColumns(DBEntry, FileEntry):
- """<summary>
-
- </summary>
- <param name="DBEntry"></param>
- <param name="FileEntry"></param>
- """
-
- def P2Detection(SqlCur):
- # Update ZoneID
- SqlCur.execute('UPDATE P2Detection '
- 'SET zoneID = (`dec`+(90.0))/(0.0083333)')
- # Update cx
- SqlCur.execute('UPDATE P2Detection '
- 'SET cx = (COS(RADIANS(`dec`))*COS(RADIANS(ra)))')
- # Update cy
- SqlCur.execute('UPDATE P2Detection '
- 'SET cy = COS(RADIANS(`dec`))*SIN(RADIANS(ra))')
- # Update cz
- SqlCur.execute('UPDATE P2Detection '
- 'SET cz = (SIN(RADIANS(`dec`)))')
-
- def P2FrameMeta(SqlCur):
- # No columns to be updated for FrameMeta
- pass
-
- def P2ImageMeta(SqlCur):
- # No columns to be updated for ImageMeta
- pass
-
- TargetTableLookup = {"P2DETECTION": P2Detection,
- "P2FRAMEMETA": P2FrameMeta,
- "P2IMAGEMETA": P2ImageMeta,
- }
-
- try:
- # connect to database instance
- SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
- SqlCur = SqlConn.cursor()
- if FileEntry.TargetTable.upper() in TargetTableLookup:
- TargetTableLookup[FileEntry.TargetTable.upper()](SqlCur)
- else:
- # none of the table types matches...invalid
- SqlCur.close()
- SqlConn.close()
- return False
-
- except Exception, e:
- print e
- # update column failed
- SqlCur.close()
- SqlConn.close()
- return False
- # update column success
- return True
-
- #endregion
-
- #region Post-Load Checks
- @staticmethod
- def IsMatchTableRowCount(DBEntry, FileEntry):
- """<summary>
-
- </summary>
- <param name="DBEntry"></param>
- <param name="FileEntry"></param>
- <returns></returns>
- """
-
- # does the number of rows expected match the number of rows loaded
- SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
- SqlCur = SqlConn.cursor()
- # execute row count command
- SqlCur.execute("SELECT COUNT(*) FROM %s" % FileEntry.TargetTable)
- RowCount = SqlCur.fetchone()[0]
- SqlCur.close()
- SqlConn.close()
- # check if row count matches expected row count
- return RowCount == FileEntry.RowCount
-
- @staticmethod
- def IsMatchTableColumnRanges(DBEntry, FileEntry):
- """<summary>
-
- </summary>
- <param name="DBEntry"></param>
- <param name="FileEntry"></param>
- <returns></returns>
- """
-
- # determine expected column ranges
- ExpectedColumnRanges = None
- ExpectedColumnRangesLookup = \
- {"P2DETECTION": LoadConstants.EXPECTED_DETECTION_COL_RANGES,
- "P2FRAMEMETA": [],
- "P2IMAGEMETA": [],
- }
- if FileEntry.TargetTable.upper() in ExpectedColumnRangesLookup:
- ExpectedColumnRanges = \
- ExpectedColumnRangesLookup[FileEntry.TargetTable.upper()]
- else:
- # none of the table types matches...invalid
- return False
-
- # connect to database instance
- SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
- SqlCur = SqlConn.cursor()
-
- # For each column in available list, test if rows in table fall
- # outside expected range
- for Column in ExpectedColumnRanges:
- # build SQL command for error count
- SqlCur.execute("SELECT COUNT(*) FROM %s "
- "WHERE (%s < %s OR %s > %s) AND %s != -999" % \
- (FileEntry.TargetTable, Column.ColumnName,
- Column.MinValue, Column.ColumnName,
- Column.MaxValue, Column.ColumnName))
-
- ErrorCount = SqlCur.fetchone()[0]
- if ErrorCount > 0:
- print "ERROR COUNT", ErrorCount
- SqlCur.close()
- SqlConn.close()
- return False
-
- SqlCur.close()
- SqlConn.close()
-
- return True # no range errors found
-
- @staticmethod
- def CompactDatabase(DBEntry):
- """<summary>
-
- </summary>
- <param name="DBEntry"></param>
- """
-
- # Shrink database instance
- SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
- SqlCur = SqlConn.cursor()
-
- SqlCur.execute("SHOW TABLES")
- SqlTables = SqlCur.fetchall()
- for SqlTable in SqlTables:
- SqlCur.execute("OPTIMIZE TABLE %s" % SqlTable)
- SqlCur.close()
- SqlConn.close()
-
- #endregion
-
- #region Histogram
- @staticmethod
- def DetectionsHistogram(DBEntry, HighQuality=False):
- SqlConn = MySQLdb.connect(**DBEntry.ConnectionString)
- SqlCur = SqlConn.cursor()
- if HighQuality:
- where_clause = "WHERE raErr < 0.1 and decErr < 0.05 "
- else:
- where_clause = ""
-
- SqlCur.execute("SELECT ceiling(zoneId/10) as zoneGroup, "
- "count(*) as detectionCount FROM P2Detection "
- "%s"
- "GROUP BY ceiling(zoneId/10) "
- "ORDER BY ceiling(zoneId/10)" % where_clause)
- return SqlCur.fetchall()
diff --git a/contrib/pc3/info/ipaw/pc3/LoadConstants.py b/contrib/pc3/info/ipaw/pc3/LoadConstants.py
deleted file mode 100644
index f9b2928..0000000
--- a/contrib/pc3/info/ipaw/pc3/LoadConstants.py
+++ /dev/null
@@ -1,19 +0,0 @@
-
-
-
-class LoadConstants(object):
- EXPECTED_TABLES = ["P2Detection", "P2FrameMeta", "P2ImageMeta"]
- EXPECTED_DETECTION_COLS = ["objID", "detectID", "ippObjID", "ippDetectID", "filterID", "imageID", "obsTime", "xPos", "yPos", "xPosErr", "yPosErr", "instFlux", "instFluxErr", "psfWidMajor", "psfWidMinor", "psfTheta", "psfLikelihood", "psfCf", "infoFlag", "htmID", "zoneID", "assocDate", "modNum", "ra", "dec", "raErr", "decErr", "cx", "cy", "cz", "peakFlux", "calMag", "calMagErr", "calFlux", "calFluxErr", "calColor", "calColorErr", "sky", "skyErr", "sgSep", "dataRelease"]
- EXPECTED_FRAME_META_COLS = ["frameID", "surveyID", "filterID", "cameraID", "telescopeID", "analysisVer", "p1Recip", "p2Recip", "p3Recip", "nP2Images", "astroScat", "photoScat", "nAstRef", "nPhoRef", "expStart", "expTime", "airmass", "raBore", "decBore"]
- EXPECTED_IMAGE_META_COLS = ["imageID", "frameID", "ccdID", "photoCalID", "filterID", "bias", "biasScat", "sky", "skyScat", "nDetect", "magSat", "completMag", "astroScat", "photoScat", "nAstRef", "nPhoRef", "nx", "ny", "psfFwhm", "psfModelID", "psfSigMajor", "psfSigMinor", "psfTheta", "psfExtra1", "psfExtra2", "apResid", "dapResid", "detectorID", "qaFlags", "detrend1", "detrend2", "detrend3", "detrend4", "detrend5", "detrend6", "detrend7", "detrend8", "photoZero", "photoColor", "proje [...]
-
- class ColumnRange(object):
- def __init__(self, ColumnName_, MinValue_, MaxValue_):
- self.ColumnName = ColumnName_
- self.MinValue = MinValue_
- self.MaxValue = MaxValue_
-
- EXPECTED_DETECTION_COL_RANGES = [ColumnRange("ra", "0", "360"),
- ColumnRange("\"dec\"", "-90", "90"),
- ColumnRange("raErr", "-2000", "9"),
- ColumnRange("decErr", "0", "9"),]
diff --git a/contrib/pc3/info/ipaw/pc3/LoadSql.py b/contrib/pc3/info/ipaw/pc3/LoadSql.py
deleted file mode 100644
index 7b16093..0000000
--- a/contrib/pc3/info/ipaw/pc3/LoadSql.py
+++ /dev/null
@@ -1,147 +0,0 @@
-class LoadSql(object):
-
- CREATE_DETECTION_TABLE = \
- """
-CREATE TABLE P2Detection(
- `objID` bigint NOT NULL,
- detectID bigint NOT NULL,
- ippObjID bigint NOT NULL,
- ippDetectID bigint NOT NULL,
- filterID smallint NOT NULL,
- imageID bigint NOT NULL,
- obsTime float NOT NULL DEFAULT -999,
- xPos real NOT NULL DEFAULT -999,
- yPos real NOT NULL DEFAULT -999,
- xPosErr real NOT NULL DEFAULT -999,
- yPosErr real NOT NULL DEFAULT -999,
- instFlux real NOT NULL DEFAULT -999,
- instFluxErr real NOT NULL DEFAULT -999,
- psfWidMajor real NOT NULL DEFAULT -999,
- psfWidMinor real NOT NULL DEFAULT -999,
- psfTheta real NOT NULL DEFAULT -999,
- psfLikelihood real NOT NULL DEFAULT -999,
- psfCf real NOT NULL DEFAULT -999,
- infoFlag int NOT NULL DEFAULT -999,
- htmID float NOT NULL DEFAULT -999,
- zoneID float NOT NULL DEFAULT -999,
- assocDate date NOT NULL DEFAULT '28881231',
- modNum smallint NOT NULL DEFAULT 0,
- ra float NOT NULL,
- `dec` float NOT NULL,
- raErr real NOT NULL DEFAULT 0,
- decErr real NOT NULL DEFAULT 0,
- cx float NOT NULL DEFAULT -999,
- cy float NOT NULL DEFAULT -999,
- cz float NOT NULL DEFAULT -999,
- peakFlux real NOT NULL DEFAULT -999,
- calMag real NOT NULL DEFAULT -999,
- calMagErr real NOT NULL DEFAULT -999,
- calFlux real NOT NULL DEFAULT -999,
- calFluxErr real NOT NULL DEFAULT -999,
- calColor real NOT NULL DEFAULT -999,
- calColorErr real NOT NULL DEFAULT -999,
- sky real NOT NULL DEFAULT -999,
- skyErr real NOT NULL DEFAULT -999,
- sgSep real NOT NULL DEFAULT -999,
- dataRelease smallint NOT NULL,
- CONSTRAINT PK_P2Detection_objID_detectID PRIMARY KEY
-(
- `objID`,
- detectID
-))
-"""
-
- CREATE_FRAME_META_TABLE = \
- """
-CREATE TABLE P2FrameMeta(
- frameID int NOT NULL PRIMARY KEY,
- surveyID smallint NOT NULL,
- filterID smallint NOT NULL,
- cameraID smallint NOT NULL,
- telescopeID smallint NOT NULL,
- analysisVer smallint NOT NULL,
- p1Recip smallint NOT NULL DEFAULT -999,
- p2Recip smallint NOT NULL DEFAULT -999,
- p3Recip smallint NOT NULL DEFAULT -999,
- nP2Images smallint NOT NULL DEFAULT -999,
- astroScat real NOT NULL DEFAULT -999,
- photoScat real NOT NULL DEFAULT -999,
- nAstRef int NOT NULL DEFAULT -999,
- nPhoRef int NOT NULL DEFAULT -999,
- expStart float NOT NULL DEFAULT -999,
- expTime real NOT NULL DEFAULT -999,
- airmass real NOT NULL DEFAULT -999,
- raBore float NOT NULL DEFAULT -999,
- decBore float NOT NULL DEFAULT -999
-)
-"""
-
- CREATE_IMAGE_META_TABLE = \
- """
-CREATE TABLE P2ImageMeta(
- imageID bigint NOT NULL PRIMARY KEY,
- frameID int NOT NULL,
- ccdID smallint NOT NULL,
- photoCalID int NOT NULL,
- filterID smallint NOT NULL,
- bias real NOT NULL DEFAULT -999,
- biasScat real NOT NULL DEFAULT -999,
- sky real NOT NULL DEFAULT -999,
- skyScat real NOT NULL DEFAULT -999,
- nDetect int NOT NULL DEFAULT -999,
- magSat real NOT NULL DEFAULT -999,
- completMag real NOT NULL DEFAULT -999,
- astroScat real NOT NULL DEFAULT -999,
- photoScat real NOT NULL DEFAULT -999,
- nAstRef int NOT NULL DEFAULT -999,
- nPhoRef int NOT NULL DEFAULT -999,
- nx smallint NOT NULL DEFAULT -999,
- ny smallint NOT NULL DEFAULT -999,
- psfFwhm real NOT NULL DEFAULT -999,
- psfModelID int NOT NULL DEFAULT -999,
- psfSigMajor real NOT NULL DEFAULT -999,
- psfSigMinor real NOT NULL DEFAULT -999,
- psfTheta real NOT NULL DEFAULT -999,
- psfExtra1 real NOT NULL DEFAULT -999,
- psfExtra2 real NOT NULL DEFAULT -999,
- apResid real NOT NULL DEFAULT -999,
- dapResid real NOT NULL DEFAULT -999,
- detectorID smallint NOT NULL DEFAULT -999,
- qaFlags int NOT NULL DEFAULT -999,
- detrend1 bigint NOT NULL DEFAULT -999,
- detrend2 bigint NOT NULL DEFAULT -999,
- detrend3 bigint NOT NULL DEFAULT -999,
- detrend4 bigint NOT NULL DEFAULT -999,
- detrend5 bigint NOT NULL DEFAULT -999,
- detrend6 bigint NOT NULL DEFAULT -999,
- detrend7 bigint NOT NULL DEFAULT -999,
- detrend8 bigint NOT NULL DEFAULT -999,
- photoZero real NOT NULL DEFAULT -999,
- photoColor real NOT NULL DEFAULT -999,
- projection1 varchar(8000) NOT NULL DEFAULT '-999',
- projection2 varchar(8000) NOT NULL DEFAULT '-999',
- crval1 float NOT NULL DEFAULT -999,
- crval2 float NOT NULL DEFAULT -999,
- crpix1 float NOT NULL DEFAULT -999,
- crpix2 float NOT NULL DEFAULT -999,
- pc001001 float NOT NULL DEFAULT -999,
- pc001002 float NOT NULL DEFAULT -999,
- pc002001 float NOT NULL DEFAULT -999,
- pc002002 float NOT NULL DEFAULT -999,
- polyOrder int NOT NULL DEFAULT -999,
- pca1x3y0 float NOT NULL DEFAULT -999,
- pca1x2y1 float NOT NULL DEFAULT -999,
- pca1x1y2 float NOT NULL DEFAULT -999,
- pca1x0y3 float NOT NULL DEFAULT -999,
- pca1x2y0 float NOT NULL DEFAULT -999,
- pca1x1y1 float NOT NULL DEFAULT -999,
- pca1x0y2 float NOT NULL DEFAULT -999,
- pca2x3y0 float NOT NULL DEFAULT -999,
- pca2x2y1 float NOT NULL DEFAULT -999,
- pca2x1y2 float NOT NULL DEFAULT -999,
- pca2x0y3 float NOT NULL DEFAULT -999,
- pca2x2y0 float NOT NULL DEFAULT -999,
- pca2x1y1 float NOT NULL DEFAULT -999,
- pca2x0y2 float NOT NULL DEFAULT -999
-)
-"""
diff --git a/contrib/pc3/info/ipaw/pc3/LoadWorkflow.py b/contrib/pc3/info/ipaw/pc3/LoadWorkflow.py
deleted file mode 100644
index 97a71cb..0000000
--- a/contrib/pc3/info/ipaw/pc3/LoadWorkflow.py
+++ /dev/null
@@ -1,112 +0,0 @@
-from LoadAppLogic import LoadAppLogic
-
-class LoadWorkflow(object):
- @staticmethod
- def run(args):
- JobID, CSVRootPath = args[1:3]
-
-
- # /////////////////////////////////////
- # ////// Batch Initialization //////
- # /////////////////////////////////////
-
- # 1. IsCSVReadyFileExists
- IsCSVReadyFileExistsOutput = \
- LoadAppLogic.IsCSVReadyFileExists(CSVRootPath)
-
- # 2. Control Flow: Decision
- if not IsCSVReadyFileExistsOutput:
- raise Exception("IsCSVReadyFileExists failed")
-
-
- # 3. ReadCSVReadyFile
- ReadCSVReadyFileOutput = LoadAppLogic.ReadCSVReadyFile(CSVRootPath)
-
-
- # 4. IsMatchCSVFileTables
- IsMatchCSVFileTablesOutput = \
- LoadAppLogic.IsMatchCSVFileTables(ReadCSVReadyFileOutput)
- # 5. Control Flow: Decision
- if not IsMatchCSVFileTablesOutput:
- raise Exception("IsMatchCSVFileTables failed")
-
-
- # 6. CreateEmptyLoadDB
- CreateEmptyLoadDBOutput = LoadAppLogic.CreateEmptyLoadDB(JobID)
-
-
- # 7. Control Flow: Loop. ForEach LoadAppLogic.CSVFileEntry
- # in ReadCSVReadyFileOutput Do...
- for FileEntry in ReadCSVReadyFileOutput:
-
- # /////////////////////////////////////
- # ////// Pre Load Validation //////
- # /////////////////////////////////////
- # 7.a. IsExistsCSVFile
- IsExistsCSVFileOutput = LoadAppLogic.IsExistsCSVFile(FileEntry)
- # 7.b. Control Flow: Decision
- if not IsExistsCSVFileOutput:
- raise Exception("IsExistsCSVFile failed")
-
-
- # 7.c. ReadCSVFileColumnNames
- ReadCSVFileColumnNamesOutput = \
- LoadAppLogic.ReadCSVFileColumnNames(FileEntry)
-
-
- # 7.d. IsMatchCSVFileColumnNames
- IsMatchCSVFileColumnNamesOutput = \
- LoadAppLogic.IsMatchCSVFileColumnNames(ReadCSVFileColumnNamesOutput)
- # 7.e. Control Flow: Decision
- if not IsMatchCSVFileColumnNamesOutput:
- raise Exception("IsMatchCSVFileColumnNames failed")
-
-
- # /////////////////////////////////////
- # ////// Load File //////
- # /////////////////////////////////////
- # 7.f. LoadCSVFileIntoTable
- IsLoadedCSVFileIntoTableOutput = \
- LoadAppLogic.LoadCSVFileIntoTable(CreateEmptyLoadDBOutput,
- ReadCSVFileColumnNamesOutput)
- # 7.g. Control Flow: Decision
- if not IsLoadedCSVFileIntoTableOutput:
- raise Exception("LoadCSVFileIntoTable failed")
-
-
- # 7.h. UpdateComputedColumns
- IsUpdatedComputedColumnsOutput = \
- LoadAppLogic.UpdateComputedColumns(CreateEmptyLoadDBOutput,
- ReadCSVFileColumnNamesOutput)
- # 7.i. Control Flow: Decision
- if not IsUpdatedComputedColumnsOutput:
- raise Exception("UpdateComputedColumns failed")
-
-
- # /////////////////////////////////////
- # ////// PostLoad Validation //////
- # /////////////////////////////////////
- # 7.j. IsMatchTableRowCount
- IsMatchTableRowCountOutput = \
- LoadAppLogic.IsMatchTableRowCount(CreateEmptyLoadDBOutput,
- ReadCSVFileColumnNamesOutput)
- # 7.k. Control Flow: Decision
- if not IsMatchTableRowCountOutput:
- raise Exception("IsMatchTableRowCount failed")
-
-
- # 7.l. IsMatchTableColumnRanges
- IsMatchTableColumnRangesOutput = \
- LoadAppLogic.IsMatchTableColumnRanges(CreateEmptyLoadDBOutput,
- ReadCSVFileColumnNamesOutput)
- # 7.m. Control Flow: Decision
- if not IsMatchTableColumnRangesOutput:
- raise Exception("IsMatchTableColumnRanges failed")
-
-
- # 8. CompactDatabase
- LoadAppLogic.CompactDatabase(CreateEmptyLoadDBOutput)
-
-if __name__ == '__main__':
- import sys
- LoadWorkflow.run(sys.argv)
diff --git a/contrib/pc3/info/ipaw/pc3/__init__.py b/contrib/pc3/info/ipaw/pc3/__init__.py
deleted file mode 100644
index 2ae2839..0000000
--- a/contrib/pc3/info/ipaw/pc3/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-pass
diff --git a/contrib/pc3/workflow.vt b/contrib/pc3/workflow.vt
deleted file mode 100644
index f363513..0000000
Binary files a/contrib/pc3/workflow.vt and /dev/null differ
diff --git a/contrib/pc3/workflow_ifs.vt b/contrib/pc3/workflow_ifs.vt
deleted file mode 100644
index d4a0609..0000000
Binary files a/contrib/pc3/workflow_ifs.vt and /dev/null differ
diff --git a/contrib/pc3/workflow_log.xml b/contrib/pc3/workflow_log.xml
deleted file mode 100644
index 7f3459e..0000000
--- a/contrib/pc3/workflow_log.xml
+++ /dev/null
@@ -1,74 +0,0 @@
-<log id="" name="" version="1.0.0" vistrail_id="" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/log.xsd">
- <workflowExec completed="1" id="1" ip="155.98.20.78" name="" parentId="" parentType="vistrail" parentVersion="121" session="9" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:46" user="koop" vtVersion="1.2">
- <moduleExec cached="0" completed="1" error="" id="1" machine_id="1" moduleId="12" moduleName="String" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="2" machine_id="1" moduleId="13" moduleName="ConcatenateString" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="3" machine_id="1" moduleId="2" moduleName="GetCSVFiles" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="1" key="used_files" value="['/vistrails/pc3/SampleData/J062945/csv_ready.csv']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="4" machine_id="1" moduleId="4" moduleName="CreateEmptyLoadDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="5" machine_id="1" moduleId="8" moduleName="Map" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
- <loopExec completed="1" error="" id="6" iteration="0" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="7" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
- <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- </groupExec>
- </loopExec>
- <loopExec completed="1" error="" id="14" iteration="1" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="15" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <moduleExec cached="0" completed="1" error="" id="16" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="17" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="18" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="6" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv.hdr']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="19" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="7" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv']" />
- <annotation id="8" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="20" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="9" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="21" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- </groupExec>
- </loopExec>
- <loopExec completed="1" error="" id="22" iteration="2" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
- <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="23" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
- <moduleExec cached="0" completed="1" error="" id="24" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="25" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="26" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="10" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2Detection.csv.hdr']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="27" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:47" tsStart="2009-05-14 16:51:46">
- <annotation id="11" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2Detection.csv']" />
- <annotation id="12" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="28" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:47">
- <annotation id="13" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="29" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48" />
- </groupExec>
- </loopExec>
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="30" machine_id="1" moduleId="26" moduleName="If" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48" />
- <moduleExec cached="0" completed="1" error="" id="31" machine_id="1" moduleId="21" moduleName="CompactDatabase" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48">
- <annotation id="14" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection'), ({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMet [...]
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="32" machine_id="1" moduleId="28" moduleName="DetectionsHistogram" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49">
- <annotation id="15" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="33" machine_id="1" moduleId="29" moduleName="MplPlot" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
- <moduleExec cached="0" completed="1" error="" id="34" machine_id="1" moduleId="30" moduleName="MplFigure" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
- <moduleExec cached="0" completed="1" error="" id="35" machine_id="1" moduleId="31" moduleName="MplFigureCell" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
- </workflowExec>
- <machine architecture="32" id="1" name="vgc-g5c.sci.utah.edu" os="Darwin" processor="powerpc" ram="4294967296" />
-</log>
diff --git a/contrib/pc3/workflow_log_err.xml b/contrib/pc3/workflow_log_err.xml
deleted file mode 100644
index b2e24c1..0000000
--- a/contrib/pc3/workflow_log_err.xml
+++ /dev/null
@@ -1,49 +0,0 @@
-<log id="" name="" version="1.0.0" vistrail_id="" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/log.xsd">
- <workflowExec completed="-1" id="1" ip="155.98.20.78" name="" parentId="" parentType="vistrail" parentVersion="121" session="9" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" user="koop" vtVersion="1.2">
- <moduleExec cached="0" completed="1" error="" id="1" machine_id="1" moduleId="12" moduleName="String" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- <moduleExec cached="0" completed="1" error="" id="2" machine_id="1" moduleId="13" moduleName="ConcatenateString" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- <moduleExec cached="0" completed="1" error="" id="3" machine_id="1" moduleId="2" moduleName="GetCSVFiles" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <annotation id="1" key="used_files" value="['/vistrails/pc3/SampleData/J062945/csv_ready.csv']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="4" machine_id="1" moduleId="4" moduleName="CreateEmptyLoadDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- <moduleExec cached="0" completed="-1" error="Error inside map: Error(s) inside group:
-ComputeColumns: IsMatchTableRowCount failed" id="5" machine_id="1" moduleId="8" moduleName="Map" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <loopExec completed="1" error="" id="6" iteration="0" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="7" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
- <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- </groupExec>
- </loopExec>
- <loopExec completed="-1" error="Error(s) inside group:
-ComputeColumns: IsMatchTableRowCount failed" id="14" iteration="1" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <groupExec cached="0" completed="-1" error="Error(s) inside group:
-ComputeColumns: IsMatchTableRowCount failed" groupName="Group" groupType="Group" id="15" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <moduleExec cached="0" completed="1" error="" id="16" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- <moduleExec cached="0" completed="1" error="" id="17" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- <moduleExec cached="0" completed="1" error="" id="18" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <annotation id="6" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv.hdr']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="19" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <annotation id="7" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv']" />
- <annotation id="8" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="-1" error="IsMatchTableRowCount failed" id="20" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <annotation id="9" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
- </moduleExec>
- </groupExec>
- </loopExec>
- </moduleExec>
- </workflowExec>
- <machine architecture="32" id="1" name="vgc-g5c.sci.utah.edu" os="Darwin" processor="powerpc" ram="4294967296" />
-</log>
diff --git a/contrib/pc3/workflow_opm.xml b/contrib/pc3/workflow_opm.xml
deleted file mode 100644
index 968e4b4..0000000
--- a/contrib/pc3/workflow_opm.xml
+++ /dev/null
@@ -1,1379 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<opmGraph xmlns="http://openprovenance.org/model/v1.01.a">
- <accounts>
- <account id="acct0">
- <value>0</value>
- </account>
- <account id="acct1">
- <value>1</value>
- </account>
- <account id="acct2">
- <value>2</value>
- </account>
- <overlaps>
- <account id="acct0" />
- <account id="acct1" />
- </overlaps>
- <overlaps>
- <account id="acct0" />
- <account id="acct2" />
- </overlaps>
- <overlaps>
- <account id="acct1" />
- <account id="acct2" />
- </overlaps>
- </accounts>
- <processes>
- <process id="p0">
- <value>
- <moduleExec cached="0" completed="1" error="" id="1" machine_id="1" moduleId="12" moduleName="String" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p1">
- <value>
- <moduleExec cached="0" completed="1" error="" id="2" machine_id="1" moduleId="13" moduleName="ConcatenateString" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p2">
- <value>
- <moduleExec cached="0" completed="1" error="" id="3" machine_id="1" moduleId="2" moduleName="GetCSVFiles" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="1" key="used_files" value="['/vistrails/pc3/SampleData/J062945/csv_ready.csv']" />
- </moduleExec>
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p3">
- <value>
- <moduleExec cached="0" completed="1" error="" id="4" machine_id="1" moduleId="4" moduleName="CreateEmptyLoadDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p4">
- <value>
- <moduleExec cached="0" completed="1" error="" id="5" machine_id="1" moduleId="8" moduleName="Map" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
- <loopExec completed="1" error="" id="6" iteration="0" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="7" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
- <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- </groupExec>
- </loopExec>
- <loopExec completed="1" error="" id="14" iteration="1" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="15" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <moduleExec cached="0" completed="1" error="" id="16" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="17" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="18" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="6" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv.hdr']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="19" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="7" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv']" />
- <annotation id="8" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="20" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="9" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="21" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- </groupExec>
- </loopExec>
- <loopExec completed="1" error="" id="22" iteration="2" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
- <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="23" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:46">
- <moduleExec cached="0" completed="1" error="" id="24" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="25" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="26" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="10" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2Detection.csv.hdr']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="27" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:47" tsStart="2009-05-14 16:51:46">
- <annotation id="11" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2Detection.csv']" />
- <annotation id="12" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="28" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:47">
- <annotation id="13" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="29" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48" />
- </groupExec>
- </loopExec>
- </moduleExec>
- </value>
- <account id="acct0" />
- </process>
- <process id="p5">
- <value>
- <moduleExec cached="0" completed="1" error="" id="30" machine_id="1" moduleId="26" moduleName="If" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48" />
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p6">
- <value>
- <moduleExec cached="0" completed="1" error="" id="31" machine_id="1" moduleId="21" moduleName="CompactDatabase" tsEnd="2009-05-14 16:51:48" tsStart="2009-05-14 16:51:48">
- <annotation id="14" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection'), ({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Fram [...]
- </moduleExec>
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p7">
- <value>
- <moduleExec cached="0" completed="1" error="" id="32" machine_id="1" moduleId="28" moduleName="DetectionsHistogram" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49">
- <annotation id="15" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2Detection')]" />
- </moduleExec>
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p8">
- <value>
- <moduleExec cached="0" completed="1" error="" id="33" machine_id="1" moduleId="29" moduleName="MplPlot" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p9">
- <value>
- <moduleExec cached="0" completed="1" error="" id="34" machine_id="1" moduleId="30" moduleName="MplFigure" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p10">
- <value>
- <moduleExec cached="0" completed="1" error="" id="35" machine_id="1" moduleId="31" moduleName="MplFigureCell" tsEnd="2009-05-14 16:51:49" tsStart="2009-05-14 16:51:49" />
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p11">
- <value>
- <moduleExec cached="" completed="1" error="" id="-1" machine_id="" moduleId="-1" moduleName="Split" tsEnd="" tsStart="" />
- </value>
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p12">
- <value>
- <moduleExec cached="" completed="1" error="" id="-1" machine_id="" moduleId="-1" moduleName="Join" tsEnd="" tsStart="" />
- </value>
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p13">
- <value>
- <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="7" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
- <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- </groupExec>
- </value>
- <account id="acct1" />
- </process>
- <process id="p14">
- <value>
- <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- </value>
- <account id="acct2" />
- </process>
- <process id="p15">
- <value>
- <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- </value>
- <account id="acct2" />
- </process>
- <process id="p16">
- <value>
- <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
- </moduleExec>
- </value>
- <account id="acct2" />
- </process>
- <process id="p17">
- <value>
- <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
- <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
- </moduleExec>
- </value>
- <account id="acct2" />
- </process>
- <process id="p18">
- <value>
- <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="5" key="used_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
- </moduleExec>
- </value>
- <account id="acct2" />
- </process>
- <process id="p19">
- <value>
- <moduleExec cached="0" completed="1" error="" id="13" machine_id="1" moduleId="6" moduleName="OutputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- </value>
- <account id="acct2" />
- </process>
- <process id="p20">
- <value>
- <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="15" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <moduleExec cached="0" completed="1" error="" id="16" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="17" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46" />
- <moduleExec cached="0" completed="1" error="" id="18" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="6" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv.hdr']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="19" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
- <annotation id="7" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2ImageMeta.csv']" />
- <annotation id="8" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2ImageMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="20" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:51:46" tsStart="2009-05-14 16:51:46">
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- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p1" />
- <role value="in" />
- <cause id="a2" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p1" />
- <role value="in" />
- <cause id="a1" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a3" />
- <role value="out" />
- <cause id="p1" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p2" />
- <role value="in" />
- <cause id="a4" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p2" />
- <role value="in" />
- <cause id="a3" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a5" />
- <role value="out" />
- <cause id="p2" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p3" />
- <role value="in" />
- <cause id="a1" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a6" />
- <role value="out" />
- <cause id="p3" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p4" />
- <role value="in" />
- <cause id="a5" />
- <account id="acct0" />
- </used>
- <wasGeneratedBy>
- <effect id="a7" />
- <role value="out" />
- <cause id="p4" />
- <account id="acct0" />
- </wasGeneratedBy>
- <used>
- <effect id="p11" />
- <role value="in" />
- <cause id="a5" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a8" />
- <role value="out" />
- <cause id="p11" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p12" />
- <role value="in" />
- <cause id="a9" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p13" />
- <role value="in" />
- <cause id="a8" />
- <account id="acct1" />
- </used>
- <wasGeneratedBy>
- <effect id="a9" />
- <role value="out" />
- <cause id="p13" />
- <account id="acct1" />
- </wasGeneratedBy>
- <used>
- <effect id="p13" />
- <role value="in" />
- <cause id="a6" />
- <account id="acct1" />
- </used>
- <wasGeneratedBy>
- <effect id="a10" />
- <role value="out" />
- <cause id="p14" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p14" />
- <role value="in" />
- <cause id="a6" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a11" />
- <role value="out" />
- <cause id="p15" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p15" />
- <role value="in" />
- <cause id="a8" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p16" />
- <role value="in" />
- <cause id="a12" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p16" />
- <role value="in" />
- <cause id="a11" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a13" />
- <role value="out" />
- <cause id="p16" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p17" />
- <role value="in" />
- <cause id="a14" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a15" />
- <role value="out" />
- <cause id="p17" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p17" />
- <role value="in" />
- <cause id="a10" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p17" />
- <role value="in" />
- <cause id="a13" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a16" />
- <role value="out" />
- <cause id="p17" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p18" />
- <role value="in" />
- <cause id="a15" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p18" />
- <role value="in" />
- <cause id="a16" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p18" />
- <role value="in" />
- <cause id="a13" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a17" />
- <role value="out" />
- <cause id="p18" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p19" />
- <role value="in" />
- <cause id="a17" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a9" />
- <role value="out" />
- <cause id="p19" />
- <account id="acct2" />
- </wasGeneratedBy>
- <wasGeneratedBy>
- <effect id="a18" />
- <role value="out" />
- <cause id="p11" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p12" />
- <role value="in" />
- <cause id="a19" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p20" />
- <role value="in" />
- <cause id="a18" />
- <account id="acct1" />
- </used>
- <wasGeneratedBy>
- <effect id="a19" />
- <role value="out" />
- <cause id="p20" />
- <account id="acct1" />
- </wasGeneratedBy>
- <used>
- <effect id="p20" />
- <role value="in" />
- <cause id="a6" />
- <account id="acct1" />
- </used>
- <wasGeneratedBy>
- <effect id="a20" />
- <role value="out" />
- <cause id="p21" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p21" />
- <role value="in" />
- <cause id="a6" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a21" />
- <role value="out" />
- <cause id="p22" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p22" />
- <role value="in" />
- <cause id="a18" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p23" />
- <role value="in" />
- <cause id="a22" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p23" />
- <role value="in" />
- <cause id="a21" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a23" />
- <role value="out" />
- <cause id="p23" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p24" />
- <role value="in" />
- <cause id="a24" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a25" />
- <role value="out" />
- <cause id="p24" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p24" />
- <role value="in" />
- <cause id="a20" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p24" />
- <role value="in" />
- <cause id="a23" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a26" />
- <role value="out" />
- <cause id="p24" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p25" />
- <role value="in" />
- <cause id="a25" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p25" />
- <role value="in" />
- <cause id="a26" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p25" />
- <role value="in" />
- <cause id="a23" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a27" />
- <role value="out" />
- <cause id="p25" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p26" />
- <role value="in" />
- <cause id="a27" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a19" />
- <role value="out" />
- <cause id="p26" />
- <account id="acct2" />
- </wasGeneratedBy>
- <wasGeneratedBy>
- <effect id="a28" />
- <role value="out" />
- <cause id="p11" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p12" />
- <role value="in" />
- <cause id="a29" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p27" />
- <role value="in" />
- <cause id="a28" />
- <account id="acct1" />
- </used>
- <wasGeneratedBy>
- <effect id="a29" />
- <role value="out" />
- <cause id="p27" />
- <account id="acct1" />
- </wasGeneratedBy>
- <used>
- <effect id="p27" />
- <role value="in" />
- <cause id="a6" />
- <account id="acct1" />
- </used>
- <wasGeneratedBy>
- <effect id="a30" />
- <role value="out" />
- <cause id="p28" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p28" />
- <role value="in" />
- <cause id="a6" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a31" />
- <role value="out" />
- <cause id="p29" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p29" />
- <role value="in" />
- <cause id="a28" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p30" />
- <role value="in" />
- <cause id="a32" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p30" />
- <role value="in" />
- <cause id="a31" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a33" />
- <role value="out" />
- <cause id="p30" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p31" />
- <role value="in" />
- <cause id="a34" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a35" />
- <role value="out" />
- <cause id="p31" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p31" />
- <role value="in" />
- <cause id="a30" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p31" />
- <role value="in" />
- <cause id="a33" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a36" />
- <role value="out" />
- <cause id="p31" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p32" />
- <role value="in" />
- <cause id="a35" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p32" />
- <role value="in" />
- <cause id="a36" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p32" />
- <role value="in" />
- <cause id="a33" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a37" />
- <role value="out" />
- <cause id="p32" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p33" />
- <role value="in" />
- <cause id="a37" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a29" />
- <role value="out" />
- <cause id="p33" />
- <account id="acct2" />
- </wasGeneratedBy>
- <wasGeneratedBy>
- <effect id="a7" />
- <role value="out" />
- <cause id="p12" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p5" />
- <role value="in" />
- <cause id="a7" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <wasTriggeredBy>
- <effect id="p6" />
- <role value="control" />
- <cause id="p5" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </wasTriggeredBy>
- <used>
- <effect id="p6" />
- <role value="in" />
- <cause id="a35" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p6" />
- <role value="in" />
- <cause id="a15" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p6" />
- <role value="in" />
- <cause id="a25" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p6" />
- <role value="in" />
- <cause id="a6" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a38" />
- <role value="out" />
- <cause id="p6" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p7" />
- <role value="in" />
- <cause id="a35" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p7" />
- <role value="in" />
- <cause id="a39" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p7" />
- <role value="in" />
- <cause id="a38" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a40" />
- <role value="out" />
- <cause id="p7" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p8" />
- <role value="in" />
- <cause id="a41" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p8" />
- <role value="in" />
- <cause id="a40" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a42" />
- <role value="out" />
- <cause id="p8" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p9" />
- <role value="in" />
- <cause id="a42" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- <wasGeneratedBy>
- <effect id="a43" />
- <role value="out" />
- <cause id="p9" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p10" />
- <role value="in" />
- <cause id="a43" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
- </causalDependencies>
-</opmGraph>
diff --git a/contrib/pc3/workflow_opm_err.xml b/contrib/pc3/workflow_opm_err.xml
deleted file mode 100644
index 008bbdc..0000000
--- a/contrib/pc3/workflow_opm_err.xml
+++ /dev/null
@@ -1,756 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<opmGraph xmlns="http://openprovenance.org/model/v1.01.a">
- <accounts>
- <account id="acct0">
- <value>0</value>
- </account>
- <account id="acct1">
- <value>1</value>
- </account>
- <account id="acct2">
- <value>2</value>
- </account>
- <overlaps>
- <account id="acct0" />
- <account id="acct1" />
- </overlaps>
- <overlaps>
- <account id="acct0" />
- <account id="acct2" />
- </overlaps>
- <overlaps>
- <account id="acct1" />
- <account id="acct2" />
- </overlaps>
- </accounts>
- <processes>
- <process id="p0">
- <value>
- <moduleExec cached="0" completed="1" error="" id="1" machine_id="1" moduleId="12" moduleName="String" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p1">
- <value>
- <moduleExec cached="0" completed="1" error="" id="2" machine_id="1" moduleId="13" moduleName="ConcatenateString" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p2">
- <value>
- <moduleExec cached="0" completed="1" error="" id="3" machine_id="1" moduleId="2" moduleName="GetCSVFiles" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <annotation id="1" key="used_files" value="['/vistrails/pc3/SampleData/J062945/csv_ready.csv']" />
- </moduleExec>
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p3">
- <value>
- <moduleExec cached="0" completed="1" error="" id="4" machine_id="1" moduleId="4" moduleName="CreateEmptyLoadDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- </value>
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </process>
- <process id="p4">
- <value>
- <moduleExec cached="0" completed="-1" error="Error inside map: Error(s) inside group: ComputeColumns: IsMatchTableRowCount failed" id="5" machine_id="1" moduleId="8" moduleName="Map" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <loopExec completed="1" error="" id="6" iteration="0" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <groupExec cached="0" completed="1" error="" groupName="Group" groupType="Group" id="7" machine_id="1" moduleId="25" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <moduleExec cached="0" completed="1" error="" id="8" machine_id="1" moduleId="5" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- <moduleExec cached="0" completed="1" error="" id="9" machine_id="1" moduleId="4" moduleName="InputPort" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47" />
- <moduleExec cached="0" completed="1" error="" id="10" machine_id="1" moduleId="3" moduleName="ReadCSVFile" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <annotation id="2" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv.hdr']" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="11" machine_id="1" moduleId="2" moduleName="LoadCSVFileIntoDB" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
- <annotation id="3" key="used_files" value="['/vistrails/pc3/SampleData/J062945/P2_J062945_B001_P2fits0_20081115_P2FrameMeta.csv']" />
- <annotation id="4" key="generated_tables" value="[({'passwd': 'pc3_load-2009', 'host': 'localhost', 'db': 'J062945_LoadDB', 'user': 'ipaw'}, 'J062945_LoadDB', 'P2FrameMeta')]" />
- </moduleExec>
- <moduleExec cached="0" completed="1" error="" id="12" machine_id="1" moduleId="1" moduleName="ComputeColumns" tsEnd="2009-05-14 16:36:47" tsStart="2009-05-14 16:36:47">
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- <effect id="a6" />
- <role value="out" />
- <cause id="p3" />
- <account id="acct0" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p4" />
- <role value="in" />
- <cause id="a5" />
- <account id="acct0" />
- </used>
- <used>
- <effect id="p5" />
- <role value="in" />
- <cause id="a5" />
- <account id="acct1" />
- <account id="acct2" />
- </used>
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- <effect id="a7" />
- <role value="out" />
- <cause id="p5" />
- <account id="acct1" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
- <effect id="p6" />
- <role value="in" />
- <cause id="a7" />
- <account id="acct1" />
- </used>
- <wasGeneratedBy>
- <effect id="a8" />
- <role value="out" />
- <cause id="p6" />
- <account id="acct1" />
- </wasGeneratedBy>
- <used>
- <effect id="p6" />
- <role value="in" />
- <cause id="a6" />
- <account id="acct1" />
- </used>
- <wasGeneratedBy>
- <effect id="a9" />
- <role value="out" />
- <cause id="p7" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
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- <account id="acct2" />
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- <wasGeneratedBy>
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- <account id="acct2" />
- </wasGeneratedBy>
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- <used>
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- <role value="in" />
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- <used>
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- <used>
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- <role value="in" />
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- <account id="acct2" />
- </used>
- <wasGeneratedBy>
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- <role value="out" />
- <cause id="p17" />
- <account id="acct2" />
- </wasGeneratedBy>
- <used>
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- <role value="in" />
- <cause id="a23" />
- <account id="acct2" />
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- <cause id="a24" />
- <account id="acct2" />
- </used>
- <used>
- <effect id="p18" />
- <role value="in" />
- <cause id="a21" />
- <account id="acct2" />
- </used>
- </causalDependencies>
-</opmGraph>
diff --git a/contrib/pc3/workflow_reg.xml b/contrib/pc3/workflow_reg.xml
deleted file mode 100644
index a1cba59..0000000
--- a/contrib/pc3/workflow_reg.xml
+++ /dev/null
@@ -1,330 +0,0 @@
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- <package codepath="basic_modules" description="basic_modules defines basic VisTrails Modules that are used in most
-pipelines." id="0" identifier="edu.utah.sci.vistrails.basic" loadConfiguration="1" name="Basic Modules" version="1.2">
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- <moduleDescriptor baseDescriptorId="0" id="1" name="Constant" namespace="" package="edu.utah.sci.vistrails.basic" version="">
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- <moduleDescriptor baseDescriptorId="1" id="2" name="Boolean" namespace="" package="edu.utah.sci.vistrails.basic" version="">
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- <portSpec id="2" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="1" id="3" name="Float" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="3" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Float)" sortKey="-1" type="input" />
- <portSpec id="4" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Float)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="1" id="4" name="Integer" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="5" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
- <portSpec id="6" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="1" id="5" name="String" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="7" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="8" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="1" id="6" name="File" namespace="" package="edu.utah.sci.vistrails.basic" version="">
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- <portSpec id="11" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="output" />
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- <portSpec id="14" name="create_file" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
- <portSpec id="15" name="local_filename" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="7" name="FileSink" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="16" name="file" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
- <portSpec id="17" name="outputName" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="18" name="overrideFile" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="1" id="8" name="Color" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="19" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Color)" sortKey="-1" type="input" />
- <portSpec id="20" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Color)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="9" name="StandardOutput" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="21" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="10" name="Tuple" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="22" name="self" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Tuple)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="11" name="TestTuple" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="23" name="tuple" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Integer,edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="12" name="Untuple" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="24" name="tuple" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Tuple)" sortKey="-1" type="input" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="13" name="ConcatenateString" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="25" name="str1" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
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- <portSpec id="27" name="str3" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="28" name="str4" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="29" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="14" name="List" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="30" name="head" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
- <portSpec id="31" name="tail" optional="0" sigstring="(edu.utah.sci.vistrails.basic:List)" sortKey="-1" type="input" />
- <portSpec id="32" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:List)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="15" name="Null" namespace="" package="edu.utah.sci.vistrails.basic" version="" />
- <moduleDescriptor baseDescriptorId="0" id="16" name="PythonSource" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="33" name="source" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="34" name="self" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="17" name="SmartSource" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="35" name="source" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="18" name="Unzip" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="36" name="archive_file" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
- <portSpec id="37" name="filename_in_archive" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="38" name="file" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="19" name="Variant" namespace="" package="edu.utah.sci.vistrails.basic" version="" />
- <moduleDescriptor baseDescriptorId="0" id="20" name="InputPort" namespace="" package="edu.utah.sci.vistrails.basic" version="">
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- <portSpec id="42" name="old_name" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
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- <portSpec id="44" name="InternalPipe" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Variant)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="21" name="OutputPort" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="45" name="name" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
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- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="22" name="Group" namespace="" package="edu.utah.sci.vistrails.basic" version="">
- <portSpec id="50" name="self" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Group)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="22" id="23" name="SubWorkflow" namespace="" package="edu.utah.sci.vistrails.basic" version="" />
- </package>
- <package codepath="pythonCalc" description="This package implements a very simple VisTrails module called
-PythonCalc. This is intended as a simple example that can be referred
-to by users to create their own packages and modules later.
-
-If you're interested in developing new modules for VisTrails, you
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- <moduleDescriptor baseDescriptorId="0" id="24" name="PythonCalc" namespace="" package="edu.utah.sci.vistrails.pythoncalc" version="">
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- <portSpec id="54" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Float)" sortKey="-1" type="output" />
- </moduleDescriptor>
- </package>
- <package codepath="spreadsheet" description="No description available" id="2" identifier="edu.utah.sci.vistrails.spreadsheet" loadConfiguration="1" name="VisTrails Spreadsheet" version="0.9.0">
- <moduleDescriptor baseDescriptorId="0" id="25" name="SheetReference" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
- <portSpec id="55" name="MinRowCount" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
- <portSpec id="56" name="MinColumnCount" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
- <portSpec id="57" name="SheetName" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="58" name="self" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:SheetReference)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="26" name="CellLocation" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
- <portSpec id="59" name="ColumnRowAddress" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="60" name="Row" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
- <portSpec id="61" name="Column" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
- <portSpec id="62" name="SheetReference" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:SheetReference)" sortKey="-1" type="input" />
- <portSpec id="63" name="self" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:CellLocation)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="27" name="SpreadsheetCell" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
- <portSpec id="64" name="Location" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:CellLocation)" sortKey="-1" type="input" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="25" id="28" name="SingleCellSheetReference" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
- <portSpec id="65" name="SheetName" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="66" name="self" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:SingleCellSheetReference)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="27" id="29" name="ImageViewerCell" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
- <portSpec id="67" name="Location" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:CellLocation)" sortKey="-1" type="input" />
- <portSpec id="68" name="File" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="27" id="30" name="RichTextCell" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
- <portSpec id="69" name="Location" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:CellLocation)" sortKey="-1" type="input" />
- <portSpec id="70" name="File" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="27" id="31" name="SVGCell" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
- <portSpec id="71" name="Location" optional="0" sigstring="(edu.utah.sci.vistrails.spreadsheet:CellLocation)" sortKey="-1" type="input" />
- <portSpec id="72" name="File" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="32" name="SVGSplitter" namespace="" package="edu.utah.sci.vistrails.spreadsheet" version="">
- <portSpec id="73" name="File" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="input" />
- </moduleDescriptor>
- </package>
- <package codepath="controlflow" description="No description available" id="6" identifier="edu.utah.sci.vistrails.control_flow" loadConfiguration="1" name="Control Flow" version="0.1">
- <moduleDescriptor baseDescriptorId="1" id="33" name="ListOfElements" namespace="" package="edu.utah.sci.vistrails.control_flow" version="">
- <portSpec id="74" name="value" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
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- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="34" name="Fold" namespace="" package="edu.utah.sci.vistrails.control_flow" version="">
- <portSpec id="76" name="FunctionPort" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
- <portSpec id="77" name="InputList" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
- <portSpec id="78" name="InputPort" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
- <portSpec id="79" name="OutputPort" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="80" name="Result" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Variant)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="34" id="35" name="Map" namespace="" package="edu.utah.sci.vistrails.control_flow" version="" />
- <moduleDescriptor baseDescriptorId="34" id="36" name="Filter" namespace="" package="edu.utah.sci.vistrails.control_flow" version="" />
- <moduleDescriptor baseDescriptorId="34" id="37" name="AreaFilter" namespace="" package="edu.utah.sci.vistrails.control_flow" version="" />
- <moduleDescriptor baseDescriptorId="34" id="38" name="SimilarityFilter" namespace="" package="edu.utah.sci.vistrails.control_flow" version="" />
- <moduleDescriptor baseDescriptorId="0" id="39" name="If" namespace="" package="edu.utah.sci.vistrails.control_flow" version="">
- <portSpec id="81" name="Condition" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
- <portSpec id="82" name="TruePort" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
- <portSpec id="83" name="FalsePort" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
- <portSpec id="84" name="TrueOutputPorts" optional="1" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
- <portSpec id="85" name="FalseOutputPorts" optional="1" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
- <portSpec id="86" name="Result" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Variant)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="40" name="Dot" namespace="" package="edu.utah.sci.vistrails.control_flow" version="">
- <portSpec id="87" name="List_1" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
- <portSpec id="88" name="List_2" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
- <portSpec id="89" name="CombineTuple" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
- <portSpec id="90" name="Result" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="41" name="Cross" namespace="" package="edu.utah.sci.vistrails.control_flow" version="">
- <portSpec id="91" name="List_1" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
- <portSpec id="92" name="List_2" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
- <portSpec id="93" name="CombineTuple" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
- <portSpec id="94" name="Result" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="output" />
- </moduleDescriptor>
- </package>
- <package codepath="HTTP" description="HTTP provides packages for HTTP-based file fetching. This provides
-a location-independent way of referring to files. This package uses a
-local cache of the files, inside the per-user VisTrails
-directory. This way, files that haven't been changed do not need
-downloading. The check is performed efficiently using the HTTP GET
-headers.
-" id="4" identifier="edu.utah.sci.vistrails.http" loadConfiguration="1" name="HTTP" version="0.9.0">
- <moduleDescriptor baseDescriptorId="0" id="42" name="HTTP" namespace="" package="edu.utah.sci.vistrails.http" version="" />
- <moduleDescriptor baseDescriptorId="42" id="43" name="HTTPFile" namespace="" package="edu.utah.sci.vistrails.http" version="">
- <portSpec id="95" name="url" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="96" name="file" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="output" />
- <portSpec id="97" name="local_filename" optional="1" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
- </moduleDescriptor>
- </package>
- <package codepath="pylab" description="Matplotlib package for VisTrails.
-
-This package wrap Matplotlib to provide a plotting tool for
-VisTrails. We are going to use the 'Qt4Agg' backend of the library.
-
-" id="5" identifier="edu.utah.sci.vistrails.matplotlib" loadConfiguration="1" name="matplotlib" version="0.9.0">
- <moduleDescriptor baseDescriptorId="16" id="44" name="MplPlot" namespace="" package="edu.utah.sci.vistrails.matplotlib" version="">
- <portSpec id="98" name="source" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="45" name="MplFigureManager" namespace="" package="edu.utah.sci.vistrails.matplotlib" version="" />
- <moduleDescriptor baseDescriptorId="0" id="46" name="MplFigure" namespace="" package="edu.utah.sci.vistrails.matplotlib" version="">
- <portSpec id="99" name="Script" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="100" name="FigureManager" optional="0" sigstring="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" sortKey="-1" type="output" />
- <portSpec id="101" name="File" optional="0" sigstring="(edu.utah.sci.vistrails.basic:File)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="27" id="47" name="MplFigureCell" namespace="" package="edu.utah.sci.vistrails.matplotlib" version="">
- <portSpec id="102" name="FigureManager" optional="0" sigstring="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" sortKey="-1" type="input" />
- </moduleDescriptor>
- </package>
- <package codepath="dialogs" description="dialogs provides modules for user-based interaction on execution.
-Users can then enter file names, numbers, strings, etc." id="3" identifier="edu.utah.sci.vistrails.dialogs" loadConfiguration="1" name="Dialogs" version="0.9.0">
- <moduleDescriptor baseDescriptorId="0" id="48" name="Dialog" namespace="" package="edu.utah.sci.vistrails.dialogs" version="" />
- <moduleDescriptor baseDescriptorId="48" id="49" name="TextDialog" namespace="" package="edu.utah.sci.vistrails.dialogs" version="">
- <portSpec id="103" name="title" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="104" name="label" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="105" name="default" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="106" name="result" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="output" />
- </moduleDescriptor>
- </package>
- <package codepath="pc3" description="No description available" id="7" identifier="edu.utah.sci.dakoop.pc3" loadConfiguration="1" name="Provenance Challenge 3" version="1.0.0">
- <moduleDescriptor baseDescriptorId="0" id="50" name="ReadCSVReadyFile" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="107" name="csvRootPath" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="108" name="csvFiles" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="51" name="IsMatchTableRowCount" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="109" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
- <portSpec id="110" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
- <portSpec id="111" name="countsMatch" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="52" name="LoadCSVFileIntoDB" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="112" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
- <portSpec id="113" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
- <portSpec id="114" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="53" name="IsMatchCSVFileColumnNames" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="115" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
- <portSpec id="116" name="columnsMatch" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="54" name="ComputeColumns" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="117" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
- <portSpec id="118" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
- <portSpec id="119" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="55" name="ReadCSVFile" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="120" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
- <portSpec id="121" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="56" name="LoadCSVFileIntoTable" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="122" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
- <portSpec id="123" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
- <portSpec id="124" name="success" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="57" name="IsMatchTableColumnRanges" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="125" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
- <portSpec id="126" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
- <portSpec id="127" name="rangesMatch" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="58" name="DetectionsHistogram" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="128" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
- <portSpec id="129" name="highQuality" optional="1" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="input" />
- <portSpec id="130" name="histogram" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="59" name="Collection" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="131" name="elements" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Module)" sortKey="-1" type="input" />
- <portSpec id="132" name="self" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:Collection)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="60" name="CompactDatabase" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="133" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
- <portSpec id="134" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="61" name="IsMatchCSVFileTables" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="135" name="csvFiles" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="input" />
- <portSpec id="136" name="tablesMatch" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="62" name="ReadCSVFileColumnNames" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="137" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
- <portSpec id="138" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="63" name="CreateEmptyLoadDB" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="139" name="jobID" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="140" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="64" name="GetCSVFiles" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="141" name="csvRootPath" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="142" name="csvFiles" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="65" name="IsExistsCSVFile" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="143" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
- <portSpec id="144" name="fileExists" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="66" name="DatabaseEntry" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="145" name="dbGuid" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="146" name="dbName" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="147" name="connectionString" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="148" name="self" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="67" name="UpdateComputedColumns" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="149" name="csvFile" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="input" />
- <portSpec id="150" name="dbEntry" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" sortKey="-1" type="input" />
- <portSpec id="151" name="success" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="68" name="CSVFileEntry" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="152" name="filePath" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="153" name="headerPath" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="154" name="rowCount" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Integer)" sortKey="-1" type="input" />
- <portSpec id="155" name="targetTable" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="156" name="checksum" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="157" name="columnNames" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:Collection)" sortKey="-1" type="input" />
- <portSpec id="158" name="self" optional="0" sigstring="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" sortKey="-1" type="output" />
- </moduleDescriptor>
- <moduleDescriptor baseDescriptorId="0" id="69" name="IsCSVReadyFileExists" namespace="" package="edu.utah.sci.dakoop.pc3" version="">
- <portSpec id="159" name="csvRootPath" optional="0" sigstring="(edu.utah.sci.vistrails.basic:String)" sortKey="-1" type="input" />
- <portSpec id="160" name="fileExists" optional="0" sigstring="(edu.utah.sci.vistrails.basic:Boolean)" sortKey="-1" type="output" />
- </moduleDescriptor>
- </package>
- <package codepath="subworkflows" description="No description available" id="8" identifier="local.abstractions" loadConfiguration="1" name="My SubWorkflows" version="1.2" />
-</registry>
diff --git a/contrib/pc3/workflow_vt.xml b/contrib/pc3/workflow_vt.xml
deleted file mode 100644
index ce68b5f..0000000
--- a/contrib/pc3/workflow_vt.xml
+++ /dev/null
@@ -1,1153 +0,0 @@
-<vistrail id="" name="" version="0.9.5" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/vistrail.xsd">
- <action date="2009-04-07 16:02:43" id="1" prevId="0" prune="" session="0" user="koop">
- <add id="0" objectId="0" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="0" name="DatabaseEntry" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
- </add>
- <add id="1" objectId="0" parentObjId="0" parentObjType="module" what="location">
- <location id="0" x="-162.420168067" y="79.5966386555" />
- </add>
- </action>
- <action date="2009-04-07 16:02:45" id="2" prevId="1" prune="" session="0" user="koop">
- <add id="2" objectId="1" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="1" name="LoadCSVFileIntoDB" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
- </add>
- <add id="3" objectId="1" parentObjId="1" parentObjType="module" what="location">
- <location id="1" x="-104.336134454" y="-118.319327731" />
- </add>
- </action>
- <action date="2009-04-07 16:04:24" id="3" prevId="2" prune="" session="0" user="koop">
- <delete id="4" objectId="0" parentObjId="0" parentObjType="module" what="location" />
- <delete id="5" objectId="0" parentObjId="" parentObjType="" what="module" />
- <delete id="6" objectId="1" parentObjId="1" parentObjType="module" what="location" />
- <delete id="7" objectId="1" parentObjId="" parentObjType="" what="module" />
- </action>
- <action date="2009-04-07 16:04:27" id="4" prevId="3" prune="" session="0" user="koop">
- <add id="8" objectId="2" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="2" name="GetCSVFiles" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
- </add>
- <add id="9" objectId="2" parentObjId="2" parentObjType="module" what="location">
- <location id="2" x="-84.974789916" y="105.411764706" />
- </add>
- </action>
- <action date="2009-04-07 16:04:58" id="5" prevId="4" prune="" session="0" user="koop">
- <change id="10" newObjId="3" oldObjId="2" parentObjId="2" parentObjType="module" what="location">
- <location id="3" x="-20.4369747899" y="129.075630252" />
- </change>
- </action>
- <action date="2009-04-07 16:04:58" id="6" prevId="5" prune="" session="0" user="koop">
- <add id="11" objectId="3" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="3" name="ComputeColumns" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
- </add>
- <add id="12" objectId="4" parentObjId="3" parentObjType="module" what="location">
- <location id="4" x="50.5546218487" y="-62.3865546218" />
- </add>
- </action>
- <action date="2009-04-07 16:05:01" id="7" prevId="6" prune="" session="0" user="koop">
- <add id="13" objectId="4" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="4" name="CreateEmptyLoadDB" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
- </add>
- <add id="14" objectId="5" parentObjId="4" parentObjType="module" what="location">
- <location id="5" x="-236.638655462" y="118.319327731" />
- </add>
- </action>
- <action date="2009-04-07 16:05:06" id="8" prevId="7" prune="" session="0" user="koop">
- <add id="15" objectId="5" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="5" name="LoadCSVFileIntoDB" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0" />
- </add>
- <add id="16" objectId="6" parentObjId="5" parentObjType="module" what="location">
- <location id="6" x="-157.042016807" y="8.60504201681" />
- </add>
- </action>
- <action date="2009-04-07 16:05:10" id="9" prevId="8" prune="" session="0" user="koop">
- <add id="17" objectId="0" parentObjId="" parentObjType="" what="connection">
- <connection id="0" />
- </add>
- <add id="18" objectId="0" parentObjId="0" parentObjType="connection" what="port">
- <port id="0" moduleId="4" moduleName="CreateEmptyLoadDB" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
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- <add id="308" objectId="72" parentObjId="36" parentObjType="connection" what="port">
- <port id="72" moduleId="30" moduleName="MplFigure" name="FigureManager" signature="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" type="source" />
- </add>
- <add id="309" objectId="73" parentObjId="36" parentObjType="connection" what="port">
- <port id="73" moduleId="31" moduleName="MplFigureCell" name="FigureManager" signature="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" type="destination" />
- </add>
- </action>
- <action date="2009-04-10 13:41:42" id="110" prevId="109" prune="" session="6" user="koop">
- <add id="310" objectId="37" parentObjId="" parentObjType="" what="connection">
- <connection id="37" />
- </add>
- <add id="311" objectId="74" parentObjId="37" parentObjType="connection" what="port">
- <port id="74" moduleId="29" moduleName="MplPlot" name="source" signature="(edu.utah.sci.vistrails.basic:String)" type="source" />
- </add>
- <add id="312" objectId="75" parentObjId="37" parentObjType="connection" what="port">
- <port id="75" moduleId="30" moduleName="MplFigure" name="Script" signature="(edu.utah.sci.vistrails.basic:String)" type="destination" />
- </add>
- </action>
- <action date="2009-04-10 13:45:54" id="111" prevId="110" prune="" session="6" user="koop">
- <add id="313" objectId="0" parentObjId="29" parentObjType="module" what="portSpec">
- <portSpec id="0" name="histogramData" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="0" type="input" />
- </add>
- <add id="314" objectId="6" parentObjId="29" parentObjType="module" what="function">
- <function id="6" name="source" pos="0" />
- </add>
- <add id="315" objectId="14" parentObjId="6" parentObjType="function" what="parameter">
- <parameter alias="" id="14" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="x%20%3D%20%5Ba%5B1%5D%20for%20a%20in%20histogramData%5D%0Abins%20%3D%20%5Ba%5B0%5D%20for%20a%20in%20histogramData%5D%0A%0Ahist%28x%2C%20bins%29%0A" />
- </add>
- </action>
- <action date="2009-04-10 13:45:58" id="112" prevId="111" prune="" session="6" user="koop">
- <add id="316" objectId="38" parentObjId="" parentObjType="" what="connection">
- <connection id="38" />
- </add>
- <add id="317" objectId="76" parentObjId="38" parentObjType="connection" what="port">
- <port id="76" moduleId="28" moduleName="DetectionsHistogram" name="histogram" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="source" />
- </add>
- <add id="318" objectId="77" parentObjId="38" parentObjType="connection" what="port">
- <port id="77" moduleId="29" moduleName="MplPlot" name="histogramData" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="destination" />
- </add>
- </action>
- <action date="2009-04-10 14:02:37" id="113" prevId="112" prune="" session="7" user="koop">
- <change id="319" newObjId="15" oldObjId="14" parentObjId="6" parentObjType="function" what="parameter">
- <parameter alias="" id="15" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="x%20%3D%20%5Ba%5B1%5D%20for%20a%20in%20histogramData%5D%0Abins%20%3D%20%5Ba%5B0%5D%20for%20a%20in%20histogramData%5D%0A%0Abar%28x%2C%20bins%29%0A" />
- </change>
- </action>
- <action date="2009-04-10 14:03:17" id="114" prevId="113" prune="" session="7" user="koop">
- <change id="320" newObjId="16" oldObjId="15" parentObjId="6" parentObjType="function" what="parameter">
- <parameter alias="" id="16" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="x%20%3D%20%5Ba%5B1%5D%20for%20a%20in%20histogramData%5D%0Abins%20%3D%20%5Ba%5B0%5D%20for%20a%20in%20histogramData%5D%0A%0Abar%28bins%2C%20x%29%0A" />
- </change>
- </action>
- <action date="2009-04-10 14:03:32" id="115" prevId="114" prune="" session="7" user="koop">
- <change id="321" newObjId="17" oldObjId="10" parentObjId="4" parentObjType="function" what="parameter">
- <parameter alias="" id="17" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="J062945" />
- </change>
- </action>
- <action date="2009-04-10 14:04:46" id="116" prevId="115" prune="" session="7" user="koop">
- <add id="322" objectId="7" parentObjId="28" parentObjType="module" what="function">
- <function id="7" name="highQuality" pos="0" />
- </add>
- <add id="323" objectId="18" parentObjId="7" parentObjType="function" what="parameter">
- <parameter alias="" id="18" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Boolean" val="" />
- </add>
- </action>
- <action date="2009-04-10 14:04:47" id="117" prevId="116" prune="" session="7" user="koop">
- <change id="324" newObjId="19" oldObjId="18" parentObjId="7" parentObjType="function" what="parameter">
- <parameter alias="" id="19" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Boolean" val="True" />
- </change>
- </action>
- <action date="2009-04-10 14:06:31" id="118" prevId="117" prune="" session="8" user="koop" />
- <action date="2009-04-10 14:06:32" id="119" prevId="118" prune="" session="8" user="koop">
- <change id="325" newObjId="20" oldObjId="19" parentObjId="7" parentObjType="function" what="parameter">
- <parameter alias="" id="20" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Boolean" val="False" />
- </change>
- </action>
- <action date="2009-04-10 14:08:48" id="120" prevId="119" prune="" session="8" user="koop">
- <change id="326" newObjId="21" oldObjId="20" parentObjId="7" parentObjType="function" what="parameter">
- <parameter alias="" id="21" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Boolean" val="True" />
- </change>
- </action>
- <action date="2009-04-10 14:09:20" id="121" prevId="120" prune="" session="8" user="koop" />
- <tag id="46" name="Working Map" />
- <tag id="60" name="SingleString" />
- <tag id="85" name="Moved Compact" />
- <tag id="99" name="Compact Outside" />
- <tag id="103" name="Fixed False Branch" />
- <tag id="119" name="Histogram" />
- <tag id="120" name="High Quality Histogram" />
-</vistrail>
diff --git a/contrib/pc3/workflow_wf.xml b/contrib/pc3/workflow_wf.xml
deleted file mode 100644
index 756df00..0000000
--- a/contrib/pc3/workflow_wf.xml
+++ /dev/null
@@ -1,169 +0,0 @@
-<workflow id="0" name="untitled" version="1.0.0" vistrail_id="" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/workflow.xsd">
- <connection id="32">
- <port id="64" moduleId="8" moduleName="Map" name="Result" signature="(edu.utah.sci.vistrails.basic:Variant)" type="source" />
- <port id="65" moduleId="26" moduleName="If" name="Condition" signature="(edu.utah.sci.vistrails.basic:Boolean)" type="destination" />
- </connection>
- <connection id="33">
- <port id="66" moduleId="4" moduleName="CreateEmptyLoadDB" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
- <port id="67" moduleId="21" moduleName="CompactDatabase" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="destination" />
- </connection>
- <connection id="34">
- <port id="68" moduleId="27" moduleName="Module" name="self" signature="(edu.utah.sci.vistrails.basic:Module)" type="source" />
- <port id="69" moduleId="26" moduleName="If" name="FalsePort" signature="(edu.utah.sci.vistrails.basic:Module)" type="destination" />
- </connection>
- <connection id="35">
- <port id="70" moduleId="21" moduleName="CompactDatabase" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
- <port id="71" moduleId="28" moduleName="DetectionsHistogram" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="destination" />
- </connection>
- <connection id="36">
- <port id="72" moduleId="30" moduleName="MplFigure" name="FigureManager" signature="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" type="source" />
- <port id="73" moduleId="31" moduleName="MplFigureCell" name="FigureManager" signature="(edu.utah.sci.vistrails.matplotlib:MplFigureManager)" type="destination" />
- </connection>
- <connection id="37">
- <port id="74" moduleId="29" moduleName="MplPlot" name="source" signature="(edu.utah.sci.vistrails.basic:String)" type="source" />
- <port id="75" moduleId="30" moduleName="MplFigure" name="Script" signature="(edu.utah.sci.vistrails.basic:String)" type="destination" />
- </connection>
- <connection id="6">
- <port id="12" moduleId="2" moduleName="GetCSVFiles" name="csvFiles" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="source" />
- <port id="13" moduleId="8" moduleName="Map" name="InputList" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="destination" />
- </connection>
- <connection id="38">
- <port id="76" moduleId="28" moduleName="DetectionsHistogram" name="histogram" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="source" />
- <port id="77" moduleId="29" moduleName="MplPlot" name="histogramData" signature="(edu.utah.sci.vistrails.control_flow:ListOfElements)" type="destination" />
- </connection>
- <connection id="11">
- <port id="22" moduleId="12" moduleName="String" name="value" signature="(edu.utah.sci.vistrails.basic:String)" type="source" />
- <port id="23" moduleId="4" moduleName="CreateEmptyLoadDB" name="jobID" signature="(edu.utah.sci.vistrails.basic:String)" type="destination" />
- </connection>
- <connection id="12">
- <port id="24" moduleId="12" moduleName="String" name="value" signature="(edu.utah.sci.vistrails.basic:String)" type="source" />
- <port id="25" moduleId="13" moduleName="ConcatenateString" name="str2" signature="(edu.utah.sci.vistrails.basic:String)" type="destination" />
- </connection>
- <connection id="13">
- <port id="26" moduleId="13" moduleName="ConcatenateString" name="value" signature="(edu.utah.sci.vistrails.basic:String)" type="source" />
- <port id="27" moduleId="2" moduleName="GetCSVFiles" name="csvRootPath" signature="(edu.utah.sci.vistrails.basic:String)" type="destination" />
- </connection>
- <connection id="26">
- <port id="52" moduleId="4" moduleName="CreateEmptyLoadDB" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
- <port id="53" moduleId="25" moduleName="Group" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="destination" />
- </connection>
- <connection id="27">
- <port id="54" moduleId="25" moduleName="Group" name="self" signature="(edu.utah.sci.vistrails.basic:Group)" type="source" />
- <port id="55" moduleId="8" moduleName="Map" name="FunctionPort" signature="(edu.utah.sci.vistrails.basic:Module)" type="destination" />
- </connection>
- <connection id="31">
- <port id="62" moduleId="21" moduleName="CompactDatabase" name="self" signature="(edu.utah.sci.vistrails.basic:Module)" type="source" />
- <port id="63" moduleId="26" moduleName="If" name="TruePort" signature="(edu.utah.sci.vistrails.basic:Module)" type="destination" />
- </connection>
- <module cache="1" id="2" name="GetCSVFiles" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
- <location id="21" x="338.293817527" y="-164.978391356" />
- </module>
- <module cache="1" id="4" name="CreateEmptyLoadDB" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
- <location id="58" x="-38.9585627535" y="15.0773161002" />
- </module>
- <module cache="1" id="8" name="Map" namespace="" package="edu.utah.sci.vistrails.control_flow" tag="" version="0.1">
- <location id="20" x="114.016806723" y="-292.571428571" />
- <function id="2" name="InputPort" pos="0">
- <parameter alias="" id="6" name="<no description>" pos="0" type="edu.utah.sci.vistrails.control_flow:ListOfElements" val="['csvFile']" />
- </function>
- <function id="3" name="OutputPort" pos="1">
- <parameter alias="" id="13" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="dbEntry" />
- </function>
- </module>
- <module cache="1" id="12" name="String" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
- <location id="37" x="150.588235294" y="152.739495798" />
- <function id="4" name="value" pos="0">
- <parameter alias="" id="17" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="J062945" />
- </function>
- </module>
- <module cache="1" id="13" name="ConcatenateString" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
- <location id="36" x="271.058823529" y="52.7058823529" />
- <function id="5" name="str1" pos="0">
- <parameter alias="" id="12" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="/vistrails/pc3/SampleData/" />
- </function>
- </module>
- <module cache="1" id="21" name="CompactDatabase" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
- <location id="68" x="360.902962881" y="-460.065238478" />
- </module>
- <group cache="1" id="25" name="Group" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="">
- <workflow id="" name="untitled" version="" vistrail_id="">
- <connection id="1">
- <port id="1" moduleId="1" moduleName="ComputeColumns" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="destination" />
- <port id="2" moduleId="2" moduleName="LoadCSVFileIntoDB" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
- </connection>
- <connection id="2">
- <port id="3" moduleId="2" moduleName="LoadCSVFileIntoDB" name="csvFile" signature="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" type="destination" />
- <port id="4" moduleId="3" moduleName="ReadCSVFile" name="csvFile" signature="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" type="source" />
- </connection>
- <connection id="3">
- <port id="5" moduleId="1" moduleName="ComputeColumns" name="csvFile" signature="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" type="destination" />
- <port id="6" moduleId="3" moduleName="ReadCSVFile" name="csvFile" signature="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" type="source" />
- </connection>
- <connection id="4">
- <port id="7" moduleId="4" moduleName="InputPort" name="InternalPipe" signature="(edu.utah.sci.vistrails.basic:Variant)" type="source" />
- <port id="8" moduleId="3" moduleName="ReadCSVFile" name="csvFile" signature="(edu.utah.sci.dakoop.pc3:CSVFileEntry)" type="destination" />
- </connection>
- <connection id="5">
- <port id="9" moduleId="5" moduleName="InputPort" name="InternalPipe" signature="(edu.utah.sci.vistrails.basic:Variant)" type="source" />
- <port id="10" moduleId="2" moduleName="LoadCSVFileIntoDB" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="destination" />
- </connection>
- <connection id="6">
- <port id="11" moduleId="1" moduleName="ComputeColumns" name="dbEntry" signature="(edu.utah.sci.dakoop.pc3:DatabaseEntry)" type="source" />
- <port id="12" moduleId="6" moduleName="OutputPort" name="InternalPipe" signature="(edu.utah.sci.vistrails.basic:Variant)" type="destination" />
- </connection>
- <module cache="1" id="1" name="ComputeColumns" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
- <location id="1" x="66.7948593185" y="-134.829855648" />
- </module>
- <module cache="1" id="2" name="LoadCSVFileIntoDB" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
- <location id="2" x="57.1141870494" y="-46.6281749756" />
- </module>
- <module cache="1" id="3" name="ReadCSVFile" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
- <location id="3" x="-134.767894144" y="65.4297450412" />
- </module>
- <module cache="1" id="4" name="InputPort" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
- <location id="4" x="-206.697188695" y="178.15512489" />
- <function id="1" name="name" pos="0">
- <parameter alias="" id="1" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="csvFile" />
- </function>
- </module>
- <module cache="1" id="5" name="InputPort" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
- <location id="5" x="56.8852296284" y="150.149492943" />
- <function id="2" name="name" pos="0">
- <parameter alias="" id="2" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="dbEntry" />
- </function>
- </module>
- <module cache="1" id="6" name="OutputPort" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
- <location id="6" x="160.670806843" y="-212.276332251" />
- <function id="3" name="name" pos="0">
- <parameter alias="" id="3" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="dbEntry" />
- </function>
- </module>
- </workflow>
- <location id="60" x="17.2473255251" y="-163.32861386" />
- </group>
- <module cache="1" id="26" name="If" namespace="" package="edu.utah.sci.vistrails.control_flow" tag="" version="0.1">
- <location id="69" x="176.22882839" y="-382.689881848" />
- </module>
- <module cache="1" id="27" name="Module" namespace="" package="edu.utah.sci.vistrails.basic" tag="" version="1.2">
- <location id="71" x="201.936522474" y="-468.673570816" />
- </module>
- <module cache="1" id="28" name="DetectionsHistogram" namespace="" package="edu.utah.sci.dakoop.pc3" tag="" version="1.0.0">
- <location id="72" x="429.549610616" y="-595.581197698" />
- <function id="7" name="highQuality" pos="0">
- <parameter alias="" id="21" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:Boolean" val="True" />
- </function>
- </module>
- <module cache="1" id="29" name="MplPlot" namespace="" package="edu.utah.sci.vistrails.matplotlib" tag="" version="0.9.0">
- <location id="73" x="549.285584018" y="-710.147790766" />
- <function id="6" name="source" pos="0">
- <parameter alias="" id="16" name="<no description>" pos="0" type="edu.utah.sci.vistrails.basic:String" val="x%20%3D%20%5Ba%5B1%5D%20for%20a%20in%20histogramData%5D%0Abins%20%3D%20%5Ba%5B0%5D%20for%20a%20in%20histogramData%5D%0A%0Abar%28bins%2C%20x%29%0A" />
- </function>
- <portSpec id="0" name="histogramData" optional="0" sigstring="(edu.utah.sci.vistrails.control_flow:ListOfElements)" sortKey="0" type="input" />
- </module>
- <module cache="1" id="30" name="MplFigure" namespace="" package="edu.utah.sci.vistrails.matplotlib" tag="" version="0.9.0">
- <location id="74" x="572.826394762" y="-823.928376027" />
- </module>
- <module cache="1" id="31" name="MplFigureCell" namespace="" package="edu.utah.sci.vistrails.matplotlib" tag="" version="0.9.0">
- <location id="75" x="590.482002819" y="-937.708961288" />
- </module>
-</workflow>
diff --git a/contrib/poissonrecon.py b/contrib/poissonrecon.py
deleted file mode 100644
index 5039182..0000000
--- a/contrib/poissonrecon.py
+++ /dev/null
@@ -1,101 +0,0 @@
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-import core.bundles
-import core.requirements
-import os
-import re
-
-from core.configuration import ConfigurationObject
-
-configuration = ConfigurationObject(executable_path=(None, str))
-
-identifier = 'edu.utah.sci.cscheid.poissonrecon'
-version = '0.1'
-name = 'Poisson Surface Reconstruction'
-
-##############################################################################
-
-class PoissonRecon(Module):
-
- def __init__(self):
- Module.__init__(self)
-
- def compute(self):
- self.checkInputPort('pts')
- f1 = self.getInputFromPort('mesh1')
-
- make_file = self.interpreter.filePool.create_file
-
- metro_output = make_file(suffix='.ply')
-
- values = ['', f1.name, f2.name, '-q']
-
- need_error_meshes = False
- if (self.outputPorts.has_key('error_mesh_1') or
- self.outputPorts.has_key('error_mesh_2')):
- need_error_meshes = True
- error_mesh_output = (make_file(suffix='.ply'),
- make_file(suffix='.ply'))
- values.append('-c')
- values.append(error_mesh_output[0].name)
- values.append(error_mesh_output[1].name)
-
- need_histograms = False
- if (self.outputPorts.has_key('error_hist_1') or
- self.outputPorts.has_key('error_hist_2')):
- need_histograms = True
- error_hist_output = (make_file(suffix='.csv'),
- make_file(suffix='.csv'))
- values.append('-h')
- values.append(error_hist_output[0].name)
- values.append(error_hist_output[1].name)
-
- print values
- print ('%s ' * len(values))
- cmdline = ('%s ' * len(values)) % tuple(values)
- cmdline += '> '
- cmdline += metro_output.name
- print cmdline
-
- result = os.system(cmdline)
- if result != 0:
- raise ModuleError(self, "Execution failed")
- l = [x for x in file(metro_output.name).readlines()
- if x.startswith('Hausdorff')][0]
- regexp = re.compile(r'Hausdorff distance: ([0123456789.]+) \(([0123456789.]+) wrt bounding box diagonal\)')
- results = regexp.match(l).groups()
-
- if need_error_meshes:
- self.setResult('error_mesh_1', error_mesh_output[0])
- self.setResult('error_mesh_2', error_mesh_output[1])
-
- if need_histograms:
- self.setResult('error_hist_1', error_hist_output[0])
- self.setResult('error_hist_2', error_hist_output[1])
-
- self.need_error_meshes = need_error_meshes
- self.need_histograms = need_histograms
-
- self.setResult('hausdorff_error', float(results[0]))
- self.setResult('normalized_hausdorff_error', float(results[1]))
-
-##############################################################################
-
-def initialize():
- if not core.requirements.executable_file_exists('PoissonRecon'):
- raise core.requirements.MissingRequirement("PoissonRecon")
-
- reg = core.modules.module_registry
-
- reg.add_module(PoissonRecon)
- reg.add_input_port(PoissonRecon, 'pts',
- core.modules.basic_modules.File)
- reg.add_input_port(PoissonRecon, 'binary',
- core.modules.basic_modules.Boolean)
- reg.add_input_port(PoissonRecon, 'depth',
- core.modules.basic_modules.Integer)
-
- reg.add_output_port(PoissonRecon, 'output',
- core.modules.basic_modules.File)
-
diff --git a/contrib/provenance/__init__.py b/contrib/provenance/__init__.py
deleted file mode 100644
index cadc047..0000000
--- a/contrib/provenance/__init__.py
+++ /dev/null
@@ -1,274 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-"""This package defines a set of methods that perform the command-line
-tools necesary for the task designed for the first Provenance Challenge:
-
-http://twiki.ipaw.info
-
-This VisTrails package requires three software packages to be installed:
-
-AIR - Automated Image Registration: http://bishopw.loni.ucla.edu/AIR5/
-FSL - http://www.fmrib.ox.ac.uk/fsl/
-netpbm - http://netpbm.sourceforge.net/
-
-"""
-
-from core.modules.vistrails_module import Module, ModuleError, new_module
-import core.modules
-import core.modules.basic_modules
-import core.modules.module_registry
-import core.utils
-from core.system import list2cmdline
-import os
-import os.path
-import stat
-import subprocess
-
-version = '0.9.0'
-name = 'Provenance Challenge'
-identifier = 'edu.utah.sci.vistrails.provenance'
-################################################################################
-
-global_airpath = ""
-global_fslpath = ""
-global_netpbmpath = ""
-
-class ProvenanceChallenge(Module):
- """ProvenanceChallenge is the base Module for all Modules in the provenance
-package. It simply define helper methods for subclasses."""
-
- __quiet = True
- __programsQuiet = True
-
- def air_cmd_line(self, cmd, *params):
- """Runs a command-line command for the AIR tools."""
- return list2cmdline([global_airpath + cmd] + list(params))
-
- def fsl_cmd_line(self, cmd, *params):
- """Runs a command-line command for the FSL tools."""
- return ('FSLOUTPUTTYPE=NIFTI_GZ ' +
- list2cmdline([global_fslpath + cmd] + list(params)))
-
- def run(self, cmd):
- if not self.__quiet:
- print cmd
- if self.__programsQuiet:
- cmd = '(' + cmd + ') 2>&1 >/dev/null'
- r = os.system(cmd)
- if r != 0:
- raise ModuleError(self, "system call failed: '%s'" % cmd)
-
-
-class AIRHeaderFile(core.modules.basic_modules.File):
- """AIRHeaderFile subclasses File to annotate the execution with header
-file information for later querying."""
-
- def get_header_annotations(self):
- """Returns the header information for the file using the AIR scanheader
-tool."""
- process = subprocess.Popen(global_airpath + 'scanheader ' + self.name,
- shell=True,
- stdout=subprocess.PIPE)
- if process.wait() != 0:
- raise ModuleError(self, "Could not open header file " + self.name)
-
- result = {}
- lines = core.utils.no_interrupt(process.stdout.readlines)
- for l in lines:
- l = l[:-1]
- if not l:
- continue
- entries = l.split('=')
- if len(entries) != 2:
- raise ModuleError(self,
- "Error parsing line '%s' of header %s" %
- (l[:-1], self.name))
- result[entries[0]] = entries[1]
- return result
-
- def compute(self):
- core.modules.basic_modules.File.compute(self)
- d = self.get_header_annotations()
- self.annotate(d)
-
-
-class AlignWarp(ProvenanceChallenge):
- """AlignWarp executes the AIR warping tool on the input."""
-
- def compute(self):
- image = self.getInputFromPort("image")
- ref = self.getInputFromPort("reference")
- model = self.getInputFromPort("model")
- o = self.interpreter.filePool.create_file(suffix='.warp')
- cmd = self.air_cmd_line('align_warp',
- image.name,
- ref.name,
- o.name,
- '-m',
- str(model),
- '-q')
- self.run(cmd)
- self.setResult("output", o)
-
-
-class Reslice(ProvenanceChallenge):
- """AlignWarp executes the AIR reslicing tool on the input."""
-
- def compute(self):
- warp = self.getInputFromPort("warp")
- o = self.interpreter.filePool.create_file()
- cmd = self.air_cmd_line('reslice',
- warp.name,
- o.name)
- self.run(cmd)
- self.setResult("output", o)
-
-
-class SoftMean(ProvenanceChallenge):
- """SoftMean executes the AIR softmean averaging tool on the input."""
-
- def compute(self):
- imageList = self.getInputFromPort("imageList")
- o = self.interpreter.filePool.create_file(suffix='.hdr')
- cmd = self.air_cmd_line('softmean',
- o.name,
- 'y',
- 'null',
- *[f.name for f in imageList])
- self.run(cmd)
- self.setResult('output', o)
-
-
-class Slicer(ProvenanceChallenge):
- """Slicer executes the FSL slicer tool on the input."""
-
- def compute(self):
- cmd = ['slicer']
- i = self.getInputFromPort("input")
- cmd.append(i.name)
- if self.hasInputFromPort("slice_x"):
- cmd.append('-x')
- cmd.append(str(self.getInputFromPort("slice_x")))
- elif self.hasInputFromPort("slice_y"):
- cmd.append('-y')
- cmd.append(str(self.getInputFromPort("slice_y")))
- elif self.hasInputFromPort("slice_z"):
- cmd.append('-z')
- cmd.append(str(self.getInputFromPort("slice_z")))
- o = self.interpreter.filePool.create_file(suffix='.pgm')
- cmd.append(o.name)
- self.run(self.fsl_cmd_line(*cmd))
- self.setResult('output', o)
-
-
-class PGMToPPM(ProvenanceChallenge):
- """PGMToPPM executes the netpbm pgmtoppm tool on the input."""
-
- def compute(self):
- cmd = ['pgmtoppm', 'white']
- i = self.getInputFromPort("input")
- cmd.append(i.name)
- o = self.interpreter.filePool.create_file(suffix='.ppm')
- cmd.append(' >')
- cmd.append(o.name)
- self.run(list2cmdline(cmd))
- self.setResult('output', o)
-
-
-class PNMToJpeg(ProvenanceChallenge):
- """PGMToPPM executes the netpbm pnmtojpeg tool on the input."""
-
- def compute(self):
- cmd = ['pnmtojpeg']
- i = self.getInputFromPort("input")
- cmd.append(i.name)
- o = self.interpreter.filePool.create_file(suffix='.jpg')
- cmd.append(' >')
- cmd.append(o.name)
- self.run(list2cmdline(cmd))
- self.setResult('output', o)
-
-################################################################################
-
-def checkProgram(fileName):
- return os.path.isfile(fileName) and os.stat(fileName) & 005
-
-def initialize(airpath=None, fslpath=None, netpbmpath=None, *args, **kwargs):
- print "Initializing Provenance Challenge Package"
-
- if not airpath:
- print "airpath not specified or incorrect: Will assume AIR tools are on the path"
- else:
- print "Will use AIR tools from ", airpath
- global global_airpath
- global_airpath = airpath + '/'
-
- if not fslpath:
- print "fslpath not specified or incorrect: Will assume fsl tools are on the path"
- else:
- print "Will use FSL tools from ", fslpath
- global global_fslpath
- global_fslpath = fslpath + '/'
-
- if not netpbmpath:
- print "netpbmpath not specified or incorrect: Will assume netpbm tools are on the path"
- else:
- print "Will use netpbm tools from ", netpbmpath
- global global_netpbmpath
- global_netpbmpath = netpbmpath + '/'
-
- reg = core.modules.module_registry
- basic = core.modules.basic_modules
- reg.add_module(ProvenanceChallenge)
-
- reg.add_module(AlignWarp)
- reg.add_input_port(AlignWarp, "image", (basic.File, 'the image file to be deformed'))
- reg.add_input_port(AlignWarp, "image_header", (basic.File, 'the header of the image to be deformed'))
- reg.add_input_port(AlignWarp, "reference", (basic.File, 'the reference image'))
- reg.add_input_port(AlignWarp, "reference_header", (basic.File, 'the header of the reference image'))
- reg.add_input_port(AlignWarp, "model", (basic.Integer, 'the deformation model'))
- reg.add_output_port(AlignWarp, "output", (basic.File, 'the output deformation'))
-
- reg.add_module(Reslice)
- reg.add_input_port(Reslice, "warp", (basic.File, 'the warping to be resliced'))
- reg.add_output_port(Reslice, "output", (basic.File, 'the new slice'))
-
- reg.add_module(SoftMean)
- reg.add_input_port(SoftMean, "imageList", (basic.List, 'image files'))
- reg.add_output_port(SoftMean, "output", (basic.File, 'average image'))
-
- reg.add_module(Slicer)
- reg.add_input_port(Slicer, "input", (basic.File, 'the input file to be sliced'))
- reg.add_input_port(Slicer, "slice_x", (basic.Float, 'sagittal slice with given value'))
- reg.add_input_port(Slicer, "slice_y", (basic.Float, 'coronal slice with given value'))
- reg.add_input_port(Slicer, "slice_z", (basic.Float, 'axial slice with given value'))
- reg.add_output_port(Slicer, "output", (basic.File, 'slice output'))
-
- reg.add_module(PGMToPPM)
- reg.add_input_port(PGMToPPM, "input", (basic.File, "input"))
- reg.add_output_port(PGMToPPM, "output", (basic.File, "output"))
-
- reg.add_module(PNMToJpeg)
- reg.add_input_port(PNMToJpeg, "input", (basic.File, "input"))
- reg.add_output_port(PNMToJpeg, "output", (basic.File, "output"))
-
- reg.add_module(AIRHeaderFile)
diff --git a/contrib/provenance2/__init__.py b/contrib/provenance2/__init__.py
deleted file mode 100644
index 7347b39..0000000
--- a/contrib/provenance2/__init__.py
+++ /dev/null
@@ -1,366 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2007 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-"""This package defines a set of methods that perform the command-line
-tools necesary for the task designed for the first Provenance Challenge:
-
-http://twiki.ipaw.info
-
-This VisTrails package requires three software packages to be installed:
-
-AIR - Automated Image Registration: http://bishopw.loni.ucla.edu/AIR5/
-FSL - http://www.fmrib.ox.ac.uk/fsl/
-netpbm - http://netpbm.sourceforge.net/
-
-"""
-
-from core.modules.vistrails_module import Module, ModuleError, new_module
-import core.modules
-import core.modules.basic_modules
-import core.modules.module_registry
-import core.utils
-import os
-import os.path
-import stat
-import subprocess
-import glob
-
-version = '0.9.0'
-name = 'Provenance Challenge'
-identifier = 'edu.utah.sci.vistrails.provenance2'
-
-################################################################################
-
-global_airpath = ""
-global_fslpath = ""
-global_netpbmpath = ""
-
-class ProvenanceChallenge(Module):
- """ProvenanceChallenge is the base Module for all Modules in the provenance
-package. It simply define helper methods for subclasses."""
-
- __quiet = True
- __programsQuiet = True
-
- def air_cmd_line(self, cmd, *params):
- """Runs a command-line command for the AIR tools."""
- return list2cmdline([global_airpath + cmd] + list(params))
-
- def fsl_cmd_line(self, cmd, *params):
- """Runs a command-line command for the FSL tools."""
- return ('FSLOUTPUTTYPE=NIFTI_GZ ' +
- list2cmdline([global_fslpath + cmd] + list(params)))
-
- def netpbm_cmd_line(self, cmd, *params):
- """Runs a command-line command for the netpbm tools."""
- return list2cmdline([global_netpbmpath + cmd] + list(params))
-
- def run(self, cmd):
- if not self.__quiet:
- print cmd
- if self.__programsQuiet:
- cmd = '(' + cmd + ') 2>&1 >/dev/null'
- r = os.system(cmd)
- if r != 0:
- raise ModuleError(self, "system call failed: '%s'" % cmd)
-
-
-class AIRHeaderFile(core.modules.basic_modules.File):
- """AIRHeaderFile subclasses File to annotate the execution with header
-file information for later querying."""
-
- def get_header_annotations(self):
- """Returns the header information for the file using the AIR scanheader
-tool."""
- process = subprocess.Popen(global_airpath + 'scanheader ' + self.name,
- shell=True,
- stdout=subprocess.PIPE)
-
- waitCode = 0
- try:
- waitCode = process.wait()
- except OSError:
- pass
- if waitCode != 0:
- raise ModuleError(self, "Could not open header file " + self.name)
-
- result = {}
- lines = core.utils.no_interrupt(process.stdout.readlines)
- for l in lines:
- l = l[:-1]
- if not l:
- continue
- entries = l.split('=')
- if len(entries) != 2:
- raise ModuleError(self,
- "Error parsing line '%s' of header %s" %
- (l[:-1], self.name))
- result[entries[0]] = entries[1]
- return result
-
- def compute(self):
- core.modules.basic_modules.File.compute(self)
- d = self.get_header_annotations()
- self.annotate(d)
-
-
-class AlignWarp(ProvenanceChallenge):
- """AlignWarp executes the AIR warping tool on the input."""
-
- def compute(self):
- image = self.getInputFromPort("image")
- ref = self.getInputFromPort("reference")
- model = self.getInputFromPort("model")
- o = self.interpreter.filePool.create_file(suffix='.warp')
- cmd = self.air_cmd_line('align_warp',
- image.baseName,
- ref.baseName,
- o.name,
- '-m',
- model,
- '-q')
- self.run(cmd)
- self.setResult("output", o)
-
-
-class Reslice(ProvenanceChallenge):
- """AlignWarp executes the AIR reslicing tool on the input."""
-
- def compute(self):
- warp = self.getInputFromPort("warp")
- o = self.interpreter.filePool.create_file()
- cmd = self.air_cmd_line('reslice',
- warp.name,
- o.name)
- self.run(cmd)
- ofs = FileSet()
- ofs.baseName = o.name
- self.setResult("output", ofs)
-
-
-class SoftMean(ProvenanceChallenge):
- """SoftMean executes the AIR softmean averaging tool on the input."""
-
- def compute(self):
- imageList = self.getInputFromPort("imageList")
- o = self.interpreter.filePool.create_file()
- cmd = self.air_cmd_line('softmean',
- o.name,
- 'y',
- 'null',
- *[f.baseName for f in imageList])
- self.run(cmd)
- ofs = FileSet()
- ofs.baseName = o.name
- self.setResult('output', ofs)
-
-class Slicer(ProvenanceChallenge):
- """Slicer executes the FSL slicer tool on the input."""
-
- def compute(self):
- cmd = ['slicer']
- i = self.getInputFromPort("input")
- cmd.append(i.baseName)
- if self.hasInputFromPort("slice_x"):
- cmd.append('-x')
- cmd.append(str(self.getInputFromPort("slice_x")))
- elif self.hasInputFromPort("slice_y"):
- cmd.append('-y')
- cmd.append(str(self.getInputFromPort("slice_y")))
- elif self.hasInputFromPort("slice_z"):
- cmd.append('-z')
- cmd.append(str(self.getInputFromPort("slice_z")))
- o = self.interpreter.filePool.create_file(suffix='.pgm')
- cmd.append(o.name)
- self.run(self.fsl_cmd_line(*cmd))
- self.setResult('output', o)
-
-
-class PGMToPPM(ProvenanceChallenge):
- """PGMToPPM executes the netpbm pgmtoppm tool on the input."""
-
- def compute(self):
- cmd = ['pgmtoppm white']
- i = self.getInputFromPort("input")
- cmd.append(i.name)
- o = self.interpreter.filePool.create_file(suffix='.ppm')
- cmd.append(' >')
- cmd.append(o.name)
- self.run(self.netpbm_cmd_line(*cmd))
- self.setResult('output', o)
-
-
-class PNMToJpeg(ProvenanceChallenge):
- """PGMToPPM executes the netpbm pnmtojpeg tool on the input."""
-
- def compute(self):
- cmd = ['pnmtojpeg']
- i = self.getInputFromPort("input")
- cmd.append(i.name)
- o = self.interpreter.filePool.create_file(suffix='.jpg')
- cmd.append(' >')
- cmd.append(o.name)
- self.run(self.netpbm_cmd_line(*cmd))
- self.setResult('output', o)
-
-class FileSet(ProvenanceChallenge):
- """FileSet stores a set of files related by a common filename base."""
-
- def compute(self):
- self.checkInputPort("baseName")
- n = self.getInputFromPort("baseName")
- if self.hasInputFromPort("file_hdr") and \
- self.hasInputFromPort("file_img"):
- n1 = self.getInputFromPort("file_hdr").name
- n2 = self.getInputFromPort("file_img").name
- if n1.endswith('.hdr'):
- n1base = n1.rsplit('.hdr',1)[0]
- else:
- n1base = n1
- if n2.endswith('.img'):
- n2base = n2.rsplit('.img',1)[0]
- else:
- n2base = n2
- if n1base != n2base:
- o = self.interpreter.filePool.create_file()
- o1 = o.name + '.hdr'
- o2 = o.name + '.img'
- try:
- core.system.link_or_copy(n1, o1)
- except OSError, e:
- msg = "error creating tmp file '%s'" % o1
- raise ModuleError(self, msg)
- try:
- core.system.link_or_copy(n2, o2)
- except OSError, e:
- msg = "error creating tmp file '%s'" % o2
- raise ModuleError(self, msg)
- else:
- self.baseName = n1base
- else:
- self.baseName = n
- self.setResult("local_basename", self.baseName)
-
-class FileSetSink(ProvenanceChallenge):
- """FileSetSink is a module that takes a file set and writes them
- in a user-specified location in the file system."""
-
- def compute(self):
- self.checkInputPort("fileSet")
- self.checkInputPort("outputBaseName")
- v1 = self.getInputFromPort("fileSet")
- v2 = self.getInputFromPort("outputBaseName")
- filenames = glob.glob('%s.*' % v1.baseName)
- for filename in filenames:
- try:
- outFilename = filename.replace(v1.baseName, v2, 1)
- core.system.link_or_copy(filename, outFilename)
- except OSError, e:
- if (self.hasInputFromPort("overrideFile") and
- self.getInputFromPort("overrideFile")):
- try:
- os.unlink(outFilename)
- core.system.link_or_copy(filename, outFilename)
- except OSError, e:
- msg = "(override true) Could not create file '%s'" % \
- outFilename
- raise ModuleError(self, msg)
- else:
- msg = "Could not create file '%s': %s" % (outFilename, e)
- raise ModuleError(self, msg)
-
-################################################################################
-
-def checkProgram(fileName):
- return os.path.isfile(fileName) and os.stat(fileName) & 005
-
-def initialize(airpath=None, fslpath=None, netpbmpath=None, *args, **kwargs):
- print "Initializing Provenance Challenge Package"
-
- if not airpath:
- print "airpath not specified or incorrect: Will assume AIR tools are on the path"
- else:
- print "Will use AIR tools from ", airpath
- global global_airpath
- global_airpath = airpath + '/'
-
- if not fslpath:
- print "fslpath not specified or incorrect: Will assume fsl tools are on the path"
- else:
- print "Will use FSL tools from ", fslpath
- global global_fslpath
- global_fslpath = fslpath + '/'
-
- if not netpbmpath:
- print "netpbmpath not specified or incorrect: Will assume netpbm tools are on the path"
- else:
- print "Will use netpbm tools from ", netpbmpath
- global global_netpbmpath
- global_netpbmpath = netpbmpath + '/'
-
- reg = core.modules.module_registry
- basic = core.modules.basic_modules
- reg.add_module(ProvenanceChallenge)
-
- reg.add_module(AlignWarp)
- reg.add_input_port(AlignWarp, "image", (FileSet, 'the image file to be deformed'))
-# reg.add_input_port(AlignWarp, "image_header", (basic.File, 'the header of the image to be deformed'))
- reg.add_input_port(AlignWarp, "reference", (FileSet, 'the reference image'))
-# reg.add_input_port(AlignWarp, "reference_header", (basic.File, 'the header of the reference image'))
- reg.add_input_port(AlignWarp, "model", (basic.Integer, 'the deformation model'))
- reg.add_output_port(AlignWarp, "output", (basic.File, 'the output deformation'))
-
- reg.add_module(Reslice)
- reg.add_input_port(Reslice, "warp", (basic.File, 'the warping to be resliced'))
- reg.add_output_port(Reslice, "output", (FileSet, 'the new slice'))
-
- reg.add_module(SoftMean)
- reg.add_input_port(SoftMean, "imageList", (basic.List, 'image files'))
- reg.add_output_port(SoftMean, "output", (FileSet, 'average image'))
-
- reg.add_module(Slicer)
- reg.add_input_port(Slicer, "input", (FileSet, 'the input file to be sliced'))
- reg.add_input_port(Slicer, "slice_x", (basic.Float, 'sagittal slice with given value'))
- reg.add_input_port(Slicer, "slice_y", (basic.Float, 'coronal slice with given value'))
- reg.add_input_port(Slicer, "slice_z", (basic.Float, 'axial slice with given value'))
- reg.add_output_port(Slicer, "output", (basic.File, 'slice output'))
-
- reg.add_module(PGMToPPM)
- reg.add_input_port(PGMToPPM, "input", (basic.File, "input"))
- reg.add_output_port(PGMToPPM, "output", (basic.File, "output"))
-
- reg.add_module(PNMToJpeg)
- reg.add_input_port(PNMToJpeg, "input", (basic.File, "input"))
- reg.add_output_port(PNMToJpeg, "output", (basic.File, "output"))
-
- reg.add_module(AIRHeaderFile)
-
- reg.add_module(FileSet)
- reg.add_input_port(FileSet, "file_hdr", basic.File)
- reg.add_input_port(FileSet, "file_img", basic.File)
- reg.add_input_port(FileSet, "baseName", basic.String)
- reg.add_output_port(FileSet, "self", FileSet)
- reg.add_output_port(FileSet, "local_basename", basic.String)
-
- reg.add_module(FileSetSink)
- reg.add_input_port(FileSetSink, "fileSet", FileSet)
- reg.add_input_port(FileSetSink, "outputBaseName", basic.String)
- reg.add_input_port(FileSetSink, "overrideFile", basic.Boolean)
diff --git a/contrib/sahm/ColorBreaks.csv b/contrib/sahm/ColorBreaks.csv
deleted file mode 100644
index ac8f0a2..0000000
--- a/contrib/sahm/ColorBreaks.csv
+++ /dev/null
@@ -1,18 +0,0 @@
-layer,StartBreak,r,g,b
-prob_map,0,0,0,255
-prob_map,0.25,85,255,255
-prob_map,0.5,0,255,0
-prob_map,0.75,255,255,0
-prob_map,1,255,0,0
-res_map,-1,0,0,255
-res_map,-0.00000001,85,255,255
-res_map,0.00000001,255,255,0
-res_map,1,255,0,0
-bin_map,0,0,0,0
-bin_map,0.499999999,0,0,0
-bin_map,0.5000001,255,255,255
-bin_map,1,255,255,255
-mes_map,-100,0,0,255
-mes_map,-0.00000001,85,255,255
-mes_map,0.00000001,255,255,0
-mes_map,100,255,0,0
diff --git a/contrib/sahm/Images/BinMap.png b/contrib/sahm/Images/BinMap.png
deleted file mode 100644
index 64c8c96..0000000
Binary files a/contrib/sahm/Images/BinMap.png and /dev/null differ
diff --git a/contrib/sahm/Images/BlackPoints.png b/contrib/sahm/Images/BlackPoints.png
deleted file mode 100644
index 590c048..0000000
Binary files a/contrib/sahm/Images/BlackPoints.png and /dev/null differ
diff --git a/contrib/sahm/Images/GreenPoints.png b/contrib/sahm/Images/GreenPoints.png
deleted file mode 100644
index 127f0a4..0000000
Binary files a/contrib/sahm/Images/GreenPoints.png and /dev/null differ
diff --git a/contrib/sahm/Images/MesMap.png b/contrib/sahm/Images/MesMap.png
deleted file mode 100644
index 180857a..0000000
Binary files a/contrib/sahm/Images/MesMap.png and /dev/null differ
diff --git a/contrib/sahm/Images/ModMap.png b/contrib/sahm/Images/ModMap.png
deleted file mode 100644
index e3f057e..0000000
Binary files a/contrib/sahm/Images/ModMap.png and /dev/null differ
diff --git a/contrib/sahm/Images/ProbMap.png b/contrib/sahm/Images/ProbMap.png
deleted file mode 100644
index cb56001..0000000
Binary files a/contrib/sahm/Images/ProbMap.png and /dev/null differ
diff --git a/contrib/sahm/Images/RedPoints.png b/contrib/sahm/Images/RedPoints.png
deleted file mode 100644
index ef4b8d5..0000000
Binary files a/contrib/sahm/Images/RedPoints.png and /dev/null differ
diff --git a/contrib/sahm/Images/ResMap.png b/contrib/sahm/Images/ResMap.png
deleted file mode 100644
index 37b24bf..0000000
Binary files a/contrib/sahm/Images/ResMap.png and /dev/null differ
diff --git a/contrib/sahm/Images/icons.pptx b/contrib/sahm/Images/icons.pptx
deleted file mode 100644
index fa9e1d0..0000000
Binary files a/contrib/sahm/Images/icons.pptx and /dev/null differ
diff --git a/contrib/sahm/SahmOutputViewer.py b/contrib/sahm/SahmOutputViewer.py
deleted file mode 100644
index 4f21f01..0000000
--- a/contrib/sahm/SahmOutputViewer.py
+++ /dev/null
@@ -1,494 +0,0 @@
-################################################################################
-# ImageViewer widgets/toolbar implementation
-################################################################################
-from PyQt4 import QtCore, QtGui, QAxContainer
-from core.modules.vistrails_module import Module
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
-from packages.spreadsheet.spreadsheet_controller import spreadsheetController
-from SahmViewerCell import Ui_Frame
-#import imageviewer_rc
-import os
-################################################################################
-
-class SAHMModelOutputViewerCell(SpreadsheetCell):
- """
- SAHMModelOutputViewerCell displays the various non-spatial
- outputs from a SAHM Model run
- """
- _input_ports = [("row", "(edu.utah.sci.vistrails.basic:Integer)"),
- ("column", "(edu.utah.sci.vistrails.basic:Integer)"),
- ('ModelWorkspace', '(edu.utah.sci.vistrails.basic:File)')]
-
- def compute(self):
- """ compute() -> None
- Dispatch the display event to the spreadsheet with images and labels
-
- """
- if self.hasInputFromPort("ModelWorkspace"):
- window = spreadsheetController.findSpreadsheetWindow()
- model_workspace = self.getInputFromPort("ModelWorkspace").name
- model_dir_full = os.path.normcase(os.path.split(model_workspace)[0])
- model_dir = os.path.split(model_dir_full)[1]
- model_name = model_dir[:model_dir.index('output')]
-
-# prob_map_path = os.path.join(model_dir_full, model_name + '_prob_map.jpeg')
-# prob_map = window.file_pool.make_local_copy(prob_map_path)
-
- auc_graph_path = os.path.join(model_dir_full, model_name + '_auc_plot.jpg')
- auc_graph = window.file_pool.make_local_copy(auc_graph_path)
-
- text_output_path = os.path.join(model_dir_full, model_name + '_output.txt')
- text_output = window.file_pool.make_local_copy(text_output_path)
-
- response_path = os.path.join(model_dir_full, model_name + '_response_curves.pdf')
- response_curves = window.file_pool.make_local_copy(response_path)
-
- model_label = model_dir.capitalize().replace('output', 'Output')
-
-
- if self.hasInputFromPort("row"):
- if not self.location:
- self.location = CellLocation()
- self.location.row = self.getInputFromPort('row') - 1
-
- if self.hasInputFromPort("column"):
- if not self.location:
- self.location = CellLocation()
- self.location.col = self.getInputFromPort('column') - 1
-
- else:
- fileValue = None
- self.cellWidget = self.displayAndWait(SAHMOutputViewerCellWidget, (auc_graph,
- text_output,
- response_curves,
- model_label))
-
-class SAHMOutputViewerCellWidget(QCellWidget):
- """
- SAHMOutputViewerCellWidget is the widget that will display the various
- non spatial outputs from a model run
- """
- def __init__(self, parent=None):
- QCellWidget.__init__(self, parent)
-
- centralLayout = QtGui.QVBoxLayout()
- self.setLayout(centralLayout)
- centralLayout.setMargin(0)
- centralLayout.setSpacing(0)
-
-
-# self.setAnimationEnabled(True)
-
- self.Frame = QtGui.QFrame()
- self.ui = Ui_Frame()
- self.ui.setupUi(self.Frame)
-
-# #add scenes to our graphicViews
-# self.gs_prob_map = QtGui.QGraphicsScene()
-# self.ui.gv_prob_map.setScene(self.gs_prob_map)
-# self.gs_prob_map.wheelEvent = self.wheel_event_prob
-
- self.gs_auc_graph = QtGui.QGraphicsScene()
- self.ui.gv_auc.setScene(self.gs_auc_graph)
- self.gs_auc_graph.wheelEvent = self.wheel_event_auc
-
- #add in ie browsers for the text and response
- self.text_browser = QAxContainer.QAxWidget(self)
- self.text_browser.setFocusPolicy(QtCore.Qt.StrongFocus)
- self.text_browser.setControl("{8856F961-340A-11D0-A96B-00C04FD705A2}")
- self.ui.text_output_layout.addWidget(self.text_browser)
- self.text_urlSrc = None
-
- self.response_browser = QAxContainer.QAxWidget(self)
- self.response_browser.setFocusPolicy(QtCore.Qt.StrongFocus)
- self.response_browser.setControl("{8856F961-340A-11D0-A96B-00C04FD705A2}")
- self.ui.response_curves_layout.addWidget(self.response_browser)
- self.response_urlSrc = None
-
-
- self.layout().addWidget(self.Frame)
-
- def updateContents(self, inputPorts):
- """ updateContents(inputPorts: tuple) -> None
- Update the widget contents based on the input data
-
- """
- (auc_graph, text_output, response_curves, model_label) = inputPorts
-
- self.images = {}
-# if prob_map:
-# #Value = (full image, sized image, scene, view, max_height)
-# pixmap = QtGui.QPixmap(prob_map.name)
-# max_size = self.getMaxSize(self.ui.gv_prob_map)
-# scaled_pixmap = pixmap.scaled(max_size, max_size,
-# QtCore.Qt.KeepAspectRatio,
-# QtCore.Qt.FastTransformation)
-#
-# self.images['prob_map'] = [pixmap,
-# scaled_pixmap,
-# self.gs_prob_map,
-# self.ui.gv_prob_map,
-# max_size]
-
- if auc_graph:
- pixmap = QtGui.QPixmap(auc_graph.name)
- max_size = self.getMaxSize(self.ui.gv_auc)
- scaled_pixmap = pixmap.scaled(max_size, max_size,
- QtCore.Qt.KeepAspectRatio,
- QtCore.Qt.SmoothTransformation)
-
- self.images['auc_graph'] = [pixmap,
- scaled_pixmap,
- self.gs_auc_graph,
- self.ui.gv_auc,
- max_size]
-
-
-
- self.text_urlSrc = QtCore.QUrl.fromLocalFile(text_output.name)
- if self.text_urlSrc!=None:
- self.text_browser.dynamicCall('Navigate(const QString&)', self.text_urlSrc.toString())
- else:
- self.text_browser.dynamicCall('Navigate(const QString&)', QtCore.QString('about:blank'))
-
- self.response_urlSrc = QtCore.QUrl.fromLocalFile(response_curves.name)
- if self.response_urlSrc!=None:
- self.response_browser.dynamicCall('Navigate(const QString&)', self.response_urlSrc.toString())
- else:
- self.response_browser.dynamicCall('Navigate(const QString&)', QtCore.QString('about:blank'))
-
- self.view_current()
-
- #QCellWidget.updateContents(self, inputPorts)
-
- def getMaxSize(self, view):
- return self.Frame.size().width() - 10
-# if view.size().width() <= view.size().height():
-# return view.size().width() * 0.95
-# else:
-# return view.size().height() * 0.95
-
- def view_current(self):
- for k,v in self.images.iteritems():
- size_img = v[1].size()
- wth, hgt = QtCore.QSize.width(size_img), QtCore.QSize.height(size_img)
- v[2].clear()
- v[2].setSceneRect(0, 0, wth, hgt)
- v[2].addPixmap(v[1])
- QtCore.QCoreApplication.processEvents()
-
- def wheel_event_prob(self, event):
- self.wheel_event(event, 'prob_map', QtCore.Qt.FastTransformation)
-
- def wheel_event_auc(self, event):
- self.wheel_event(event, 'auc_graph', QtCore.Qt.SmoothTransformation)
-
- def wheel_event (self, event, id, transform):
- numDegrees = event.delta() / 8
- numSteps = numDegrees / 15.0
- self.zoom(numSteps, self.images[id], transform)
- event.accept()
-
- def zoom(self, step, images, transform):
- zoom_step = 0.06
- images[2].clear()
- w = images[1].size().width()
- h = images[1].size().height()
- w, h = w * (1 + zoom_step*step), h * (1 + zoom_step*step)
- images[1] = images[0].scaled(w, h,
- QtCore.Qt.KeepAspectRatio,
- transform)
- self.view_current()
-
- def saveToPNG(self, filename):
- """ saveToPNG(filename: str) -> bool
- Save the current widget contents to an image file
-
- """
-
- pixmap = QtGui.QPixmap(self.Frame.size())
- painter = QtGui.QPainter(pixmap)
- self.Frame.render(painter)
- painter.end()
-
- if pixmap and (not pixmap.isNull()):
- return pixmap.save(filename)
- return False
-
- def saveToPDF(self, filename):
- """ saveToPDF(filename: str) -> bool
- Save the current widget contents to a pdf file
-
- """
- printer = QtGui.QPrinter()
-
- printer.setOutputFormat(QtGui.QPrinter.PdfFormat)
- printer.setOutputFileName(filename)
- painter = QtGui.QPainter()
- painter.begin(printer)
- rect = painter.viewport()
- pixmap = self.label.pixmap()
- size = pixmap.size()
- size.scale(rect.size(), QtCore.Qt.KeepAspectRatio)
- painter.setViewport(rect.x(), rect.y(), size.width(), size.height())
- painter.setWindow(pixmap.rect())
- painter.drawPixmap(0, 0, pixmap)
- painter.end()
-#
-# def resizeEvent(self, e):
-# if self.originalPix!=None:
-# self.label.setPixmap(self.originalPix.scaled(self.label.size(),
-# QtCore.Qt.KeepAspectRatio,
-# QtCore.Qt.SmoothTransformation))
-#
-
-class ImageViewerFitToCellAction(QtGui.QAction):
- """
- ImageViewerFitToCellAction is the action to stretch the image to
- fit inside a cell
-
- """
- def __init__(self, parent=None):
- """ ImageViewerFitToCellAction(parent: QWidget)
- -> ImageViewerFitToCellAction
- Setup the image, status tip, etc. of the action
-
- """
- QtGui.QAction.__init__(self,
- QtGui.QIcon(":/images/fittocell.png"),
- "&Fit To Cell",
- parent)
- self.setStatusTip("Scale image content to fit cell frame")
- self.setCheckable(True)
- self.setChecked(True)
-
- def toggledSlot(self, checked):
- """ toggledSlot(checked: boolean) -> None
- Execute the action when the button is toggled
-
- """
- cellWidget = self.toolBar.getSnappedWidget()
- cellWidget.label.setScaledContents(checked)
- self.toolBar.slider.updateStatus((self.toolBar.sheet,
- self.toolBar.row,
- self.toolBar.col,
- cellWidget))
-
- def updateStatus(self, info):
- """ updateStatus(info: tuple) -> None
- Updates the status of the button based on the input info
-
- """
- (sheet, row, col, cellWidget) = info
- self.setChecked(cellWidget.label.hasScaledContents())
-
-class ImageViewerSaveAction(QtGui.QAction):
- """
- ImageViewerSaveAction is the action to save the image to file
-
- """
- def __init__(self, parent=None):
- """ ImageViewerSaveAction(parent: QWidget) -> ImageViewerSaveAction
- Setup the image, status tip, etc. of the action
-
- """
- QtGui.QAction.__init__(self,
- QtGui.QIcon(":/images/save.png"),
- "&Save image as...",
- parent)
- self.setStatusTip("Save image to file")
-
- def triggeredSlot(self, checked=False):
- """ toggledSlot(checked: boolean) -> None
- Execute the action when the button is clicked
-
- """
- cellWidget = self.toolBar.getSnappedWidget()
- if not cellWidget.label.pixmap() or cellWidget.label.pixmap().isNull():
- return
- fn = QtGui.QFileDialog.getSaveFileName(None, "Save image as...",
- "screenshot.png",
- "Images (*.png);;PDF files (*.pdf)")
- if not fn:
- return
- if fn.endsWith(QtCore.QString("png"), QtCore.Qt.CaseInsensitive):
- cellWidget.label.pixmap().toImage().save(fn, "png")
- elif fn.endsWith(QtCore.QString("pdf"), QtCore.Qt.CaseInsensitive):
- cellWidget.saveToPDF(str(fn))
-
-#class testButton(QtGui.QAction):
-# def __init__(self, parent=None):
-# """ ImageViewerRotateAction(parent: QWidget)
-# -> ImageViewerRotateAction
-# Setup the image, status tip, etc. of the action
-#
-# """
-# QtGui.QAction.__init__(self,
-# QtGui.QIcon(":/images/grass_split_line.png"),
-# "&Do Something...",
-# parent)
-# self.setStatusTip("We'll do something with this soon")
-# self.rotationMatrix = QtGui.QMatrix(0,1,-1,0,0,0)
-#
-#class ModelLabel(QtGui.QLabel):
-# def __init__(self, parent=None):
-# """A lable to indicate which model the output pertains to
-# """
-# self.text = QtCore.QString("testing")
-#
-#class ImageViewerZoomSlider(QtGui.QSlider):
-# """
-# ImageViewerZoomSlider is a slider that allows user to zoom in and
-# out by dragging it
-# """
-# def __init__(self, parent=None):
-# """ ImageViewerZoomSlider(parent: QWidget) -> ImageViewerZoomSlider
-# Setup the ranges, status tip, etc. of the slider
-#
-# """
-# QtGui.QSlider.__init__(self, QtCore.Qt.Horizontal, parent)
-# self.setRange(100, 600)
-# self.setValue(100)
-# self.setTracking(True)
-# self.setStatusTip("Zoom in the image")
-# self.connect(self, QtCore.SIGNAL("valueChanged(int)"), self.updateZoom)
-# self.connect(self, QtCore.SIGNAL("needUpdateStatus"), self.updateStatus)
-# self.setSizePolicy(QtGui.QSizePolicy.Preferred,
-# QtGui.QSizePolicy.Expanding)
-#
-# def updateZoom(self, value):
-# """ updateZoom(value: int) -> None
-# Update the image when the slider value changed
-#
-# """
-# if self.toolBar:
-# cellWidget = self.toolBar.getSnappedWidget()
-# if not cellWidget.label.hasScaledContents():
-# newWidth = cellWidget.originalPix.width()*value/100
-# pixmap = cellWidget.originalPix.scaledToWidth(newWidth)
-# cellWidget.label.setPixmap(pixmap)
-#
-# def updateStatus(self, info):
-# """ updateStatus(info: tuple) -> None
-# Updates the status of the button based on the input info
-#
-# """
-# (sheet, row, col, cellWidget) = info
-# if cellWidget:
-# if (not cellWidget.label.hasScaledContents() and
-# not cellWidget._playing):
-# self.setEnabled(True)
-# originalWidth = cellWidget.originalPix.width()
-# self.setValue(cellWidget.label.pixmap().width()*100/originalWidth)
-# else:
-# self.setEnabled(False)
-# self.setValue(100)
-#
-#class ImageViewerZoomLabel(QtGui.QLabel):
-# """
-# ImageViewerZoomLabel is the label sitting next to the ImageViewerZoomSlider
-#
-# """
-# def __init__(self, parent=None):
-# """ ImageViewerZoomSlider(parent: QWidget) -> None
-# Setup the label with a status tip
-#
-# """
-# QtGui.QLabel.__init__(self, "100%", parent)
-# self.setStatusTip("Zoom in the image")
-#
-# def updateValue(self, value):
-# """ updateValue(value: int)
-# Updates the label with the new percentage value
-# """
-# self.setText(str(value)+"%")
-#
-#class ImageViewerRotateAction(QtGui.QAction):
-# """
-# ImageViewerRotateAction is the action to rotate the image
-#
-# """
-# def __init__(self, parent=None):
-# """ ImageViewerRotateAction(parent: QWidget)
-# -> ImageViewerRotateAction
-# Setup the image, status tip, etc. of the action
-#
-# """
-# QtGui.QAction.__init__(self,
-# QtGui.QIcon(":/images/rotate.png"),
-# "&Rotate CW...",
-# parent)
-# self.setStatusTip("Rotate 90 degrees CW")
-# self.rotationMatrix = QtGui.QMatrix(0,1,-1,0,0,0)
-#
-# def triggeredSlot(self, checked=False):
-# """ toggledSlot(checked: boolean) -> None
-# Execute the action when the button is clicked
-#
-# """
-# cellWidget = self.toolBar.getSnappedWidget()
-# if not cellWidget.label.pixmap() or cellWidget.label.pixmap().isNull():
-# return
-# cellWidget.originalPix = cellWidget.originalPix.transformed(
-# self.rotationMatrix)
-# cellWidget.label.setPixmap(cellWidget.label.pixmap().transformed(
-# self.rotationMatrix))
-#
-#class ImageViewerFlipAction(QtGui.QAction):
-# """
-# ImageViewerFlipAction is the action to flip the image
-#
-# """
-# def __init__(self, parent=None):
-# """ ImageViewerFlipAction(parent: QWidget) -> ImageViewerFlipAction
-# Setup the image, status tip, etc. of the action
-#
-# """
-# QtGui.QAction.__init__(self,
-# QtGui.QIcon(":/images/flip.png"),
-# "&Flip Horizontal...",
-# parent)
-# self.setStatusTip("Flip the image horizontally")
-# self.flipMatrix = QtGui.QMatrix(-1,0,0,1,0,0)
-#
-# def triggeredSlot(self, checked=False):
-# """ toggledSlot(checked: boolean) -> None
-# Execute the action when the button is clicked
-#
-# """
-# cellWidget = self.toolBar.getSnappedWidget()
-# label = cellWidget.label
-# if not label.pixmap() or label.pixmap().isNull():
-# return
-# cellWidget.originalPix = cellWidget.originalPix.transformed(
-# self.flipMatrix)
-# label.setPixmap(label.pixmap().transformed(self.flipMatrix))
-#
-#class ImageViewerToolBar(QCellToolBar):
-# """
-# ImageViewerToolBar derives from CellToolBar to give the ImageViewerCellWidget
-# a customizable toolbar
-#
-# """
-# def createToolBar(self):
-# """ createToolBar() -> None
-# This will get call initiallly to add customizable widgets
-#
-# """
-# global SAHMModelOutputViewerCell
-#
-## self.appendAction(QtCore.QString(SAHMModelOutputViewerCell.model_label))
-# self.appendAction(testButton(self))
-# self.appendAction(ImageViewerFitToCellAction(self))
-# self.appendAction(ImageViewerSaveAction(self))
-# self.appendAction(ImageViewerRotateAction(self))
-# self.appendAction(ImageViewerFlipAction(self))
-# self.slider = ImageViewerZoomSlider(self)
-# label = ImageViewerZoomLabel(self)
-# self.connect(self.slider,
-# QtCore.SIGNAL("valueChanged(int)"),
-# label.updateValue)
-# self.appendWidget(self.slider)
-# self.appendWidget(label)
-# self.addAnimationButtons()
\ No newline at end of file
diff --git a/contrib/sahm/SahmSpatialOutputViewer.py b/contrib/sahm/SahmSpatialOutputViewer.py
deleted file mode 100644
index c5f2696..0000000
--- a/contrib/sahm/SahmSpatialOutputViewer.py
+++ /dev/null
@@ -1,483 +0,0 @@
-################################################################################
-# ImageViewer widgets/toolbar implementation
-################################################################################
-from PyQt4 import QtCore, QtGui, QAxContainer
-from core.modules.vistrails_module import Module
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
-from packages.spreadsheet.spreadsheet_controller import spreadsheetController
-from SahmSpatialViewerCell import Ui_Frame
-#import imageviewer_rc
-import os
-
-import csv
-
-from packages.sahm.pySAHM.utilities import mds_to_shape
-from utils import getrasterminmax
-################################################################################
-
-def setQGIS(qgis):
- globals()["qgis"] = qgis
-
-class SAHMSpatialOutputViewerCell(SpreadsheetCell):
- """
- SAHMModelOutputViewerCell displays the various output from a SAHM Model run
-
- """
- _input_ports = [("row", "(edu.utah.sci.vistrails.basic:Integer)"),
- ("column", "(edu.utah.sci.vistrails.basic:Integer)"),
- ('model_workspace', '(edu.utah.sci.vistrails.basic:File)')]
-
- def __init__(self):
- SpreadsheetCell.__init__(self)
-
-# globals()["qgis"] = qgis
-
- def compute(self):
- inputs = {}
- inputs["model_workspace"] = self.forceGetInputFromPort('model_workspace').name
- inputs["model_dir"] = os.path.split(inputs["model_workspace"])[0]
-
- inputs["prob_map"] = os.path.join(inputs["model_dir"],
- self.find_file(inputs["model_dir"], "_prob_map.tif"))
- inputs["bin_map"] = os.path.join(inputs["model_dir"],
- self.find_file(inputs["model_dir"], "_bin_map.tif"))
- inputs["res_map"] = os.path.join(inputs["model_dir"],
- self.find_file(inputs["model_dir"], "_resid_map.tif"))
- try:
- inputs["mes_map"] = os.path.join(inputs["model_dir"],
- self.find_file(inputs["model_dir"], "_mess_map.tif"))
- except:
- inputs["mes_map"] = ""
-
- try:
- inputs["mod_map"] = os.path.join(inputs["model_dir"],
- self.find_file(inputs["model_dir"], "_MoD_map.tif"))
- except:
- inputs["mod_map"] = ""
-
- mds = self.find_mds(inputs["model_dir"])
- shaperoot = self.gen_points_shp(mds)
- inputs["pres_points"] = shaperoot + "_pres.shp"
- inputs["abs_points"] = shaperoot + "_abs.shp"
- inputs["backs_points"] = shaperoot + "_backs.shp"
-
- inputs["model_tag"] = os.path.split(inputs["model_dir"])[1]
-
- if self.hasInputFromPort("row"):
- if not self.location:
- self.location = CellLocation()
- self.location.row = self.getInputFromPort('row') - 1
-
- if self.hasInputFromPort("column"):
- if not self.location:
- self.location = CellLocation()
- self.location.col = self.getInputFromPort('column') - 1
-
- self.displayAndWait(SAHMSpatialOutputViewerCellWidget,
- inputs)
-
-
- def find_file(self, model_dir, suffix):
- return [file_name for file_name in os.listdir(model_dir)
- if file_name.endswith(suffix)][0]
-
- def find_mds(self, model_dir):
- model_text = os.path.join(model_dir,
- self.find_file(model_dir, "_output.txt"))
-
- f = open(model_text, 'rb')
- lines = f.read().splitlines()
-
- # grab the line after "Data:"
- result = [lines[i + 1] for i in range(len(lines))
- if lines[i].startswith("Data:")][0].strip()
-
- if os.path.exists(result):
- return result
- else:
- raise RuntimeError('Valid input MDS file not found in Model text output.')
-
- def gen_points_shp(self, mds):
- """I couldn't figure out how to use a render on a shapefile
- instead I split the shapefile into three separate files for each
- class.
- This split only occurs once per mds though.
- """
- parentfolder, filename = os.path.split(mds)
- filenoext = os.path.splitext(filename)[0]
- shpfolder = os.path.join(parentfolder, "PointShapefiles")
-
- if not os.path.exists(shpfolder):
- os.mkdir(shpfolder)
- fileroot = os.path.join(shpfolder, filenoext)
-
- pregenerated = True
- for type in ["_pres", "_abs", "_backs"]:
- shape_file = fileroot + type + ".shp"
- if not os.path.exists(shape_file):
- pregenerated = False
-
- if not pregenerated:
- mds_to_shape(mds, shpfolder)
-
- return fileroot
-
-
-class SAHMSpatialOutputViewerCellWidget(QCellWidget):
- """
-
- """
- def __init__(self, parent=None):
- """ QGISCellWidget(parent: QWidget) -> QGISCellWidget
- Initialize the widget with its central layout
-
- """
- QCellWidget.__init__(self, parent)
-
- centralLayout = QtGui.QVBoxLayout()
- self.setLayout(centralLayout)
- centralLayout.setMargin(0)
- centralLayout.setSpacing(0)
-
-# self.setAnimationEnabled(True)
-
- self.Frame = QtGui.QFrame()
- self.ui = Ui_Frame()
- self.ui.setupUi(self.Frame)
-
- self.toolBarType = SAHMSpatialViewerToolBar
- self.controlBarType = SAHMSpatialViewerToolBar
-
- self.layout().addWidget(self.Frame)
-
-
- def updateContents(self, inputs):
- """ updateContents(inputs: dictionary) -> None
- Update the widget contents based on the input data
- """
-
- self.canvas = qgis.gui.QgsMapCanvas()
- self.canvas.show()
-
- self.ui.legend_label.setText(QtCore.QString(inputs["model_tag"]))
-
- self.toolPan = qgis.gui.QgsMapToolPan(self.canvas)
-
- self.canvas.setMapTool(self.toolPan)
- self.canvas.setWheelAction(2)
- self.canvas.setCanvasColor(QtCore.Qt.white)
- self.canvas.enableAntiAliasing(True)
-
- self.all_layers = {}
- self.add_raster(inputs["prob_map"], "prob_map")
- self.add_raster(inputs["bin_map"], "bin_map")
- self.add_raster(inputs["res_map"], "res_map")
- self.add_raster(inputs["mes_map"], "mes_map")
- self.add_raster(inputs["mod_map"], "mod_map")
-
- self.add_vector(inputs['pres_points'], "pres_points", '255,0,0')
- self.add_vector(inputs['abs_points'], "abs_points", '0,255,0')
- self.add_vector(inputs['backs_points'], "backs_points", '0,0,0')
-
- self.canvas.setExtent(self.all_layers["prob_map"].layer().extent())
- self.canvas.setLayerSet([self.all_layers["pres_points"],
- self.all_layers["abs_points"],
- self.all_layers["prob_map"]])
-
- self.ui.map_frame.layout().addWidget(self.canvas)
- legend = self.create_legend_ramp("prob_map", None, (0, 1), 6)
-
- self.ui.legend.layout().addWidget(legend)
- # Update the new figure canvas
- self.update()
-
- def dumpToFile(self, filename):
- pass
-
- def saveToPDF(self, filename):
- pass
-
- def add_raster(self, path, tag):
- if os.path.exists(path):
- fileInfo = QtCore.QFileInfo(path)
- baseName = fileInfo.baseName()
- raster = qgis.core.QgsRasterLayer(path, baseName)
-
- if tag=="res_map":
- min_max = getrasterminmax(path)
- else:
- min_max = None
-
- self.set_color_ramp(tag, raster)
- qgis.core.QgsMapLayerRegistry.instance().addMapLayer(raster)
- self.all_layers[tag] = qgis.gui.QgsMapCanvasLayer(raster)
- else:
- print "The file " + path + " could not be found on the file system."
- print " tag will not be enabled"
-
- def set_color_ramp(self, layer_type, raster, min_max=None):
- QgsColorRampShader = qgis.core.QgsColorRampShader
-
-
- if layer_type == "mod_map":
- #raster.setDrawingStyle(qgis.core.QgsRasterLayer.PalettedColor)
- raster.setDrawingStyle(qgis.core.QgsRasterLayer.SingleBandPseudoColor)
- raster.setColorShadingAlgorithm(qgis.core.QgsRasterLayer.PseudoColorShader)
-
- #raster.setColorShadingAlgorithm(qgis.core.QgsRasterLayer.ColorRampShader)
-# raster.setDrawingStyle(qgis.core.QgsRasterLayer.SingleBandGray)
- return None
- else:
- raster.setDrawingStyle(qgis.core.QgsRasterLayer.SingleBandPseudoColor)
-
- csv_file = os.path.abspath(os.path.join(os.path.dirname(__file__), "ColorBreaks.csv"))
- csvfile = open(csv_file, "r")
- reader = csv.reader(csvfile)
- header = reader.next() #skip the header
-
- color_ramp_items = []
- for row in reader:
- if row[0] == layer_type:
- r, g, b = [int(val) for val in row[2:5]]
- cur_color = QtGui.QColor(r, g, b)
- cur_val = float(row[1])
- color_item = QgsColorRampShader.ColorRampItem(cur_val, cur_color)
- color_ramp_items.append(color_item)
-
- raster.setColorShadingAlgorithm(qgis.core.QgsRasterLayer.ColorRampShader)
- fcn = raster.rasterShader().rasterShaderFunction()
- fcn.setColorRampType(QgsColorRampShader.INTERPOLATED)
- fcn.setColorRampItemList(color_ramp_items)
-
- if hasattr(raster, "setCacheImage"): raster.setCacheImage(None)
- raster.triggerRepaint()
-
- qgis.core.QgsMapLayerRegistry.instance().addMapLayer(raster)
-
- csvfile.close()
-
- return None
-
- def create_legend_ramp(self, layer_type, raster, min_max, num_tags):
- legend = QtGui.QFrame()
- legend.setObjectName(QtCore.QString.fromUtf8("legend"))
- mainlayout = QtGui.QVBoxLayout(legend)
- mainlayout.setSpacing(0)
- mainlayout.setMargin(0)
-
- frame_colorbar = QtGui.QFrame(legend)
- frame_colorbar.setObjectName(QtCore.QString.fromUtf8("frame_colorbar"))
- layout_colorbar = QtGui.QHBoxLayout(frame_colorbar)
- layout_colorbar.setSpacing(0)
- layout_colorbar.setContentsMargins(-1, 2, -1, 0)
-
- frame_ticks = QtGui.QFrame(legend)
- frame_ticks.setFrameShape(QtGui.QFrame.StyledPanel)
- frame_ticks.setFrameShadow(QtGui.QFrame.Raised)
- frame_ticks.setObjectName(QtCore.QString.fromUtf8("frame_ticks"))
- layout_ticks = QtGui.QHBoxLayout(frame_ticks)
- layout_ticks.setSpacing(0)
- layout_ticks.setContentsMargins(-1, 0, -1, 0)
-
- frame_labels = QtGui.QFrame(legend)
- frame_labels.setObjectName(QtCore.QString.fromUtf8("frame_labels"))
- layout_labels = QtGui.QHBoxLayout(frame_labels)
- layout_labels.setSpacing(0)
- layout_labels.setContentsMargins(4, 0, 4, 0)
-
- csv_file = os.path.abspath(os.path.join(os.path.dirname(__file__), "ColorBreaks.csv"))
- csvfile = open(csv_file, "r")
- reader = csv.reader(csvfile)
- header = reader.next() #skip the header
-
- color_ramp_items = []
- prev_color = None
- for row in reader:
- if row[0] == layer_type:
- cur_color = ", ".join(row[2:5])
-
- if prev_color:
- color_label = QtGui.QLabel(frame_colorbar)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.MinimumExpanding)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(color_label.sizePolicy().hasHeightForWidth())
- color_label.setSizePolicy(sizePolicy)
- color_label.setMinimumSize(QtCore.QSize(0, 4))
- stylesheet = "background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba("
- stylesheet += prev_color
- stylesheet += ", 255), stop:1 rgba("
- stylesheet += cur_color
- stylesheet += ", 255));"
- color_label.setStyleSheet(QtCore.QString.fromUtf8(stylesheet))
- color_label.setText(QtCore.QString.fromUtf8(""))
- layout_colorbar.addWidget(color_label)
-
- prev_color = cur_color
-
- min = min_max[0]
- max = min_max[1]
- step = float(max - min) / num_tags
- curStep = min
-
- while curStep <= max:
- line = QtGui.QFrame(frame_ticks)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Minimum)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(line.sizePolicy().hasHeightForWidth())
- line.setSizePolicy(sizePolicy)
- line.setMinimumSize(QtCore.QSize(0, 4))
- line.setSizeIncrement(QtCore.QSize(0, 0))
- line.setFrameShadow(QtGui.QFrame.Plain)
- line.setFrameShape(QtGui.QFrame.VLine)
- line.setFrameShadow(QtGui.QFrame.Sunken)
- line.setObjectName(QtCore.QString.fromUtf8("line"))
- layout_ticks.addWidget(line)
- spacerItem = QtGui.QSpacerItem(133, 2, QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
- layout_ticks.addItem(spacerItem)
-
- lbl = QtGui.QLabel(frame_labels)
- lbl.setMinimumSize(QtCore.QSize(0, 10))
- txt = "%.1f" %curStep
- lbl.setText(QtCore.QString.fromUtf8(txt))
- lbl.setAlignment(QtCore.Qt.AlignCenter)
- #lbl.setObjectName(QtCore.QString.fromUtf8("lbl"))
- layout_labels.addWidget(lbl)
- spacerItem2 = QtGui.QSpacerItem(5, 5, QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
- layout_labels.addItem(spacerItem2)
-
- curStep += step
-
- layout_ticks.removeItem(spacerItem)
- layout_labels.removeItem(spacerItem2)
-
- mainlayout.addWidget(frame_colorbar)
- mainlayout.addWidget(frame_ticks)
- mainlayout.addWidget(frame_labels)
- return legend
-
-
- def add_vector(self, path, tag, strcolor):
- fileInfo = QtCore.QFileInfo(path)
- baseName = fileInfo.baseName()
- points_layer = qgis.core.QgsVectorLayer(path, baseName, "ogr")
-
- props = {'color':strcolor, 'radius':'3' }
- s = qgis.core.QgsMarkerSymbolV2.createSimple(props)
-
- points_layer.setRendererV2( qgis.core.QgsSingleSymbolRendererV2( s ) )
-
- qgis.core.QgsMapLayerRegistry.instance().addMapLayer(points_layer)
- self.all_layers[tag] = qgis.gui.QgsMapCanvasLayer(points_layer)
-
-#
-#def update_displayed_layers(cellWidget):
-# pass
-#
-#
-## [qgis.gui.QgsMapCanvasLayer(layer) for layer in layers]
-
-# layer = cellWidget.cur_layers[layer]
-# layers = cellWidget.canvas.layers()
-#
-# if visible:
-# layers.insert(0, layer.layer())
-# else:
-# layers.remove(layer.layer())
-#
-# cellWidget.canvas.setLayerSet(layerset)
-# cellWidget.canvas.repaint()
-
-
-class ViewLayerAction(QtGui.QAction):
- def __init__(self, action_dict, parent=None):
- icon = os.path.abspath(os.path.join(
- os.path.dirname(__file__), "Images", action_dict["icon"]))
- QtGui.QAction.__init__(self,
- QtGui.QIcon(icon),
- action_dict["label"],
- parent)
- self.setCheckable(True)
- self.setChecked(action_dict["checked"])
- self.tag = action_dict["tag"]
- self.group = action_dict["group"]
-
- def triggeredSlot(self, checked=False):
-# cellWidget = self.toolBar.getSnappedWidget()
- self.toggleOthers()
- self.displayLayer()
-
- def toggleOthers(self):
- for action in self.toolBar.actions():
- if "group" in dir(action) and \
- action.group == self.group and \
- action.tag <> self.tag:
- action.setChecked(False)
-
- def displayLayer(self):
- cellWidget = self.toolBar.getSnappedWidget()
-
- all_layers = cellWidget.all_layers
- layerset = []
- for action in self.toolBar.actions():
- if action.isChecked() and all_layers.has_key(action.tag):
- layer = all_layers[action.tag]
- layerset.append(qgis.gui.QgsMapCanvasLayer(layer))
-
- cellWidget.canvas.setLayerSet(layerset)
- cellWidget.canvas.repaint()
-
-
-class SAHMSpatialViewerToolBar(QCellToolBar):
- """
- The toolbar that allows users to toggle layers on and off
- in the widget
-
- """
- def createToolBar(self):
- """ createToolBar() -> None
- This will get call initiallly to add customizable widgets
-
- """
- sw = self.getSnappedWidget()
-
- actions = [{"tag":"pres_points", "icon":"RedPoints.png",
- "checked":True, "label":"Display presence points",
- "group":"pres_points"},
- {"tag":"abs_points", "icon":"GreenPoints.png",
- "checked":True, "label":"Display absence points",
- "group":"abs_points"},
- {"tag":"backs_points", "icon":"BlackPoints.png",
- "checked":False, "label":"Display background points",
- "group":"backs_points"},
- {"tag":"prob_map", "icon":"ProbMap.png",
- "checked":True, "label":"Display probability map",
- "group":"Grids"},
- {"tag":"bin_map", "icon":"BinMap.png",
- "checked":False, "label":"Display binary map",
- "group":"Grids"},
- {"tag":"res_map", "icon":"ResMap.png",
- "checked":False, "label":"Display residuals map",
- "group":"Grids"},
- {"tag":"mes_map", "icon":"MesMap.png",
- "checked":False, "label":"Display Multivariate Environmental Similarity Surface (Mess) map",
- "group":"Grids"},
- {"tag":"mod_map", "icon":"ModMap.png",
- "checked":False, "label":"Display Most Dissimilar Variable (MoD) map",
- "group":"Grids"}]
-
-
- for action_dict in actions:
- self.appendAction(ViewLayerAction(action_dict, self))
-
- def updateToolBar(self):
- QCellToolBar.updateToolBar(self)
- sw = self.getSnappedWidget()
- for action in self.actions():
- if type(action) == ViewLayerAction:
- #disenable all action refering to data we don't have
- action.setEnabled(action.tag in sw.all_layers)
-
-
\ No newline at end of file
diff --git a/contrib/sahm/SahmSpatialViewerCell.py b/contrib/sahm/SahmSpatialViewerCell.py
deleted file mode 100644
index 0f5db47..0000000
--- a/contrib/sahm/SahmSpatialViewerCell.py
+++ /dev/null
@@ -1,89 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Form implementation generated from reading ui file 'I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\SahmSpatialViewerCell.ui'
-#
-# Created: Tue Oct 11 16:20:25 2011
-# by: PyQt4 UI code generator 4.8.5
-#
-# WARNING! All changes made in this file will be lost!
-
-from PyQt4 import QtCore, QtGui
-
-try:
- _fromUtf8 = QtCore.QString.fromUtf8
-except AttributeError:
- _fromUtf8 = lambda s: s
-
-class Ui_Frame(object):
- def setupUi(self, Frame):
- Frame.setObjectName(_fromUtf8("Frame"))
- Frame.resize(734, 706)
- Frame.setWindowTitle(QtGui.QApplication.translate("Frame", "Frame", None, QtGui.QApplication.UnicodeUTF8))
- Frame.setFrameShape(QtGui.QFrame.StyledPanel)
- Frame.setFrameShadow(QtGui.QFrame.Plain)
- self.gridLayout = QtGui.QGridLayout(Frame)
- self.gridLayout.setMargin(0)
- self.gridLayout.setSpacing(0)
- self.gridLayout.setObjectName(_fromUtf8("gridLayout"))
- self.splitter = QtGui.QSplitter(Frame)
- self.splitter.setOrientation(QtCore.Qt.Vertical)
- self.splitter.setObjectName(_fromUtf8("splitter"))
- self.legend_frame_2 = QtGui.QFrame(self.splitter)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Preferred)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.legend_frame_2.sizePolicy().hasHeightForWidth())
- self.legend_frame_2.setSizePolicy(sizePolicy)
- self.legend_frame_2.setMinimumSize(QtCore.QSize(0, 0))
- self.legend_frame_2.setBaseSize(QtCore.QSize(0, 0))
- self.legend_frame_2.setFrameShape(QtGui.QFrame.StyledPanel)
- self.legend_frame_2.setFrameShadow(QtGui.QFrame.Sunken)
- self.legend_frame_2.setObjectName(_fromUtf8("legend_frame_2"))
- self.horizontalLayout_2 = QtGui.QHBoxLayout(self.legend_frame_2)
- self.horizontalLayout_2.setSpacing(5)
- self.horizontalLayout_2.setContentsMargins(9, 0, 0, 0)
- self.horizontalLayout_2.setObjectName(_fromUtf8("horizontalLayout_2"))
- self.legend_label = QtGui.QLabel(self.legend_frame_2)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Minimum)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.legend_label.sizePolicy().hasHeightForWidth())
- self.legend_label.setSizePolicy(sizePolicy)
- self.legend_label.setText(QtGui.QApplication.translate("Frame", "TextLabel", None, QtGui.QApplication.UnicodeUTF8))
- self.legend_label.setObjectName(_fromUtf8("legend_label"))
- self.horizontalLayout_2.addWidget(self.legend_label)
- self.legend = QtGui.QFrame(self.legend_frame_2)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.legend.sizePolicy().hasHeightForWidth())
- self.legend.setSizePolicy(sizePolicy)
- self.legend.setFrameShape(QtGui.QFrame.NoFrame)
- self.legend.setFrameShadow(QtGui.QFrame.Plain)
- self.legend.setLineWidth(0)
- self.legend.setObjectName(_fromUtf8("legend"))
- self.legend_layout = QtGui.QHBoxLayout(self.legend)
- self.legend_layout.setMargin(0)
- self.legend_layout.setObjectName(_fromUtf8("legend_layout"))
- self.horizontalLayout_2.addWidget(self.legend)
- self.map_frame = QtGui.QFrame(self.splitter)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Expanding)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(1)
- sizePolicy.setHeightForWidth(self.map_frame.sizePolicy().hasHeightForWidth())
- self.map_frame.setSizePolicy(sizePolicy)
- self.map_frame.setFrameShape(QtGui.QFrame.StyledPanel)
- self.map_frame.setFrameShadow(QtGui.QFrame.Sunken)
- self.map_frame.setObjectName(_fromUtf8("map_frame"))
- self.horizontalLayout = QtGui.QHBoxLayout(self.map_frame)
- self.horizontalLayout.setSpacing(0)
- self.horizontalLayout.setMargin(0)
- self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
- self.gridLayout.addWidget(self.splitter, 0, 0, 1, 1)
-
- self.retranslateUi(Frame)
- QtCore.QMetaObject.connectSlotsByName(Frame)
-
- def retranslateUi(self, Frame):
- pass
-
diff --git a/contrib/sahm/SahmViewerCell.py b/contrib/sahm/SahmViewerCell.py
deleted file mode 100644
index af0be39..0000000
--- a/contrib/sahm/SahmViewerCell.py
+++ /dev/null
@@ -1,72 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Form implementation generated from reading ui file 'SahmViewerCell.ui'
-#
-# Created: Thu Sep 29 18:41:54 2011
-# by: PyQt4 UI code generator 4.8.5
-#
-# WARNING! All changes made in this file will be lost!
-
-from PyQt4 import QtCore, QtGui
-
-try:
- _fromUtf8 = QtCore.QString.fromUtf8
-except AttributeError:
- _fromUtf8 = lambda s: s
-
-class Ui_Frame(object):
- def setupUi(self, Frame):
- Frame.setObjectName(_fromUtf8("Frame"))
- Frame.resize(546, 402)
- Frame.setWindowTitle(QtGui.QApplication.translate("Frame", "Frame", None, QtGui.QApplication.UnicodeUTF8))
- Frame.setFrameShape(QtGui.QFrame.StyledPanel)
- Frame.setFrameShadow(QtGui.QFrame.Raised)
- self.horizontalLayout = QtGui.QHBoxLayout(Frame)
- self.horizontalLayout.setSpacing(0)
- self.horizontalLayout.setMargin(0)
- self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
- self.tabWidget = QtGui.QTabWidget(Frame)
- self.tabWidget.setEnabled(True)
- self.tabWidget.setTabPosition(QtGui.QTabWidget.North)
- self.tabWidget.setObjectName(_fromUtf8("tabWidget"))
- self.text_output = QtGui.QWidget()
- self.text_output.setObjectName(_fromUtf8("text_output"))
- self.text_output_layout = QtGui.QHBoxLayout(self.text_output)
- self.text_output_layout.setSpacing(0)
- self.text_output_layout.setMargin(0)
- self.text_output_layout.setObjectName(_fromUtf8("text_output_layout"))
- self.tabWidget.addTab(self.text_output, _fromUtf8(""))
- self.tabWidget.setTabToolTip(self.tabWidget.indexOf(self.text_output), QtGui.QApplication.translate("Frame", "Textual model output ", None, QtGui.QApplication.UnicodeUTF8))
- self.response_curves = QtGui.QWidget()
- self.response_curves.setObjectName(_fromUtf8("response_curves"))
- self.response_curves_layout = QtGui.QHBoxLayout(self.response_curves)
- self.response_curves_layout.setSpacing(0)
- self.response_curves_layout.setMargin(0)
- self.response_curves_layout.setObjectName(_fromUtf8("response_curves_layout"))
- self.tabWidget.addTab(self.response_curves, _fromUtf8(""))
- self.tabWidget.setTabToolTip(self.tabWidget.indexOf(self.response_curves), QtGui.QApplication.translate("Frame", "Response curves", None, QtGui.QApplication.UnicodeUTF8))
- self.auc = QtGui.QWidget()
- self.auc.setObjectName(_fromUtf8("auc"))
- self.horizontalLayout_4 = QtGui.QHBoxLayout(self.auc)
- self.horizontalLayout_4.setSpacing(0)
- self.horizontalLayout_4.setMargin(0)
- self.horizontalLayout_4.setObjectName(_fromUtf8("horizontalLayout_4"))
- self.gv_auc = QtGui.QGraphicsView(self.auc)
- self.gv_auc.setDragMode(QtGui.QGraphicsView.ScrollHandDrag)
- self.gv_auc.setTransformationAnchor(QtGui.QGraphicsView.AnchorUnderMouse)
- self.gv_auc.setResizeAnchor(QtGui.QGraphicsView.AnchorUnderMouse)
- self.gv_auc.setObjectName(_fromUtf8("gv_auc"))
- self.horizontalLayout_4.addWidget(self.gv_auc)
- self.tabWidget.addTab(self.auc, _fromUtf8(""))
- self.tabWidget.setTabToolTip(self.tabWidget.indexOf(self.auc), QtGui.QApplication.translate("Frame", "Area under the curve (AUC)", None, QtGui.QApplication.UnicodeUTF8))
- self.horizontalLayout.addWidget(self.tabWidget)
-
- self.retranslateUi(Frame)
- self.tabWidget.setCurrentIndex(2)
- QtCore.QMetaObject.connectSlotsByName(Frame)
-
- def retranslateUi(self, Frame):
- self.tabWidget.setTabText(self.tabWidget.indexOf(self.text_output), QtGui.QApplication.translate("Frame", "Model Results", None, QtGui.QApplication.UnicodeUTF8))
- self.tabWidget.setTabText(self.tabWidget.indexOf(self.response_curves), QtGui.QApplication.translate("Frame", "Response", None, QtGui.QApplication.UnicodeUTF8))
- self.tabWidget.setTabText(self.tabWidget.indexOf(self.auc), QtGui.QApplication.translate("Frame", "AUC", None, QtGui.QApplication.UnicodeUTF8))
-
diff --git a/contrib/sahm/SelectPredictorsLayers.py b/contrib/sahm/SelectPredictorsLayers.py
deleted file mode 100644
index 1815c27..0000000
--- a/contrib/sahm/SelectPredictorsLayers.py
+++ /dev/null
@@ -1,428 +0,0 @@
-'''
-Created on Sep 17, 2010
-
- at author: talbertc
-'''
-from core.modules.vistrails_module import Module
-from PyQt4 import QtCore, QtGui
-import csv
-import utils
-from utils import writetolog
-import shutil
-import os
-from core.system import execute_cmdline
-import subprocess
-
-try:
- _fromUtf8 = QtCore.QString.fromUtf8
-except AttributeError:
- _fromUtf8 = lambda s: s
-
-class SelectListDialog(QtGui.QDialog):
-
- def __init__(self, inputMDS, outputMDS, displayJPEG, rPath, parent=None):
- #print inputMDS, outputMDS, rPath, modelsPath
- self.rPath = rPath
-
- self.selection_name = os.path.split(outputMDS)[1]
- self.selection_name = os.path.splitext(self.selection_name)[0]
- self.selection_name = self.selection_name.split('_')[-1]
-
- self.displayJPEG = displayJPEG
-
- QtGui.QDialog.__init__(self, parent)
-
- self.inputMDS = inputMDS
- self.outputMDS = outputMDS
- self.outputDir = os.path.split(outputMDS)[0]
-
- layout = QtGui.QVBoxLayout()
- self.setWindowFlags(QtCore.Qt.Window)
- ##begin autogenerated code from QtDesigner
- #
-
- self.horizontalLayout_4 = QtGui.QHBoxLayout()
- self.horizontalLayout_4.setSpacing(5)
- self.horizontalLayout_4.setMargin(5)
- self.horizontalLayout_4.setObjectName(_fromUtf8("horizontalLayout_4"))
- self.verticalLayout_3 = QtGui.QVBoxLayout()
- self.verticalLayout_3.setObjectName(_fromUtf8("verticalLayout_3"))
- self.splitter = QtGui.QSplitter()
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.splitter.sizePolicy().hasHeightForWidth())
- self.splitter.setSizePolicy(sizePolicy)
- self.splitter.setMinimumSize(QtCore.QSize(0, 0))
- self.splitter.setFrameShape(QtGui.QFrame.Box)
- self.splitter.setFrameShadow(QtGui.QFrame.Plain)
- self.splitter.setLineWidth(1)
- self.splitter.setOrientation(QtCore.Qt.Horizontal)
- self.splitter.setHandleWidth(10)
- self.splitter.setObjectName(_fromUtf8("splitter"))
- self.widget = QtGui.QWidget(self.splitter)
- self.widget.setObjectName(_fromUtf8("widget"))
- self.verticalLayout = QtGui.QVBoxLayout(self.widget)
- self.verticalLayout.setSpacing(4)
- self.verticalLayout.setSizeConstraint(QtGui.QLayout.SetDefaultConstraint)
- self.verticalLayout.setContentsMargins(6, 6, 3, 3)
- self.verticalLayout.setObjectName(_fromUtf8("verticalLayout"))
- self.label_2 = QtGui.QLabel(self.widget)
- self.label_2.setObjectName(_fromUtf8("label_2"))
- self.verticalLayout.addWidget(self.label_2)
- self.treeview = QtGui.QTreeWidget(self.widget)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Ignored, QtGui.QSizePolicy.Expanding)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.treeview.sizePolicy().hasHeightForWidth())
- self.treeview.setSizePolicy(sizePolicy)
- self.treeview.setMinimumSize(QtCore.QSize(75, 0))
- self.treeview.setMaximumSize(QtCore.QSize(16777215, 16777215))
- self.treeview.setSizeIncrement(QtCore.QSize(100, 0))
- self.treeview.setBaseSize(QtCore.QSize(0, 0))
- self.treeview.setObjectName(_fromUtf8("treeview"))
- self.verticalLayout.addWidget(self.treeview)
- self.horizontalLayout_3 = QtGui.QHBoxLayout()
- self.horizontalLayout_3.setSizeConstraint(QtGui.QLayout.SetDefaultConstraint)
- self.horizontalLayout_3.setObjectName(_fromUtf8("horizontalLayout_3"))
- self.btnRunR = QtGui.QPushButton(self.widget)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.btnRunR.sizePolicy().hasHeightForWidth())
- self.btnRunR.setSizePolicy(sizePolicy)
- self.btnRunR.setObjectName(_fromUtf8("btnRunR"))
- self.horizontalLayout_3.addWidget(self.btnRunR)
- spacerItem = QtGui.QSpacerItem(10, 0, QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
- self.horizontalLayout_3.addItem(spacerItem)
- self.label = QtGui.QLabel(self.widget)
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Preferred)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.label.sizePolicy().hasHeightForWidth())
- self.label.setSizePolicy(sizePolicy)
- self.label.setObjectName(_fromUtf8("label"))
- self.horizontalLayout_3.addWidget(self.label)
- self.lineEdit = QtGui.QLineEdit(self.widget)
- self.lineEdit.setText(_fromUtf8("0.7"))
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.lineEdit.sizePolicy().hasHeightForWidth())
- self.lineEdit.setSizePolicy(sizePolicy)
- self.lineEdit.setMaximumSize(QtCore.QSize(75, 16777215))
- self.lineEdit.setObjectName(_fromUtf8("lineEdit"))
- self.horizontalLayout_3.addWidget(self.lineEdit)
-
- self.chkPresence = QtGui.QCheckBox(self.widget)
- self.chkPresence.setChecked(True)
- self.chkPresence.setText(_fromUtf8("Include presence/count points"))
- self.chkPresence.setObjectName(_fromUtf8("chkPresence"))
- self.verticalLayout.addWidget(self.chkPresence)
- self.chkAbsence = QtGui.QCheckBox(self.widget)
- self.chkAbsence.setChecked(True)
- self.chkAbsence.setText(_fromUtf8("Include absence points"))
- self.chkAbsence.setObjectName(_fromUtf8("chkAbsence"))
- self.verticalLayout.addWidget(self.chkAbsence)
- self.chkBackground = QtGui.QCheckBox(self.widget)
- self.chkBackground.setChecked(True)
- self.chkBackground.setText(_fromUtf8("Include background points"))
- self.chkBackground.setObjectName(_fromUtf8("chkBackground"))
- self.verticalLayout.addWidget(self.chkBackground)
-
- self.verticalLayout.addLayout(self.horizontalLayout_3)
-
- self.scene = QtGui.QGraphicsScene()
- self.view = QtGui.QGraphicsView(self.scene)
- #self.view = customGraphicsView(self.scene)
- self.view.setDragMode(QtGui.QGraphicsView.ScrollHandDrag)
-
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
- sizePolicy.setHorizontalStretch(4)
- sizePolicy.setVerticalStretch(0)
- #sizePolicy.setHeightForWidth(self.view.sizePolicy().hasHeightForWidth())
- self.view.setSizePolicy(sizePolicy)
- self.view.setResizeAnchor(QtGui.QGraphicsView.AnchorUnderMouse)
- self.view.setObjectName(_fromUtf8("view"))
-
- self.splitter.addWidget(self.view)
-
- self.verticalLayout_3.addWidget(self.splitter)
- self.horizontalLayout = QtGui.QHBoxLayout()
- self.horizontalLayout.setContentsMargins(-1, 3, -1, 3)
- self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
- self.btnOK = QtGui.QPushButton()
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.btnOK.sizePolicy().hasHeightForWidth())
- self.btnOK.setSizePolicy(sizePolicy)
- self.btnOK.setBaseSize(QtCore.QSize(100, 0))
- self.btnOK.setToolTip(_fromUtf8(""))
- self.btnOK.setObjectName(_fromUtf8("btnOK"))
- self.horizontalLayout.addWidget(self.btnOK)
- self.btnCancel = QtGui.QPushButton()
- sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
- sizePolicy.setHorizontalStretch(0)
- sizePolicy.setVerticalStretch(0)
- sizePolicy.setHeightForWidth(self.btnCancel.sizePolicy().hasHeightForWidth())
- self.btnCancel.setSizePolicy(sizePolicy)
- self.btnCancel.setBaseSize(QtCore.QSize(100, 0))
- self.btnCancel.setObjectName(_fromUtf8("btnCancel"))
- self.horizontalLayout.addWidget(self.btnCancel)
- self.verticalLayout_3.addLayout(self.horizontalLayout)
- self.horizontalLayout_4.addLayout(self.verticalLayout_3)
-
- self.setWindowTitle(_fromUtf8("Covariate Coorelation viewer"))
- self.label_2.setText(_fromUtf8("Covariates"))
- self.btnRunR.setText(_fromUtf8("Update"))
- self.label.setText(_fromUtf8("Threshold"))
- self.btnOK.setText(_fromUtf8("OK"))
- self.btnCancel.setText(_fromUtf8("Cancel"))
- self.resize(1100, 800)
- self.view.resize(800, 750)
-
- ##End autogenerated code from QtDesigner
-
- layout.addLayout(self.horizontalLayout_4)
-
- self.btnCancel.setShortcut('Esc')
- self.connect(self.btnOK, QtCore.SIGNAL('clicked(bool)'),
- self.okTriggered)
- self.connect(self.btnCancel, QtCore.SIGNAL('clicked(bool)'),
- self.cancel)
- self.connect(self.btnRunR, QtCore.SIGNAL('clicked(bool)'),
- self.updateROutput)
-# self.connect(self.view, QtCore.SIGNAL('resize()'),
-# self.resize)
-
- self.scene.wheelEvent = self.wheel_event
-# self.resizeEvent = self.resize_event
- #code to populate the treeview with the contents of our MDS
- self.PopulateTreeview()
-
- self.setLayout(layout)
- self.repaint()
- #utils.breakpoint()
- #code to add in pictureviewer stuff
- outputPic = self.runR(self.inputMDS)
-# self.setup_view()
- self.load_picture(outputPic)
-
- def okTriggered(self):
- self.SaveMDSFromTreeview()
- self.done(0)
-
- def cancel(self):
- self.done(1)
- #raise Exception
-# shutil.copyfile(self.inputMDS, self.outputMDS)
-
-
- def PopulateTreeview(self):
- ''' Reads in the input MDS and populates the treeview widget
- with the items in covariate columns.
- Sets the check state to be the same as the 0/1 include flag.
- '''
- writetolog(" PopulateTreeview inputMDS = " + self.inputMDS, False, False)
- self.treeview.setColumnCount(1)
- #If an outputMDS already exists then the user has run this module before.
- #We need to pull and apply their previous selections from that output file
-
-
-
- csvfile = open(self.inputMDS, "r")
- #print "MDS", self.inputMDS
- reader = csv.reader(csvfile)
- header = reader.next() #store the header
- header2 = reader.next() #the 2nd line of the mds with use/don't use
- header3 = reader.next() #the 3rd line of the mds with the path
-
- self.responseCol = header[2]
-
- headerList = []
- n = 0
- for i in range(0, len(header)):
- headerList.append([header[i], header2[i], header3[i]])
-
- #headerList.sort()
- for item in headerList[3:]:
- child_item = QtGui.QTreeWidgetItem([item[0],])
- child_item.setFlags(QtCore.Qt.ItemIsUserCheckable |
- QtCore.Qt.ItemIsEnabled)
- checked = True
- if int(item[1]) == 0:
- checked = False
-
- if not checked:
- child_item.setCheckState(0, QtCore.Qt.Unchecked)
- else:
- child_item.setCheckState(0, QtCore.Qt.Checked)
-
- self.treeview.addTopLevelItem(child_item)
- #self.tree_items[file] = child_item
- n += 1
- csvfile.close()
- #update the tree view label to show how many covariates there are
- self.label_2.setText(_fromUtf8("Covariates (n=" + str(n) + ")"))
-
- def SaveMDSFromTreeview(self):
- #updates the second header line on the input MDS file
- #to reflect the checked items in the tree view
- #and saves the results to the output MDS.
-
- reader = csv.reader(open(self.inputMDS, "r"))
- header = reader.next() #store the header
- header2 = reader.next() #the 2nd line of the mds with use/don't use
- header3 = reader.next() #the 3rd line of the mds with the path
-
- headerList = []
- for i in range(0, len(header)):
- headerList.append([header[i], header2[i], header3[i]])
-
- outHeader2 = header2[:2] + [self.selection_name]
-
- treeviewIter = QtGui.QTreeWidgetItemIterator(self.treeview)
- while treeviewIter.value():
- if treeviewIter.value().checkState(0) == QtCore.Qt.Checked:
- outHeader2.append("1")
- else:
- outHeader2.append ("0")
- treeviewIter += 1
-
-
- oFile = open(self.outputMDS, 'wb')
- writer = csv.writer(oFile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
- writer.writerow(header)
- writer.writerow(outHeader2)
- writer.writerow(header3)
- for row in reader:
- writer.writerow(row)
- oFile.close
-
- def updateROutput(self):
- self.SaveMDSFromTreeview()
- outputPic = self.runR(self.outputMDS)
- self.load_picture(outputPic)
-
- def runR(self, MDSfile):
-#
-# program = os.path.join(self.rPath, "i386", "Rterm.exe")
-# script = os.path.join(utils.getModelsPath(), "PairsExplore.r")
-
- args = "i=" + '"' + MDSfile + '"' + " o=" + '"' + self.displayJPEG + '"' + " m=" + str(self.lineEdit.text())
- args += " rc=" + self.responseCol
-
- if self.chkPresence.checkState() == QtCore.Qt.Checked:
- args += " pres=TRUE"
- else:
- args += " pres=FALSE"
- if self.chkAbsence.checkState() == QtCore.Qt.Checked:
- args += " absn=TRUE"
- else:
- args += " absn=FALSE"
- if self.chkBackground.checkState() == QtCore.Qt.Checked:
- args += " bgd=TRUE"
- else:
- args += " bgd=FALSE"
-
-# command = program + " --vanilla -f " + script + " --args " + args
-# writetolog(" " + command, False, False)
- if os.path.exists(os.path.join(self.outputDir, "Predictor_Correlation.jpg")):
- os.remove(os.path.join(self.outputDir, "Predictor_Correlation.jpg"))
-
- utils.runRScript('PairsExplore.r', args)
-
-# p = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
-#
-# writetolog(" Calculating covariate correlation in r R ")
-
-# ret = p.communicate()
-# if ret[1]:
-# msg = "An error was encountered in the R script for this module. The R error message is below - \n"
-# msg += ret[1]
-# writetolog(msg)
-# raise Exception, msg
-# else:
-# writetolog(" Finished in R. ")
-# del(ret)
-
- if os.path.exists(os.path.join(self.displayJPEG)):
- return os.path.join(self.displayJPEG)
- else:
- writetolog("Missing output from R processing: " + self.displayJPEG)
- raise Exception, "Missing output from R processing"
-
- def load_picture(self, strPicture):
- #utils.breakpoint()
- self.l_pix = QtGui.QPixmap(strPicture)
- if self.view.size().width() <= self.view.size().height():
- self.max_vsize = self.view.size().width() * 0.95
- else:
- self.max_vsize = self.view.size().height() * 0.95
-
- self.c_view = self.l_pix.scaled(self.max_vsize, self.max_vsize,
- QtCore.Qt.KeepAspectRatio,
- QtCore.Qt.SmoothTransformation)
- self.view_current()
-
- def view_current(self):
- #print "view_current"
- size_img = self.c_view.size()
- wth, hgt = QtCore.QSize.width(size_img), QtCore.QSize.height(size_img)
- self.scene.clear()
- self.scene.setSceneRect(0, 0, wth, hgt)
- self.scene.addPixmap(self.c_view)
- QtCore.QCoreApplication.processEvents()
-
-# def load_current(self, filePath):
-# print "load_current"
-# self.l_pix = QtGui.QPixmap(filePath)
-# self.c_view = self.l_pix.scaled(self.max_vsize, self.max_vsize,
-# QtCore.Qt.KeepAspectRatio,
-# QtCore.Qt.FastTransformation)
-# #change the previous line with QtCore.Qt.SmoothTransformation eventually
-# self.view_current()
-
- def wheel_event (self, event):
- numDegrees = event.delta() / 8
- numSteps = numDegrees / 15.0
- self.zoom(numSteps)
- event.accept()
-
- def zoom(self, step):
- zoom_step = 0.06
- self.scene.clear()
- w = self.c_view.size().width()
- h = self.c_view.size().height()
- w, h = w * (1 + zoom_step*step), h * (1 + zoom_step*step)
- self.c_view = self.l_pix.scaled(w, h,
- QtCore.Qt.KeepAspectRatio,
- QtCore.Qt.SmoothTransformation)
- self.view_current()
-
- def closeEvent(self, event):
- self.cancel()
-
- def resizeEvent(self, event):
- self.load_picture(self.displayJPEG)
-
-# def resize_event(self, event):
-# utils.breakpoint()
-# origsize = self.c_view.size()
-# size = event.size()
-# w = size.width()
-# h = size.height()
-# self.c_view = self.l_pix.scaled(origsize.width(), origsize.height(),
-# QtCore.Qt.KeepAspectRatio,
-# QtCore.Qt.SmoothTransformation)
-# self.view_current()
-
-
-#class customGraphicsView(QtGui.QGraphicsView):
-#
-# def __init__(self, parent=None):
-# QtGui.QGraphicsView.__init__(self, parent)
-#
-# def resizeEvent(self, evt=None):
-# self.emit(QtCore.SIGNAL("resize()"))
diff --git a/contrib/sahm/__init__.py b/contrib/sahm/__init__.py
deleted file mode 100644
index 7a0d593..0000000
--- a/contrib/sahm/__init__.py
+++ /dev/null
@@ -1,14 +0,0 @@
-from core.configuration import ConfigurationObject
-
-name = "SAHM"
-identifier = "gov.usgs.sahm"
-version = '0.0.5'
-
-configuration = \
- ConfigurationObject(output_dir= r'C:\temp\SAHM_workspace',
- r_path = r'..\\Central_R\R-2.12.1\bin',
- gdal_path = r'..\\Central_GDAL',
- maxent_path = r'..\\Central_Maxent',
- qgis_path = r'..\\Central_QGIS',
- projection_layers_path = r'I:\WorldClim_Future_Climate\RenamedBILs', #This only applies to instances running in the FORT Infrastructure
- verbose = 'True')
diff --git a/contrib/sahm/enum_modules.py b/contrib/sahm/enum_modules.py
deleted file mode 100644
index 142c0e8..0000000
--- a/contrib/sahm/enum_modules.py
+++ /dev/null
@@ -1,11 +0,0 @@
-from core.modules.basic_modules import String
-from enum_widget import build_enum_widget
-
-class MyEnum(String):
- _input_ports = [('value', '(gov.usgs.sahm:MyEnum:DataInput)')]
- _widget_class = build_enum_widget('MyEnumWidget',
- ['abc', 'def', 'ghi'])
-
- @staticmethod
- def get_widget_class():
- return MyEnum._widget_class
diff --git a/contrib/sahm/enum_widget.py b/contrib/sahm/enum_widget.py
deleted file mode 100644
index 3a61264..0000000
--- a/contrib/sahm/enum_widget.py
+++ /dev/null
@@ -1,44 +0,0 @@
-from PyQt4 import QtCore, QtGui
-from core.modules.constant_configuration import ConstantWidgetMixin
-
-class EnumWidget(QtGui.QComboBox, ConstantWidgetMixin):
- param_values = []
- def __init__(self, param, parent=None):
- """__init__(param: core.vistrail.module_param.ModuleParam,
- parent: QWidget)
-
- """
- contents = param.strValue
- contentType = param.type
- QtGui.QComboBox.__init__(self, parent)
- ConstantWidgetMixin.__init__(self, param.strValue)
- # want to look up in registry based on parameter type
-
- self.addItem('')
- for val in self.param_values:
- self.addItem(val)
-
- curIdx = self.findText(contents)
- if curIdx != -1:
- self.setCurrentIndex(curIdx)
- self._contentType = contentType
- self.connect(self,
- QtCore.SIGNAL('currentIndexChanged(int)'),
- self.update_parent)
-
- def contents(self):
- curIdx = self.currentIndex()
- if curIdx == -1:
- print '*** ""'
- return ''
- print '*** "%s"' % str(self.itemText(curIdx))
- return str(self.itemText(curIdx))
-
- def setContents(self, strValue, silent=True):
- curIdx = self.findText(contents)
- self.setCurrentIndex(curIdx)
- if not silent:
- self.update_parent()
-
-def build_enum_widget(name, param_values):
- return type(name, (EnumWidget,), {'param_values': param_values})
diff --git a/contrib/sahm/init.py b/contrib/sahm/init.py
deleted file mode 100644
index 6e12900..0000000
--- a/contrib/sahm/init.py
+++ /dev/null
@@ -1,1788 +0,0 @@
-#test from marian
-import csv
-from datetime import datetime
-import glob
-import itertools
-import os
-import shutil
-import sys
-import subprocess
-import traceback
-
-from core.modules.vistrails_module import Module, ModuleError, ModuleConnector
-from core.modules.basic_modules import File, Directory, Path, new_constant, Constant
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
-#from packages.persistence.init import PersistentPath, PersistentFile, PersistentDir
-
-from core.modules.basic_modules import List
-from core.modules.basic_modules import String
-
-from PyQt4 import QtCore, QtGui
-
-from widgets import get_predictor_widget, get_predictor_config
-from enum_widget import build_enum_widget
-
-from SelectPredictorsLayers import SelectListDialog
-
-import utils
-#import our python SAHM Processing files
-import packages.sahm.pySAHM.FieldDataQuery as FDQ
-import packages.sahm.pySAHM.MDSBuilder as MDSB
-import packages.sahm.pySAHM.PARC as parc
-import packages.sahm.pySAHM.RasterFormatConverter as RFC
-import packages.sahm.pySAHM.MaxentRunner as MaxentRunner
-from SahmOutputViewer import SAHMModelOutputViewerCell
-from SahmSpatialOutputViewer import SAHMSpatialOutputViewerCell
-
-from utils import writetolog
-from pySAHM.utilities import TrappedError
-
-from SahmSpatialOutputViewer import setQGIS
-
-identifier = 'gov.usgs.sahm'
-
-def menu_items():
- """ Add a menu item which allows users to specify their session directory
- """
- def change_session_folder():
- global session_dir
-
- path = str(QtGui.QFileDialog.getExistingDirectory(None,
- 'Browse to new session folder -'))
- session_dir = path
- utils.setrootdir(path)
-
- writetolog("*" * 79 + "\n" + "*" * 79)
- writetolog(" output directory: " + session_dir)
- writetolog("*" * 79 + "\n" + "*" * 79)
-
- lst = []
- lst.append(("Change session folder", change_session_folder))
- return(lst)
-
-
-
-
-def expand_ports(port_list):
- new_port_list = []
- for port in port_list:
- port_spec = port[1]
- if type(port_spec) == str: # or unicode...
- if port_spec.startswith('('):
- port_spec = port_spec[1:]
- if port_spec.endswith(')'):
- port_spec = port_spec[:-1]
- new_spec_list = []
- for spec in port_spec.split(','):
- spec = spec.strip()
- parts = spec.split(':', 1)
-# print 'parts:', parts
- namespace = None
- if len(parts) > 1:
- mod_parts = parts[1].rsplit('|', 1)
- if len(mod_parts) > 1:
- namespace, module_name = mod_parts
- else:
- module_name = parts[1]
- if len(parts[0].split('.')) == 1:
- id_str = 'edu.utah.sci.vistrails.' + parts[0]
- else:
- id_str = parts[0]
- else:
- mod_parts = spec.rsplit('|', 1)
- if len(mod_parts) > 1:
- namespace, module_name = mod_parts
- else:
- module_name = spec
- id_str = identifier
- if namespace:
- new_spec_list.append(id_str + ':' + module_name + ':' + \
- namespace)
- else:
- new_spec_list.append(id_str + ':' + module_name)
- port_spec = '(' + ','.join(new_spec_list) + ')'
- new_port_list.append((port[0], port_spec) + port[2:])
-# print new_port_list
- return new_port_list
-
-class FieldData(Path):
- '''
- Field Data
-
- The FieldData module allows a user to add presence/absence points or count data recorded across a
- landscape for the phenomenon being modeled (e.g., plant sightings, evidence of animal presence, etc.).
- The input data for this module must be in the form of a .csv file that follows one of two formats:
-
- Format 1
- A .csv file with the following column headings, in order: "X," "Y," and "responseBinary".
- In this case, the "X" field should be populated with the horizontal (longitudinal) positional
- data for a sample point. The "Y" field should be populated with the vertical (latitudinal) data
- for a sample point. These values must be in the same coordinate system/units as the template
- layer used in the workflow. The column "responseBinary" should be populated with either a '0'
- (indicating absence at the point) or a '1' (indicating presence at the point).
-
- Format 2
- A .csv file with the following column headings, in order: "X," "Y," and "responseCount".
- In this case, the "X" field should be populated with the horizontal (longitudinal) positional
- data for a sample point. The "Y" field should be populated with the vertical (latitudinal) data
- for a sample point. These values must be in the same coordinate system/units as the template
- layer used in the workflow. The column "responseCount" should be populated with either a '-9999'
- (indicating that the point is a background point) or a numerical value (either '0' or a positive integer)
- indicating the number of incidences of the phenomenon recorded at that point.
- '''
-# _input_ports = [('csvFile', '(edu.utah.sci.vistrails.basic:File)')]
- _output_ports = [('value', '(gov.usgs.sahm:FieldData:DataInput)'),
- ('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
-
-
-
-class AggregationMethod(String):
- '''
- This module is a required class for other modules and scripts within the
- SAHM package. It is not intended for direct use or incorporation into
- the VisTrails workflow by the user.
- '''
- _input_ports = [('value', '(gov.usgs.sahm:AggregationMethod:Other)')]
- _output_ports = [('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
- _widget_class = build_enum_widget('AggregationMethod',
- ['Mean', 'Max', 'Min', 'Majority', 'None'])
-
- @staticmethod
- def get_widget_class():
- return AggregationMethod._widget_class
-
-class ResampleMethod(String):
- '''
- This module is a required class for other modules and scripts within the
- SAHM package. It is not intended for direct use or incorporation into
- the VisTrails workflow by the user.
- '''
- _input_ports = [('value', '(gov.usgs.sahm:ResampleMethod:Other)')]
- _output_ports = [('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
- _widget_class = build_enum_widget('ResampleMethod',
- ['NearestNeighbor', 'Bilinear', 'Cubic', 'CubicSpline', 'Lanczos'])
-
- @staticmethod
- def get_widget_class():
- return ResampleMethod._widget_class
-
-class Predictor(Constant):
- '''
- Predictor
-
- The Predictor module allows a user to select a single raster layer for consideration in the
- modeled analysis. Four parameters must be specified by the user:
-
- 1. Aggregation Method: The aggregation method to be used in the event that the raster layer
- must be up-scaled to match the template layer (e.g., generalizing a 10 m input layer to a
- 100 m output layer). Care should be taken to ensure that the aggregation method that
- best preserves the integrity of the data is used.
-
- 2. Resample Method: The resample method employed to interpolate new cell values when
- transforming the raster layer to the coordinate space or cell size of the template layer,
- if necessary.
-
- 3. Categorical (Boolean): Checking this box indicates that the data contained in the raster
- layer is categorical (e.g. landcover categories). Leaving this box unchecked indicates that
- the data contained in the raster is continuous (e.g., a DEM layer). This distinction is important
- in determining an appropriate resampling method.
-
- 4. File Path: The location of the raster predictor file, which a user can specify by navigating to the
- file's location on their file system. When a user is selecting an ESRI grid raster, the user should navigate
- to the 'hdr.adf' file contained within the grid folder.
-
- '''
- _input_ports = [('categorical', '(edu.utah.sci.vistrails.basic:Boolean)'),
- ('ResampleMethod', '(gov.usgs.sahm:ResampleMethod:Other)', {'defaults':str(['Bilinear'])}),
- ('AggregationMethod', '(gov.usgs.sahm:AggregationMethod:Other)', {'defaults':str(['Mean'])}),
- ('file', '(edu.utah.sci.vistrails.basic:Path)')]
- _output_ports = [('value', '(gov.usgs.sahm:Predictor:DataInput)'),
- ('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
-
- def compute(self):
- if (self.hasInputFromPort("ResampleMethod")):
- resampleMethod = self.getInputFromPort("ResampleMethod")
- if resampleMethod.lower() not in ['nearestneighbor', 'bilinear', 'cubic', 'cubicspline', 'lanczos']:
- raise ModuleError(self,
- "Resample Method not one of 'nearestneighbor', 'bilinear', 'cubic', 'cubicspline', or 'lanczos'")
- else:
- resampleMethod = 'Bilinear'
-
- if (self.hasInputFromPort("AggregationMethod")):
- aggregationMethod = self.getInputFromPort("AggregationMethod")
- if self.getInputFromPort("AggregationMethod").lower() not in ['mean', 'max', 'min', 'majority', 'none']:
- raise ModuleError(self, "No Aggregation Method specified")
- else:
- aggregationMethod = "Mean"
-
- if (self.hasInputFromPort("categorical")):
- if self.getInputFromPort("categorical") == True:
- categorical = '1'
- else:
- categorical = '0'
- else:
- categorical = '0'
-
- if (self.hasInputFromPort("file")):
- inFile = utils.getRasterName(self.getInputFromPort("file").name)
- else:
- raise ModuleError(self, "No input file specified")
- self.setResult('value', (inFile, categorical, resampleMethod, aggregationMethod))
-
-class PredictorList(Constant):
- '''
- This module is a required class for other modules and scripts within the
- SAHM package. It is not intended for direct use or incorporation into
- the VisTrails workflow by the user.
- '''
- _input_ports = expand_ports([('value', 'Other|PredictorList'),
- ('addPredictor', 'DataInput|Predictor')])
- _output_ports = expand_ports([('value', 'Other|PredictorList')])
-
- @staticmethod
- def translate_to_string(v):
- return str(v)
-
- @staticmethod
- def translate_to_python(v):
- v_list = eval(v)
- return v_list
-
- @staticmethod
- def validate(x):
- return type(x) == list
-
- def compute(self):
- p_list = self.forceGetInputListFromPort("addPredictor")
- v = self.forceGetInputFromPort("value", [])
-
- b = self.validate(v)
- if not b:
- raise ModuleError(self, "Internal Error: Constant failed validation")
- if len(v) > 0 and type(v[0]) == tuple:
- f_list = [utils.create_file_module(v_elt[1]) for v_elt in v]
- else:
- f_list = v
- p_list += f_list
- #self.setResult("value", p_list)
- self.setResult("value", v)
-
-class PredictorListFile(Module):
- '''
- Predictor List File
-
- The PredictorListFile module allows a user to load a .csv file containing a list
- of rasters for consideration in the modeled analysis. The .csv file should contain
- a header row and four columns containing the following information, in order, for
- each raster input.
-
- Column 1: The full file path to the input raster layer.
-
- Column 2: A binary value indicating whether the input layer is categorical or not.
- A value of "0" indicates that an input raster is non-categorical data (continuous),
- while a value of "1" indicates that an input raster is categorical data.
-
- Column 3: The resampling method employed to interpolate new cell values when
- transforming the raster layer to the coordinate space or cell size of the template
- layer, if necessary. The resampling type should be specified using one of the following
- values: "nearestneighbor," "bilinear," "cubic," or "lanczos."
-
- Column 4: The aggregation method to be used in the event that the raster layer
- must be up-scaled to match the template layer (e.g., generalizing a 10 m input layer to a
- 100 m output layer). Care should be taken to ensure that the aggregation method that
- best preserves the integrity of the data is used. The aggregation should be specified
- using one of the following values: "Min," "Mean," "Max," "Majority," or "None."
-
- In formatting the list of predictor files, the titles assigned to each of the columns
- are unimportant as the module retrieves the information based on the order of the
- values in the .csv file (the ordering of the information and the permissible values
- in the file however, are strictly enforced). The module also anticipates a header row
- and will ignore the first row in the .csv file.
-
- '''
- _input_ports = expand_ports([('csvFileList', '(edu.utah.sci.vistrails.basic:File)'),
- ('addPredictor', 'DataInput|Predictor')])
- _output_ports = expand_ports([('RastersWithPARCInfoCSV', '(gov.usgs.sahm:RastersWithPARCInfoCSV:Other)')])
-
- #copies the input predictor list csv to our working directory
- #and appends any additionally added predictors
-
- @staticmethod
- def translate_to_string(v):
- return str(v)
-
- @staticmethod
- def translate_to_python(v):
- v_list = eval(v)
- return v_list
-
- @staticmethod
- def validate(x):
- return type(x) == list
-
- def compute(self):
- if not (self.hasInputFromPort("csvFileList") or
- self.hasInputFromPort("addPredictor")):
- raise ModuleError(self, "No inputs or CSV file provided")
-
- output_fname = utils.mknextfile(prefix='PredictorList_', suffix='.csv')
- if (self.hasInputFromPort("csvFileList") and
- os.path.exists(self.getInputFromPort("csvFileList").name)):
- shutil.copy(self.getInputFromPort("csvFileList").name,
- output_fname)
- csv_writer = csv.writer(open(output_fname, 'ab'))
- else:
- #create an empty file to start with.
- csv_writer = csv.writer(open(output_fname, 'wb'))
- csv_writer.writerow(["file", "Resampling", "Aggregation"])
-
- if self.hasInputFromPort("addPredictor"):
- p_list = self.forceGetInputListFromPort("addPredictor")
- for p in p_list:
- if p.hasInputFromPort('resampleMethod'):
- resMethod = p.getInputFromPort('resampleMethod')
- else:
- resMethod = "NearestNeighbor"
- if p.hasInputFromPort('aggregationMethod'):
- aggMethod = p.getInputFromPort('aggregationMethod')
- else:
- aggMethod = "Mean"
- csv_writer.writerow([os.path.normpath(p.name), resMethod, aggMethod])
-
- del csv_writer
-
- output_file = utils.create_file_module(output_fname)
- self.setResult('RastersWithPARCInfoCSV', output_file)
-
-class TemplateLayer(Path):
- '''
- Template Layer
-
- The TemplateLayer is a raster data layer with a defined coordinate system, a known cell size,
- and an extent that defines the study area. This raster layer serves as the template for all
- the other inputs in the analysis. All additional raster layers used in the analysis will be
- resampled and reprojected as needed to match the template, snapped to the template, and
- clipped to have an extent that matches the template. Users should ensure that any additional
- layers considered in the analysis have coverage within the extent of the template layer.
-
- The TemplateLayer is a required input for the PARC module.
-
- '''
-# _input_ports = [('FilePath', '(edu.utah.sci.vistrails.basic:File)')]
- _output_ports = [('value', '(gov.usgs.sahm:TemplateLayer:DataInput)'),
- ('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
-# def compute(self):
-# output_file = create_file_module(self.forceGetInputFromPort('FilePath', []))
-# self.setResult('value', output_file)
-
-#class SingleInputPredictor(Predictor):
-# pass
-#
-#class SpatialDef(Module):
-# _output_ports = [('spatialDef', '(gov.usgs.sahm:SpatialDef:DataInput)')]
-
-class MergedDataSet(File):
- '''
- This module is a required class for other modules and scripts within the
- SAHM package. It is not intended for direct use or incorporation into
- the VisTrails workflow by the user.
- '''
- _input_ports = expand_ports([('mdsFile', '(edu.utah.sci.vistrails.basic:File)')])
- _output_ports = expand_ports([('value', '(gov.usgs.sahm:MergedDataSet:Other)')])
-
- pass
-
-class RastersWithPARCInfoCSV(File):
- '''
- This module is a required class for other modules and scripts within the
- SAHM package. It is not intended for direct use or incorporation into
- the VisTrails workflow by the user.
- '''
- _input_ports = expand_ports([('mdsFile', '(edu.utah.sci.vistrails.basic:File)')])
- _output_ports = expand_ports([('value', '(gov.usgs.sahm:MergedDataSet:Other)')])
-
- pass
-# def compute(self, is_input=None):
-# PersistentPath.compute(self, is_input, 'blob')
-
-class ApplyModel(Module):
- '''
- Apply Model
-
- The ApplyModel module allows the user to apply a model developed using a
- particular package within the workflow and generate output probability and binary
- maps. The process of creating an output probability map and binary map based on
- a particular model can be time-consuming, depending on the input data. By
- existing as a stand-alone process in the workflow, the ApplyModel module allows
- a user to investigate the performance metrics for a particular model (such as
- the ROC curve or the AUC) before dedicating the processing time needed to generate
- the output maps. In most cases, a user will "fine tune" a model by exploring the
- performance metrics of different model iterations before applying the model and
- generating the actual maps as a final step.
-
- The ApplyModel module also provides the user with the option of projecting the results
- of a model developed from one set of environmental predictors onto a new modeled space
- containing that same set of environmental predictors but representing data captured at
- a different temporal or spatial location. For example, a user could generate a model
- predicting habitat suitability using recorded presence points and certain environmental
- predictors such as elevation, landcover, and proximity to water in one geographic
- location. Based on the training from this information, the modeled results could be
- generated for (or "projected to") a new location based on the range of values seen in
- elevation, landcover, and proximity to water in the second geographic area. Similarly,
- modeling predicted results through time is also possible. A model trained using field
- data and a set of predictor layers representative of one time period could be projected
- onto the same geographical area using a new set of layers corresponding to the same
- predictors but representing data from a different time period (e.g., different climate
- data).
-
- The ApplyModel module accepts two inputs from the user:
-
- 1. Model Workspace: The model workspace field accepts as an input a modeling
- package element (complete with all required parameters) from upstream in the workflow.
- The inputs and specifications provided in the dialogue fields of the model will be applied
- and used to generate the output maps. A user should populate the model workspace field by
- connecting a model element to the appropriate input port of the ApplyModel module in the
- visual display of the model workflow.
-
- 2. Projection Target: The projection target is an optional parameter that allows a user to
- apply a model to a particular geographic area and or set of predictors (other than those
- used to train the model) and create output maps within the spatial extent of the projection
- target layers. This input field should be populated by connecting either the output of the
- ProjectionLayers module or a separate MDSBuilder element to the appropriate input port of
- the ApplyModel module.
-
- '''
-
- _input_ports = [('projectionTarget', '(gov.usgs.sahm:MergedDataSet:Other)'),
- ('modelWorkspace', '(edu.utah.sci.vistrails.basic:File)'),
- ('makeBinMap', '(edu.utah.sci.vistrails.basic:Boolean)'),
- ('makeProbabilityMap', '(edu.utah.sci.vistrails.basic:Boolean)'),]
- _output_ports = [('BinaryMap', '(edu.utah.sci.vistrails.basic:File)'),
- ('ProbabilityMap', '(edu.utah.sci.vistrails.basic:File)')]
-
-
-
- def compute(self):
-
- workspace = self.forceGetInputFromPort('modelWorkspace').name
- output_dname = utils.mknextdir(prefix='AppliedModel_')
- if self.hasInputFromPort('projectionTarget'):
- mdsFile = self.forceGetInputFromPort('projectionTarget').name
- args = "ws=" + '"' + workspace + '"' + " c=" + '"' + mdsFile + '"' + " o=" + '"' + output_dname + '"'
- else:
- args = "ws=" + '"' + workspace + '"' + " o=" + '"' + output_dname + '"'
-
- if self.hasInputFromPort('makeBinMap'):
- makeBinMap = self.forceGetInputFromPort('makeBinMap')
- args += ' mbt=' + str(makeBinMap).upper()
- else:
- args += ' mbt=TRUE'
-
- if self.hasInputFromPort('makeProbabilityMap'):
- makeProbabilityMap = self.forceGetInputFromPort('makeProbabilityMap')
- args += ' mpt=' + str(makeProbabilityMap).upper()
- else:
- args += ' mpt=TRUE'
-
-
- utils.runRScript('PredictModel.r', args, self)
-
- input_fname = os.path.join(output_dname, "prob_map.tif")
- output_fname = os.path.join(output_dname, 'prob_map.jpeg')
- if os.path.exists(input_fname):
- utils.tif_to_color_jpeg(input_fname, output_fname, color_breaks_csv)
- output_file1 = utils.create_file_module(output_fname)
- self.setResult('ProbabilityMap', output_file1)
- else:
- msg = "Expected output from ApplyModel was not found."
- msg += "\nThis likely indicates problems with the inputs to the R module."
- writetolog(msg, False, True)
- raise ModuleError(self, msg)
-
- if os.path.exists(os.path.join(output_dname, "bin_map.tif")):
- outFileName = os.path.join(output_dname, "bin_map.tif")
- output_file2 = utils.create_file_module(outFileName)
- self.setResult('BinaryMap', output_file2)
-
-class Model(Module):
- '''
- This module is a required class for other modules and scripts within the
- SAHM package. It is not intended for direct use or incorporation into
- the VisTrails workflow by the user.
- '''
- _input_ports = [('mdsFile', '(gov.usgs.sahm:MergedDataSet:Other)'),
- ('makeBinMap', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['True']), 'optional':False}),
- ('makeProbabilityMap', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['True']), 'optional':False}),
- ('makeMESMap', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['False']), 'optional':False}),
- ('ThresholdOptimizationMethod', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['2']), 'optional':False})
- ]
- _output_ports = [('modelWorkspace', '(edu.utah.sci.vistrails.basic:File)'),
- ('BinaryMap', '(edu.utah.sci.vistrails.basic:File)'),
- ('ProbabilityMap', '(edu.utah.sci.vistrails.basic:File)'),
- ('AUC_plot', '(edu.utah.sci.vistrails.basic:File)'),
- ('ResponseCurves', '(edu.utah.sci.vistrails.basic:File)'),
- ('Text_Output', '(edu.utah.sci.vistrails.basic:File)')]
-
- def compute(self):
- global color_breaks_csv
-
- ModelOutput = {"FIT_BRT_pluggable.r":"brt",
- "FIT_GLM_pluggable.r":"glm",
- "FIT_RF_pluggable.r":"rf",
- "FIT_MARS_pluggable.r":"mars"}
- ModelAbbrev = ModelOutput[self.name]
-
- output_dname = utils.mknextdir(prefix=ModelAbbrev + 'output_')
- argsDict = utils.map_ports(self, self.port_map)
- mdsFile = self.forceGetInputFromPort('mdsFile').name
-
- args = ''
- for k, v in argsDict.iteritems():
- if k == 'c':
- args += ' ' + '='.join([str(k),'"' + str(v) + '"'])
- else:
- args += ' ' + '='.join([str(k),str(v)])
- args += " o=" + '"' + output_dname + '"'
- args += " rc=" + utils.MDSresponseCol(mdsFile)
-# if self.hasInputFromPort('makeBinMap'):
-# makeBinMap = self.forceGetInputFromPort('makeBinMap')
-# args += ' mbt=' + str(makeBinMap).upper()
-# else:
-# makeBinMap = True
-# args += ' mbt=TRUE'
-#
-# if self.hasInputFromPort('makeProbabilityMap'):
-# makeProbabilityMap = self.forceGetInputFromPort('makeProbabilityMap')
-# args += ' mpt=' + str(makeProbabilityMap).upper()
-# else:
-# makeProbabilityMap = True
-# args += ' mpt=TRUE'
-#
-# if self.hasInputFromPort('seed'):
-# args += ' seed=' + str(self.forceGetInputFromPort('seed'))
-#
-# if self.hasInputFromPort('someParam'):
-# x = self.forceGetInputFromPort('someParam')
-# if x > 1:
-# msg = "Expected output from " + ModelAbbrev + " was not found."
-# msg += "\nThis likely indicates problems with the inputs to the R module."
-# writetolog(msg, False, True)
-# args += " abr=" + x
-
- utils.runRScript(self.name, args, self)
-# utils.runRScript('FIT_BRT_pluggableErrorMessage.r', args, self)
-
- input_fname = os.path.join(output_dname, ModelAbbrev + "_prob_map.tif")
- output_fname = os.path.join(output_dname, ModelAbbrev + "_prob_map.jpeg")
- if os.path.exists(input_fname):
-# utils.tif_to_color_jpeg(input_fname, output_fname, color_breaks_csv)
-# output_file4 = utils.create_file_module(output_fname)
- self.setResult('ProbabilityMap', input_fname)
- elif (argsDict.has_key('mpt') and argsDict['mpt'] == True) or \
- not argsDict.has_key('mpt'):
- msg = "Expected output from " + ModelAbbrev + " was not found."
- msg += "\nThis might indicate problems with the inputs to the R module."
- msg += "\nCheck the console output for additional R warnings "
- writetolog(msg, False, True)
- raise ModuleError(self, msg)
-
- if (argsDict.has_key('mbt') and argsDict['mbt'] == True) or \
- not argsDict.has_key('mbt'):
- outFileName = os.path.join(output_dname, ModelAbbrev + "_bin_map.tif")
- output_file1 = utils.create_file_module(outFileName)
- self.setResult('BinaryMap', output_file1)
-
- outFileName = os.path.join(output_dname, ModelAbbrev + "_output.txt")
- output_file2 = utils.create_file_module(outFileName)
- self.setResult('Text_Output', output_file2)
-
- outFileName = os.path.join(output_dname, ModelAbbrev + "_auc_plot.jpg")
-# print "out auc: ", outFileName
- output_file3 = utils.create_file_module(outFileName)
- self.setResult('AUC_plot', output_file3)
-
- outFileName = os.path.join(output_dname, ModelAbbrev + "_response_curves.pdf")
- output_file5 = utils.create_file_module(outFileName)
- self.setResult('ResponseCurves', output_file5)
-
- outFileName = os.path.join(output_dname, "modelWorkspace")
-# print "out auc: ", outFileName
- output_file6 = utils.create_file_module(outFileName)
- self.setResult('modelWorkspace', output_file6)
-
- writetolog("Finished " + ModelAbbrev + " builder\n", True, True)
-
-class GLM(Model):
- _input_ports = list(Model._input_ports)
- _input_ports.extend([('ModelFamily', '(edu.utah.sci.vistrails.basic:String)', {'defaults':str(['binomial']), 'optional':True}),
- ('SimplificationMethod', '(edu.utah.sci.vistrails.basic:String)', {'defaults':str(['AIC']), 'optional':True}),
- ])
- def __init__(self):
- global models_path
- Model.__init__(self)
- self.name = 'FIT_GLM_pluggable.r'
- self.port_map = {'mdsFile':('c', None, True),#These ports are for all Models
- 'makeProbabilityMap':('mpt', utils.R_boolean, False),
- 'makeBinMap':('mbt', utils.R_boolean, False),
- 'makeMESMap':('mes', utils.R_boolean, False),
- 'ThresholdOptimizationMethod':('om', None, False),
- 'ModelFamily':('mf', None, False), #This is a GLM specific port
- 'SimplificationMethod':('sm', None, False) #This is a GLM specific port
- }
-
-class RandomForest(Model):
- _input_ports = list(Model._input_ports)
- _input_ports.extend([('MTRY', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['1']), 'optional':True}),
- ])
- def __init__(self):
- global models_path
- Model.__init__(self)
- self.name = 'FIT_RF_pluggable.r'
- self.port_map = {'mdsFile':('c', None, True),#These ports are for all Models
- 'makeProbabilityMap':('mpt', utils.R_boolean, False),
- 'makeBinMap':('mbt', utils.R_boolean, False),
- 'makeMESMap':('mes', utils.R_boolean, False),
- 'ThresholdOptimizationMethod':('om', None, False),
- 'MTRY': ('mtry', None, False) #This is a Random Forest specific port
- }
-
-class MARS(Model):
- _input_ports = list(Model._input_ports)
- _input_ports.extend([('MarsDegree', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['1']), 'optional':True}),
- ('MarsPenalty', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['2']), 'optional':True}),
- ])
- def __init__(self):
- global models_path
- Model.__init__(self)
- self.name = 'FIT_MARS_pluggable.r'
- self.port_map = {'mdsFile':('c', None, True),#These ports are for all Models
- 'makeProbabilityMap':('mpt', utils.R_boolean, False),
- 'makeBinMap':('mbt', utils.R_boolean, False),
- 'makeMESMap':('mes', utils.R_boolean, False),
- 'ThresholdOptimizationMethod':('om', None, False),
- 'MarsDegree':('deg', None, False), #This is a MARS specific port
- 'MarsPenalty':('pen', None, False), #This is a MARS specific port
- }
-
-class BoostedRegressionTree(Model):
- _input_ports = list(Model._input_ports)
- _input_ports.extend([('Seed', '(edu.utah.sci.vistrails.basic:Integer)', True),
- ('TreeComplexity', '(edu.utah.sci.vistrails.basic:Integer)', True),
- ('NumberOfTrees', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['10000']), 'optional':True}),
- ('BagFraction', '(edu.utah.sci.vistrails.basic:Float)', {'defaults':str(['0.5']), 'optional':True}),
- ('NumberOfFolds', '(edu.utah.sci.vistrails.basic:Integer)', {'defaults':str(['3']), 'optional':True}),
- ('Alpha', '(edu.utah.sci.vistrails.basic:Float)', {'defaults':str(['1']), 'optional':True}),
- ('PrevalenceStratify', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['True']), 'optional':True}),
- ('ToleranceMethod', '(edu.utah.sci.vistrails.basic:String)', {'defaults':str(['auto']), 'optional':True}),
- ('Tolerance', '(edu.utah.sci.vistrails.basic:Float)', {'defaults':str(['0.001']), 'optional':True})
- ])
- def __init__(self):
- global models_path
- Model.__init__(self)
- self.name = 'FIT_BRT_pluggable.r'
- self.port_map = {'mdsFile':('c', None, True),#These ports are for all Models
- 'makeProbabilityMap':('mpt', utils.R_boolean, False),
- 'makeBinMap':('mbt', utils.R_boolean, False),
- 'makeMESMap':('mes', utils.R_boolean, False),
- 'ThresholdOptimizationMethod':('om', None, False),
- 'Seed':('seed', None, False), #This is a BRT specific port
- 'TreeComplexity':('tc', None, False), #This is a BRT specific port
- 'NumberOfTrees':('nf', None, False), #This is a BRT specific port
- 'BagFraction':('bf', None, False), #This is a BRT specific port
- 'NumberOfFolds':('nf', None, False), #This is a BRT specific port
- 'Alpha':('alp', None, False), #This is a BRT specific port
- 'PrevalenceStratify':('ps', None, False), #This is a BRT specific port
- 'ToleranceMethod':('tolm', None, False), #This is a BRT specific port
- 'Tolerance':('tol', None, False) #This is a BRT specific port
- }
-
-class MDSBuilder(Module):
- '''
- MDS Builder
-
- The Merged Data Set (MDS) Builder module is a utility that extracts the values of each predictor
- layer to the point locations included in the field data set. The module produces a .csv file that
- contains the x and y locations of the sample points and a column indicating whether each point
- represents a presence recording, an absence recording, a presence count, or a background point.
- Following these first three columns, each environmental predictor layer is appended as a column
- with row entries representing the value present in the raster layer at each field sample point.
- There are a total of three header rows in the output .csv of the MDSBuilder. The first row contains
- the columns "x," "y," "ResponseBinary" or "ResponseCount," and the names of each of the raster
- predictor files that were passed to the MDS Builder. The second row contains a binary value
- indicating whether the column should be included when the model is finally applied; these values
- are later modified during the Covariate Correlation and Selection process that takes place downstream
- in the workflow. The final header row contains the full path on the file system to each of the raster
- predictor files.
-
- The MDSBuilder accepts four inputs from the user:
-
- 1. Rasters with PARC Info .csv File: The raster layers listed in this file will have their values
- extracted to the points in the field data .csv file. This parameter should be supplied by connecting
- the output of a PARC module within the workflow to the MDSBuilder module. (In order to properly
- extract the values of each predictor layer to the field data points, all the layers must have matching
- coordinate systems and cell sizes; outputs from the PARC module will have had the prerequisite processing).
-
- 2. Background Point Count: This is an optional value that applies only to workflows that employ the
- Maxent modeling package. The dialogue box provides the option of specifying a number of background points
- to be randomly scattered throughout the study area (the extent of the template layer) to capture a more
- complete sample of the range of values present for each predictor layer. These points will be added to
- the field data .csv file with a value of "-999" denoting them as background points.
-
- 3. Background Probability Surface: This is an optional parameter that applies only to workflows that
- employ the Maxent modeling package. In some analyses, it may be appropriate to spatially limit background
- points to a particular subset of the study area (e.g., islands within a study area polygon, particular
- regions within a study area polygon, or a region determined by the known bias present in the field data).
- Specifying a background probability surface raster allows a user to control where random points will be
- scattered within the extent of the study area. The raster layer specified by a user should have the same
- projection and extent as the template layer and contain values ranging from 0 to 100. These values represent
- the probability that a randomly generated point will be retained should it fall within a particular cell.
- That is, randomly generated points will not be generated in any part of the probability grid with a value
- of "0" while all points falling in an area with a value of "100" will be retained. A point falling in an
- area with a value of "50" will be kept as a background point 50% of the time.
-
- 4. Field Data: The field data input corresponds to a .csv file containing presence/absence points or count
- data recorded across a landscape for the phenomenon being modeled (e.g., plant sightings, evidence of
- animal presence, etc.). This input file must be in a particular format, and in most cases, a user should
- populate this field by connecting a FieldData element to the MDSBuilder in the visual display within VisTrails.
- Please see the documention for the FieldData module for more details.
-
- '''
-
-# _input_ports = expand_ports([('RastersWithPARCInfoCSV', '(gov.usgs.sahm:RastersWithPARCInfoCSV:Other)'),
-# ('fieldData', '(gov.usgs.sahm:FieldData:DataInput)'),
-# ('backgroundPointCount', '(edu.utah.sci.vistrails.basic:Integer)'),
-# ('backgroundProbSurf', '(edu.utah.sci.vistrails.basic:File)')]
-# )
-# _input_ports = expand_ports([('RastersWithPARCInfoCSV', '(edu.utah.sci.vistrails.persistence:PersistentFile)'),
-# ('fieldData', '(gov.usgs.sahm:FieldData:DataInput)'),
-# ('backgroundPointCount', '(edu.utah.sci.vistrails.basic:Integer)'),
-# ('backgroundProbSurf', '(edu.utah.sci.vistrails.basic:File)')]
-# )
- _input_ports = expand_ports([('RastersWithPARCInfoCSV', '(edu.utah.sci.vistrails.basic:File)'),
- ('fieldData', '(gov.usgs.sahm:FieldData:DataInput)'),
- ('backgroundPointCount', '(edu.utah.sci.vistrails.basic:Integer)'),
- ('backgroundProbSurf', '(edu.utah.sci.vistrails.basic:File)')]
- )
-
- _output_ports = expand_ports([('mdsFile', '(gov.usgs.sahm:MergedDataSet:Other)')])
-
- def compute(self):
- port_map = {'fieldData': ('fieldData', None, True),
- 'backgroundPointCount': ('pointcount', None, False),
- 'backgroundProbSurf': ('probsurf', None, False),}
-
- MDSParams = utils.map_ports(self, port_map)
- MDSParams['outputMDS'] = utils.mknextfile(prefix='MergedDataset_', suffix='.csv')
-
- #allow multiple CSV of inputs to be provided.
- #if more than one then combine into a single CSV before sending to MDSBuilder
- inputs_csvs = self.forceGetInputListFromPort('RastersWithPARCInfoCSV')
- if len(inputs_csvs) == 0:
- raise ModuleError(self, "Must supply at least one 'RastersWithPARCInfoCSV'/nThis is the output from the PARC module")
- if len(inputs_csvs) > 1:
- inputs_csv = utils.mknextfile(prefix='CombinedPARCFiles_', suffix='.csv')
- inputs_names = [f.name for f in inputs_csvs]
- utils.merge_inputs_csvs(inputs_names, inputs_csv)
- else:
- inputs_csv = inputs_csvs[0].name
- MDSParams['inputsCSV'] = inputs_csv
-
- #inputsCSV = utils.path_port(self, 'RastersWithPARCInfoCSV')
-
- ourMDSBuilder = MDSB.MDSBuilder()
- utils.PySAHM_instance_params(ourMDSBuilder, MDSParams)
-
- writetolog(" inputsCSV=" + ourMDSBuilder.inputsCSV, False, False)
- writetolog(" fieldData=" + ourMDSBuilder.fieldData, False, False)
- writetolog(" outputMDS=" + ourMDSBuilder.outputMDS, False, False)
-
- try:
- ourMDSBuilder.run()
- except TrappedError as e:
- raise ModuleError(self, e.message)
- except:
- utils.informative_untrapped_error(self, "MDSBuilder")
-
- output_file = utils.create_file_module(ourMDSBuilder.outputMDS)
-
- self.setResult('mdsFile', output_file)
-
-class FieldDataAggregateAndWeight(Module):
- '''
- Documentation to be updated when module finalized.
- '''
- _input_ports = expand_ports([('templateLayer', '(gov.usgs.sahm:TemplateLayer:DataInput)'),
- ('fieldData', '(gov.usgs.sahm:FieldData:DataInput)'),
- ('aggregateRows', 'basic:Boolean'),
- ('aggregateRowsByYear', 'basic:Boolean')])
- _output_ports = expand_ports([('fieldData', '(gov.usgs.sahm:FieldData:DataInput)')])
-
- def compute(self):
- writetolog("\nRunning FieldDataQuery", True)
- port_map = {'templateLayer': ('template', None, True),
- 'fieldData': ('csv', None, True),
- 'aggregateRowsByYear': ('aggRows', None, False),
- 'addKDE': ('addKDE', None, False),}
-
- KDEParams = utils.map_ports(self, port_map)
- output_fname = utils.mknextfile(prefix='FDQ_', suffix='.csv')
- writetolog(" output_fname=" + output_fname, True, False)
- KDEParams['output'] = output_fname
-
- output_fname = utils.mknextfile(prefix='FDQ_', suffix='.csv')
- writetolog(" output_fname=" + output_fname, True, False)
-
- ourFDQ = FDQ.FieldDataQuery()
- utils.PySAHM_instance_params(ourFDQ, KDEParams)
-
- ourFDQ.processCSV()
-
- output_file = utils.create_file_module(output_fname)
- writetolog("Finished running FieldDataQuery", True)
- self.setResult('fieldData', output_file)
-
-class PARC(Module):
- '''
- PARC
-
- The Projection, Aggregation, Resampling, and Clipping (PARC) module is a powerful
- utility that automates the preparation steps required for using raster layers in
- most geospatial modeling packages. In order to successfully consider multiple
- environmental predictors in raster format, each layer must have coincident cells
- (pixels) of the same size, have the same coordinate system (and projection, if
- applicable), and the same geographic extent. The PARC module ensures that all of
- these conditions are met for the input layers by transforming and or reprojecting
- each raster to match the coordinate system of the template layer. This process
- usually involves aggregation (necessary when an input raster layer must be up-scaled
- to match the template layer-- e.g., generalizing a 10 m input layer to a 100 m output
- layer), and or resampling (necessary for interpolating new cell values when transforming
- the raster layer to the coordinate space or cell size of the template layer). Lastly,
- each raster predictor layer is clipped to match the extent of the template layer.
-
- The settings used during these processing steps follow a particular set of decision rules
- designed to preserve the integrity of data as much as possible. However, it is important
- for a user to understand how these processing steps may modify the data inputs. For
- additional information about the PARC module, please see the extended help and
- documentation for the SAHM package.
-
- The PARC module accepts four kinds of inputs:
-
- 1. Predictor List: A user should not have to populate this field. This field is populated
- when a selection is made from the pre-loaded .csv file of raster predictor layer inputs
- (specified during the SAHM install) and connected to the PARC module in the visual display.
-
- 2. .csv File List: The .csv file list corresponds to the Predictor List File element and
- allows a user to load a .csv file containing a list of rasters for consideration in the
- modeled analysis. For additional information, please see the documentation for the Predictor
- List File element.
-
- 3. Predictor: The predictor input allows a user to select a single raster predictor layer
- to be considered in the analysis. It is recommended that a user add this input as a separate
- element in the visual display (and then link it to the PARC module) so that the aggregation
- and resampling settings can be established. The PARC module can accept multiple predictor
- elements. For additional information, please see the documentation for the Predictor element.
-
- 4. Template Layer: The template layer is a raster data layer with a defined coordinate system,
- a known cell size, and an extent that defines the study area. This raster layer serves as the
- template for all the other inputs in the analysis. All additional raster layers used in the
- analysis will be resampled and reprojected as needed to match the template, snapped to the
- template, and clipped to have an extent that matches the template. Users should ensure that
- any additional layers considered in the analysis have coverage within the extent of the
- template layer. The template layer is a required input for the PARC module.
-
- '''
-
- #configuration = []
- _input_ports = [('predictor', "(gov.usgs.sahm:Predictor:DataInput)"),
- ('PredictorList', '(gov.usgs.sahm:PredictorList:Other)'),
- ('RastersWithPARCInfoCSV', '(gov.usgs.sahm:RastersWithPARCInfoCSV:Other)'),
- ('templateLayer', '(gov.usgs.sahm:TemplateLayer:DataInput)'),
- ('multipleCores', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['True']), 'optional':True})]
-
-# _output_ports = [('RastersWithPARCInfoCSV', '(gov.usgs.sahm:RastersWithPARCInfoCSV:Other)')]
-# _output_ports = [('RastersWithPARCInfoCSV', '(edu.utah.sci.vistrails.persistence:PersistentFile)')]
- _output_ports = [('RastersWithPARCInfoCSV', '(edu.utah.sci.vistrails.basic:File)')]
-
- def compute(self):
- #writetolog("\nRunning PARC", True)
-
- ourPARC = parc.PARC()
- output_dname = utils.mknextdir(prefix='PARC_')
-
- if configuration.verbose:
- ourPARC.verbose = True
- ourPARC.logger = utils.getLogger()
-
- ourPARC.out_dir = output_dname
-
- if self.hasInputFromPort("multipleCores"):
- if self.getInputFromPort("multipleCores"):
- ourPARC.multicores = "True"
-
- workingCSV = utils.mknextfile(prefix='tmpFilesToPARC_', suffix='.csv')
- outputCSV = utils.mknextfile(prefix='PARCOutput_', suffix='.csv')
-
- #append additional inputs to the existing CSV if one was supplied
- #otherwise start a new CSV
- if self.hasInputFromPort("RastersWithPARCInfoCSV"):
- inputCSV = self.forceGetInputFromPort("RastersWithPARCInfoCSV").name
- shutil.copy(inputCSV, workingCSV)
- f = open(workingCSV, "ab")
- csvWriter = csv.writer(f)
- else:
- f = open(workingCSV, "wb")
- csvWriter = csv.writer(f)
- csvWriter.writerow(["FilePath", "Categorical", "Resampling", "Aggregation"])
-
- if self.hasInputFromPort("PredictorList"):
- predictor_lists = self.forceGetInputListFromPort('PredictorList')
- for predictor_list in predictor_lists:
- for predictor in predictor_list:
- csvWriter.writerow(list(predictor))
-
- if self.hasInputFromPort("predictor"):
- predictor_list = self.forceGetInputListFromPort('predictor')
- for predictor in predictor_list:
- csvWriter.writerow(list(predictor))
- f.close()
- del csvWriter
- ourPARC.inputs_CSV = workingCSV
- ourPARC.template = self.forceGetInputFromPort('templateLayer').name
- writetolog(' template layer = ' + self.forceGetInputFromPort('templateLayer').name)
- writetolog(" output_dname=" + output_dname, False, False)
- writetolog(" workingCSV=" + workingCSV, False, False)
- try:
- ourPARC.parcFiles()
- except TrappedError as e:
- writetolog(e.message)
- raise ModuleError(self, e.message)
- except:
- utils.informative_untrapped_error(self, "PARC")
-
- #delete our temp working file
- os.remove(workingCSV)
-
- predictorsDir = utils.create_dir_module(output_dname)
- outputCSV = os.path.join(output_dname, "PARC_Files.csv")
- output_file = utils.create_file_module(outputCSV)
-
-
- writetolog("Finished running PARC", True)
- self.setResult('RastersWithPARCInfoCSV', output_file)
-
-
-class RasterFormatConverter(Module):
- '''
- Raster Format Converter
-
- The RasterFormatConverter module allows a user to easily convert .tif raster layers
- into a different raster format for use and display in other software packages. The
- module accepts as an input either a list of rasters in a Merged Dataset File (MDS)
- or the location of a directory containing multiple raster files. All outputs will be
- sent to a folder named "ConvertedRasters" (followed by an underscore and a number
- corresponding to the run sequence of the module) within the user's current VisTrail
- session folder.
-
- Three parameters can be specified by the user:
-
- 1. Format: The format corresponds to the desired raster output format. The following
- output file formats are supported: Arc/Info ASCII Grid, ESRI BIL, ERDAS Imagine, and JPEG.
-
- To specify the desired output, users should enter the values shown below.
- For an ASCII (.asc) output, enter: "asc"
- For an ESRI BIL output, enter: "bil"
- For an Erdas Imagine (.img) output, enter: "img"
- For a JPEG (.jpg) output, enter: "jpg"
-
- If no value is entered by the user, the module will default to an ASCII (.asc) output
- format.
-
- 2. Input Directory: The input directory allows a user to point to an entire folder as
- an input to the RasterFormatConverter. The contents of the specified folder will be
- checked for raster files and all the raster files contained within the directory will
- be converted to the format specified in the "Format" dialogue box. The module will
- identify and convert files of the following raster types: .bil, .img, .tif, .jpg, and .asc.
-
- 3. Input Merged Dataset (MDS): The input merged dataset allows a user to specify a .csv
- file created in the VisTrails workflow (containing a list of .tif raster files) as an
- input to the raster converter. All of the files listed in the MDS will be converted to
- the raster format specified in the "Format" dialogue box.
-
- '''
-
- #configuration = []
- _input_ports = [("inputMDS", "(gov.usgs.sahm:MergedDataSet:Other)"),
- ('inputDir', '(edu.utah.sci.vistrails.basic:Directory)'),
- ('format', '(edu.utah.sci.vistrails.basic:String)'),
- ('multipleCores', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':str(['True']), 'optional':True})]
-
- _output_ports = [('outputDir', '(edu.utah.sci.vistrails.basic:Directory)')]
-
- def compute(self):
- writetolog("\nRunning TiffConverter", True)
- ourRFC = RFC.FormatConverter()
- if self.hasInputFromPort('inputMDS'):
- ourRFC.MDSFile = self.forceGetInputFromPort('inputMDS').name
- elif self.hasInputFromPort('inputDir'):
- ourRFC.inputDir = self.forceGetInputFromPort('inputDir').name
-
- if self.hasInputFromPort('format'):
- format = self.forceGetInputFromPort('format')
- if format == '':
- format = 'asc'
- ourRFC.format = format
-
- if self.hasInputFromPort("multipleCores"):
- if self.getInputFromPort("multipleCores"):
- ourRFC.multicores = "True"
-
- ourRFC.outputDir = utils.mknextdir(prefix='ConvertedRasters_')
- if configuration.verbose:
- ourRFC.verbose = True
- ourRFC.logger = utils.getLogger()
- writetolog(" output directory = " + ourRFC.outputDir, False, False)
-
- try:
- ourRFC.run()
- except TrappedError as e:
- raise ModuleError(self, e.message)
- except:
- utils.informative_untrapped_error(self, "RasterFormatConverter")
-
-
- outputDir = utils.create_dir_module(ourRFC.outputDir)
- self.setResult('outputDir', outputDir)
- writetolog("\nFinished running TiffConverter", True)
-
-class TestTrainingSplit(Module):
- '''
- Test Training Split
-
- The TestTrainingSplit module provides the opportunity to establish specific settings
- for how field data will be used in the modeling process. Three parameters can be set
- by the user:
-
- 1. Ratio of Presence/Absence Points:
- This field is populated with a number corresponding to the desired proportion of
- presence and absence points to be used in the analysis. If populated, this entry should
- be a number greater than zero. (A value of '1' will result in an equal number of both
- presence and absence points being used, a value of '2' indicates that twice as many
- presence points will be used, a value of 0.5 indicates that twice as many absence points
- will be used, etc.). All field data points with a value equal to or greater than 1 are
- interpreted as presence points. Although the original field data is unmodified, this
- option will reduce the sample size as the merged dataset containing sample points will
- have points deleted from it to achieve the specified ratio. A warning will be generated
- if more than 50% of either the presence or absence points will be deleted based on the
- ratio specified by the user. Background points are ignored by this module (they are read
- in and written out, but not assigned to either the test or training split).
-
- When left empty, this field will default to 'null' and the model will use the existing
- presence/absence ratio present in the field data.
-
- 2. Input Merged Data Set (MDS):
- This is the input data set consisting of locational data for each sample point, the
- values of each predictor variable at those points, and if established, a field denoting
- the weight that will be assigned to each point in modeling. This input is usually provided
- by the upstream steps that precede the Test Training Split module. Any value entered here
- (e.g., specifying another existing MDS on the file system) will override the input
- specified by a model connection in the visual display.
-
- 3. Training Proportion:
- This is the proportion of the sample points that will be used to train the model, relative
- to the total number of points. Entered values should be greater than 0 but less than 1.
- For example, a value of '0.9' will result in 90% of the sample points being used to train
- the model, with 10% of the sample being held out to test the model's performance. Choosing
- an appropriate training proportion can depend on various factors, such as the total number
- of sample points available.
-
- '''
-
- _input_ports = [("inputMDS", "(gov.usgs.sahm:MergedDataSet:Other)"),
- ('trainingProportion', '(edu.utah.sci.vistrails.basic:Float)',
- {'defaults':str(['0.7'])}),
- ('RatioPresAbs', '(edu.utah.sci.vistrails.basic:Float)')]
- _output_ports = [("outputMDS", "(gov.usgs.sahm:MergedDataSet:Other)")]
-
- def compute(self):
- if self.hasInputFromPort('trainingProportion'):
- print 'real input'
- writetolog("\nGenerating Test Training split ", True)
- inputMDS = utils.dir_path_value(self.forceGetInputFromPort('inputMDS', []))
- outputMDS = utils.mknextfile(prefix='TestTrainingSplit_', suffix='.csv')
-
- global models_path
-
- args = "i=" + '"' + inputMDS + '"' + " o=" + '"' + outputMDS + '"'
- args += " rc=" + utils.MDSresponseCol(inputMDS)
- if (self.hasInputFromPort("trainingProportion")):
- try:
- trainingProportion = float(self.getInputFromPort("trainingProportion"))
- if trainingProportion <= 0 or trainingProportion > 1:
- raise ModuleError(self, "Train Proportion (trainProp) must be a number between 0 and 1 excluding 0")
- args += " p=" + str(trainingProportion)
- except:
- raise ModuleError(self, "Train Proportion (trainProp) must be a number between 0 and 1 excluding 0")
- if (self.hasInputFromPort("RatioPresAbs")):
- try:
- RatioPresAbs = float(self.getInputFromPort("RatioPresAbs"))
- if RatioPresAbs <= 0:
- raise ModuleError(self, "The ratio of presence to absence (RatioPresAbs) must be a number greater than 0")
- args += " m=" + str(trainingProportion)
- except:
- raise ModuleError(self, "The ratio of presence to absence (RatioPresAbs) must be a number greater than 0")
-
- utils.runRScript("TestTrainSplit.r", args, self)
-
- output = os.path.join(outputMDS)
- if os.path.exists(output):
- output_file = utils.create_file_module(output)
- writetolog("Finished Test Training split ", True)
- else:
- msg = "Problem encountered generating Test Training split. Expected output file not found."
- writetolog(msg, False)
- raise ModuleError(self, msg)
- self.setResult("outputMDS", output_file)
-
-class CovariateCorrelationAndSelection(Module):
- '''
- Covariate Correlation And Selection
-
- The CovariateCorrelationAndSelection view provides a breakpoint in the modeling workflow
- for the user to assess how well each variable explains the distribution of the sampled
- data points and to remove any variables that may exhibit high correlation with others.
-
- The display shows the 10 most correlated variables of those selected. These variables
- are displayed on the diagonal and their respective graphical display and correlation with
- other variables can be found by locating the row/column intersection between each (above
- and below the diagonal). The column heading over each variable displays the number of
- other variables with which the environmental predictor is correlated. The user defined
- "Threshold" option allows a user to specify the degree of correlation required between
- two variables for them to be counted in this tally.
-
- A user is provided with the opportunity to select a new set of the environmental predictor
- variables and "Update" the Covariate Correlation screen to investigate the relationships
- among the new variables selected. The options are provided to include or exclude the
- presence/count points, the absence points (when applicable), and the background points in
- this correlation test. Variables with a high degree of correlation with other variables
- should generally be unchecked in their respective radio buttons, and will be excluded from
- subsequent analysis steps in the model workflow.
-
- Multiple iterations can be run at this screen, allowing the user to investigate the
- relationships among the environmental predictor variables and choose the most appropriate
- set to be used in the subsequent modeling. When the desired set of variables has been chosen,
- the "OK" button is selected and processing will resume in the VisTrails workflow.
-
- '''
- kwargs = {}
- kwargs['defaults'] = str(['initial'])
- _input_ports = [("inputMDS", "(gov.usgs.sahm:MergedDataSet:Other)"),
- ('selectionName', '(edu.utah.sci.vistrails.basic:String)', kwargs),
- ('ShowGUI', '(edu.utah.sci.vistrails.basic:Boolean)')]
- _output_ports = [("outputMDS", "(gov.usgs.sahm:MergedDataSet:Other)")]
-
- def compute(self):
- writetolog("\nOpening Select Predictors Layers widget", True)
- inputMDS = utils.dir_path_value(self.forceGetInputFromPort('inputMDS'))
- selectionName = self.forceGetInputFromPort('selectionName', 'initial')
-# outputMDS = utils.mknextfile(prefix='SelectPredictorsLayers_' + selectionName + "_", suffix='.csv')
-# displayJPEG = utils.mknextfile(prefix='PredictorCorrelation_' + selectionName + "_", suffix='.jpg')
- global session_dir
- outputMDS = os.path.join(session_dir, "CovariateCorrelationOutputMDS_" + selectionName + ".csv")
- displayJPEG = os.path.join(session_dir, "CovariateCorrelationDisplay.jpg")
- writetolog(" inputMDS = " + inputMDS, False, False)
- writetolog(" displayJPEG = " + displayJPEG, False, False)
- writetolog(" outputMDS = " + outputMDS, False, False)
-
- if os.path.exists(outputMDS):
- utils.applyMDS_selection(outputMDS, inputMDS)
- os.remove(outputMDS)
-
- self.callDisplayMDS(inputMDS, outputMDS, displayJPEG)
-
- output_file = utils.create_file_module(outputMDS)
- writetolog("Finished Select Predictors Layers widget", True)
- self.setResult("outputMDS", output_file)
-
- def callDisplayMDS(self, inputMDS, outputMDS, displayJPEG):
- dialog = SelectListDialog(inputMDS, outputMDS, displayJPEG, configuration.r_path)
- #dialog.setWindowFlags(QtCore.Qt.WindowMaximizeButtonHint)
-# print " ... finished with dialog "
- retVal = dialog.exec_()
- #outputPredictorList = dialog.outputList
- if retVal == 1:
- raise ModuleError(self, "Cancel or Close selected (not OK) workflow halted.")
-
-
-class ProjectionLayers(Module):
- '''
- Projection Layers
-
- Note: as of June 2011, this module offers some functionality that is only available
- to users running the SAHM package within the USGS Fort Collins Science Center (FORT).
-
- The ProjectionLayers module provides the option to prepare a separate set of predictor
- layers so that the results of a model developed from one set of environmental predictors
- can be projected onto a new modeled space. This second set of environmental predictors
- (corresponding to the "projection target") most often contains the same environmental
- predictors but represents data captured at a different temporal or spatial location. For
- example, a user could generate a model predicting habitat suitability using recorded
- presence points and certain environmental predictors such as elevation, landcover, and
- proximity to water in one geographic location. Based on the training from this information,
- the modeled results could be generated for (or "projected to") a new location based on the
- range of values seen in elevation, landcover, and proximity to water in the second geographic
- area. Similarly, modeling predicted results through time is also possible. A model trained
- using field data and a set of predictor layers representative of one time period could be
- projected onto the same geographical area using a new set of predictor layers corresponding
- to the same predictors but representing data from a different time period (e.g., different
- climate data).
-
- The output of this module is subsequently used as the projection target in the ApplyModel module.
-
- (As part of the process of preparing the layers for modeling, the ProjectionLayers module runs
- the PARC module internally on the inputs. Outputs from the ProjectionLayers module will possess
- matching coordinate systems, cell sizes, and extents and do not need to be run through PARC
- before being used downstream in the workflow.)
-
- Six parameters can be set by the user:
-
- 1. Directory Crosswalk CSV: This is a .csv file containing two columns designating
- the layers that should be swapped out in the projected model. The first column
- contains a list of the full paths to the predictor layers used to develop the original
- model that will be replaced in the projection process. The second column contains the
- full paths to the new predictor layers that will substitute the respective layers used
- in the original model. Each original layer in the first column should be paired with
- its replacement in the second column (e.g., Column 1 = C:\ModelLayers\Precipitation1980.tif,
- Column 2 = C:\ModelLayers\Precipitation2000.tif). In the case of any file used to develop
- the first model that is not expressly listed in the Directory Crosswalk CSV with a
- replacement, the original file will be used in the new model projection. The module
- anticipates a header row in this .csv file (thus, the first row of data will be ignored).
-
- 2. File List CSV: This is a .csv file containing the list of predictor files used to
- develop the first model. Effectively, this file will be updated based on the information
- provided in the directory crosswalk .csv and used as the input to the training process
- for the projected model. The output of the PARC module from the first model iteration
- should be used as the input to this parameter.
-
- 3. Model (available only to users at the FORT): This parameter allows VisTrail users
- running the SAHM package on site at the USGS Science Center in Fort Collins (FORT) to
- specify one of three models to use for the projected model run ("CCCMA," "CSIRO,"
- or "hadcm3").
-
- 4. Scenario (available only to users at the FORT): This parameter allows VisTrail
- users running the SAHM package on site at the USGS Science Center in Fort Collins
- FORT) to specify one of two scenarios for the projected model run ("A2a" or "B2b").
-
- 5. Template: This parameter allows a user to specify the new template layer to be used
- in the projected model run. The template layer is a raster data layer with a defined
- coordinate system, a known cell size, and an extent that defines the (new) study area.
- This raster layer serves as the template for all the other inputs in the analysis. All
- additional raster layers used in the analysis will be resampled and reprojected as
- needed to match the template, snapped to the template, and clipped to have an extent
- that matches the template. Users should ensure that all the layers used for the projected
- analysis have coverage within the extent of the template layer.
-
- 6. Year (available only to users at the FORT): This parameter allows VisTrail users
- running the SAHM package on site at the USGS Science Center in Fort Collins (FORT)
- to specify one of three years to use for the projected model run ("2020," "2050," or "2080").
-
- '''
- _input_ports = [('RastersWithPARCInfoCSV', '(gov.usgs.sahm:RastersWithPARCInfoCSV:Other)'),
- ('templateLayer', '(gov.usgs.sahm:TemplateLayer:DataInput)'),
- ('model', '(edu.utah.sci.vistrails.basic:String)'),
- ('scenario', '(edu.utah.sci.vistrails.basic:String)'),
- ('year', '(edu.utah.sci.vistrails.basic:String)'),
- ('directoryCrosswalkCSV', '(edu.utah.sci.vistrails.basic:File)')
- ]
- _output_ports = [("MDS", "(gov.usgs.sahm:MergedDataSet:Other)")]
-
- def compute(self):
- models = ['CCCMA', 'CSIRO', 'hadcm3']
- scenarioss = ['A2a', 'B2b']
- years = ['2020', '2050', '2080']
-
- writetolog("\nRunning make Projection Layers", True)
-
- inputCSV = self.forceGetInputFromPort('RastersWithPARCInfoCSV').name
-
- if self.hasInputFromPort('templateLayer'):
- template = self.forceGetInputFromPort('templateLayer').name
- else:
- template = '' #we'll get a template below
-
- fromto = []
- climargs = {}
-
- for input in ['model', 'scenario', 'year']:
- if self.hasInputFromPort(input):
- climargs[input] = self.forceGetInputFromPort(input)
- if climargs <> {} and climargs.keys() <> ['model', 'scenario', 'year']:
- #they did not add in one of each, Not going to fly
- raise ModuleError(self, "All of model, scenario, and year must be supplied if any are used.")
- elif climargs <> {} and climargs.keys <> ['model', 'scenario', 'year']:
- #they specified a alt climate scenario add this to our list to search for
- fromto.append([r'K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio',
- os.path.join('I:\WorldClim_Future_Climate\RenamedBILs',
- climargs['model'], climargs['scenario'], climargs['year'])])
-
- if self.hasInputFromPort('directoryCrosswalkCSV'):
- crosswalkCSV = csv.reader(open(self.forceGetInputFromPort('directoryCrosswalkCSV'), 'r'))
- header = crosswalkCSV
- for row in crosswalkCSV:
- fromto.append(row[0], row[1])
- del crosswalkCSV
-
- #write out the outputs to an empty MDS file (just the header is needed to PARC the outputs)
-
-
- inCSV = csv.reader(open(inputCSV, 'r'))
- inCSV.next() #skip header
- workingCSV = utils.mknextfile(prefix='tmpFilesToPARC_', suffix='.csv')
- tmpCSV = csv.writer(open(workingCSV, 'wb'))
- tmpCSV.writerow(["FilePath", "Categorical", "Resampling", "Aggregation"])
- outHeader1 = ['x', 'y', 'response']
- outHeader2 = ['', '', '']
- outHeader3 = ['', '', '']
-
- output_dname = utils.mknextdir(prefix='ProjectionLayers_')
-
- for row in inCSV:
- if template == '':
- template = row[0]
- fileShortName = utils.getShortName(row[0])
- if row[1] == 1:
- outHeader1.append(fileShortName + '_categorical')
- else:
- outHeader1.append(fileShortName)
- outHeader2.append('1')
- outHeader3.append(os.path.join(output_dname, fileShortName + '.tif'))
-
- origFile = row[4]
- newOrigFile = origFile
- for lookup in fromto:
- if lookup[0] in origFile:
- newOrigFile = origFile.replace(lookup[0], lookup[1])
- tmpCSV.writerow([newOrigFile,] + row[1:4])
- del tmpCSV
-
- #PARC the files here
- ourPARC = parc.PARC()
-
-
- if configuration.verbose:
- ourPARC.verbose = True
- writetolog(" output_dname=" + output_dname, False, False)
- ourPARC.outDir = output_dname
- ourPARC.inputsCSV = workingCSV
- ourPARC.template = template
-
- try:
- ourPARC.parcFiles()
- except TrappedError as e:
- raise ModuleError(self, e.message)
- except :
- utils.informative_untrapped_error(self, "PARC")
-
- #loop through our workingCSV and format it into an MDS header
-
- #outputMDS = utils.mknextfile(prefix='ProjectionLayersMDS_', suffix = '.csv')
- outputMDS = os.path.join(output_dname, 'ProjectionLayersMDS.csv')
- outCSV = csv.writer(open(outputMDS, 'wb'))
- outCSV.writerow(outHeader1)
- outCSV.writerow(outHeader2)
- outCSV.writerow(outHeader3)
-
- output_file = utils.create_file_module(outputMDS)
- self.setResult("MDS", output_file)
- writetolog("Finished Select Projection Layers widget", True)
-
-#class ClimateModel(String):
-# _input_ports = [('value', '(gov.usgs.sahm:ClimateModel:Other)')]
-# _output_ports = [('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
-# _widget_class = build_enum_widget('ClimateModel',
-# ['CCCMA', 'CSIRO', 'hadcm3'])
-#
-# @staticmethod
-# def get_widget_class():
-# return ClimateModel._widget_class
-#
-#class ClimateScenario(String):
-# _input_ports = [('value', '(gov.usgs.sahm:ClimateScenario:Other)')]
-# _output_ports = [('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
-# _widget_class = build_enum_widget('ClimateScenario',
-# ['A2a', 'B2b'])
-#
-# @staticmethod
-# def get_widget_class():
-# return ClimateScenario._widget_class
-#
-#class ClimateYear(String):
-# _input_ports = [('value', '(gov.usgs.sahm:ClimateYear:Other)')]
-# _output_ports = [('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True)]
-# _widget_class = build_enum_widget('ClimateYear',
-# ['2020', '2050', '2080'])
-#
-# @staticmethod
-# def get_widget_class():
-# return ClimateYear._widget_class
-
-class MAXENT(Module):
-
- _output_ports = [("lambdas", "(edu.utah.sci.vistrails.basic:File)"),
- ("report", "(edu.utah.sci.vistrails.basic:File)"),
- ("roc", "(edu.utah.sci.vistrails.basic:File)")]
-
- def compute(self):
- global maxent_path
-
- ourMaxent = MaxentRunner.MAXENTRunner()
- ourMaxent.outputDir = utils.mknextdir(prefix='maxentFiles_')
-
- ourMaxent.inputMDS = self.forceGetInputFromPort('inputMDS').name
-
- ourMaxent.maxentpath = maxent_path
-
- MaxentArgsCSV = utils.mknextfile(prefix='MaxentArgs', suffix='.csv')
- argWriter = csv.writer(open(MaxentArgsCSV, 'wb'))
- argWriter.writerow(['parameter','value'])
- for port in self._input_ports:
- #print port
- if port[0] <> 'inputMDS' and port[0] <> 'projectionlayers':
- if self.hasInputFromPort(port[0]):
- port_val = self.getInputFromPort(port[0])
- if port[1] == "(edu.utah.sci.vistrails.basic:Boolean)":
- port_val = str(port_val).lower()
- elif (port[1] == "(edu.utah.sci.vistrails.basic:Path)" or \
- port[1] == "(edu.utah.sci.vistrails.basic:File)"):
- port_val = port_val.name
- argWriter.writerow([port[0], port_val])
- else:
- #print " has no input "
- kwargs = port[2]
- #print kwargs
- try:
- if port[1] == "(edu.utah.sci.vistrails.basic:Boolean)":
- default = kwargs['defaults'][2:-2].lower()
- else:
- default = kwargs['defaults'][2:-2]
- #args[port[0]] = default
- argWriter.writerow([port[0], default])
- except KeyError:
- pass
- if self.hasInputFromPort('projectionlayers'):
- value = self.forceGetInputListFromPort('projectionlayers')
- projlayers = ','.join([path.name for path in value])
- argWriter.writerow(['projectionlayers', projlayers])
-
- del argWriter
- ourMaxent.argsCSV = MaxentArgsCSV
- ourMaxent.logger = utils.getLogger()
- try:
- ourMaxent.run()
- except TrappedError as e:
- raise ModuleError(self, e.message)
- except:
- utils.informative_untrapped_error(self, "Maxent")
-
- #set outputs
- lambdasfile = os.path.join(ourMaxent.outputDir, ourMaxent.args["species_name"] + ".lambdas")
- output_file = utils.create_file_module(lambdasfile)
- self.setResult("lambdas", output_file)
-
-
- rocfile = os.path.join(ourMaxent.outputDir, 'plots', ourMaxent.args["species_name"] + "_roc.png")
- output_file = utils.create_file_module(rocfile)
- self.setResult("roc", output_file)
-
- htmlfile = os.path.join(ourMaxent.outputDir, ourMaxent.args["species_name"] + ".html")
- print htmlfile
- output_file = utils.create_file_module(htmlfile)
- self.setResult("report", output_file)
-
- writetolog("Finished Maxent widget", True)
-
-def load_max_ent_params():
- maxent_fname = os.path.join(os.path.dirname(__file__), 'maxent.csv')
- csv_reader = csv.reader(open(maxent_fname, 'rU'))
- # pass on header
- csv_reader.next()
- input_ports = []
-
- input_ports.append(('inputMDS', '(gov.usgs.sahm:MergedDataSet:Other)'))
-
- docs = {}
- basic_pkg = 'edu.utah.sci.vistrails.basic'
- p_type_map = {'file/directory': 'Path',
- 'double': 'Float'}
- for row in csv_reader:
- [name, flag, p_type, default, doc, notes] = row
- name = name.strip()
- p_type = p_type.strip()
- if p_type in p_type_map:
- p_type = p_type_map[str(p_type)]
- else:
- p_type = str(p_type).capitalize()
- kwargs = {}
- default = default.strip()
- if default:
- if p_type == 'Boolean':
- default = default.capitalize()
- kwargs['defaults'] = str([default])
- if p_type == 'Boolean':
- kwargs['optional'] = True
- input_ports.append((name, '(' + basic_pkg + ':' + p_type + ')', kwargs))
- # FIXME set documentation
- #print 'port:', (name, '(' + basic_pkg + ':' + p_type + ')', kwargs)
- docs[name] = doc
-
-
- #print 'MAXENT:', input_ports
- MAXENT._input_ports = input_ports
- MAXENT._port_docs = docs
-
- def provide_input_port_documentation(cls, port_name):
- return cls._port_docs[port_name]
- MAXENT.provide_input_port_documentation = \
- classmethod(provide_input_port_documentation)
-
-
-#class ModelOutputCell(SpreadsheetCell):
-# _input_ports = [("row", "(edu.utah.sci.vistrails.basic:Integer)"),
-# ("column", "(edu.utah.sci.vistrails.basic:Integer)"),
-# ('ProbabilityMap', '(edu.utah.sci.vistrails.basic:File)')]
-#
-# def __init__(self):
-# SpreadsheetCell.__init__(self)
-# self.cellWidget = None
-#
-# def compute(self):
-# renderView = self.forceGetInputFromPort('SetRenderView')
-# if renderView==None:
-# raise ModuleError(self, 'A vtkRenderView input is required.')
-# self.cellWidget = self.displayAndWait(QVTKViewWidget, (renderView,))
-
-#class SAHMViewWidget(QCellWidget):
-# def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
-# QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
-#
-
-#class RasterLayer(Module):
-# _input_ports = [('file', '(edu.utah.sci.vistrails.basic:File)'),
-# ('name', '(edu.utah.sci.vistrails.basic:String)')]
-# _output_ports = [('self', '(gov.usgs.sahm:RasterLayer:DataInput)')]
-#
-# def __init__(self):
-# Module.__init__(self)
-# self.qgis_obj = None
-#
-# def compute(self):
-# fname = self.getInputFromPort('file').name
-# if self.hasInputFromPort('name'):
-# name = self.getInputFromPort('name')
-# else:
-# name = os.path.splitext(os.path.basename(fname))[0]
-# self.qgis_obj = qgis.core.QgsRasterLayer(fname, name)
-# self.setResult('self', self)
-#
-#class VectorLayer(Module):
-# _input_ports = [('file', '(edu.utah.sci.vistrails.basic:File)'),
-# ('name', '(edu.utah.sci.vistrails.basic:String)')]
-# _output_ports = [('self', '(gov.usgs.sahm:VectorLayer:DataInput)')]
-#
-# def __init__(self):
-# Module.__init__(self)
-# self.qgis_obj = None
-#
-# def compute(self):
-# fname = self.getInputFromPort('file').name
-# if self.hasInputFromPort('name'):
-# name = self.getInputFromPort('name')
-# else:
-# name = os.path.splitext(os.path.basename(fname))[0]
-# self.qgis_obj = qgis.core.QgsVectorLayer(fname, name, "ogr")
-# self.setResult('self', self)
-
-
-
-def initialize():
- global maxent_path, color_breaks_csv
- global session_dir
- utils.config = configuration
-
- r_path = os.path.abspath(configuration.r_path)
- maxent_path = os.path.abspath(configuration.maxent_path)
-
-
- #I was previously setting the following environmental variables and path additions
- #so that each user wouldn't have to do this on their individual machines.
- #I was running into problems with imports occuring before this initialize routine so
- #I moved the setting of these to an external .net application that sets these before
- #starting up VisTrails.py.
-
- #This should also make this package easier to port to other systems as this stuff would
- #only work on a windows instance.
- #the current dependencies are:
- #an installation of GDAL and Proj.4
- # this includes the GDAL_DATA and PROJ_LIB directories as environmental variables
- #GDAL bindings for python in the python path.
- #QGIS built for the version of Python, QT, PyQt, and SIP used by VisTrails.
- # This one was a painful bear on Windows.
- #All of the DLLs required by the above QGIS build must be on the path.
- #In my case these were in a folder in the OSGeoW installation that QGIS was built
- #off of.
- #And finally QGIS bindings for python in the python path.
-
-
- import qgis.core
- import qgis.gui
- globals()["qgis"] = qgis
- setQGIS(qgis)
-
- qgis_prefix = os.path.join(configuration.qgis_path, "qgis1.7.0")
- qgis.core.QgsApplication.setPrefixPath(qgis_prefix, True)
- qgis.core.QgsApplication.initQgis()
-
-
- session_dir = utils.createrootdir(configuration.output_dir)
- utils.createLogger(session_dir, configuration.output_dir)
- #log_file = Utilities.createsessionlog(session_dir, configuration.verbose)
-
- color_breaks_csv = os.path.abspath(os.path.join(os.path.dirname(__file__), "ColorBreaks.csv"))
-
- load_max_ent_params()
-
- global layers_csv_fname
-
- writetolog("*" * 79)
- writetolog("Initializing:", True, True)
- writetolog(" Locations of dependencies")
-# writetolog(" Layers CSV = " + os.path.join(os.path.dirname(__file__), 'layers.csv'))
- writetolog(" Layers CSV = " + layers_csv_fname)
- writetolog(" R path = " + r_path)
- writetolog(" GDAL folder = " + os.path.abspath(configuration.gdal_path))
- writetolog(" Must contain subfolders proj, gdal-data, GDAL")
- writetolog(" Maxent folder = " + maxent_path)
- writetolog(" QGIS folder = " + os.path.abspath(configuration.qgis_path))
- writetolog(" Must contain subfolders qgis1.7.0, OSGeo4W")
- writetolog(" ")
- writetolog("*" * 79)
-
- writetolog("*" * 79)
- writetolog(" output directory: " + session_dir)
- writetolog("*" * 79)
- writetolog("*" * 79)
-
-def finalize():
- pass
- #utils.cleantemps()#No longer used
-
-def generate_namespaces(modules):
- module_list = []
- for namespace, m_list in modules.iteritems():
- for module in m_list:
- m_dict = {'namespace': namespace}
- if type(module) == tuple:
- m_dict.update(module[1])
- module_list.append((module[0], m_dict))
- #print 'm_dict:', m_dict
- else:
- module_list.append((module, m_dict))
- return module_list
-
-def build_available_trees():
- trees = {}
- global layers_csv_fname
- layers_csv_fname = os.path.join(os.path.dirname(__file__), 'layers.csv')
- csv_reader = csv.reader(open(layers_csv_fname, 'rU'))
- csv_reader.next()
- first_file = csv_reader.next()[0]
-
- #if the first file in the layers file does not exist assume that none
- #of them do and use the exampledata version
- if not os.path.exists(first_file):
- print (("!" * 30) + " WARNING " + ("!" * 30) + "\n")*3
- print "The first grid in your layers CSV could not be found."
- print "Defaulting to the example data csv."
- print "fix/set paths in file " + layers_csv_fname + " to enable this functionality."
- print "See documentation for more information on setting up the layers.csv\n"
- print (("!" * 30) + " WARNING " + ("!" * 30) + "\n")*3
- layers_csv_fname = os.path.join(os.path.dirname(__file__), 'layers.exampledata.csv')
-
- csv_reader = csv.reader(open(layers_csv_fname, 'rU'))
- # pass on header
- csv_reader.next()
- for row in csv_reader:
- if row[2] not in trees:
- trees[row[2]] = {}
- available_dict = trees[row[2]]
-# if 'Daymet' not in available_dict:
-# available_dict['Daymet'] = []
-# available_dict['Daymet'].append((row[0], row[1], row[3]))
- if row[3] not in available_dict:
- available_dict[row[3]] = []
- available_dict[row[3]].append((row[0], row[1], row[4]))
-
- return trees
-
-def build_predictor_modules():
- available_trees = build_available_trees()
- modules = []
- for name, tree in available_trees.iteritems():
- name_arr = name.strip().split()
- class_base = ''.join(n.capitalize() for n in name_arr)
- widget_class = get_predictor_widget(class_base, tree)
- config_class = get_predictor_config(class_base, tree)
- class_name = class_base + "Predictors"
- def get_widget_method(w_class):
- @staticmethod
- def get_widget_class():
- return w_class
- return get_widget_class
- module = type(class_name, (PredictorList,),
- {'get_widget_class': get_widget_method(widget_class),
- '_input_ports': \
- [('value',
- '(gov.usgs.sahm:%s:DataInput)' % class_name, True)]})
-
- modules.append((module, {'configureWidgetType': config_class}))
- for module in modules:
- module[0]._output_ports.append(('value_as_string', '(edu.utah.sci.vistrails.basic:String)', True))
-
- return modules
-
-
-
-
-_modules = generate_namespaces({'DataInput': [
- Predictor,
- PredictorListFile,
- FieldData,
- TemplateLayer] + \
- build_predictor_modules(),
- 'Tools': [FieldDataAggregateAndWeight,
- MDSBuilder,
- PARC,
- RasterFormatConverter,
- ProjectionLayers,
- TestTrainingSplit,
- CovariateCorrelationAndSelection,
- ApplyModel],
- 'Models': [GLM,
- RandomForest,
- MARS,
- MAXENT,
- BoostedRegressionTree],
- 'Other': [(Model, {'abstract': True}),
- (ResampleMethod, {'abstract': True}),
- (AggregationMethod, {'abstract': True}),
- (PredictorList, {'abstract': True}),
- (MergedDataSet, {'abstract': True}),
- (RastersWithPARCInfoCSV, {'abstract': True})],
- 'Output': [SAHMModelOutputViewerCell,
- SAHMSpatialOutputViewerCell,
- ]
-# ClimateModel,
-# ClimateScenario,
-# ClimateYear
-
- })
\ No newline at end of file
diff --git a/contrib/sahm/layers.csv b/contrib/sahm/layers.csv
deleted file mode 100644
index dcf138b..0000000
--- a/contrib/sahm/layers.csv
+++ /dev/null
@@ -1,820 +0,0 @@
-FileName,LayerName,Group,Source,Categorical
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_1.tif,Annual mean temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_2.tif,Mean diurnal range,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_3.tif,Isothermality,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_4.tif,Temperature seasonality,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_5.tif,Max. temperature of warmest month,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_6.tif,Min. temperature of coldest month,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_7.tif,Temperature annual range,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_8.tif,Mean temperature of wettest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_9.tif,Mean temperature of driest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_10.tif,Mean temperature of warmest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_11.tif,Mean temperature of coldest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_12.tif,Annual precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_13.tif,Precipitation of wettest month,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_14.tif,Precipitation of driest month,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_15.tif,Precipitation seasonality,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_16.tif,Precipitation of wettest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_17.tif,Precipitation of driest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_18.tif,Precipitiation of warmest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\DerivedData\bio_19.tif,Precipitation of coldest quarter,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax1.tif,Average Jan. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax2.tif,Average Feb. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax3.tif,Average March Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax4.tif,Average April Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax5.tif,Average May Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax6.tif,Average June Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax7.tif,Average July Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax8.tif,Average Aug. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax9.tif,Average Sept. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax10.tif,Average Oct. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax11.tif,Average Nov. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMaxTemp\tmax12.tif,Average Dec. Max. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean1.tif,Average Jan. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean2.tif,Average Feb. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean3.tif,Average March Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean4.tif,Average April Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean5.tif,Average May Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean6.tif,Average June Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean7.tif,Average July Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean8.tif,Average Aug. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean9.tif,Average Sept. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean10.tif,Average Oct. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean11.tif,Average Nov. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMeanTemp\tmean12.tif,Average Dec. Mean Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin1.tif,Average Jan. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin2.tif,Average Feb. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin3.tif,Average March Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin4.tif,Average April Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin5.tif,Average May Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin6.tif,Average June Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin7.tif,Average July Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin8.tif,Average Aug. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin9.tif,Average Sept. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin10.tif,Average Oct. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin11.tif,Average Nov. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMinTemp\tmin12.tif,Average Dec. Min. Temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt1.tif,Average Jan. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt2.tif,Average Feb. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt3.tif,Average March Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt4.tif,Average April Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt5.tif,Average May Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt6.tif,Average June Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt7.tif,Average July Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt8.tif,Average Aug. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt9.tif,Average Sept. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt10.tif,Average Oct. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt11.tif,Average Nov. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\DAYMET\SourceData\AvgMonthlyMonthlyPrecip\ppt12.tif,Average Dec. Precipitation,Climate,"Daymet (1980-1997) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_1,Average Jan. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_2,Average Feb. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_3,Average March Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_4,Average April Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_5,Average May Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_6,Average June Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_7,Average July Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_8,Average Aug. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_9,Average Sept. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_10,Average Oct. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_11,Average Nov. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MaxTempAvg1950-2000\tmax_30s_esri\tmax\tmax_12,Average Dec. Max. Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_1,Average Jan. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_2,Average Feb. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_3,Average March Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_4,Average April Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_5,Average May Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_6,Average June Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_7,Average July Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_8,Average Aug. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_9,Average Sept. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_10,Average Oct. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_11,Average Nov. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MeanTempAvg1950-2000\tmean_30s_esri\tmean\tmean_12,Average Dec. Mean Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_1,Average Jan. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_2,Average Feb. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_3,Average March Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_4,Average April Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_5,Average May Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_6,Average June Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_7,Average July Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_8,Average Aug. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_9,Average Sept. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_10,Average Oct. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_11,Average Nov. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\MinTempAvg1950-2000\tmin_30s_esri\tmin\tmin_12,Average Dec. Min Temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_1,Average Jan. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_2,Average Feb. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_3,Average March Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_4,Average April Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_5,Average May Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_6,Average June Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_7,Average July Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_8,Average Aug. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_9,Average Sept. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_10,Average Oct. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_11,Average Nov. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\TotPrecipAvg1950-2000\prec_30s_esri\prec\prec_12,Average Dec. Precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_1,Annual mean temperature,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_2,Mean diurnal range,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_3,Isothermality,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_4,Temperature seasonality,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_5,Max. temperature of warmest month,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_6,Min. temperature of coldest month,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_7,Temperature annual range,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_8,Mean temperature of wettest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_9,Mean temperature of driest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_10,Mean temperature of warmest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_11,Mean temperature of coldest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_12,Annual precipitation,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_13,Precipitation of wettest month,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_14,Precipitation of driest month,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_15,Precipitation seasonality,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_16,Precipitation of wettest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_17,Precipitation of driest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_18,Precipitiation of warmest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\WorldClim\BioclimaticVariables\bio_30s_esri\bio\bio_19,Precipitation of coldest quarter,Climate,"WorldClim (1950-2000) Normals, 1km.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_01.img,Average Jan. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_02.img,Average Feb. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_03.img,Average March Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_04.img,Average April Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_05.img,Average May Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_06.img,Average June Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_07.img,Average July Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_08.img,Average Aug. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_09.img,Average Sept. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_10.img,Average Oct. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_11.img,Average Nov. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\ppt_1971_2000_12.img,Average Dec. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_01.img,Average Jan. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_02.img,Average Feb. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_03.img,Average March Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_04.img,Average April Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_05.img,Average May Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_06.img,Average June Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_07.img,Average July Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_08.img,Average Aug. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_09.img,Average Sept. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_10.img,Average Oct. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_11.img,Average Nov. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmax_1971_2000_12.img,Average Dec. Max. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_01.img,Average Jan. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_02.img,Average Feb. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_03.img,Average March Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_04.img,Average April Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_05.img,Average May Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_06.img,Average June Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_07.img,Average July Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_08.img,Average Aug. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_09.img,Average Sept. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_10.img,Average Oct. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_11.img,Average Nov. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\Input_1971_2000\tmin_1971_2000_12.img,Average Dec. Min. Temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_01_1971_2000.img,Annual mean temperature,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_02_1971_2000.img,Mean diurnal range,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_03_1971_2000.img,Isothermality,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_04_1971_2000.img,Temperature seasonality,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_05_1971_2000.img,Max. temperature of warmest month,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_06_1971_2000.img,Min. temperature of coldest month,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_07_1971_2000.img,Temperature annual range,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_08_1971_2000.img,Mean temperature of wettest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_09_1971_2000.img,Mean temperature of driest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_10_1971_2000.img,Mean temperature of warmest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_11_1971_2000.img,Mean temperature of coldest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_12_1971_2000.img,Annual precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_13_1971_2000.img,Precipitation of wettest month,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_14_1971_2000.img,Precipitation of driest month,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_15_1971_2000.img,Precipitation seasonality,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_16_1971_2000.img,Precipitation of wettest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_17_1971_2000.img,Precipitation of driest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_18_1971_2000.img,Precipitiation of warmest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Climate\PRISM\OregonStateUniversity_Normal_1971_2000_800m\BioClim_1971_2000\bio_19_1971_2000.img,Precipitation of coldest quarter,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.NA.2001.bare.tif,VCF Bare Landcover,Remote Sensing,MODIS / GLCF North America (2001) .5 km,N
-K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.NA.2001.herbaceous.tif,VCF Herbaceous Landcover,Remote Sensing,MODIS / GLCF North America (2001) .5 km,N
-K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.NA.2001.tree.tif,VCF Tree Landcover,Remote Sensing,MODIS / GLCF North America (2001) .5 km,N
-K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.SA.2001.bare.tif,VCF Bare Landcover,Remote Sensing,MODIS / GLCF South America (2001) .5 km,N
-K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.SA.2001.herbaceous.tif,VCF Herbaceous Landcover,Remote Sensing,MODIS / GLCF South America (2001) .5 km,N
-K:\GIS_LIBRARY\Veg_LandCover\MODIS\LatLon.SA.2001.tree.tif,VCF Tree Landcover,Remote Sensing,MODIS / GLCF South America (2001) .5 km,N
-K:\GIS_LIBRARY\Elevation\EDNA\dem\dem,DEM,Elevation / Topography,"EDNA Continental US, 30 m.",N
-K:\GIS_LIBRARY\Elevation\EDNA\aspect\aspect,DEM Derivative: Aspect,Elevation / Topography,"EDNA Continental US, 30 m.",N
-K:\GIS_LIBRARY\Elevation\EDNA\slopedeg\slopedeg,DEM Derivative: Slope in Degrees,Elevation / Topography,"EDNA Continental US, 30 m.",N
-K:\GIS_LIBRARY\Elevation\EDNA\facc\facc,DEM Derivative: Flow Accumulation,Hydrology,"EDNA Continental US, 30 m.",N
-K:\GIS_LIBRARY\Elevation\EDNA\fdir\fdir,DEM Derivative: Flow Direction,Hydrology,"EDNA Continental US, 30 m.",N
-K:\GIS_LIBRARY\Elevation\EDNA\cti\cti,DEM Derivative: CTI/Steady State Wetness,Hydrology,"EDNA Continental US, 30 m.",N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2000.tif,amplitudes1_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2001.tif,amplitudes1_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2002.tif,amplitudes1_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2003.tif,amplitudes1_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2004.tif,amplitudes1_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2005.tif,amplitudes1_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2006.tif,amplitudes1_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2007.tif,amplitudes1_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2008.tif,amplitudes1_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_2009.tif,amplitudes1_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes1\NDVI_amplitudes1_Average.tif,amplitudes1_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2000.tif,amplitudes2_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2001.tif,amplitudes2_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2002.tif,amplitudes2_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2003.tif,amplitudes2_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2004.tif,amplitudes2_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2005.tif,amplitudes2_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2006.tif,amplitudes2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2007.tif,amplitudes2_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2008.tif,amplitudes2_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_2009.tif,amplitudes2_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\amplitudes2\NDVI_amplitudes2_Average.tif,amplitudes2_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2000.tif,annualMaximumValue_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2001.tif,annualMaximumValue_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2002.tif,annualMaximumValue_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2003.tif,annualMaximumValue_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2004.tif,annualMaximumValue_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2005.tif,annualMaximumValue_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2006.tif,annualMaximumValue_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2007.tif,annualMaximumValue_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2008.tif,annualMaximumValue_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_2009.tif,annualMaximumValue_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMaximumValue\NDVI_annualMaximumValue_Average.tif,annualMaximumValue_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2000.tif,annualMeanValue_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2001.tif,annualMeanValue_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2002.tif,annualMeanValue_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2003.tif,annualMeanValue_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2004.tif,annualMeanValue_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2005.tif,annualMeanValue_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2006.tif,annualMeanValue_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2007.tif,annualMeanValue_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2008.tif,annualMeanValue_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_2009.tif,annualMeanValue_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMeanValue\NDVI_annualMeanValue_Average.tif,annualMeanValue_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2000.tif,annualMinimumValue_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2001.tif,annualMinimumValue_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2002.tif,annualMinimumValue_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2003.tif,annualMinimumValue_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2004.tif,annualMinimumValue_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2005.tif,annualMinimumValue_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2006.tif,annualMinimumValue_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2007.tif,annualMinimumValue_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2008.tif,annualMinimumValue_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_2009.tif,annualMinimumValue_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\annualMinimumValue\NDVI_annualMinimumValue_Average.tif,annualMinimumValue_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2000.tif,baselevels1_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2001.tif,baselevels1_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2002.tif,baselevels1_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2003.tif,baselevels1_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2004.tif,baselevels1_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2005.tif,baselevels1_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2006.tif,baselevels1_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2007.tif,baselevels1_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2008.tif,baselevels1_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_2009.tif,baselevels1_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels1\NDVI_baselevels1_Average.tif,baselevels1_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2000.tif,baselevels2_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2001.tif,baselevels2_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2002.tif,baselevels2_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2003.tif,baselevels2_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2004.tif,baselevels2_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2005.tif,baselevels2_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2006.tif,baselevels2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2007.tif,baselevels2_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2008.tif,baselevels2_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_2009.tif,baselevels2_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\baselevels2\NDVI_baselevels2_Average.tif,baselevels2_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2000.tif,browndownrates1_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2001.tif,browndownrates1_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2002.tif,browndownrates1_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2003.tif,browndownrates1_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2004.tif,browndownrates1_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2005.tif,browndownrates1_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2006.tif,browndownrates1_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2007.tif,browndownrates1_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2008.tif,browndownrates1_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_2009.tif,browndownrates1_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates1\NDVI_browndownrates1_Average.tif,browndownrates1_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2000.tif,browndownrates2_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2001.tif,browndownrates2_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2002.tif,browndownrates2_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2003.tif,browndownrates2_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2004.tif,browndownrates2_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2005.tif,browndownrates2_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2006.tif,browndownrates2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2007.tif,browndownrates2_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2008.tif,browndownrates2_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_2009.tif,browndownrates2_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndownrates2\NDVI_browndownrates2_Average.tif,browndownrates2_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2000.tif,browndowns1_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2001.tif,browndowns1_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2002.tif,browndowns1_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2003.tif,browndowns1_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2004.tif,browndowns1_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2005.tif,browndowns1_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2006.tif,browndowns1_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2007.tif,browndowns1_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2008.tif,browndowns1_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_2009.tif,browndowns1_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns1\NDVI_browndowns1_Average.tif,browndowns1_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2000.tif,browndowns2_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2001.tif,browndowns2_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2002.tif,browndowns2_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2003.tif,browndowns2_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2004.tif,browndowns2_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2005.tif,browndowns2_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2006.tif,browndowns2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2007.tif,browndowns2_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2008.tif,browndowns2_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_2009.tif,browndowns2_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\browndowns2\NDVI_browndowns2_Average.tif,browndowns2_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2000.tif,greenuprates1_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2001.tif,greenuprates1_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2002.tif,greenuprates1_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2003.tif,greenuprates1_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2004.tif,greenuprates1_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2005.tif,greenuprates1_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2006.tif,greenuprates1_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2007.tif,greenuprates1_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2008.tif,greenuprates1_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_2009.tif,greenuprates1_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates1\NDVI_greenuprates1_Average.tif,greenuprates1_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2000.tif,greenuprates2_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2001.tif,greenuprates2_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2002.tif,greenuprates2_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2003.tif,greenuprates2_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2004.tif,greenuprates2_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2005.tif,greenuprates2_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2006.tif,greenuprates2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2007.tif,greenuprates2_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2008.tif,greenuprates2_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_2009.tif,greenuprates2_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenuprates2\NDVI_greenuprates2_Average.tif,greenuprates2_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2000.tif,greenups1_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2001.tif,greenups1_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2002.tif,greenups1_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2003.tif,greenups1_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2004.tif,greenups1_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2005.tif,greenups1_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2006.tif,greenups1_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2007.tif,greenups1_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2008.tif,greenups1_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_2009.tif,greenups1_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups1\NDVI_greenups1_Average.tif,greenups1_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2000.tif,greenups2_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2001.tif,greenups2_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2002.tif,greenups2_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2003.tif,greenups2_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2004.tif,greenups2_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2005.tif,greenups2_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2006.tif,greenups2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2007.tif,greenups2_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2008.tif,greenups2_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_2009.tif,greenups2_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\greenups2\NDVI_greenups2_Average.tif,greenups2_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2000.tif,landcover_2000,MODIS Phenology,NDVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2001.tif,landcover_2001,MODIS Phenology,NDVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2002.tif,landcover_2002,MODIS Phenology,NDVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2003.tif,landcover_2003,MODIS Phenology,NDVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2004.tif,landcover_2004,MODIS Phenology,NDVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2005.tif,landcover_2005,MODIS Phenology,NDVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2006.tif,landcover_2006,MODIS Phenology,NDVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2007.tif,landcover_2007,MODIS Phenology,NDVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2008.tif,landcover_2008,MODIS Phenology,NDVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_2009.tif,landcover_2009,MODIS Phenology,NDVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\landcover\NDVI_landcover_Average.tif,landcover_Average,MODIS Phenology,NDVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2000.tif,largeintegrals1_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2001.tif,largeintegrals1_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2002.tif,largeintegrals1_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2003.tif,largeintegrals1_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2004.tif,largeintegrals1_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2005.tif,largeintegrals1_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2006.tif,largeintegrals1_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2007.tif,largeintegrals1_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2008.tif,largeintegrals1_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_2009.tif,largeintegrals1_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals1\NDVI_largeintegrals1_Average.tif,largeintegrals1_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2000.tif,largeintegrals2_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2001.tif,largeintegrals2_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2002.tif,largeintegrals2_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2003.tif,largeintegrals2_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2004.tif,largeintegrals2_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2005.tif,largeintegrals2_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2006.tif,largeintegrals2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2007.tif,largeintegrals2_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2008.tif,largeintegrals2_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_2009.tif,largeintegrals2_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\largeintegrals2\NDVI_largeintegrals2_Average.tif,largeintegrals2_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2000.tif,maxpeakvalues1_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2001.tif,maxpeakvalues1_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2002.tif,maxpeakvalues1_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2003.tif,maxpeakvalues1_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2004.tif,maxpeakvalues1_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2005.tif,maxpeakvalues1_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2006.tif,maxpeakvalues1_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2007.tif,maxpeakvalues1_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2008.tif,maxpeakvalues1_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_2009.tif,maxpeakvalues1_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues1\NDVI_maxpeakvalues1_Average.tif,maxpeakvalues1_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2000.tif,maxpeakvalues2_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2001.tif,maxpeakvalues2_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2002.tif,maxpeakvalues2_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2003.tif,maxpeakvalues2_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2004.tif,maxpeakvalues2_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2005.tif,maxpeakvalues2_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2006.tif,maxpeakvalues2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2007.tif,maxpeakvalues2_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2008.tif,maxpeakvalues2_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_2009.tif,maxpeakvalues2_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\maxpeakvalues2\NDVI_maxpeakvalues2_Average.tif,maxpeakvalues2_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2000.tif,peakdates1_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2001.tif,peakdates1_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2002.tif,peakdates1_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2003.tif,peakdates1_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2004.tif,peakdates1_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2005.tif,peakdates1_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2006.tif,peakdates1_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2007.tif,peakdates1_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2008.tif,peakdates1_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_2009.tif,peakdates1_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates1\NDVI_peakdates1_Average.tif,peakdates1_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2000.tif,peakdates2_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2001.tif,peakdates2_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2002.tif,peakdates2_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2003.tif,peakdates2_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2004.tif,peakdates2_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2005.tif,peakdates2_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2006.tif,peakdates2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2007.tif,peakdates2_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2008.tif,peakdates2_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_2009.tif,peakdates2_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\peakdates2\NDVI_peakdates2_Average.tif,peakdates2_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2000.tif,qualityFlag_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2001.tif,qualityFlag_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2002.tif,qualityFlag_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2003.tif,qualityFlag_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2004.tif,qualityFlag_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2005.tif,qualityFlag_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2006.tif,qualityFlag_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2007.tif,qualityFlag_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2008.tif,qualityFlag_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_2009.tif,qualityFlag_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\qualityFlag\NDVI_qualityFlag_Average.tif,qualityFlag_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2000.tif,RMSE_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2001.tif,RMSE_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2002.tif,RMSE_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2003.tif,RMSE_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2004.tif,RMSE_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2005.tif,RMSE_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2006.tif,RMSE_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2007.tif,RMSE_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2008.tif,RMSE_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_2009.tif,RMSE_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\RMSE\NDVI_RMSE_Average.tif,RMSE_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2000.tif,seasonlengths1_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2001.tif,seasonlengths1_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2002.tif,seasonlengths1_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2003.tif,seasonlengths1_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2004.tif,seasonlengths1_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2005.tif,seasonlengths1_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2006.tif,seasonlengths1_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2007.tif,seasonlengths1_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2008.tif,seasonlengths1_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_2009.tif,seasonlengths1_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths1\NDVI_seasonlengths1_Average.tif,seasonlengths1_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2000.tif,seasonlengths2_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2001.tif,seasonlengths2_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2002.tif,seasonlengths2_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2003.tif,seasonlengths2_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2004.tif,seasonlengths2_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2005.tif,seasonlengths2_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2006.tif,seasonlengths2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2006.tif,seasonlengths2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2007.tif,seasonlengths2_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2008.tif,seasonlengths2_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_2009.tif,seasonlengths2_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\seasonlengths2\NDVI_seasonlengths2_Average.tif,seasonlengths2_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2000.tif,smallintegrals1_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2001.tif,smallintegrals1_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2002.tif,smallintegrals1_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2003.tif,smallintegrals1_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2004.tif,smallintegrals1_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2005.tif,smallintegrals1_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2006.tif,smallintegrals1_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2007.tif,smallintegrals1_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2008.tif,smallintegrals1_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_2009.tif,smallintegrals1_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals1\NDVI_smallintegrals1_Average.tif,smallintegrals1_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2000.tif,smallintegrals2_2000,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2001.tif,smallintegrals2_2001,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2002.tif,smallintegrals2_2002,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2003.tif,smallintegrals2_2003,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2004.tif,smallintegrals2_2004,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2005.tif,smallintegrals2_2005,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2006.tif,smallintegrals2_2006,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2007.tif,smallintegrals2_2007,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2008.tif,smallintegrals2_2008,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_2009.tif,smallintegrals2_2009,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_NDVI\smallintegrals2\NDVI_smallintegrals2_Average.tif,smallintegrals2_Average,MODIS Phenology,NDVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2000.tif,amplitudes1_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2001.tif,amplitudes1_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2002.tif,amplitudes1_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2003.tif,amplitudes1_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2004.tif,amplitudes1_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2005.tif,amplitudes1_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2006.tif,amplitudes1_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2007.tif,amplitudes1_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2008.tif,amplitudes1_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_2009.tif,amplitudes1_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes1\EVI_amplitudes1_Average.tif,amplitudes1_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2000.tif,amplitudes2_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2001.tif,amplitudes2_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2002.tif,amplitudes2_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2003.tif,amplitudes2_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2004.tif,amplitudes2_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2005.tif,amplitudes2_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2006.tif,amplitudes2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2007.tif,amplitudes2_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2008.tif,amplitudes2_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_2009.tif,amplitudes2_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\amplitudes2\EVI_amplitudes2_Average.tif,amplitudes2_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2000.tif,annualMaximumValue_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2001.tif,annualMaximumValue_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2002.tif,annualMaximumValue_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2003.tif,annualMaximumValue_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2004.tif,annualMaximumValue_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2005.tif,annualMaximumValue_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2006.tif,annualMaximumValue_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2007.tif,annualMaximumValue_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2008.tif,annualMaximumValue_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_2009.tif,annualMaximumValue_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMaximumValue\EVI_annualMaximumValue_Average.tif,annualMaximumValue_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2000.tif,annualMeanValue_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2001.tif,annualMeanValue_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2002.tif,annualMeanValue_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2003.tif,annualMeanValue_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2004.tif,annualMeanValue_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2005.tif,annualMeanValue_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2006.tif,annualMeanValue_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2007.tif,annualMeanValue_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2008.tif,annualMeanValue_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_2009.tif,annualMeanValue_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMeanValue\EVI_annualMeanValue_Average.tif,annualMeanValue_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2000.tif,annualMinimumValue_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2001.tif,annualMinimumValue_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2002.tif,annualMinimumValue_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2003.tif,annualMinimumValue_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2004.tif,annualMinimumValue_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2005.tif,annualMinimumValue_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2006.tif,annualMinimumValue_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2007.tif,annualMinimumValue_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2008.tif,annualMinimumValue_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_2009.tif,annualMinimumValue_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\annualMinimumValue\EVI_annualMinimumValue_Average.tif,annualMinimumValue_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2000.tif,baselevels1_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2001.tif,baselevels1_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2002.tif,baselevels1_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2003.tif,baselevels1_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2004.tif,baselevels1_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2005.tif,baselevels1_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2006.tif,baselevels1_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2007.tif,baselevels1_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2008.tif,baselevels1_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_2009.tif,baselevels1_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels1\EVI_baselevels1_Average.tif,baselevels1_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2000.tif,baselevels2_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2001.tif,baselevels2_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2002.tif,baselevels2_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2003.tif,baselevels2_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2004.tif,baselevels2_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2005.tif,baselevels2_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2006.tif,baselevels2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2007.tif,baselevels2_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2008.tif,baselevels2_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_2009.tif,baselevels2_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\baselevels2\EVI_baselevels2_Average.tif,baselevels2_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2000.tif,browndownrates1_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2001.tif,browndownrates1_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2002.tif,browndownrates1_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2003.tif,browndownrates1_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2004.tif,browndownrates1_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2005.tif,browndownrates1_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2006.tif,browndownrates1_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2007.tif,browndownrates1_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2008.tif,browndownrates1_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_2009.tif,browndownrates1_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates1\EVI_browndownrates1_Average.tif,browndownrates1_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2000.tif,browndownrates2_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2001.tif,browndownrates2_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2002.tif,browndownrates2_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2003.tif,browndownrates2_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2004.tif,browndownrates2_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2005.tif,browndownrates2_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2006.tif,browndownrates2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2007.tif,browndownrates2_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2008.tif,browndownrates2_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_2009.tif,browndownrates2_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndownrates2\EVI_browndownrates2_Average.tif,browndownrates2_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2000.tif,browndowns1_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2001.tif,browndowns1_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2002.tif,browndowns1_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2003.tif,browndowns1_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2004.tif,browndowns1_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2005.tif,browndowns1_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2006.tif,browndowns1_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2007.tif,browndowns1_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2008.tif,browndowns1_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_2009.tif,browndowns1_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns1\EVI_browndowns1_Average.tif,browndowns1_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2000.tif,browndowns2_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2001.tif,browndowns2_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2002.tif,browndowns2_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2003.tif,browndowns2_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2004.tif,browndowns2_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2005.tif,browndowns2_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2006.tif,browndowns2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2007.tif,browndowns2_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2008.tif,browndowns2_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_2009.tif,browndowns2_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\browndowns2\EVI_browndowns2_Average.tif,browndowns2_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2000.tif,greenuprates1_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2001.tif,greenuprates1_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2002.tif,greenuprates1_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2003.tif,greenuprates1_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2004.tif,greenuprates1_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2005.tif,greenuprates1_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2006.tif,greenuprates1_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2007.tif,greenuprates1_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2008.tif,greenuprates1_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_2009.tif,greenuprates1_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates1\EVI_greenuprates1_Average.tif,greenuprates1_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2000.tif,greenuprates2_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2001.tif,greenuprates2_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2002.tif,greenuprates2_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2003.tif,greenuprates2_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2004.tif,greenuprates2_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2005.tif,greenuprates2_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2006.tif,greenuprates2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2007.tif,greenuprates2_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2008.tif,greenuprates2_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_2009.tif,greenuprates2_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenuprates2\EVI_greenuprates2_Average.tif,greenuprates2_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2000.tif,greenups1_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2001.tif,greenups1_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2002.tif,greenups1_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2003.tif,greenups1_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2004.tif,greenups1_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2005.tif,greenups1_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2006.tif,greenups1_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2007.tif,greenups1_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2008.tif,greenups1_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_2009.tif,greenups1_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups1\EVI_greenups1_Average.tif,greenups1_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2000.tif,greenups2_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2001.tif,greenups2_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2002.tif,greenups2_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2003.tif,greenups2_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2004.tif,greenups2_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2005.tif,greenups2_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2006.tif,greenups2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2007.tif,greenups2_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2008.tif,greenups2_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_2009.tif,greenups2_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\greenups2\EVI_greenups2_Average.tif,greenups2_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2000.tif,landcover_2000,MODIS Phenology,EVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2001.tif,landcover_2001,MODIS Phenology,EVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2002.tif,landcover_2002,MODIS Phenology,EVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2003.tif,landcover_2003,MODIS Phenology,EVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2004.tif,landcover_2004,MODIS Phenology,EVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2005.tif,landcover_2005,MODIS Phenology,EVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2006.tif,landcover_2006,MODIS Phenology,EVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2007.tif,landcover_2007,MODIS Phenology,EVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2008.tif,landcover_2008,MODIS Phenology,EVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_2009.tif,landcover_2009,MODIS Phenology,EVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\landcover\EVI_landcover_Average.tif,landcover_Average,MODIS Phenology,EVI (230 m),Y
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2000.tif,largeintegrals1_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2001.tif,largeintegrals1_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2002.tif,largeintegrals1_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2003.tif,largeintegrals1_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2004.tif,largeintegrals1_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2005.tif,largeintegrals1_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2006.tif,largeintegrals1_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2007.tif,largeintegrals1_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2008.tif,largeintegrals1_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_2009.tif,largeintegrals1_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals1\EVI_largeintegrals1_Average.tif,largeintegrals1_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2000.tif,largeintegrals2_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2001.tif,largeintegrals2_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2002.tif,largeintegrals2_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2003.tif,largeintegrals2_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2004.tif,largeintegrals2_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2005.tif,largeintegrals2_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2006.tif,largeintegrals2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2007.tif,largeintegrals2_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2008.tif,largeintegrals2_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_2009.tif,largeintegrals2_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\largeintegrals2\EVI_largeintegrals2_Average.tif,largeintegrals2_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2000.tif,maxpeakvalues1_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2001.tif,maxpeakvalues1_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2002.tif,maxpeakvalues1_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2003.tif,maxpeakvalues1_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2004.tif,maxpeakvalues1_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2005.tif,maxpeakvalues1_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2006.tif,maxpeakvalues1_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2007.tif,maxpeakvalues1_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2008.tif,maxpeakvalues1_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_2009.tif,maxpeakvalues1_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues1\EVI_maxpeakvalues1_Average.tif,maxpeakvalues1_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2000.tif,maxpeakvalues2_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2001.tif,maxpeakvalues2_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2002.tif,maxpeakvalues2_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2003.tif,maxpeakvalues2_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2004.tif,maxpeakvalues2_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2005.tif,maxpeakvalues2_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2006.tif,maxpeakvalues2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2007.tif,maxpeakvalues2_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2008.tif,maxpeakvalues2_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_2009.tif,maxpeakvalues2_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\maxpeakvalues2\EVI_maxpeakvalues2_Average.tif,maxpeakvalues2_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2000.tif,peakdates1_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2001.tif,peakdates1_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2002.tif,peakdates1_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2003.tif,peakdates1_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2004.tif,peakdates1_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2005.tif,peakdates1_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2006.tif,peakdates1_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2007.tif,peakdates1_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2008.tif,peakdates1_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_2009.tif,peakdates1_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates1\EVI_peakdates1_Average.tif,peakdates1_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2000.tif,peakdates2_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2001.tif,peakdates2_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2002.tif,peakdates2_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2003.tif,peakdates2_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2004.tif,peakdates2_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2005.tif,peakdates2_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2006.tif,peakdates2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2007.tif,peakdates2_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2008.tif,peakdates2_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_2009.tif,peakdates2_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\peakdates2\EVI_peakdates2_Average.tif,peakdates2_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2000.tif,qualityFlag_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2001.tif,qualityFlag_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2002.tif,qualityFlag_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2003.tif,qualityFlag_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2004.tif,qualityFlag_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2005.tif,qualityFlag_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2006.tif,qualityFlag_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2007.tif,qualityFlag_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2008.tif,qualityFlag_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_2009.tif,qualityFlag_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\qualityFlag\EVI_qualityFlag_Average.tif,qualityFlag_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2000.tif,RMSE_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2001.tif,RMSE_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2002.tif,RMSE_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2003.tif,RMSE_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2004.tif,RMSE_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2005.tif,RMSE_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2006.tif,RMSE_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2007.tif,RMSE_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2008.tif,RMSE_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_2009.tif,RMSE_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\RMSE\EVI_RMSE_Average.tif,RMSE_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2000.tif,seasonlengths1_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2001.tif,seasonlengths1_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2002.tif,seasonlengths1_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2003.tif,seasonlengths1_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2004.tif,seasonlengths1_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2005.tif,seasonlengths1_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2006.tif,seasonlengths1_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2007.tif,seasonlengths1_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2008.tif,seasonlengths1_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_2009.tif,seasonlengths1_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths1\EVI_seasonlengths1_Average.tif,seasonlengths1_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2000.tif,seasonlengths2_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2001.tif,seasonlengths2_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2002.tif,seasonlengths2_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2003.tif,seasonlengths2_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2004.tif,seasonlengths2_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2005.tif,seasonlengths2_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2006.tif,seasonlengths2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2006.tif,seasonlengths2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2007.tif,seasonlengths2_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2008.tif,seasonlengths2_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_2009.tif,seasonlengths2_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\seasonlengths2\EVI_seasonlengths2_Average.tif,seasonlengths2_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2000.tif,smallintegrals1_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2001.tif,smallintegrals1_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2002.tif,smallintegrals1_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2003.tif,smallintegrals1_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2004.tif,smallintegrals1_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2005.tif,smallintegrals1_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2006.tif,smallintegrals1_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2007.tif,smallintegrals1_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2008.tif,smallintegrals1_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_2009.tif,smallintegrals1_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals1\EVI_smallintegrals1_Average.tif,smallintegrals1_Average,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2000.tif,smallintegrals2_2000,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2001.tif,smallintegrals2_2001,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2002.tif,smallintegrals2_2002,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2003.tif,smallintegrals2_2003,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2004.tif,smallintegrals2_2004,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2005.tif,smallintegrals2_2005,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2006.tif,smallintegrals2_2006,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2007.tif,smallintegrals2_2007,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2008.tif,smallintegrals2_2008,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_2009.tif,smallintegrals2_2009,MODIS Phenology,EVI (230 m),N
-\\IGSKBACBVMFS002\InvasivesNAS$\Phenology Share\FinalMosaics_WGS84Sinusoidal\MOD09Q1P_EVI\smallintegrals2\EVI_smallintegrals2_Average.tif,smallintegrals2_Average,MODIS Phenology,EVI (230 m),N
diff --git a/contrib/sahm/layers.exampledata.csv b/contrib/sahm/layers.exampledata.csv
deleted file mode 100644
index f93f24c..0000000
--- a/contrib/sahm/layers.exampledata.csv
+++ /dev/null
@@ -1,6 +0,0 @@
-FileName,LayerName,Group,Source,Categorical
-..\examples\SAHM_example\PredictorLayers\Climate\DAYMET_WGS84\bio_1_wgs84.tif,Annual mean temperature,Climate,"Daymet (1980-1997) Normals, 1km.",N
-..\examples\SAHM_example\PredictorLayers\Climate\DAYMET_WGS84\bio_2_wgs84.tif,Mean diurnal range,Climate,"Daymet (1980-1997) Normals, 1km.",N
-..\examples\SAHM_example\PredictorLayers\Climate\PRISM\ppt_1971_2000_011.img,Average Jan. Precipitation,Climate,"PRISM (1971-2000) Normals, 800 m.",N
-..\examples\SAHM_example\PredictorLayers\NLCD\nlcd01_11.tif,NLCD Landcover,Remote Sensing,NLCD,Y
-..\examples\SAHM_example\PredictorLayers\Elevation\dem.tif,30m EDNA Elevation resampled to 90m,Elevation / Topography,"EDNA, NED",N
diff --git a/contrib/sahm/maxent.csv b/contrib/sahm/maxent.csv
deleted file mode 100644
index f9c2c8d..0000000
--- a/contrib/sahm/maxent.csv
+++ /dev/null
@@ -1,33 +0,0 @@
-Flag ,Abbrv ,Type ,Default ,Meaning ,VisTrailsNotes
-projectionlayers ,j ,file/directory ,,"Location of an alternate set of environmental variables. Maxent models will be projected onto these variables.
Can be a .csv file (in SWD format) or a directory containing one file per variable.
Multiple projection files/directories can be separated by commas. ",
-randomtestpoints ,X ,integer ,0,"Percentage of presence localities to be randomly set aside as test points, used to compute AUC, omission etc. ","If the MDS input is from the test training split the will not be used, but instead this file will be generated from the input MDS Split column where it equals 'test'"
-betamultiplier ,b ,double ,1,Multiply all automatic regularization parameters by this number. A higher number gives a more spread-out distribution. ,
-maximumbackground ,MB ,integer ,10000,"If the number of background points / grid cells is larger than this number, then this number of cells is chosen randomly for background points ",
-testsamplesfile ,T ,file ,,"Use the presence localities in this file to compute statistics (AUC, omission etc.)
The file can contain different localities for different species.
It takes precedence over the random test percentage. ",
-replicates ,,integer ,1,"Number of replicate runs to do when cross-validating, bootstrapping or doing sampling with replacement runs ",If we supply the testsamples file or generate one from our testtraining split data can this also supplied? I think not.
-replicatetype ,,string ,subsample,"If replicates > 1, do multiple runs of this type:
Crossvalidate: samples divided into replicates folds; each fold in turn used for test data.
Bootstrap: replicate sample sets chosen by sampling with replacement.
Subsample: replicate sample sets chosen by removing random test percentage without replacement to be used for evaluation.
(Options)",same as above
-writebackgroundpredictions ,,boolean ,false ,Write .csv file with predictions at background points ,
-linear ,l ,boolean ,true ,Allow linear features to be used ,
-quadratic ,q ,boolean ,true ,Allow quadratic features to be used ,
-product ,p ,boolean ,true ,Allow product features to be used ,
-threshold ,,boolean ,true ,Allow threshold features to be used ,
-hinge ,h ,boolean ,true ,Allow hinge features to be used ,
-writeplotdata ,,boolean ,false ,"Write output files containing the data used to make response curves, for import into external plotting software ",
-fadebyclamping ,,boolean ,false ,"Reduce prediction at each point in projections by the difference between
clamped and non-clamped output at that point ",
-extrapolate ,,boolean ,true ,Predict to regions of environmental space outside the limits encountered during training ,
-autofeature ,A ,boolean ,true ,"Automatically select which feature classes to use, based on number of training samples ",
-doclamp ,,boolean ,true ,Apply clamping when projecting ,
-maximumiterations ,m ,integer ,500,Stop training after this many iterations of the optimization algorithm ,
-convergencethreshold ,c ,double ,1.00E-05,Stop training when the drop in log loss per iteration drops below this number ,
-beta_threshold ,,double ,-1,Regularization parameter to be applied to all threshold features; negative value enables automatic setting ,
-beta_categorical ,,double ,-1,Regularization parameter to be applied to all categorical features; negative value enables automatic setting ,
-beta_lqp ,,double ,-1,"Regularization parameter to be applied to all linear, quadratic and product features; negative value enables automatic setting ",
-beta_hinge ,,double ,-1,Regularization parameter to be applied to all hinge features; negative value enables automatic setting ,
-applythresholdrule ,,string ,,"Apply a threshold rule, generating a binary output grid in addition to the regular prediction grid. Options:
������ Fixed cumulative value 1
������ Fixed cumulative value 5
������ Fixed cumulative value 10
������ Minimum training presence
������ 10 percentile training presence
������ Equal training sensitivity and specificity
������ Maximum training sensitivity plus specificity
",
-prefixes,,boolean ,false ,,
-species_name,,string ,species,Used only by VisTrails to set the species name,
-responsecurves,p ,boolean ,true ,Create graphs showing how predicted relative probability of occurrence depends on the value of each environmental variable,
-jackknife,,boolean ,true ,Do jackknife to measure variable importance,
-writeclampgrid,,boolean ,false ,Do not create clamping grids when projecting,
-writemess,,boolean ,false ,Do not do MESS analysis when projecting,
-outputgrids,,boolean ,false ,Only create the summary grids when doing multiple iterations,
diff --git a/contrib/sahm/pySAHM/FieldDataQuery.py b/contrib/sahm/pySAHM/FieldDataQuery.py
deleted file mode 100644
index 6565ca7..0000000
--- a/contrib/sahm/pySAHM/FieldDataQuery.py
+++ /dev/null
@@ -1,385 +0,0 @@
-'''
-Created on Dec 29, 2010
-
-This module was created to
-
- at author: talbertc
-'''
-
-import sys, os
-import math
-import csv
-
-from osgeo import gdalconst
-from osgeo import gdal
-from osgeo import osr
-from math import floor
-
-from optparse import OptionParser
-
-import utilities
-
-def main(argv):
- usageStmt = "usage: options: -t --template -f --fieldData -a --aggPixel -y --aggYears -o --output"
- desc = "Aggregates sample points by pixel and/or year."
-
- parser = OptionParser(usage=usageStmt, description=desc)
- parser.add_option("-t", "--template",
- dest="template",
- help="The template grid in Tif, ESRI grid, or ASC format")
- parser.add_option("-f", "--fieldData",
- dest="csv",
- help="The CSV of field data")
- parser.add_option("-o", "--output",
- dest="output",
- help="The output CSV file with appended frequency and numPresence")
- parser.add_option("-p", "--aggregate",
- dest="bAgg",
- default=True,
- action="store_true",
- help="Flag to aggregate by pixel in the template")
- parser.add_option("-y", "--aggregateYears",
- dest="bAggYears",
- default=False,
- action="store_true",
- help="Flag to aggregate by years in the template")
- parser.add_option("-v", "--verbose",
- dest="verbose",
- default=False,
- action="store_true",
- help="the verbose flag causes diagnostic output to print")
-
- (options, args) = parser.parse_args(argv)
-
- ourFDQ = FieldDataQuery()
- ourFDQ.template = options.template
- ourFDQ.csv = options.csv
- ourFDQ.output = options.output
- ourFDQ.AggByPixel = options.bAgg
- ourFDQ.AggByYear = options.bAggYears
- ourFDQ.verbose = options.verbose
- ourFDQ.processCSV()
-
-class FieldDataQuery(object):
-
- def __init__(self):
- #instance level variables
- self.csv = None
- self.template = None
- self.output = None
- self.templateParams = {}
- self.AggByYear = False
- self.AggByPixel = True
- self.verbose = False
- self.countdata = False
- self.logger = None
-
- def validateArgs(self):
- """
- Make sure the user sent us some stuff we can work with
- """
-
- # Validate template image.
- if self.template is None:
- raise Exception, "template raster not provided (-t command line argument missing)"
-
- if not os.path.exists(self.template):
- raise Exception, "Template file, " + self.template + ", does not exist on file system"
-
- self.templateParams = self.getRasterParams(self.template)
- if len(self.templateParams["Error"]) <> 0:
- print ("There was a problem with the provided template: \n " +
- " " + "\n ".join(self.templateParams["Error"]))
- raise Exception, ("There was a problem with the provided template: \n " +
- " " + "\n ".join(self.templateParams["Error"]))
-
- # Ensure the template has square pixels.
- if abs(abs(self.templateParams["xScale"]) - abs(self.templateParams["yScale"])) > 1e-6:
- print "The template raster must have square pixels."
- print "x pixel scale = " + str(xScale)
- print "y pixel scale = " + str(yScale)
- raise Exception, "template image must have square pixels."
-
- #Validate the CSV
- if self.csv is None:
- raise Exception, "No csv provided"
-
- if not os.path.exists(self.csv):
- raise Exception, "CSV file, " + self.csv + ", does not exist on file system"
-
- #make sure the directory the mds file is going into exists:
- outDir = os.path.split(self.output)[0]
- if not os.path.exists(outDir):
- raise RuntimeError, "The directory of the supplied MDS output file path, " + self.output +", does not appear to exist on the filesystem"
-
- if self.logger is None:
- self.logger = utilities.logger(outDir, self.verbose)
- self.writetolog = self.logger.writetolog
-
- def getRasterParams(self, rasterFile):
- """
- Extracts a series of bits of information from a passed raster
- All values are stored in a dictionary which is returned.
- If errors are encountered along the way the error messages will
- be returned as a list in the Error element.
- """
- try:
- #initialize our params dictionary to have None for all parma
- params = {}
- allRasterParams = ["Error", "xScale", "yScale", "width", "height",
- "ulx", "uly", "lrx", "lry", "Wkt",
- "tUlx", "tUly", "tLrx", "tLry",
- "srs", "gt", "prj", "NoData", "PixelType"]
-
- for param in allRasterParams:
- params[param] = None
- params["Error"] = []
-
- # Get the PARC parameters from the rasterFile.
- dataset = gdal.Open(rasterFile, gdalconst.GA_ReadOnly)
- if dataset is None:
- params["Error"].append("Unable to open file")
- #print "Unable to open " + rasterFile
- #raise Exception, "Unable to open specifed file " + rasterFile
-
-
- xform = dataset.GetGeoTransform()
- params["xScale"] = xform[1]
- params["yScale"] = xform[5]
-
- params["width"] = dataset.RasterXSize
- params["height"] = dataset.RasterYSize
-
- params["ulx"] = xform[0]
- params["uly"] = xform[3]
- params["lrx"] = params["ulx"] + params["width"] * params["xScale"]
- params["lry"] = params["uly"] + params["height"] * params["yScale"]
-
-
- except:
- #print "We ran into problems extracting raster parameters from " + rasterFile
- params["Error"].append("Some untrapped error was encountered")
- finally:
- del dataset
- return params
-
- def processCSV(self):
-
- self.validateArgs()
- if self.verbose:
- self.writetolog("Starting on Field Data Query for " + os.path.split(self.csv)[1])
- self.writetolog(" using template " + os.path.split(self.template)[1])
-
- templatename = os.path.split(self.template)[1]
- if templatename == 'hdr.adf':
- templatename = os.path.split(os.path.split(self.template)[0])[1]
-
-
- csvfile = open(self.csv, "r")
- #dialect = csv.Sniffer().sniff(csvfile.read(1024))
- reader = csv.reader(csvfile)
- usedPixels = {}
- header = reader.next()
- if header[2].lower() == 'responsecount':
- self.countdata = True
-
- #Commented this out because it is causing an error
- #to be thrown by the java, uncomment out when the
- #java has been replaced
- header.append("frequency")
- header.append("numPresence")
- header.append("pixelColumn")
- header.append("pixelRow")
- header.append(os.path.abspath(self.template))
- header.append(os.path.abspath(self.csv))
-
- #loop through each row (observation) and
- #if that particular pixel hasn't been encountered before
- #add it to a dictionary containing a key of the pixel X,Y
- #and values of each row encountered for that pixel
- #if pixel
- lineCount = linesInFile(self.csv)
- extraPoints = []
- pointCount = 0
- pcntDone = 0
- for row in reader:
- if self.pointInTemplate(row[0], row[1]):
- pixelColumn = int(floor((float(row[0]) - self.templateParams["ulx"])
- / self.templateParams["xScale"]))
- pixelRow = int(floor((float(row[1]) - self.templateParams["uly"])
- / self.templateParams["yScale"]))
- pixel = "".join(["X:",str(pixelColumn),":Y:",str(pixelRow)])
- #if verbose == True:
- if not pixel in usedPixels:
- usedPixels[pixel] = [row]
- #usedPixels[pixel] = usedPixels[pixel].append(row)
- else:
- curVal = usedPixels[pixel]
- curVal.append(row)
- usedPixels[pixel] = curVal
- else:
- extraPoints.append([row[0], row[1], row[2]])
- pointCount += 1
- if self.verbose:
- if float(pointCount)/lineCount > float(pcntDone)/100:
- pcntDone += 10
- if self.verbose:
- print str(pcntDone) + "...",
-
- #Open up and write to an output file
- oFile = open(self.output, 'wb')
- fOut = csv.writer(oFile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
- fOut.writerow(header)
-
- #Add each used pixel to the output file
- for k in usedPixels:
- v = usedPixels[k]
- outputLine = v[0]
-
- pixelColumn = int(k.rsplit(':')[1])
- pixelRow = int(k.rsplit(':')[3])
- outPixelX = (self.templateParams["ulx"] + (self.templateParams["xScale"] * pixelColumn) +
- self.templateParams["xScale"]/2)
- outPixelY = (self.templateParams["uly"] + (self.templateParams["yScale"] * pixelRow) +
- self.templateParams["yScale"]/2)
- frequency = len(v)
-
- #loop though the 'points' in each pixel
- #for count data the value is the sum of the 'points'
- # if there were any 'hits' not equal to 0
- # otherwise if there were any absences the value is 0
- # what's left is background points
- #for presense/absense data
- # The value is 1 if there were any 1s in our points
- # Or 0 if there were any zeros (absenses)
- # Otherwise it's a background pixel.
- total = 0
- numAbsense = 0
- for i in range (frequency):
- if int(float(v[i][2])) > 0:
- total += int(float(v[i][2]))
- if int(float(v[i][2])) == 0:
- numAbsense += 1
-
- outputLine[0] = outPixelX
- outputLine[1] = outPixelY
-
- if self.countdata and total > 0:
- outputLine[2] = total
- elif total > 0:
- outputLine[2] = 1
- elif numAbsense > 0:
- outputLine[2] = 0
- else:
- outputLine[2] = -9999
-
- outputLine.append(frequency)
- outputLine.append(total)
- outputLine.append(pixelColumn)
- outputLine.append(pixelRow)
-
-
- fOut.writerow(outputLine)
- oFile.close
- if self.verbose:
- self.writetolog("Done\nFinished creating field data query output.\n")
- if len(extraPoints) > 0:
- self.writetolog (" WARNING: " + str(len(extraPoints)) + " points" +
- " out of " + str(pointCount) + " total points in the " +
- "original CSV were outside the template extent and WERE NOT " +
- "INCLUDED IN THE FDQ OUTPUT.")
- else:
- pass
-
- def pointInTemplate(self, x, y):
- if (float(x) >= self.templateParams["ulx"] and
- float(x) <= self.templateParams["lrx"] and
- float(y) >= self.templateParams["lry"] and
- float(y) <= self.templateParams["uly"]):
- return True
- else:
- return False
-
-def linesInFile(filename):
- f = open(filename)
- lines = 0
- buf_size = 1024 * 1024
- read_f = f.read # loop optimization
-
- buf = read_f(buf_size)
- while buf:
- lines += buf.count('\n')
- buf = read_f(buf_size)
-
- return lines
-#def getTemplateParams(template, verbose):
-# # Get the PARC parameters from the template.
-# dataset = gdal.Open(template, gdalconst.GA_ReadOnly)
-#
-# if dataset is None:
-# print "Unable to open " + template
-# raise RuntimeError
-# xform = dataset.GetGeoTransform()
-# xScale = xform[1]
-# yScale = xform[5]
-# # Ensure the template has square pixels.
-# if abs(math.fabs(xScale) - math.fabs(yScale)) > 1e-6:
-# print "The template image must have square pixels."
-# print "x pixel scale = " + str(math.fabs(xScale))
-# print "y pixel scale = " + str(math.fabs(yScale))
-# raise RuntimeError
-# width = dataset.RasterXSize
-# height = dataset.RasterYSize
-# ulx = xform[0]
-# uly = xform[3]
-# lrx = ulx + width * xScale
-# lry = uly + height * yScale
-# if verbose == True:
-# print "upper left = (" + str(ulx) + ", " + str(uly) + ")"
-# print "lower right = (" + str(lrx) + ", " + str(lry) + ")"
-# # Store the extent in geographic coordinates.
-# tEPSG = getEPSG(dataset)
-# if int(tEPSG) == 4326:
-# tGeoUlX = ulx
-# tGeoUlY = uly
-# tGeoLrX = lrx
-# tGeoLrY = lry
-# else:
-# tGeoUlX, tGeoUlY, tGeoLrX, tGeoLrY = getExtentInGeog(ulx, uly, lrx, lry, tEPSG)
-# return ulx, uly, lrx, lry, getEPSG(dataset), xScale, yScale
-#
-#def getEPSG(dataset):
-# #Returns code for the projection/datum used in the layer
-# wkt = dataset.GetProjection()
-# s_srs = osr.SpatialReference(wkt)
-# s_srs.AutoIdentifyEPSG()
-# epsg = s_srs.GetAuthorityCode("PROJCS")
-# if epsg == None:
-# epsg = s_srs.GetAuthorityCode("GEOGCS")
-# if epsg == None:
-# print "Unable to extract the EPSG code from the image."
-# raise RuntimeError
-# return epsg
-#
-#def getExtentInGeog(ulx, uly, lrx, lry, EPSG):
-#
-# s_srs = osr.SpatialReference()
-# s_srs.ImportFromEPSG(int(EPSG))
-#
-# t_srs = osr.SpatialReference()
-# t_srs.ImportFromEPSG(4326)
-#
-# coordXform = osr.CoordinateTransformation(s_srs, t_srs)
-#
-# result = coordXform.TransformPoint(ulx, uly)
-# gulx = result[0]
-# guly = result[1]
-#
-# result = coordXform.TransformPoint(lrx, lry)
-# glrx = result[0]
-# glry = result[1]
-#
-# return gulx, guly, glrx, glry
-
-if __name__ == '__main__':
- main(sys.argv)
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/MDSBuilder.py b/contrib/sahm/pySAHM/MDSBuilder.py
deleted file mode 100644
index 7bf9739..0000000
--- a/contrib/sahm/pySAHM/MDSBuilder.py
+++ /dev/null
@@ -1,473 +0,0 @@
-'''
-Created on Jan 31, 2011
-
-This module creates a Merged Data Set (MDS)
-from an input CSV and directory
-or list of rasters. The MDS consists of three
-header lines 1st is a x, y, ResponseBinary,
-{other info fields}, then a list of raster covariates.
-The next header line contains ones and zeros for each of the
-raster covariates and indicates if the covariate is to be
-used in subsequent analyses. The last header line contains
-the full network path the raster dataset for that covariate.
-After the header lines comes the data which is the
-covariate values pulled from the raster cell
-with those coordinates.
-
- at author: talbertc
-
-'''
-
-import sys
-import csv
-import os
-import time
-import random
-import shutil
-
-from osgeo import gdalconst
-from osgeo import gdal
-
-from optparse import OptionParser
-import utilities
-#from Utilities import self.writetolog
-
-class MDSBuilder(object):
- '''Takes a csv with animal location x,y and attributes each with the values
- extracted from each of the grids (covariates) indicated in the supplied
- csv list of files
- '''
- def __init__(self):
- #instance level variables
- self.verbose = False
- self.inputsCSV = ''
- self.inputs = []
- self.fieldData = ''
- self.outputMDS = ''
- self.probsurf = ''
- self.pointcount = 0
- self.NDFlag = -9999
- self.deleteTmp = False
- self.logger = None
-
- def validateArgs(self):
- #check our CSV file for expectations
- if not os.path.exists(self.fieldData):
- raise RuntimeError, "Could not find CSV file of fieldData provided. Please check input file: " + str(self.fieldData)
-
- if not os.path.exists(self.inputsCSV):
- raise RuntimeError, "Could not find CSV file of inputs provided. Please check input file: " + str(self.inputsCSV)
-
- #check the input CSV file of inputs
- reader = csv.reader(open(self.inputsCSV, 'r'))
- header = reader.next()
- missingfiles = []
- for row in reader:
- if not self.isRaster(row[0]):
- missingfiles.append(row[0])
- if not len(missingfiles) ==0:
- msg = "One or more of the files in the input covariate list CSV could not be identified as rasters by GDAL."
- msg += "\n ".join(missingfiles)
- raise RuntimeError, msg
-
- if self.probsurf <> '':
- if not self.isRaster(self.probsurf):
- raise RuntimeError, "The supplied probability surface, " + self.probsurf + ", does not appear to be a valid raster."
-
- try:
- self.pointcount = int(self.pointcount)
- except:
- raise RuntimeError, "The supplied point count parameter, " + self.pointcount +", does not appear to be an integer"
-
- #make sure the directory the mds file is going into exists:
- outDir = os.path.split(self.outputMDS)[0]
- if not os.path.exists(outDir):
- raise RuntimeError, "The directory of the supplied MDS output file path, " + self.outputMDS +", does not appear to exist on the filesystem"
-
- if self.logger is None:
- self.logger = utilities.logger(outDir, self.verbose)
- self.writetolog = self.logger.writetolog
-
- def run(self):
- '''
- This routine loops through a set of rasters and creates an MDS file
- '''
-
- self.validateArgs()
- self.writetolog('\nRunning MDSBuilder', True, True)
- # start timing
- startTime = time.time()
- gdal.UseExceptions()
- gdal.AllRegister()
-
- self.constructEmptyMDS()
-
- if self.pointcount <> 0:
- self.addBackgroundPoints()
-
- outputRows = self.readInPoints()
-
- #loop though each of the supplied rasters and add the
- #extracted values to
- for input in self.inputs:
- inputND = self.getND(input)
- rasterDS = gdal.Open(input, gdalconst.GA_ReadOnly)
- # get image size
- rows = rasterDS.RasterYSize
- cols = rasterDS.RasterXSize
- band = rasterDS.GetRasterBand(1)
- # get georeference info
- transform = rasterDS.GetGeoTransform()
- xOrigin = transform[0]
- yOrigin = transform[3]
- pixelWidth = transform[1]
- pixelHeight = transform[5]
-
- if self.verbose:
- self.writetolog(" Extracting raster values for " + input)
- print " ",
-
- pcntDone = 0
- i = 1
- badpoints = []
- for row in outputRows:
- x = float(row[0])
- y = float(row[1])
- # compute pixel offset
- xOffset = int((x - xOrigin) / pixelWidth)
- yOffset = int((y - yOrigin) / pixelHeight)
-# try:
- if xOffset < 0 or yOffset < 0:
- if row[:3] not in badpoints:
- badpoints.append(row[:3])
- row.append(str(self.NDFlag))
- else:
- try:
- data = band.ReadAsArray(xOffset, yOffset, 1, 1)
- value = data[0,0]
- if value <> inputND:
- row.append(value)
- else:
- row.append(str(self.NDFlag))
- except:
- badpoints.append(row[:3])
- row.append(str(self.NDFlag))
-
- if self.verbose:
- if i/float(len(outputRows)) > float(pcntDone)/100:
- pcntDone += 10
- print str(pcntDone) + "...",
- i += 1
- if self.verbose:
- self.writetolog(" Done")
- if len(badpoints) > 0:
- msg = "\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
- msg += "\n!!!!!!!!!!!!!!!!!!!!!WARNING!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n"
- msg += str(len(badpoints)) + " point fell outside the Covariate coverage."
- msg += "\nThese points were assigned the NoData value of -9999 for all covariates and will"
- msg += "not be included in subsequent models.\n These points are:"
- for badpoint in badpoints:
- msg += " x:" + str(row[0]) + " Y: " + str(row[1]) + " response: " + str(row[2])
- self.writetolog(msg)
-
-
- outputMDS = csv.writer(open(self.outputMDS, 'ab'))
- thrownOut = 0
- kept = 0
- for row in outputRows:
- #remove this if when Marian handles the ND
- if not str(self.NDFlag) in row[3:]:
- outputMDS.writerow(row)
- kept += 1
- else:
- outputMDS.writerow(row)
- thrownOut += 1
- if thrownOut > 0:
- msg = "\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
- msg += "\n!!!!!!!!!!!!!!!!!!!!!WARNING!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n"
- msg += str(thrownOut) + " points had 'nodata' in at least one of the covariates."
- msg += "\nThese points will not be considered in subsequent Models."
- msg += "\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
- msg += "\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
- self.writetolog(msg)
- del outputMDS
-
- #convert the mds csv to a shapefile
- output_shp = self.outputMDS.replace(".csv", ".mds")
- utilities.mds_to_shape(self.outputMDS, output_shp)
-
- # figure out how long the script took to run
- endTime = time.time()
-
- if self.deleteTmp:
- #if this flag is trud the field data we're working with is
- # a temporary copy which we created so that we could add
- # background points. Delete it to clean up our working file.
- os.remove(self.fieldData)
-
- if self.verbose:
- self.writetolog('Finished running MDSBuilder', True, True)
- self.writetolog(' The process took ' + str(endTime - startTime) + ' seconds')
-
- def constructEmptyMDS(self):
- '''Creates the triple header line format of our output file.
- Also parses the inputs file to append the '_categorical' flag
- to the covariate names of all categorical inputs.
- '''
-
- field_data_CSV = csv.reader(open(self.fieldData, "r"))
- orig_header = field_data_CSV.next()
- full_header = ["x", "y"]
- if orig_header[2].lower not in ["responsebinary", "responsecount"]:
- #inputs not conforming to our expected format will be assumed
- #to be binary data
- full_header.append("responseBinary")
- else:
- full_header.append(orig_header[2])
-
- inputs_CSV = csv.reader(open(self.inputsCSV, "r"))
- inputs_header = inputs_CSV.next()
- self.inputs = []
-
- #each row contains a covariate raster layer
- #item 0 is the full path to the file
- #item 1 is 0/1 indicating categorical
- #Construct our output header by extracting each individual
- #file (raster) name and appending '_categorical' if the flag is 1
- rasters = {}
- for row in inputs_CSV:
- temp_raster = row[0]
-# self.inputs.append(temp_raster)
- raster_shortname = os.path.split(temp_raster)[1]
- raster_shortname = os.path.splitext(raster_shortname)[0]
- if len(row) > 1 and row[1] == '1':
- raster_shortname += "_categorical"
- rasters[raster_shortname] = temp_raster
-
- keys = rasters.keys()
- keys.sort(key=lambda s: s.lower())
- keys.sort(key=lambda s: s.lower())
- for key in keys:
- self.inputs.append(rasters[key])
- full_header.append(key)
-
- #Open up and write to an output file
- oFile = open(self.outputMDS, 'wb')
- fOut = csv.writer(oFile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
-
- #Format and write out our three header lines
- # the original template, fieldData, and parc folder are
- # stored in spots 1,2,3 in the second header line
- if len(orig_header) > 7 and os.path.exists(orig_header[7]):
- #The input is an output from Field data query
- original_field_data = orig_header[7]
- field_data_template = orig_header[8]
- else:
- #The input is a raw field data file
- original_field_data = self.fieldData
- field_data_template = "NA"
-
- if len(inputs_header) > 5:
- parc_template = inputs_header[5]
- parc_workspace = inputs_header[6]
- else:
- parc_template = "Unknown"
- parc_workspace = "Unknown"
-
- secondRow = [original_field_data, field_data_template, ""] + ["1" for elem in self.inputs]
- thirdRow = [parc_template, parc_workspace, ""] + self.inputs
- fOut.writerow(full_header)
- fOut.writerow(secondRow)
- fOut.writerow(thirdRow)
- oFile.close()
- del fOut
-
- def readInPoints(self):
- '''Loop through each row in our field data and add the X, Y, response
- to our in memory list of rows to write to our output MDS file
- '''
- fieldDataCSV = csv.reader(open(self.fieldData, "r"))
- origHeader = fieldDataCSV.next()
- points = []
- for row in fieldDataCSV:
- points.append(row[:3])
-
- del fieldDataCSV
- return points
-
- def addBackgroundPoints(self):
- '''Add pointcount number of points to the supplied field data
- If a probability surface was provided the distribution will
- follow this otherwise it will be uniform within the extent of the first of our inputs.
- No more than one per pixel is used.
- '''
- #First we'll create a temp copy of the Field Data to work with.
- shutil.copy(self.fieldData, self.fieldData + ".tmp.csv")
- self.fieldData = self.fieldData + ".tmp.csv"
- self.deleteTmp = True
-
- if self.probsurf <> '':
- rasterDS = gdal.Open(self.probsurf, gdalconst.GA_ReadOnly)
- useProbSurf = True
- else:
- print self.inputs[0]
- rasterDS = gdal.Open(self.inputs[0], gdalconst.GA_ReadOnly)
- useProbSurf = False
-
- # get image size
- rows = rasterDS.RasterYSize
- cols = rasterDS.RasterXSize
- band = rasterDS.GetRasterBand(1)
- # get georeference info
- transform = rasterDS.GetGeoTransform()
- xOrigin = transform[0]
- yOrigin = transform[3]
- pixelWidth = transform[1]
- pixelHeight = transform[5]
- xRange = [xOrigin, xOrigin * pixelWidth * cols]
- yRange = [yOrigin, yOrigin * pixelHeight * rows]
-
- #Open up and write to an output file
- oFile = open(self.fieldData, 'ab')
- fOut = csv.writer(oFile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
-
-
- if self.verbose:
- self.writetolog(' Starting generation of ' + str(self.pointcount) + ' random background points, ')
- if self.probsurf <> '':
- self.writetolog(' using ' + self.probsurf + ' as the probability surface.')
- print " Percent Done: ",
-
- foundPoints = 0 # The running count of how many we've found
- pcntDone = 0 #for status bar
- while foundPoints < self.pointcount: #loop until we find enough
- x = random.randint(0, cols - 1)
- y = random.randint(0, rows - 1)
- #print x, y
- tmpPixel = [x, y, -9999] # a random pixel in the entire image
- if useProbSurf:
- # if they supplied a probability surface ignore the random pixel
- # if a random number between 1 and 100 is > the probability surface value
- pixelProb = int(band.ReadAsArray(tmpPixel[0], tmpPixel[1], 1, 1)[0,0])
- #pixelProb is the extracted probability from the probability surface
- rand = random.randint(1,100)
- #rand is a uniform random integer between 1 and 100 inclusive
- if rand > pixelProb:
- continue
- #don't record this pixel in our output file
- #because our rand number was lower (or equal) than that pixel's probability
-
- #convert our outValues for row, col to coordinates
- tmpPixel[0] = xOrigin + tmpPixel[0] * pixelWidth
- tmpPixel[1] = yOrigin + tmpPixel[1] * pixelHeight
-
- fOut.writerow(tmpPixel)
- foundPoints += 1
- if self.verbose:
- if float(foundPoints)/self.pointcount > float(pcntDone)/100:
- pcntDone += 10
- print str(pcntDone) + "...",
- print "Done!\n"
- oFile.close()
- del fOut
-
- def getRasters(self, directory):
- #the list of rasters in the given directory
- rasters = []
- dirList = os.listdir(directory)
- for file in [elem for elem in dirList if elem[-4:].lower() == ".tif"]:
- if isRaster(os.path.join(directory, file)):
- rasters.append(os.path.join(directory, file))
- for file in [elem for elem in dirList if elem[-4:].lower() == ".asc"]:
- if isRaster(os.path.join(directory,file)):
- rasters.append(os.path.join(directory, file))
- for folder in [name for name in dirList if os.path.isdir(os.path.join(directory, name)) ]:
- if isRaster(os.path.join(directory, folder)):
- rasters.append(os.path.join(directory, folder))
-
- return rasters
-
- def isRaster(self, filePath):
- '''Verifies that a pased file and path is recognized by
- GDAL as a raster file.
- '''
- try:
- dataset = gdal.Open(filePath, gdalconst.GA_ReadOnly)
- if dataset is None:
- return False
- else:
- return True
- del dataset
- except:
- return False
-
- def getND(self, raster):
- dataset = gdal.Open(raster, gdalconst.GA_ReadOnly)
- ND = dataset.GetRasterBand(1).GetNoDataValue()
- if ND is None:
- if dataset.GetRasterBand(1).DataType == 1:
- print "Warning: Could not extract NoData value. Using assumed nodata value of 255"
- return 255
- elif dataset.GetRasterBand(1).DataType == 2:
- print "Warning: Could not extract NoData value. Using assumed nodata value of 65536"
- return 65536
- elif dataset.GetRasterBand(1).DataType == 3:
- print "Warning: Could not extract NoData value. Using assumed nodata value of 32767"
- return 32767
- elif dataset.GetRasterBand(1).DataType == 4:
- print "Warning: Could not extract NoData value. Using assumed nodata value of 2147483647"
- return 2147483647
- elif dataset.GetRasterBand(1).DataType == 5:
- print "Warning: Could not extract NoData value. Using assumed nodata value of 2147483647"
- return 2147483647
- elif dataset.GetRasterBand(1).DataType == 6:
- print "Warning: Could not extract NoData value. Using assumed nodata value of -3.40282346639e+038"
- return -3.40282346639e+038
- else:
- return None
- else:
- return ND
-
-def main(argv):
-
- usageStmt = "usage: options: -f --fieldData -i --inCSV -o --output -pc --pointcount -ps --probsurf"
- desc = "Creates a merged dataset file (mds) from a csv of field points and rasters located in a csv listing one raster per line. Optionally this module adds a number of background points to the output."
- parser = OptionParser(usage=usageStmt, description=desc)
-
- parser.add_option("-v",
- dest="verbose",
- default=False,
- action="store_true",
- help="the verbose flag causes diagnostic output to print")
- parser.add_option("-f", "--fieldData",
- dest="fieldData",
- help="The input CSV of field data points")
- parser.add_option("-i", "--inCSV",
- dest="inputsCSV",
- help="The input CSV containing a list of our inputs, one per line.")
- parser.add_option("-o", "--output",
- dest="outputMDS",
- help="Output MDS file to save to.")
- parser.add_option("-p", "--probsurf",
- dest="probsurf",
- default='',
- help="Probability surface to use for generation of background points (optional)")
- parser.add_option("-c", "--pointcount",
- dest="pointcount",
- default=0,
- help="Number of random background points to add(optional)")
-
- (options, args) = parser.parse_args(argv)
-
- ourMDS = MDSBuilder()
- ourMDS.verbose = options.verbose
- ourMDS.fieldData = options.fieldData
- ourMDS.inputsCSV = options.inputsCSV
- ourMDS.probsurf = options.probsurf
- ourMDS.pointcount = options.pointcount
- ourMDS.outputMDS = options.outputMDS
- ourMDS.run()
-
-
-if __name__ == '__main__':
- sys.exit(main(sys.argv))
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/MaxentRunner.py b/contrib/sahm/pySAHM/MaxentRunner.py
deleted file mode 100644
index fa8b762..0000000
--- a/contrib/sahm/pySAHM/MaxentRunner.py
+++ /dev/null
@@ -1,319 +0,0 @@
-'''
-Created on Sep 17, 2010
-
- at author: talbertc
-'''
-
-import time
-import os, sys
-import csv
-import itertools
-import traceback
-
-import subprocess
-
-from optparse import OptionParser
-
-#from core.modules.vistrails_module import Module, ModuleError, ModuleConnector
-#from core.system import execute_cmdline
-
-
-
-import utilities
-#from packages.sahm.pySAHM.Utilites import self.writetolog
-
-from osgeo import gdalconst
-from osgeo import gdal
-from osgeo import osr
-
-class MAXENTRunner(object):
-
- def __init__(self):
- self.verbose = False
- self.maxentpath = ''
- self.inputMDS = ''
- self.projectionlayers = ''
- self.testCSV = ''
- self.trainingCSV = ''
- self.backgroundCSV = ''
- self.outputDir = ''
- self.categoricals = []
- self.argsCSV = ''
- self.logger = None
-
- def run(self):
- self.loadArgs()
- self.args['outputdirectory'] = self.outputDir
-
-# if self.projectionlayers <> '':
-# #A command line input overrides an input in the args csv
-# self.args['projectionlayers'] = self.projectionlayers
-#
- self.validateInputs()
-
- if self.inputMDS <> '':
- self.prepInputs()
- else:
- raise Exception, "No MDS supplied."
-
- if not self.args.has_key('projectionlayers'):
- self.args['projectionlayers'] = ''
-
- if self.trainingCSV <> '':
- self.args['samplesfile'] = self.trainingCSV
- else:
- raise Exception, "No Samples file supplied"
-
- if self.testCSV <> '':
- self.args['testsamplesfile'] = self.testCSV
-
- if self.backgroundCSV <> '':
- self.args['environmentallayers'] = self.backgroundCSV
-
-
- self.args['autorun'] = 'true'
- #self.args['outputgrids'] = 'false'
-
- if ' ' in self.args['species_name']:
- self.args['species_name'] = self.args['species_name'].replace(' ', '_')
-
- strargs = ['='.join((str(k),str(v))) for k,v in self.args.iteritems() if k <> "species_name"]
- for categorical in self.categoricals:
- strargs += ['togglelayertype=' + categorical.replace('_categorical', '')]
- #strargs = ' '.join(strargs)
- #print strargs
-
- if not self.maxentpath.endswith('.jar'):
- jar = os.path.join(self.maxentpath, 'maxent.jar')
- else:
- jar = self.maxentpath
-
- self.run_cmd_line_jar(jar, strargs)
-
-
- def run_cmd_line_jar(self, jar_name, args):
- #arg_items = list(itertools.chain(*args.items()))
- #arg_items = ['='.join((str(k),str(v))) for k,v in args.iteritems()]
-
- cmd = ' '.join(['java', '-mx512m', '-jar', jar_name] + args)
-
- self.writetolog(' running: ' + cmd, True, False)
- #res = execute_cmdline(['java', '-jar', jar_name] + args, output)
- p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
- self.writetolog(' Finished running: ', True, False)
-
-
- ret = p.communicate()
- self.writetolog(' Maxent strOut: ' + str(ret[0]))
- if ret[1] is not None:
- msg = "An error was encountered running the Maxent jar file. The error message is below - \n"
- msg += ret[1]
- writetolog(msg)
- raise RuntimeError , msg
- del ret
-
- def loadArgs(self):
- argsReader = csv.reader(open(self.argsCSV, 'r'))
- header = argsReader.next()
- self.args = {}
- for row in argsReader:
- self.args[row[0]] = row[1]
-
- def validateInputs(self):
- if not os.path.exists(self.argsCSV):
- raise RuntimeError(self, 'Input argsFile, ' + self.argsCSV + ', could not be found on file system')
-
- if not os.path.exists(self.inputMDS):
- raise RuntimeError(self, 'Input MDS, ' + self.inputMDS + ', could not be found on file system')
-
- if not self.args.has_key('projectionlayers'):
- self.args['projectionlayers'] = ''
-
- if self.args['projectionlayers'] <> '':
- dirs = self.args['projectionlayers'].split(',')
- for dir in dirs:
- if not os.path.isdir(dir):
- raise RuntimeError(self, "Input 'projectionlayers' must be a directory")
-
- if not utilities.isMDSFile(self.inputMDS):
- raise RuntimeError(self, 'Input MDS, ' + self.inputMDS + ', does not appear to be formated as an MDS file.')
-
- if not os.path.exists(self.outputDir):
- raise RuntimeError(self, 'Output directory, ' + self.outputDir + ', could not be found on file system')
-
- if self.logger is None:
- self.logger = utilities.logger(outDir, self.verbose)
- self.writetolog = self.logger.writetolog
-
- def prepInputs(self):
- '''parses out input MDS file into the 1 to 3 SWD files that Maxent requires.
- '''
-
- #Create the outputs in our outputdirectory
- self.testCSV = os.path.join(self.outputDir, 'testSamples.csv')
- self.trainingCSV = os.path.join(self.outputDir, 'trainingSamples.csv')
- self.backgroundCSV = os.path.join(self.outputDir, 'backgroundPoints.csv')
-
- testWriter = csv.writer(open(self.testCSV, 'wb'))
- trainingWriter = csv.writer(open(self.trainingCSV, 'wb'))
- backgroundWriter = csv.writer(open(self.backgroundCSV, 'wb'))
-
- #Read through the MDS and pull the headers
- MDSreader = csv.reader(open(self.inputMDS, 'r'))
- header1 = MDSreader.next()
- header2 = MDSreader.next()
- header3 = MDSreader.next()
-
- self.pullCategoricals(header1)
-
- #The split column indicates that this file has been run through the
- #test training split and testing data should be writen to the test file.
- splitcol = None
- try:
- splitcol = header1.index('Split')
- deleteTest = False
- except ValueError:
- self.writetolog(" The supplied MDS does not have a 'Split' column defaulting to having Maxent apply test/training split.")
- deleteTest = True
-
- covariateIndexes = self.usedIndexes(header1, header2)
- covariateNames = self.usedValues(header1, covariateIndexes)
- covariateNamesClean = [name.replace('_categorical', '') for name in covariateNames]
- usedCovariateFiles = self.usedValues(header3, covariateIndexes)
-
- self.writetolog(' Used covariates:' + ", ".join(covariateNames), False, False)
-
- testWriter.writerow(['full_name', 'x', 'y'] + covariateNamesClean)
- trainingWriter.writerow(['full_name', 'x', 'y'] + covariateNamesClean)
- backgroundWriter.writerow(['full_name', 'x', 'y'] + covariateNamesClean)
-
- #loop through the rows sending each row to the appropriate file
- hasBackground = False
- for row in MDSreader:
- if row[2] == '-9999':
- hasBackground = True
- vals = self.usedValues(row, covariateIndexes)
- backgroundWriter.writerow([''] + row[:2] + vals)
- elif splitcol is None and row[2] <> 0:
- vals = self.usedValues(row, covariateIndexes)
- trainingWriter.writerow([self.args['species_name']] + row[:2] + vals)
- elif (row[splitcol] == 'test' and row[2] <> 0) or \
- self.testCSV == '':
- vals = self.usedValues(row, covariateIndexes)
- testWriter.writerow([self.args['species_name']] + row[:2] + vals)
- elif row[splitcol] == 'train' and row[2] <> 0:
- vals = self.usedValues(row, covariateIndexes)
- trainingWriter.writerow([self.args['species_name']] + row[:2] + vals)
- #any absense points (row[2] == 0) will be ignored for maxent
-
- if not hasBackground:
- msg = " No background points were detected in the input file."
- msg += "\n This implementation of Maxent does not have access to prepared ASCII environmental layers"
- msg += " from which to extract values. Background points must be supplied in the MDS file."
- self.writetolog(msg)
- raise RuntimeError(msg)
-
- #del our writers
- try:
- del testWriter
- if deleteTest:
- os.remove(self.testCSV)
- self.testCSV = ''
- del backgroundWriter
- if not hasBackground:
- os.remove(self.backgroundCSV)
- self.backgroundCSV = ''
- del trainingWriter
- except:
- print ' '.join([str(i) for i in sys.exc_info()[:2]])
- pass
-
- #First we have to figure out what they passed us
- #either a directory, a SWD file, or a csv with a list of files
-
- if self.args['projectionlayers'] <> '':
- pass
- else:
- self.args['outputgrids'] = 'false'
-
- def usedIndexes(self, header1, header2):
- covariateIndexes = []
- for i in range(len(header1)):
- if header2[i] == '1' and header1[i] <> 'Split':
- covariateIndexes.append(i)
- return covariateIndexes
-
- def usedValues(self, values, indexes):
- usedvals = []
- for i in indexes:
- usedvals.append(values[i])
- return usedvals
-
- def pullCategoricals(self, headerline):
- for item in headerline:
- if item.endswith('_categorical'):
- self.categoricals.append(item)
-
-
- def isSWD(self, file):
- '''Checks the format of a file to see if it is in the
- Maxent samples with data (SWD) format.
- '''
- if os.path.exists(file):
- reader = csv.reader(open(file, 'r'))
- header = reader.next()
- if header[0].lower() in ['species', 'full_name', 'fullname']:
- return True
-
- return False
-
-
-def main(argv):
- '''Process our command line args and initiate a Maxent run
- '''
- usageStmt = "usage: -m --MDSFile -a --argsCSV -o --outputDir"
- desc = "Formats and prepares input for running the Maxent Jar in a SAHM workflow"
-
- parser = OptionParser(usage=usageStmt, description=desc)
- parser.add_option("-m", "--MDSFile",
- dest="MDSFile",
- help="The MDS file with our sample data.")
-# parser.add_option("-p", "--projectionData",
-# dest="projectionData",
-# help="An optional CSV with a projection file for each of our environemnetal layers.")
- parser.add_option("-a", "--argsCSV",
- dest="argsCSV",
- help="A CSV with each Maxent argument name and it's value on separate lines.")
- parser.add_option("-e", "--maxentExecutable",
- dest="maxentExecutable",
- help="The full path to the maxent executable jar file.")
- parser.add_option("-o", "--outputDir",
- dest="outputDir",
- help="The directory to save output files.")
- parser.add_option("-v", "--verbose",
- dest="verbose",
- default=False,
- action="store_true",
- help="the verbose flag causes diagnostic output to print")
-
- (options, args) = parser.parse_args(argv)
-
- ourMaxent = MAXENTRunner()
- ourMaxent.verbose = options.verbose
- ourMaxent.maxentpath = options.maxentExecutable
- ourMaxent.inputMDS = options.MDSFile
- ourMaxent.outputDir = options.outputDir
- ourMaxent.argsCSV = options.argsCSV
- ourMaxent.projectionDataFile = options.projectionData
-
- utilities.createsessionlog(options.outputDir, options.verbose)
- ourMaxent.run()
-
-if __name__ == "__main__":
- sys.exit(main(sys.argv[1:]))
-
-
-
-
-
-
diff --git a/contrib/sahm/pySAHM/PARC.py b/contrib/sahm/pySAHM/PARC.py
deleted file mode 100644
index 3417301..0000000
--- a/contrib/sahm/pySAHM/PARC.py
+++ /dev/null
@@ -1,776 +0,0 @@
-#!/usr/bin/python
-
-import glob
-import math
-import os
-import shutil
-import struct
-import sys
-import csv
-import Queue
-import thread
-import subprocess
-
-from optparse import OptionParser
-
-from osgeo import gdalconst
-from osgeo import gdal
-from osgeo import osr
-
-
-from numpy import *
-import numpy as np
-
-import utilities
-
-def main(args_in):
- """
- Process commandline Arguments,
- Create an instance of PARC with the Variables,
- Kick off the parkFiles function of our PARC instance
- """
- # Process command-line args.
- usageStmt = "usage: %prog [options] <template image> <input dir or list of input files>"
- desc = "This application projects, aggregates, resamples, and clips imagery."
-
- parser = OptionParser(usage=usageStmt, description=desc)
- parser.add_option("-l", dest="listMethodFlag", default=False, action="store_true", help="print the names of all known aggregation methods")
- parser.add_option("-o", dest="out_dir", default="./", help="directory in which to put processed images, defaults to current directory")
- parser.add_option("-v", dest="verbose", default=False, action="store_true", help="the verbose flag causes diagnostic output to print")
- parser.add_option("-t", dest="templateRaster", help="The template raster used for projection, origin, cell size and extent")
- parser.add_option("-i", dest="inputs_CSV", help="The CSV containing the list of files to process. Format is 'FilePath, Categorical, Resampling, Aggreagtion")
- parser.add_option("-m", dest="multicore", default=True, help="'True', 'False' indicating whether to use multiple cores or not")
- (options, args) = parser.parse_args(args_in)
-
- ourPARC = PARC()
- ourPARC.verbose = options.verbose
- ourPARC.template = options.templateRaster
- ourPARC.out_dir = options.out_dir
- ourPARC.inputs_CSV = options.inputs_CSV
- ourPARC.multicores = options.multicore
- ourPARC.parcFiles()
-
-class PARC:
- '''
- PARC: Project, Aggregate, Resample, Clip
- The workflow on this beast is as follows:
- For each dataset
- Step 1: RePrject the source raster into a tmp raster using
- the projection info from the template and the method if
- supplied or the default of nearest if not.
- At this stage the tmp output will have a cell size about
- the same as the input. We just use the default for this
- setting.
- Step 2: Aggregate the tmpRaster to have the same origin,
- cell size and extent as our template.
- '''
-
- def __init__(self):
- #instance level variables
- self.verbose = False
- self.template = ""
- self.template_params = {}
- self.out_dir = ""
- self.inputs_CSV = ''
- self.inputs = []
- self.agg_methods = ['Min', 'Mean', 'Max', 'Majority']
- self.resample_methods = ['NearestNeighbor', 'Bilinear', 'Cubic', 'CubicSpline', 'Lanczos']
- self.logger = None
- self.multicores = 'False'
- self.module = None
-
- def parcFiles(self):
- '''
- 1: Parse the inputs_CSV into our inputs list
- 2: Make sure all of our instance variables are good and proper
- 3: Loop through the list of sourceImages and PARC each one.
- 4: The outputs will be stored in the output directory
- 5: Additionally an output CSV will be produced that lists the
- inputs, parameters used, and outputs
- '''
-
- self.logger.writetolog("Starting PARC", True, True)
- self.validateArgs()
- self.logger.writetolog(" Arguments validated successfully", True, True)
- if self.multicores.lower() in ['true', 'yes', 't', 'y', '1']:
- self.processFilesMC()
- else:
- self.processFiles()
-
- self.logger.writetolog("Finished PARC", True, True)
-
- def processFiles(self):
- # Clip and reproject each source image.
- for image in self.inputs:
- # Ensure source is different from template.
- #if not os.path.samefile(template, image):
- inPath, inFileName = os.path.split(image[0])
- outFile, ext = os.path.splitext(inFileName)
- outFile = os.path.join(self.out_dir, outFile + ".tif")
-
- # os.path.samefile(image, outFile):
- if os.path.exists(outFile) and \
- os.path.abspath(image[0]) == os.path.abspath(outFile):
-
- baseName, extension = os.path.splitext(outFile)
- outFile = baseName + "-PARC.tif"
-
- if os.path.abspath(self.template) != os.path.abspath(image[0]):
- self.parcFile(image, outFile)
- elif os.path.abspath(self.template) == os.path.abspath(image[0]):
- shutil.copyfile(self.template, outFile)
-
-
-
- def processFilesMC(self):
- '''This function has the same functionality as parcFiles
- with the addition of utilizing multiple cores to do the processing.
- '''
- results= Queue.Queue()
- process_count= 0
-
- for image in self.inputs:
- # Ensure source is different from template.
- #if not os.path.samefile(template, image):
- inPath, inFileName = os.path.split(image[0])
- outFile, ext = os.path.splitext(inFileName)
- outFile = os.path.join(self.out_dir, outFile + ".tif")
-
- # os.path.samefile(image, outFile):
- if os.path.exists(outFile) and \
- os.path.abspath(image[0]) == os.path.abspath(outFile):
-
- baseName, extension = os.path.splitext(outFile)
- outFile = baseName + "-PARC.tif"
-
- if os.path.abspath(self.template) != os.path.abspath(image[0]):
- image_short_name = os.path.split(image[0])[1]
- args = '-s ' + '"' + os.path.abspath(image[0]) + '"'
- args += ' -c ' + '"' + image[1] + '"'
- args += ' -d ' + os.path.abspath(outFile)
- args += ' -t ' + os.path.abspath(self.template)
- args += ' -r ' + image[2]
- args += ' -a ' + image[3]
-
- execDir = os.path.split(__file__)[0]
- executable = os.path.join(execDir, 'singlePARC.py')
-
- pyEx = sys.executable
- command = ' '.join([pyEx, executable, args])
- self.logger.writetolog(command, False, False)
- proc = subprocess.Popen( command )
- thread.start_new_thread(utilities.process_waiter,
- (proc, image_short_name, results))
- process_count+= 1
-
- while process_count > 0:
- description, rc= results.get()
-
- if rc == 0:
- if self.verbose:
- msg = " " + description + " finished successfully: " + \
- str(len(self.inputs) - process_count + 1) + " done out of " \
- + str(len(self.inputs))
- self.logger.writetolog(msg, True, True)
- else:
- self.logger.writetolog("There was a problem with: " + description , True, True)
- process_count-= 1
-
-
-
- self.logger.writetolog("Finished PARC", True, True)
-
- def parcFile(self, source, dest):
- """
- Processes a single file
- """
- gdal.UseExceptions()
-
- shortName = os.path.split(os.path.splitext(source[0])[0])[1]
- self.logger.writetolog(" Starting processing of " + source[0])
- sourceParams = self.getRasterParams(source[0])
-
- gdalType = None
- if source[2].lower() == "nearestneighbor":
- gdalType = gdalconst.GRA_NearestNeighbour
- if source[2].lower() == "bilinear":
- gdalType = gdalconst.GRA_Bilinear
- if source[2].lower() == "cubic":
- gdalType = gdalconst.GRA_Cubic
- if source[2].lower() == "cubicspline":
- gdalType = gdalconst.GRA_CubicSpline
- if source[2].lower() == "lanczos":
- gdalType = gdalconst.GRA_Lanczos
- if gdalType == None:
- self.logger.writetolog(" Specified resampling method (" + source[2] + ") not one of 'NearestNeighbor', 'Bilinear', 'Cubic', 'CubicSpline', or 'Lanczos'. Defaulting to 'NearestNeighbor'")
- gdalType = gdalconst.GRA_NearestNeighbour
-
- #Open dgal dataset of the source to pull some values from
- srcDs = gdal.Open(source[0])
-
- cellRatio = self.getTemplateSRSCellSize(sourceParams)/self.template_params["xScale"]
- msg = " ratio of source cell size to template cell size = " + str(cellRatio)
- msg += " template cell size = " + str(self.template_params["xScale"])
- msg += " " + shortName + " cell size = " + str(self.getTemplateSRSCellSize(sourceParams))
- self.writetolog(msg)
-
- if cellRatio > 0.5:
- #The source cell size is close enough to our template cell size,
- #or smaller so
- #that all we need to do is reproject and resample.
- self.logger.writetolog(" cell ratio > .5: reprojecting and resampling to template parameters only")
- self.reprojectRaster(srcDs, sourceParams, self.template_params, dest,
- gdalType, shortName, self.template_params["xScale"])
- else:
- #Our Target cell size is much bigger than our source we need to do
- #some aggregation to make things work.
- msg = ' cell ratio <= .5: reprojecting and resampling to template parameters'
- msg += ' then aggregating the reprojected raster to match template parameters'
- self.writetolog(msg)
-
- targetCellSize, numSourcePerTarget = self.getAggregateTargetCellSize(sourceParams)
- tmpOutput = os.path.join(os.path.dirname(dest), "tmp_" + os.path.basename(dest))
-
- self.reprojectRaster(srcDs, sourceParams, self.template_params,
- tmpOutput, gdalType, shortName, targetCellSize)
- self.writetolog(" Starting on Aggregating: " + shortName)
-
- tmpOutput2 = os.path.splitext(tmpOutput)[0] + ".tif"
- self.Aggregate(tmpOutput2, dest,
- sourceParams, self.template_params,
- source[3], numSourcePerTarget)
-
- try:
- os.remove(tmpOutput2)
- except WindowsError:
- pass
-
-
- def getTemplateSRSCellSize(self, sourceParams):
- """
- Calculate what size our source image pixels would be in the template SRS
- """
- #first convert our template origin into the source srs
- tOriginX, tOriginY = self.transformPoint(self.template_params["west"], self.template_params["north"],
- self.template_params["srs"], sourceParams["srs"])
- #next add the source xScale to the converted origin x and convert that back to template srs
- tOriginX1 = self.transformPoint (tOriginX + sourceParams["xScale"], tOriginY,
- sourceParams["srs"], self.template_params["srs"])[0]
-
-
-# templateCellXCorner1 = (self.template_params["west"], self.template_params["north"],
-# self.template_params["srs"], sourceParams["srs"])[0]
-#
-# targetCellXCorner1 = (sourceParams["west"], sourceParams["north"],
-# sourceParams["srs"], self.template_params["srs"])[0]
-# targetCellXCorner2 = self.transformPoint(sourceParams["west"] + sourceParams["xScale"],
-# sourceParams["north"], sourceParams["srs"], self.template_params["srs"])[0]
- templateSRSCellSize = abs(abs(tOriginX1) - abs(self.template_params["west"]))
- return templateSRSCellSize
-
- def getAggregateTargetCellSize(self, sourceParams):
- """
- This function determines the appropriate cell size to
- reproject/resample our source raster into before
- aggregating.
- This size is the cell size that results in a template
- cell containing a whole number of cells which are as
- close as possible to the cell dimension that would
- result if you reprojected the source cells into the
- target srs without changing cell size.
- """
- #first determine what cell size we are going to use for the initial reproject/resample
- #step 1: Determine the native cell size in the template coordinate system.
- templateSRSCellSize = self.getTemplateSRSCellSize(sourceParams)
- #step 2: round this up or down to an even fraction of the template cell size
- # for example source = 30, target = 250 resampledSource = 250/round(250/30)
- sourcePixelsPerTarget = round(self.template_params["xScale"]/templateSRSCellSize)
- nearestWholeCellSize = (self.template_params["xScale"] /
- sourcePixelsPerTarget)
- return nearestWholeCellSize, sourcePixelsPerTarget
-
-
- def Aggregate(self, inFile, outFile, sourceParams, templateParams, method=None, numSourcePerTarget=10):
- sourceDs = gdal.Open(inFile, gdalconst.GA_ReadOnly)
- sourceBand = sourceDs.GetRasterBand(1)
-
- tmpOutput = os.path.splitext(outFile)[0] + ".tif"
- tmpOutDataset = self.generateOutputDS(sourceParams, templateParams, tmpOutput)
- outBand = tmpOutDataset.GetRasterBand(1)
-
- rows = int(sourceParams["height"])
- cols = int(sourceParams["width"])
-
- row = 0
- col = 0
-
-
- pcntDone = 0.0
- if self.verbose:
- print " % Done: 0.0",
-
- while row < templateParams["width"]:
- while col < templateParams["height"]:
- sourceRow = row * numSourcePerTarget
- sourceCol = col * numSourcePerTarget
-
- #kernel = self.getKernel(sourceRow, sourceCol, numSourcePerTarget, sourceDs)
- kernel = sourceDs.GetRasterBand(1).ReadAsArray(int(sourceRow),
- int(sourceCol),
- int(numSourcePerTarget),
- int(numSourcePerTarget))
- #convert kernel values of our nodata to nan
- ndMask = ma.masked_array(kernel, mask=(kernel==sourceParams["NoData"]))
- #print kernel
- if method == "Min":
- ans = ndMask.min()
- elif method == "Max":
- ans = ndMask.max()
- elif method == "Majority":
-# ndMask = ndMask.flatten()
- uniques = np.unique(ndMask)
- curMajority = -3.40282346639e+038
- for val in uniques:
- numOccurances = (array(ndMask)==val).sum()
- if numOccurances > curMajority:
- ans = val
- curMajority = numOccurances
-
-# histogram = np.histogram(ndMask, uniques)
-# ans = histogram[1][histogram[0].argmax()]
- else:
- ans = ndMask.mean()
-
-# print ndMask
-# print ans
- #special case real ugly
- if ans < 0 and sourceParams["signedByte"]:
- ans = ans + 255
-
- ansArray = empty([1, 1])
- if type(ans) == ma.core.MaskedArray:
- ansArray[0, 0] = sourceParams["NoData"]
- else:
- ansArray[0, 0] = ans
-
- outBand.WriteArray(ansArray, row, col)
-
- col += 1
-
- row += 1
- col = 0
- if self.verbose:
- if float(row)/templateParams["width"] > float(pcntDone)/100:
- pcntDone += 2.5
- if int(pcntDone) % 10 == 0:
- print str(pcntDone),
- else:
- print ".",
- if self.verbose:
- print "Done"
-# if self.verbose:
-# print "Done\nSaving to ASCII format"
-#
-# driver = gdal.GetDriverByName("AAIGrid")
-# driver.Register()
-#
-# dst_ds = driver.CreateCopy(outFile, tmpOutDataset, 0)
-# if self.verbose:
-# print " Finished Saving ", self.shortName
-
- dst_ds = None
- tmpOutDataset=None
-
- def getRasterParams(self, rasterFile):
- """
- Extracts properties from a passed raster
- All values are stored in a dictionary which is returned.
- If errors are encountered along the way the error messages will
- be returned as a list in the 'Error' element.
- """
- try:
- #initialize our params dictionary to have None for all parma
- params = {}
- allRasterParams = ["Error", "xScale", "yScale", "width", "height",
- "east", "north", "west", "south",
- "tEast", "tNorth", "tWest", "tSouth",
- "gEast", "gNorth", "gWest", "gSouth",
- "Wkt", "srs", "gt", "prj", "NoData", "PixelType", "file_name"]
-
- for param in allRasterParams:
- params[param] = None
- params["Error"] = []
- params["file_name"] = rasterFile
-
-
- # Get the PARC parameters from the rasterFile.
- dataset = gdal.Open(rasterFile, gdalconst.GA_ReadOnly)
- if dataset is None:
- params["Error"].append("Unable to open file")
- return params
-
- #print "Unable to open " + rasterFile
- #raise Exception, "Unable to open specifed file " + rasterFile
-
-
- xform = dataset.GetGeoTransform()
- params["xScale"] = xform[1]
- params["yScale"] = xform[5]
-
- params["width"] = dataset.RasterXSize
- params["height"] = dataset.RasterYSize
-
- params["west"] = xform[0]
- params["north"] = xform[3]
- params["east"] = params["west"] + params["width"] * params["xScale"]
- params["south"] = params["north"] + params["height"] * params["yScale"]
-
- try:
- wkt = dataset.GetProjection()
- params["gt"] = dataset.GetGeoTransform()
- params["prj"] = dataset.GetProjectionRef()
- params["srs"] = osr.SpatialReference(wkt)
- if wkt == '':
- params["Error"].append("Undefined projection")
- else:
-
- if rasterFile == self.template:
- params["tWest"], params["tNorth"] = params["west"], params["north"]
- params["tEast"], params["tSouth"] = params["east"], params["south"]
- elif params["srs"].ExportToWkt() == self.template_params["srs"].ExportToWkt():
- params["tWest"], params["tNorth"] = params["west"], params["north"]
- params["tEast"], params["tSouth"] = params["east"], params["south"]
- else:
- try:
- params["tWest"], params["tNorth"] = self.transformPoint(params["west"], params["north"], params["srs"], self.template_params["srs"])
- params["tEast"], params["tSouth"] = self.transformPoint(params["east"], params["south"], params["srs"], self.template_params["srs"])
- except:
- params["Error"].append("Could not transform extent coordinates to template spatial reference")
- #params["Error"] = "We ran into problems converting projected coordinates to template for " + rasterFile
- try:
- geographic = osr.SpatialReference()
- geographic.ImportFromEPSG(4326)
- params["gWest"], params["gNorth"] = self.transformPoint(params["west"], params["north"], params["srs"], geographic)
- params["gEast"], params["gSouth"] = self.transformPoint(params["east"], params["south"], params["srs"], geographic)
- except:
- pass
-
- except:
- #print "We ran into problems getting the projection information for " + rasterFile
- params["Error"].append("Undefined problems extracting the projection information")
-
- try:
- params["signedByte"] = dataset.GetRasterBand(1).GetMetadata('IMAGE_STRUCTURE')['PIXELTYPE'] == 'SIGNEDBYTE'
- except KeyError:
- params["signedByte"] = False
-
- params["NoData"] = dataset.GetRasterBand(1).GetNoDataValue()
- if params["NoData"] == None:
- if dataset.GetRasterBand(1).DataType == 1:
- print "Warning: Could not extract NoData value. Using assumed nodata value of 255"
- params["NoData"] = 255
- elif dataset.GetRasterBand(1).DataType == 2:
- print "Warning: Could not extract NoData value. Using assumed nodata value of 65536"
- params["NoData"] = 65536
- elif dataset.GetRasterBand(1).DataType == 3:
- print "Warning: Could not extract NoData value. Using assumed nodata value of 32767"
- params["NoData"] = 32767
- elif dataset.GetRasterBand(1).DataType == 4:
- print "Warning: Could not extract NoData value. Using assumed nodata value of 2147483647"
- params["NoData"] = 2147483647
- elif dataset.GetRasterBand(1).DataType == 5:
- print "Warning: Could not extract NoData value. Using assumed nodata value of 2147483647"
- params["NoData"] = 2147483647
- elif dataset.GetRasterBand(1).DataType == 6:
- print "Warning: Could not extract NoData value. Using assumed nodata value of -3.40282346639e+038"
- params["NoData"] = -3.40282346639e+038
- else:
- params["Error"].append("Could not identify nodata value")
- params["PixelType"] = dataset.GetRasterBand(1).DataType
- if params["PixelType"] == None:
- params["Error"].append("Could not identify pixel type (bit depth)")
-
- except:
- #print "We ran into problems extracting raster parameters from " + rasterFile
- params["Error"].append("Some untrapped error was encountered")
- finally:
- del dataset
- return params
-
- def transformPoint(self, x, y, from_srs, to_srs):
- """
- Transforms a point from one srs to another
- """
- coordXform = osr.CoordinateTransformation(from_srs, to_srs)
- yRound = round(y, 4)
- xRound = round(x, 4)
-
- result = coordXform.TransformPoint(xRound, yRound)
-
- gx = result[0]
- gy = result[1]
-
- return gx, gy
-
- def ImageCoversTemplate(self, sourceParams):
- """
- Checks to see if the template images
- falls completely inside the source raster
-
- it does this by generating a list of 16 coordinate
- pairs equally distributed across the template,
- including the four absolute corners.
- These points are in the CRS of the image.
- If all of these points have a valid data or nodata
- value in the image, then the image covers the template.
- (in nearly every case anyway)
- """
-
- n = 5
- xOffset = (self.template_params["east"] - self.template_params["west"]) / (n) - \
- ((self.template_params["east"] - self.template_params["west"]) / self.template_params["width"] / 1000)
- yOffset = (self.template_params["north"] - self.template_params["south"]) / (n) - \
- ((self.template_params["north"] - self.template_params["south"]) / self.template_params["height"] / 1000)
- curX = self.template_params["west"]
- curY = self.template_params["north"]
- testPoints =[]
-
- for x in range(n + 1):
- for y in range(n + 1):
- testPoints.append(self.transformPoint(curX, curY, self.template_params["srs"],
- sourceParams["srs"]))
- curY -= yOffset
-
- curX += xOffset
- curY = self.template_params["north"]
-
- rasterDS = gdal.Open(sourceParams["file_name"], gdalconst.GA_ReadOnly)
- band = rasterDS.GetRasterBand(1)
- badPoint = False
- for point in testPoints:
- try:
- xOffset = int((point[0] - sourceParams["west"]) / sourceParams["xScale"])
- yOffset = int((point[1] - sourceParams["north"]) / sourceParams["yScale"])
- data = band.ReadAsArray(xOffset, yOffset, 1, 1)
- value = data[0,0]
- except:
- badPoint = True
-
- #if valid values were returned from each of our points then
- #the template falls entirely within the Source image.
- if badPoint:
- return False
- else:
- return True
-
-
- def validateArgs(self):
- """
- Make sure the user sent us some stuff we can work with
- """
-
- if not os.path.exists(self.out_dir):
- raise utilities.TrappedError("Specified Output directory " + self.out_dir + " not found on file system")
-
- if not os.path.isdir(self.out_dir):
- raise utilities.TrappedError("Specified Output directory " + self.out_dir + " is not a directory")
-
- if self.logger is None:
- self.logger = utilities.logger(self.out_dir, self.verbose)
- self.writetolog = self.logger.writetolog
-
- # Validate template image.
- if self.template is None:
- raise utilities.TrappedError("template raster not provided.")
-
- if not os.path.exists(self.template):
- raise utilities.TrappedError("Template file, " + self.template + ", does not exist on file system")
-
- self.template_params = self.getRasterParams(self.template)
- if len(self.template_params["Error"]) <> 0:
- raise utilities.TrappedError("There was a problem with the provided template: \n " +
- " " + "\n ".join(self.template_params["Error"]))
-
- # Ensure the template has square pixels.
- if abs(abs(self.template_params["xScale"]) - abs(self.template_params["yScale"])) > 1e-6:
- raise utilities.TrappedError("template image must have square pixels." +
- "/n x pixel scale = " + str(xScale) +
- "/n y pixel scale = " + str(yScale))
-
-
- #Validate input rasters
- if not os.path.exists(self.inputs_CSV):
- raise utilities.TrappedError("Inputs CSV, " + self.inputs_CSV + ", does not exist on file system.")
-
- inputsCSV = csv.reader(open(self.inputs_CSV, 'r'))
- header = inputsCSV.next()
- strInputFileErrors = ""
-
- outputCSV = os.path.join(self.out_dir, "PARC_Files.csv")
- output = csv.writer(open(outputCSV, "wb"))
- output.writerow(["PARCOutputFile", "Categorical", "Resampling", "Aggregation", "OriginalFile", os.path.abspath(self.template), os.path.abspath(self.out_dir)])
-
- for row in inputsCSV:
- inputFile = row[0]
- sourceParams = self.getRasterParams(inputFile)
- if len(sourceParams["Error"]) > 0:
- strInputFileErrors += (" " + os.path.split(inputFile)[1] + " had the following errors:\n" +
- " " + "\n ".join(sourceParams["Error"])) + "\n"
- else:
- pass
- if not self.ImageCoversTemplate(sourceParams):
- strInputFileErrors += ("\n Some part of the template image falls outside of " + os.path.split(inputFile)[1])
- strInputFileErrors += "\n template upper left = (" + str(self.template_params["gWest"]) + ", " + str(self.template_params["gNorth"]) + ")"
- strInputFileErrors += "\n template lower right = (" + str(self.template_params["gEast"]) + ", " + str(self.template_params["gSouth"]) + ")"
- strInputFileErrors += "\n image upper left = (" + str(sourceParams["gWest"]) + ", " + str(sourceParams["gNorth"]) + ")"
- strInputFileErrors += "\n image lower right = (" + str(sourceParams["gEast"]) + ", " + str(sourceParams["gSouth"]) + ")"
-# strInputFileErrors += "\n points are given in projected coordinates."
-# strInputFileErrors += "\n template upper left = (" + str(self.template_params["tWest"]) + ", " + str(self.template_params["tNorth"]) + ")"
-# strInputFileErrors += "\n template lower right = (" + str(self.template_params["tEast"]) + ", " + str(self.template_params["tSouth"]) + ")"
-# strInputFileErrors += "\n image upper left = (" + str(sourceParams["tWest"]) + ", " + str(sourceParams["tNorth"]) + ")"
-# strInputFileErrors += "\n image lower right = (" + str(sourceParams["tEast"]) + ", " + str(sourceParams["tSouth"]) + ")"
-# strInputFileErrors += "\n Note: points are given in the template coordinates." + "\n"
-#
- if len(row) < 2 or not row[1] in ['0', '1']:
- self.writetolog(" " + os.path.split(inputFile)[1] + " categorical either missing or not 0 or 1:\n Defaulting to 0 (continuous)")
- if len(row) < 2:
- row.append('0')
- else:
- row[1] = '0'
-
- if len(row) < 3 or not row[2].lower() in [item.lower() for item in self.resample_methods]:
- self.writetolog(" " + os.path.split(inputFile)[1] + " resample method either missing or not one of " +
- ", ".join(self.resample_methods) + "\n Defaulting to 'Bilinear'")
-
- if row[1] == '0':
- default = 'Bilinear'
- else:
- default = 'NearestNeighbor'
- if len(row) < 3:
- row.append(default)
- else:
- row[2] = default
-
- if len(row) < 4 or not row[3].lower() in [item.lower() for item in self.agg_methods]:
- self.writetolog(" " + os.path.split(inputFile)[1] + " aggregation method either missing or not one of " +
- ", ".join(self.agg_methods) + "\n Defaulting to 'Mean'")
- if row[1] == '0':
- default = 'Mean'
- else:
- default = 'Majority'
- if len(row) < 4:
- row.append(default)
- else:
- row[3] = default
-
- self.inputs.append(row)
- #also write the output row, reconfigured to our output file
- fileName = self.getShortName(row[0])
- fileName = os.path.abspath(os.path.join(self.out_dir, fileName + ".tif"))
- outputrow = [fileName] + row[1:4] + [os.path.abspath(row[0]), os.path.abspath(self.out_dir)]
- output.writerow(outputrow)
- del output
-
- if strInputFileErrors <> "":
- self.writetolog(strInputFileErrors)
- raise utilities.TrappedError("There was one or more problems with your input rasters: \n" + strInputFileErrors)
-
- def reprojectRaster(self, srcDs, sourceParams, templateParams,
- destFile, resamplingType, shortName='', outputCellSize = None):
- """
- Reprojects a raster to match the template_params
- if outputCellSize is not provided defaults to the template cellSize
- """
-# driver = gdal.GetDriverByName("AAIGrid")
-# driver.Register()
-
- tmpOutput = os.path.splitext(destFile)[0] + ".tif"
-
- tmpOutDataset = self.generateOutputDS(sourceParams, templateParams, tmpOutput, outputCellSize)
-
- self.writetolog(" Starting intermediate reprojection of: " + shortName)
-
- err = gdal.ReprojectImage(srcDs, tmpOutDataset, sourceParams["srs"].ExportToWkt(),
- templateParams["srs"].ExportToWkt(), resamplingType)
-
-# dst_ds = driver.CreateCopy(destFile, tmpOutDataset, 0)
- self.writetolog(" Finished reprojection " + shortName)
- dst_ds = None
- tmpOutDataset = None
-
- def generateOutputDS(self, sourceParams, templateParams,
- tmpOutput, outputCellSize = None):
- """
- Creates an output dataset (tiff format) that
- has the nodata value of the sourceParams but
- all other attributes from the template_params
- This output is saved to tmpOutput.
-
- The optional cell size will override the cell size
- specified in the template_params
- """
- tifDriver = gdal.GetDriverByName("GTiff")
-
- if outputCellSize == None:
- width = templateParams["width"]
- height = templateParams["height"]
- else:
- width = templateParams["width"] * int(templateParams["xScale"]/outputCellSize)
- height = templateParams["height"] * int(templateParams["xScale"]/outputCellSize)
-
- if sourceParams["signedByte"]:
- tmpOutDataset = tifDriver.Create(tmpOutput,
- width,
- height,
- 1, sourceParams["PixelType"], ["PIXELTYPE=SIGNEDBYTE"])
- else:
- tmpOutDataset = tifDriver.Create(tmpOutput,
- width,
- height,
- 1, sourceParams["PixelType"])
-
-
- if outputCellSize == None:
- outputCellSize = templateParams["xScale"]
- gtList = list(templateParams["gt"])
- if templateParams["xScale"] < 0:
- gtList[1] = -1 * outputCellSize
- else:
- gtList[1] = outputCellSize
- if templateParams["yScale"] < 0:
- gtList[5] = -1 * outputCellSize
- else:
- gtList[5] = outputCellSize
- gt = tuple(gtList)
-
- tmpOutDataset.SetGeoTransform(gt)
- tmpOutDataset.SetProjection(templateParams["prj"])
- tmpOutDataset.GetRasterBand(1).SetNoDataValue(sourceParams["NoData"])
- if sourceParams["signedByte"]:
- #tmpOutDataset.GetRasterBand(1).SetMetadataItem('PIXELTYPE', "SIGNEDBYTE")
- tmpOutDataset.GetRasterBand(1).PixelType = "SIGNEDBYTE"
- tmpOutDataset.GetRasterBand(1).SetMetadata({'PIXELTYPE': 'SIGNEDBYTE'}, 'IMAGE_STRUCTURE')
-
-# if self.verbose:
-# print tmpOutput
-# print "noDataValue = ", tmpOutDataset.GetRasterBand(1).GetNoDataValue()
-# print "Pixel type = ", gdal.GetDataTypeName(tmpOutDataset.GetRasterBand(1).DataType)
- return tmpOutDataset
-
- def getShortName(self, fullPathName):
- if fullPathName.endswith('hdr.adf'):
- shortname = os.path.split(fullPathName)[0]
- shortname = os.path.split(shortname)[1]
- else:
- shortname = os.path.split(fullPathName)[1]
- shortname = os.path.splitext(shortname)[0]
- return shortname
-
-if __name__ == "__main__":
- sys.exit(main(sys.argv[1:]))
-# try:
-## PARC().testing()
-# sys.exit(PARC().main(sys.argv[1:]))
-# except Exception as e:
-# print e
-# sys.exit(1)
diff --git a/contrib/sahm/pySAHM/RasterFormatConverter.py b/contrib/sahm/pySAHM/RasterFormatConverter.py
deleted file mode 100644
index 9004bd7..0000000
--- a/contrib/sahm/pySAHM/RasterFormatConverter.py
+++ /dev/null
@@ -1,204 +0,0 @@
-#!/usr/bin/python
-'''Takes an MDS file and converts all of the tiff files into
-ascii format in a supplied directory
-The optional parameter format can be used to specify other
-conversion types.
-'''
-import sys
-import csv
-import os
-import time
-import random
-import shutil
-
-import Queue
-import thread
-import subprocess
-
-from osgeo import gdalconst
-from osgeo import gdal
-
-from optparse import OptionParser
-
-import utilities
-from utilities import isMDSFile
-
-class FormatConverter(object):
- def __init__(self):
- #instance level variables
- self.verbose = False
- self.MDSFile = ''
- self.inputDir = ''
- self.outputDir = ''
- self.format = 'asc'
- self.logger = None
- self.multicore = True
- self.driverExt = {'asc':'AAIGrid', 'bil':'EHdr', 'img':'HFA', 'jpg':'JPEG'}
-
- def run(self):
- self.validateArgs()
- if self.MDSFile <> '':
- usedTifs = self.extractFileNames()
- else:
- usedTifs = self.fileNamesFromFolder()
- #self.writetolog(' Converting: ' + ','.join(usedTifs))
- if self.multicore:
- self.convertEnvironmentalLayers_mc(usedTifs, self.outputDir, self.format)
- else:
- self.convertEnvironmentalLayers(usedTifs, self.outputDir, self.format)
-
- def validateArgs(self):
- argProblem = ""
-
- if self.logger is None:
- self.logger = utilities.logger(outDir, self.verbose)
- self.writetolog = self.logger.writetolog
-
- if os.path.isdir(self.inputDir):
- pass
- elif os.path.exists(self.MDSFile):
- if not isMDSFile(self.MDSFile):
- argProblem += "The supplied MDS file, " + self.MDSFile + ", does not appear to be in the appropriate format."
- else:
- argProblem += "Neither an input Directory or MDS File was supplied."
-
- if not os.path.isdir(self.outputDir):
- try:
- os.mkdir(self.outputDir)
- except:
- argProblem += 'The supplied output directory, ' + self.outputDir + ", does not exist and could not be created."
- if not self.format.lower() in self.driverExt.keys():
- argProblem += "The supplied format must be one of " + ", ".join(self.driverExt.keys())
-
- if argProblem:
- raise utilities.TrappedError("There was a problem with one or more of the inputs to RasterFormatConverter")
-
- def extractFileNames(self):
- #Read through the MDS and pull the headers
- MDSreader = csv.reader(open(self.MDSFile, 'r'))
- header1 = MDSreader.next()
- header2 = MDSreader.next()
- header3 = MDSreader.next()
-
- usedTifs = []
- for i in range(3, len(header1)):
- if header2[i] == '1' and header1[i] <> 'Split':
- usedTifs.append(header3[i])
- return usedTifs
-
- def fileNamesFromFolder(self):
- usedRasters = []
- items = os.listdir(self.inputDir)
- for item in items:
-# print item
- fullPath = os.path.join(self.inputDir, item)
- try:
- if os.path.isdir(fullPath) or \
- os.path.splitext(item)[1].lower() in \
- ['.bil', '.img', '.tif', '.jpg', '.bmp', '.asc']:
- inds = None
- inds = gdal.Open(fullPath, gdalconst.GA_ReadOnly)
- if inds is not None:
- usedRasters.append(fullPath)
- except:
- pass
- return usedRasters
-
- def convertEnvironmentalLayers(self, files, outputFolder, type):
-
- i = 1
- for f in files:
- f_name = os.path.splitext(os.path.split(f)[1])[0]
- self.writetolog(' Starting on ' + f_name)
- outputfile = os.path.join(outputFolder, f_name + '.' + type)
- self.convertFormat(f, outputfile, self.driverExt[type])
- if self.verbose:
- self.writetolog(' Finished converting ' + f_name + ' ' + str(i) + ' out of ' + str(len(files)) + ' finished.')
- i += 1
-
- def convertEnvironmentalLayers_mc(self, files, outputFolder, type):
- '''This function has the same functionality as convertEnvironmentalLayers
- with the addition of utilizing multiple cores to do the processing.
- '''
- results = Queue.Queue()
- process_count= 0
-
- i = 1
- for f in files:
- f_name = os.path.splitext(os.path.split(f)[1])[0]
- args = '-i ' + '"' + f + '"'
- args += ' -o ' + '"' + outputFolder + '"'
- args += ' -f ' + type
-# if self.verbose:
-# args += " -v"
-
- execDir = os.path.split(__file__)[0]
- executable = os.path.join(execDir, 'singleRasterFormatConverter.py')
-
- pyEx = sys.executable
- command = ' '.join([pyEx, executable, args])
- self.logger.writetolog(command, False, False)
- proc = subprocess.Popen( command )
- thread.start_new_thread(utilities.process_waiter,
- (proc, f_name, results))
- process_count+= 1
-
- while process_count > 0:
- description, rc= results.get()
-
- if rc == 0:
- if self.verbose:
- msg = " " + description + " finished successfully: " + \
- str(len(files) - process_count + 1) + " done out of " \
- + str(len(files))
- self.logger.writetolog(msg, True, True)
- else:
- self.logger.writetolog("There was a problem with: " + description , True, True)
- process_count-= 1
-
-
- def convertFormat(self, file, outfile, driver):
- inds = gdal.Open(file, gdalconst.GA_ReadOnly)
-
- #ascii = "AAIGrid"
- #bil = "EHdr"
- Driver = gdal.GetDriverByName(driver)
- Driver.CreateCopy(outfile, inds, 0)
-
-def main(argv):
- usageStmt = "usage: options: -m --MDSFile -o --outputDir -f --format -v --verbose"
- desc = "Converts all of the tif files specified in an MDS to ASCII format (or optionally other formats)"
- parser = OptionParser(usage=usageStmt, description=desc)
-
- parser.add_option("-v",
- dest="verbose",
- default=False,
- action="store_true",
- help="the verbose flag causes diagnostic output to print.")
- parser.add_option("-m", "--MDSFile",
- dest="MDSFile",
- help="The input MDS used to determine tif inputs.")
- parser.add_option("-o", "--outputDir",
- dest="outputDir",
- help="Output directory to save files in.")
- parser.add_option("-f", "--format",
- dest="format",
- default='asc',
- help="The format to convert into. 'bil', 'img', 'tif', 'jpg', 'bmp', 'asc'")
- parser.add_option("-s", dest="multicore",
- default=True,
- action="store_true",
- help="the use single-core flag causes each iteration to run on the same thread.")
-
- (options, args) = parser.parse_args(argv)
-
- ourFC = FormatConverter()
- ourFC.verbose = options.verbose
- ourFC.MDSFile = options.MDSFile
- ourFC.outputDir = options.outputDir
- ourFC.format = options.format
- ourFC.multicore = options.multicore
- ourFC.run()
-
-if __name__ == "__main__":
- sys.exit(main(sys.argv[1:]))
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/Docs/SAHM User Help.docx b/contrib/sahm/pySAHM/Resources/Docs/SAHM User Help.docx
deleted file mode 100644
index db2a430..0000000
Binary files a/contrib/sahm/pySAHM/Resources/Docs/SAHM User Help.docx and /dev/null differ
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/AppendOut.r b/contrib/sahm/pySAHM/Resources/R_Modules/AppendOut.r
deleted file mode 100644
index 2c2d8ee..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/AppendOut.r
+++ /dev/null
@@ -1,170 +0,0 @@
-AppendOut<-function(compile.out,Header,x,out,test.split,parent){
- Header.Length<-nrow(Header)
- Parm.Len<-nrow(x)
- if(file.access(compile.out,mode=0)==-1){ #if very first time through little to do
- #A more complex than necessary way of writing a csv with several header lines
- write.table(Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=",")
- if(!is.null(out$dat$ma$ma.test))
- write.table(cbind("","Train Split"),file=compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=",")
- write.table(x,file=compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=",")
- } else { #this else (not the first time through) goes to the very end of the function
- input<-read.table(compile.out,fill=TRUE,sep=",")
- Orig.Header<-input[1:Header.Length,]
-
- if(!is.null(out$dat$ma$ma.test)){ #if there is a test train split this if lasts until after plotting
- Train.x<-input[(Header.Length+2):(Header.Length+Parm.Len+1),]
- Orig.Train<-input[(Header.Length+1),]
-
- if(nrow(input)>15){ #if there is a test split in input (not in very first loop)
- Test.x<-input[(Header.Length+Parm.Len+4):nrow(input),]
- Orig.Test<-input[(Header.Length+Parm.Len+2):(Header.Length+Parm.Len+3),]
- if(test.split){ # if we're hitting this on a test and not a train
- Test.x[,ncol(Test.x)]<-x[,2]
- class(Orig.Test[,ncol(Orig.Test)])="character"
- Orig.Test[1,ncol(Orig.Test)]<-""
- Orig.Test[2,ncol(Orig.Test)]<-"Test Split"
- } else{
- Orig.Header<-cbind(Orig.Header,Header[,2])
- Train.x<-cbind(Train.x,x[,2])
- Orig.Train<-cbind(Orig.Train,"Train Split")
- }
- } else{
- Orig.Test=rbind(c("",""),cbind("","Test Split"))
- Test.x=x
- }
-
- temp<-try(write.table(Orig.Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
-
- while(class(temp)=="try-error"){
- modalDialog("","Please Close the AppendedOutput.exe\ so that R can write to it then press ok to continue ","")
- temp<-try(write.table(Orig.Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
- }
- try(write.table(Orig.Train,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
- try(write.table(Train.x,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
- try(write.table(Orig.Test,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
- try(write.table(Test.x,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
- if(ncol(Train.x)==ncol(Test.x) & ncol(Test.x)>2){
-
- jpeg(file=paste(parent,"AcrossModelPerformTestTrain.jpg",sep="//"),width=1000,height=1000,pointsize=13)
- par(mfrow=c(nrow(Train.x),1),mar=c(.2, 5, .6, 2),cex=1.1,oma=c(5, 0, 3, 0))
- temp<-Train.x[,2:ncol(Train.x)]
- temp<-matrix(data=as.numeric(as.matrix(temp,nrow=Par.Len)),nrow=Parm.Len,ncol=(ncol(Train.x)-1))
- temp1<-temp
- temp[2,]<-temp[2,]/100
- temp[3,]<-temp[3,]/100
- temp2<-Test.x[,2:ncol(Test.x)]
- temp2<-matrix(data=as.numeric(as.matrix(temp2,nrow=Par.Len)),nrow=Parm.Len,ncol=(ncol(Test.x)-1))
- temp2[2,]<-temp2[2,]/100
- temp2[3,]<-temp2[3,]/100
- ss<-seq(from=1,to=(ncol(Train.x)-1),by=1)
- x.labs<-sub(" ","\n",Train.x[,1])
- x.labs<-sub("Percent","Proportion",x.labs)
- colors.test=c("chocolate3","gold1","darkolivegreen2","steelblue1","brown3")
- colors.train=c("chocolate4","gold3","darkolivegreen4","steelblue4","brown4")
- #Plot 1.
- plot(c(0,(ncol(Test.x)+2)),c(0,1.1),type="n",xaxt="n",
- xlab=paste("Corresponding Column in ",ifelse(!is.null(out$dat$ma$ma.test),"AppendedOutputTestTrain.csv","AppendedOutput.csv"),sep=""),
- ylab=x.labs[1])
- grid(nx=10)
- legend(ncol(Test.x),y=.75,legend=c("Test","Train"),fill=c(colors.test[1],colors.train[1]))
- rect(xleft=ss-.4,ybottom=0,xright=ss,ytop=temp[1,],col=colors.train[1],lwd=2)
- rect(xleft=ss,ybottom=0,xright=(ss+.4),ytop=pmax(0,temp2[1,]),col=colors.test[1],lwd=2)
- text((which(temp1[1,]==max(temp1[1,],na.rm=TRUE),arr.ind=TRUE)-.25),
- max(temp1[1,],na.rm=TRUE)+.05,labels=as.character(round(max(temp1[1,]),digits=2)),cex=.8)
- text((which(temp2[1,]==max(temp2[1,],na.rm=TRUE),arr.ind=TRUE)+.25),
- max(temp2[1,],na.rm=TRUE)+.05,labels=as.character(round(max(temp2[1,]),digits=2)),cex=.8)
- par(mar=c(.2, 5, .6, 2))
- #Middle Plots.
- for(i in 2:(nrow(Train.x)-1)){
- plot(c(0,(ncol(Test.x)+2)),c(0,1.1),type="n",xaxt="n",
- ylab=x.labs[i])
- grid(nx=10)
- rect(xleft=ss-.4,ybottom=0,xright=ss,ytop=temp[i,],col=colors.train[i],lwd=2)
- rect(xleft=ss,ybottom=0,xright=(ss+.4),ytop=pmax(0,temp2[i,]),col=colors.test[i],lwd=2)
- legend(ncol(Test.x),y=.75,legend=c("Test","Train"),fill=c(colors.test[i],colors.train[i]))
- text((which(temp[i,]==max(temp[i,],na.rm=TRUE),arr.ind=TRUE)-.25),
- max(temp[i,],na.rm=TRUE)+.05,labels=as.character(round(max(temp[i,]),digits=2)),cex=.8)
- text((which(temp2[i,]==max(temp2[i,],na.rm=TRUE),arr.ind=TRUE)+.25),
- max(temp2[i,],na.rm=TRUE)+.05,labels=as.character(round(max(temp2[i,]),digits=2)),cex=.8)
- par(mar=c(.3, 5, .4, 2))
- }
- par(mar=c(2, 5, .4, 2))
- #Last Plot.
- i=nrow(Train.x)
- plot(c(0,(ncol(Test.x)+2)),c(0,1.1),type="n",xaxt="n",
- xlab="n",
- ylab=x.labs[i])
- grid(nx=10)
- rect(xleft=ss-.4,ybottom=0,xright=ss,ytop=temp[i,],col=colors.train[i],lwd=2)
- rect(xleft=ss,ybottom=0,xright=(ss+.4),ytop=pmax(0,temp2[i,]),col=colors.test[i],lwd=2)
- legend(ncol(Test.x),y=.75,legend=c("Test","Train"),fill=c(colors.test[i],colors.train[i]))
- text((which(temp1[i,]==max(temp1[i,],na.rm=TRUE),arr.ind=TRUE)-.25),
- max(temp1[i,],na.rm=TRUE)+.05,labels=as.character(round(max(temp1[i,]),digits=2)),cex=.8)
- text((which(temp2[i,]==max(temp2[i,],na.rm=TRUE),arr.ind=TRUE)+.25),
- max(temp2[i,],na.rm=TRUE)+.05,labels=as.character(round(max(temp2[i,]),digits=2)),cex=.8)
- #Outer margin labels
- for(i in 2:ncol(Orig.Header)) mtext(Orig.Header[1,i],line=-12,at=(i-1),las=2)
- mtext("Evaluation Metrics Performance Across Model Runs",outer=TRUE,side=3,cex=1.3)
- mtext(paste("Folder Name where model is found in ",
- ifelse(!is.null(out$dat$ma$ma.test),"AppendedOutputTestTrain.csv","AppendedOutput.csv"),sep=""),side=1,outer=TRUE,line=3)
- dev.off()
- }
- } else{
-
- Orig.x<-input[(Header.Length+1):nrow(input),]
- temp<-try(write.table(cbind(Orig.Header,Header[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
- while(class(temp)=="try-error"){
- modalDialog("","Please Close the AppendedOutput.exe\ so that R can write to it then press ok to continue ","")
- temp<-try(write.table(cbind(Orig.Header,Header[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
- }
- if(ncol(Orig.x)>2){
-
- jpeg(file=paste(parent,"AcrossModelPerform.jpg",sep="//"),width=1000,height=1000,pointsize=13)
- par(mfrow=c(5,1),mar=c(.2, 5, .6, 2),cex=1.1,oma=c(5, 0, 3, 0))
- temp<-Orig.x[,2:ncol(Orig.x)]
- temp<-matrix(data=as.numeric(as.matrix(temp,nrow=Par.Len)),nrow=Parm.Len,ncol=(ncol(Orig.x)-1))
- temp1<-temp
- temp[2,]<-temp[2,]/100
- temp[3,]<-temp[3,]/100
- ss<-seq(from=1,to=(ncol(Orig.x)-1),by=1)
- x.labs<-sub(" ","\n",Orig.x[,1])
- x.labs<-sub("Percent","Proportion",x.labs)
- colors.train=c("chocolate4","gold3","darkolivegreen4","steelblue4","brown4")
- #Plot 1.
- plot(c(0,(ncol(Orig.x))),c(0,1.1),type="n",xaxt="n",ylab=x.labs[1])
- grid(nx=10)
- rect(xleft=ss-.3,ybottom=0,xright=ss+.3,ytop=temp[1,],col=colors.train[1],lwd=2)
- text((which(temp1[1,]==max(temp1[1,],na.rm=TRUE),arr.ind=TRUE)),
- max(temp1[1,],na.rm=TRUE)+.06,labels=as.character(round(max(temp1[1,]),digits=2)),cex=.8)
- par(mar=c(.2, 5, .6, 2))
- #Plot 2-4.
- for(i in 2:(nrow(x)-1)){
- plot(c(0,(ncol(Orig.x))),c(0,1.1),type="n",xaxt="n",
- ylab=x.labs[i])
- grid(nx=10)
- rect(xleft=ss-.3,ybottom=0,xright=ss+.3,ytop=temp[i,],col=colors.train[i],lwd=2)
- text((which(temp[i,]==max(temp[i,],na.rm=TRUE),arr.ind=TRUE)),
- max(temp[i,],na.rm=TRUE)+.06,labels=as.character(round(max(temp[i,]),digits=2)),cex=.8)
- par(mar=c(.3, 5, .4, 2))
- }
- par(mar=c(2, 5, .4, 2))
- #Plot 5.
- i=nrow(x)
- plot(c(0,(ncol(Orig.x))),c(0,1.1),type="n",xaxt="n",
- ylab=x.labs[i])
- grid(nx=10)
- rect(xleft=ss-.3,ybottom=0,xright=ss+.3,ytop=temp[i,],col=colors.train[i],lwd=2)
- text((which(temp[i,]==max(temp[i,],na.rm=TRUE),arr.ind=TRUE)),
- max(temp[i,],na.rm=TRUE)+.06,labels=as.character(round(max(temp[i,]),digits=2)),cex=.8)
- #Outer margin labels
- for(i in 2:ncol(Orig.Header)) mtext(Orig.Header[1,i],line=-12,at=(i-1),las=2)
- mtext("Evaluation Metrics Performance Across Model Runs",outer=TRUE,side=3,cex=1.3)
- mtext(paste("Folder Name where model is found in ",
- ifelse(!is.null(out$dat$ma$ma.test),"AppendedOutputTestTrain.csv","AppendedOutput.csv"),sep=""),side=1,outer=TRUE,line=3)
- dev.off()
- }
-
- try(write.table(cbind(Orig.x,x[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
- }}
- }
-
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/CompileOutput.r b/contrib/sahm/pySAHM/Resources/R_Modules/CompileOutput.r
deleted file mode 100644
index 82b38d9..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/CompileOutput.r
+++ /dev/null
@@ -1,12 +0,0 @@
-Compile.Output<-function(out){
-last.dir<-strsplit(out$input$output.dir,split="/")
-length(last.dir[[1]])
-parent<-sub(paste("/",last.dir[[1]][length(last.dir[[1]])],sep=""),"",out$input$output.dir)
-
-txt0 <- paste("Generalized Liinear Results\n",out$input$run.time,"\n\n","Data:\n\t ",ma.name,"\n\t ","n(pres)=",
- out$dat$ma$n.pres[2],"\n\t n(abs)=",out$dat$ma$n.abs[2],"\n\t number of covariates considered=",(length(names(out$dat$ma$ma))-1),
- "\n\n","Settings:\n","\n\t model family=",out$input$model.family,
- "\n\n","Results:\n\t ","number covariates in final model=",length(out$dat$ma$used.covs),
- "\n\t pct deviance explained on train data =",round(out$mods$auc.output$pct.dev.exp,1),"%\n",
- "\n\t total time for model fitting=",round((unclass(Sys.time())-t0)/60,2),"min\n",sep="")
-}
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/CrossValidationSplit.r b/contrib/sahm/pySAHM/Resources/R_Modules/CrossValidationSplit.r
deleted file mode 100644
index a87e425..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/CrossValidationSplit.r
+++ /dev/null
@@ -1,99 +0,0 @@
-CrossValidationSplit<-function(input.file,output.file,response.col="ResponseBinary",n.folds=10,stratify=FALSE){
-
-#Description:
-#this code takes as input an mds file with the first line being the predictor or
-#response name, the second line an indicator of predictors to include and the
-#third line being paths where tif files can be found. An output file and a
-#response column must also be specified. Given a number of folds, a new
-#column is created indicating which fold each observation will be assigned to
-#if a Split Column is also found (test/train split) then only the train portion
-#will be assigned a fold. Optional stratification by response is also available
-#Background points are ignored
-#by this module (they are read in, written out, but not assigned to cv folds.
-#Output is written to a csv that can be used by the
-#SAHM R modules.
-
-#Written by Marian Talbert 9/29/2011
-
- if(n.folds<=1 | n.folds%%1!=0) stop("n.folds must be an integer greater than 1")
- browser()
-
- #Read input data and remove any columns to be excluded
- dat.in<-read.csv(input.file,header=FALSE,as.is=TRUE)
- dat<-as.data.frame(dat.in[4:dim(dat.in)[1],])
- names(dat)<-dat.in[1,]
-
- response<-dat[,match(tolower(response.col),tolower(names(dat)))]
-
- if(sum(as.numeric(response)==0)==0 && !is.null(stratify)) stop("The ratio of presence to absence cannot be set with only presence data")
-
- #Ignoring background data that might be present in the mds
-
- bg.dat<-dat[response==-9999,]
-
- if(dim(bg.dat)[1]!=0){
- dat<-dat[-c(which(response==-9999,arr.ind=TRUE)),]
- dat.in<-dat.in[-c(which(response==-9999,arr.ind=TRUE)+3),]
- response<-response[-c(which(response==-9999,arr.ind=TRUE))]
- bg.dat$TrainSplit=""
- }
-
- #this splits the training set
- split.mask<-dat[,match(tolower("split"),tolower(names(dat)))]=="train"
- index<-seq(1:nrow(dat))[split.mask]
- if(stratify==TRUE){
- dat[,ncol(dat)+1]<-NA
- for(i in 1:names(table(response))){
- index.i<-index[response[split.mask]==names(table(response))[i]]
- index.i<-index.i[order(runif(length(index.i)))]
- dat[index.i,ncol(dat)]<-c(rep(seq(1:n.folds),each=floor(length(index.i)/n.folds)),sample(seq(1:n.folds),size=length(index.i)%%n.folds,replace=FALSE))
- }
- } else{
- index<-index[order(runif(length(index)))]
- dat[index,ncol(dat)+1]<-c(rep(seq(1:n.folds),each=floor(length(index)/n.folds)),sample(seq(1:n.folds),size=length(index)%%n.folds,replace=FALSE))
- }
-
- #inserting data must be done in 3 steps because dat.in isn't a proper dataframe in that
- #not all elements in a column are of the same type
- dat.in<-dat.in[c(1:3,rownames(dat)),] #removing rows that weren't selected for the test train split
- dat.in[4:(dim(dat.in)[1]),(dim(dat.in)[2]+1)]<-dat$TrainSplit
- dat.in[c(1,3),(dim(dat.in)[2])]<-c("Split","")
- dat.in[2,(dim(dat.in)[2])]<-1
-
- if(dim(bg.dat)[1]!=0) {
- names(bg.dat)<-names(dat.in)
- dat.in<-rbind(dat.in,bg.dat)}
-
- #write output files for R modules
- write.table(dat.in,file=output.file,row.names=FALSE,col.names=FALSE,sep=",",quote=FALSE)
-
-
- }
-
-
- #Reading in command line arguments
- Args <- commandArgs(T)
- print(Args)
- #assign default values
-
- responseCol <- "responseBinary"
- trainProp=.7
- RatioPresAbs=NULL
- #replace the defaults with passed values
- for (arg in Args) {
- argSplit <- strsplit(arg, "=")
- argSplit[[1]][1]
- argSplit[[1]][2]
- if(argSplit[[1]][1]=="p") trainProp <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="m") RatioPresAbs <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="o") output.file <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="i") infil <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
- }
-
- RatioResAbs<-as.numeric(RatioPresAbs)
- trainProp<-as.numeric(trainProp)
-
- #Run the Test training split with these parameters
- CrossValidationSplit(input.file=infil,output.file=output.file,response.col=responseCol,
- trainProp=trainProp,RatioPresAbs=RatioPresAbs)
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/EvalStats.r b/contrib/sahm/pySAHM/Resources/R_Modules/EvalStats.r
deleted file mode 100644
index 6d566d5..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/EvalStats.r
+++ /dev/null
@@ -1,25 +0,0 @@
-EvaluationStats<-function(out,thresh,train,train.pred,opt.methods=opt.methods){
- response<-out$dat$ma$ma.test[,1]
-
- if(out$input$model.source.file=="rf.r") {pred<-tweak.p(as.vector(predict(out$mods$final.mod,newdata=out$dat$ma$ma.test[,-1],type="prob")[,2]))
- modelname="Random Forest"
- }
-
- if(out$input$model.source.file=="mars.r") {pred<-mars.predict(out$mods$final.mod,out$dat$ma$ma.test)$prediction[,1]
- modelname="MARS"
- }
-
- if(out$input$model.source.file=="glm.r") {pred=glm.predict(out$mods$final.mod,out$dat$ma$ma.test)
- modelname="GLM"
- }
-
- if(out$input$model.source.file=="brt.r") {pred=predict.gbm(out$mods$final.mod,out$dat$ma$ma.test,out$mods$final.mod$target.trees,type="response")
- modelname="BRT"
- }
-
- auc.output<-make.auc.plot.jpg(out$dat$ma$ma.test,pred=pred,plotname=paste(out$dat$bname,"_auc_plot.jpg",sep=""),
- modelname=modelname,test.split=TRUE,thresh=thresh,train=train,train.pred,opt.methods=opt.methods,weight=out$dat$ma$test.weights,out=out)
-
- out$mods$auc.output<-auc.output
-
-}
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/EvalStatsHelperFcts.r b/contrib/sahm/pySAHM/Resources/R_Modules/EvalStatsHelperFcts.r
deleted file mode 100644
index 7fb65fd..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/EvalStatsHelperFcts.r
+++ /dev/null
@@ -1,122 +0,0 @@
-"calibration" <-
- function(obs, preds, family = "binomial")
- {
- #
- # j elith/j leathwick 17th March 2005
- # calculates calibration statistics for either binomial or count data
- # but the family argument must be specified for the latter
- # a conditional test for the latter will catch most failures to specify
- # the family
- #
-
- if (family == "bernoulli") family <- "binomial"
- pred.range <- max(preds) - min(preds)
- if(pred.range > 1.2 & family == "binomial") {
- print(paste("range of response variable is ", round(pred.range, 2)), sep = "", quote = F)
- print("check family specification", quote = F)
- return()
- }
- if(family == "binomial") {
- pred <- preds + 1e-005
- pred[pred >= 1] <- 0.99999
- mod <- glm(obs ~ log((pred)/(1 - (pred))), family = binomial)
- lp <- log((pred)/(1 - (pred)))
- a0b1 <- glm(obs ~ offset(lp) - 1, family = binomial)
- miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
- ab1 <- glm(obs ~ offset(lp), family = binomial)
- miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
- miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
- }
- if(family == "poisson") {
- mod <- glm(obs ~ log(preds), family = poisson)
- lp <- log(preds)
- a0b1 <- glm(obs ~ offset(lp) - 1, family = poisson)
- miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
- ab1 <- glm(obs ~ offset(lp), family = poisson)
- miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
- miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
- }
- calibration.result <- c(mod$coef, miller1, miller2, miller3)
- names(calibration.result) <- c("intercept", "slope", "testa0b1", "testa0|b1", "testb1|a")
- return(calibration.result)
-}
-
-"calc.dev" <-
- function(obs.values, fitted.values, weights = rep(1,length(obs.values)), family="binomial", calc.mean = TRUE)
- {
- # j. leathwick/j. elith
- #
- # version 2.1 - 5th Sept 2005
- #
- # function to calculate deviance given two vectors of raw and fitted values
- # requires a family argument which is set to binomial by default
- #
- #
-
- if (length(obs.values) != length(fitted.values))
- stop("observations and predictions must be of equal length")
-
- y_i <- obs.values
-
- u_i <- fitted.values
-
- if (family == "binomial" | family == "bernoulli") {
-
- deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
- deviance <- -2 * sum(deviance.contribs * weights)
-
- }
-
- if (family == "poisson" | family == "Poisson") {
-
- deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
- deviance <- 2 * sum(deviance.contribs * weights)
-
- }
-
- if (family == "laplace") {
- deviance <- sum(abs(y_i - u_i))
- }
-
- if (family == "gaussian") {
- deviance <- sum((y_i - u_i) * (y_i - u_i))
- }
-
-
-
- if (calc.mean) deviance <- deviance/length(obs.values)
- dev=list(deviance=deviance,dev.cont=deviance.contribs)
- return(dev)
-
-}
-
-beachcolours<-function (heightrange, sealevel = 0, monochrome = FALSE, ncolours = if (monochrome) 16 else 64)
-{
-#this function was robbed from the spatstat library internals
- if (monochrome)
- return(grey(seq(0, 1, length = ncolours)))
- stopifnot(is.numeric(heightrange) && length(heightrange) ==
- 2)
- stopifnot(all(is.finite(heightrange)))
- depths <- heightrange[1]
- peaks <- heightrange[2]
- dv <- diff(heightrange)/(ncolours - 1)
- epsilon <- dv/2
- lowtide <- max(sealevel - epsilon, depths)
- hightide <- min(sealevel + epsilon, peaks)
- countbetween <- function(a, b, delta) {
- max(0, round((b - a)/delta))
- }
- nsea <- countbetween(depths, lowtide, dv)
- nbeach <- countbetween(lowtide, hightide, dv)
- nland <- countbetween(hightide, peaks, dv)
- colours <- character(0)
- if (nsea > 0)
- colours <- rev(rainbow(nsea, start = 3/6, end = 4/6))
- if (nbeach > 0)
- colours <- c(colours, rev(rainbow(nbeach, start = 3/12,
- end = 5/12)))
- if (nland > 0)
- colours <- c(colours, rev(rainbow(nland, start = 0, end = 1/6)))
- return(colours)
-}
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/EvaluationStats.r b/contrib/sahm/pySAHM/Resources/R_Modules/EvaluationStats.r
deleted file mode 100644
index ca62d3d..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/EvaluationStats.r
+++ /dev/null
@@ -1,436 +0,0 @@
-make.auc.plot.jpg<-function(ma.reduced,pred,plotname,modelname,test.split=FALSE,thresh=NULL,train=NULL,train.pred=NULL,opt.methods=2,weight,out){
-
- if(is.null(weight)) weight=rep(1,times=dim(ma.reduced)[1])
- auc.data <- data.frame(ID=1:nrow(ma.reduced),pres.abs=ma.reduced[,1],pred=pred)
- p.bar <- sum(auc.data$pres.abs * weight) / sum(weight)
- n.pres <- sum(auc.data$pres.abs)
- n.abs <- nrow(auc.data)-n.pres
-
- null.dev<-calc.dev(auc.data$pres.abs, rep(p.bar,times=length(auc.data$pres.abs)), weight, family="binomial")$deviance*nrow(ma.reduced)
- dev.fit<-calc.dev(auc.data$pres.abs, pred, weight, family="binomial")$deviance*nrow(ma.reduced)
- dev.exp <- null.dev - dev.fit
- pct.dev.exp <- dev.exp/null.dev*100
- correlation<-cor(auc.data$pres.abs,pred)
-
- if(is.null(thresh)){
- thresh <- as.numeric(optimal.thresholds(auc.data,opt.methods=opt.methods))[2]}
- auc.fit <- auc(auc.data,st.dev=T)
- if(test.split==TRUE){
-
- jpeg(file=plotname)
- d<-data.frame(ID=1:nrow(train),pres.abs=train[,1],pred=train.pred)
- thresh<- as.numeric(optimal.thresholds(d,opt.methods=opt.methods))[2]
- TestTrainRocPlot(DATA=d,opt.thresholds=thresh,add.legend=FALSE,lwd=2)
- TestTrainRocPlot(auc.data,model.names=modelname,opt.thresholds=thresh,add.roc=TRUE,line.type=2,color="red",add.legend=FALSE)
- legend(x=.66,y=.2,c("Training Split","Testing Split"),lty=2,col=c("black","red"),lwd=2)
- graphics.off()} else {
- jpeg(file=plotname)
- TestTrainRocPlot(auc.data,model.names=modelname,opt.thresholds=thresh)
- graphics.off()
-
- }
-
- cmx <- cmx(auc.data,threshold=thresh)
- PCC <- pcc(cmx,st.dev=F)*100
- SENS <- sensitivity(cmx,st.dev=F)
- SPEC <- specificity(cmx,st.dev=F)
- KAPPA <- Kappa(cmx,st.dev=F)
- TSS <- SENS+SPEC-1
- response<-ma.reduced$response
-
- capture.output(cat("\n\n============================================================",
- "\n\nEvaluation Statistics"),file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
- if(!is.null(out$dat$ma$ma.test))
- capture.output(cat(" applied to",ifelse(!test.split,"train","test"), "split:\n",sep=" "),
- file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
- capture.output(cat( "\n",
- "\n\t Correlation Coefficient : ",cor.test(pred,response)$estimate,
- "\n\t NULL Deviance : ",null.dev,
- "\n\t Fit Deviance : ",dev.fit,
- "\n\t Explained Deviance : ",dev.exp,
- "\n\t Percent Deviance Explained : ",pct.dev.exp,
- file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE))
-
- capture.output(cat(
- "\n\n Threshold Methods based on", switch(opt.methods,
- "1"=".5 threshold",
- "2"="Sens=Spec",
- "3"="maximize (sensitivity+specificity)/2",
- "4"="maximize Kappa",
- "5"="maximize percent correctly classified",
- "6"="predicted prevalence=observed prevalence",
- "7"="threshold=observed prevalence",
- "8"="mean predicted probability",
- "9"="minimize distance between ROC plot and (0,1)",
- ),
- "\n\t Threshold : ",
- thresh,
- "\n\n\t Confusion Matrix: \n\n"),
- print.table(cmx),
- cat("\n\t AUC : ",auc.fit[1,1],
- "\n\t Percent Correctly Classified : ",PCC,
- "\n\t Sensitivity : ",SENS,
- "\n\t Specificity : ",SPEC,
- "\n\t Kappa : ",KAPPA,
- "\n\t True Skill Statistic : ",TSS,"\n"),
- file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
-
- last.dir<-strsplit(out$input$output.dir,split="\\\\")
- parent<-sub(paste("\\\\",last.dir[[1]][length(last.dir[[1]])],sep=""),"",out$input$output.dir)
-
- if(!is.null(out$dat$ma$ma.test)) compile.out<-paste(parent,"AppendedOutputTestTrain.csv",sep="/")
- else compile.out<-paste(parent,"AppendedOutput.csv",sep="/")
-
- x=data.frame(cbind(c("Correlation Coefficient","Percent Deviance Explained","Percent Correctly Classified","Sensitivity","Specificity"),
- c(as.vector(cor.test(pred,response)$estimate),pct.dev.exp,PCC,SENS,SPEC)))
-
-
- Header<-cbind(c("","Original Field Data","Field Data Template","PARC Output Folder","PARC Template","Covariate Selection Name",""),
- c(last.dir[[1]][length(last.dir[[1]])],
- out$dat$ma$input$OrigFieldData,out$dat$ma$input$FieldDataTemp,out$dat$ma$input$ParcOutputFolder,
- out$dat$ma$input$ParcTemplate,ifelse(length(out$dat$ma$input$CovSelectName)==0,"NONE",out$dat$ma$input$CovSelectName),""))
- Header.Length<-nrow(Header)
- Parm.Len<-nrow(x)
-
- #Very first time through
- if(file.access(compile.out,mode=0)==-1){
- #A more complex than necessary way of writing a csv with several header lines
- write.table(Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=",")
- if(!is.null(out$dat$ma$ma.test))
- write.table(cbind("","Train Split"),file=compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=",")
- write.table(x,file=compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=",")
- } else {
- input<-read.table(compile.out,fill=TRUE,sep=",")
- Orig.Header<-input[1:Header.Length,]
-
- if(!is.null(out$dat$ma$ma.test)){
- Train.x<-input[(Header.Length+2):(Header.Length+Parm.Len+1),]
- Orig.Train<-input[(Header.Length+1),]
-
- if(nrow(input)>15){
- Test.x<-input[(Header.Length+Parm.Len+4):nrow(input),]
- Orig.Test<-input[(Header.Length+Parm.Len+2):(Header.Length+Parm.Len+3),]
- if(test.split){
- Test.x[,ncol(Test.x)]<-x[,2]
- class(Orig.Test[,ncol(Orig.Test)])="character"
- Orig.Test[1,ncol(Orig.Test)]<-""
- Orig.Test[2,ncol(Orig.Test)]<-"Test Split"
- } else{
- Orig.Header<-cbind(Orig.Header,Header[,2])
- Train.x<-cbind(Train.x,x[,2])
- Orig.Train<-cbind(Orig.Train,"Train Split")
- }
- } else{
- Orig.Test=rbind(c("",""),cbind("","Test Split"))
- Test.x=x
- }
-
- temp<-try(write.table(Orig.Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
-
- while(class(temp)=="try-error"){
- modalDialog("","Please Close the AppendedOutput.exe\ so that R can write to it then press ok to continue ","")
- temp<-try(write.table(Orig.Header,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
- }
-
- try(write.table(Orig.Train,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
- try(write.table(Train.x,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
- try(write.table(Orig.Test,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
- try(write.table(Test.x,file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
- } else{
-
- Orig.x<-input[(Header.Length+1):nrow(input),]
- temp<-try(write.table(cbind(Orig.Header,Header[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
- while(class(temp)=="try-error"){
- modalDialog("","Please Close the AppendedOutput.exe\ so that R can write to it then press ok to continue ","")
- temp<-try(write.table(cbind(Orig.Header,Header[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,sep=","),silent=TRUE)
- }
-
-
- try(write.table(cbind(Orig.x,x[,2]),file =compile.out,row.names=FALSE,col.names=FALSE,quote=FALSE,append=TRUE,sep=","))
- }}
-
- return(list(thresh=thresh,cmx=cmx,null.dev=null.dev,dev.fit=dev.fit,dev.exp=dev.exp,pct.dev.exp=pct.dev.exp,auc=auc.fit[1,1],auc.sd=auc.fit[1,2],
- plotname=plotname,pcc=PCC,sens=SENS,spec=SPEC,kappa=KAPPA,tss=TSS,correlation=correlation))
-}
-
-
-make.poisson.jpg<-function(ma.reduced,pred,plotname,modelname,test.split=FALSE,thresh=NULL,train=NULL,train.pred=NULL,weight,train.weight=NULL,out){
-
- pois.data <- data.frame(ID=1:nrow(ma.reduced),pres.abs=ma.reduced[,1],pred=pred)
- p.bar <- sum(pois.data$pres.abs * weight) / sum(weight)
- n.pres <- sum(pois.data$pres.abs>=1)
- n.abs <- nrow(pois.data)-n.pres
-
- #takes into account potential weights but not offset
-
- null.dev<-calc.dev(pois.data$pres.abs, rep(p.bar,times=length(pois.data$pres.abs)), weight, family="poisson")$deviance*nrow(ma.reduced)
- dev.fit<-calc.dev(pois.data$pres.abs, pred, weight, family="poisson")$deviance*nrow(ma.reduced)
- dev.exp <- null.dev - dev.fit
- pct.dev.exp <- dev.exp/null.dev*100 #this is the pseudo R^2 using definition in the course notes
- correlation<-cor(pois.data$pres.abs,pred)
- #calibration(pois.data$pres.abs,pred,family="poisson") gbm hasn't implimented this for poisson though elith and leathwich use it, I can't find much
- prediction.error<-sum((pois.data$pres.abs-pred)^2)
-
- ## ADD Weights and offset?
- #function (y, mu, wt)
- #2 * wt * (y * log(ifelse(y == 0, 1, y/mu)) - (y - mu))
-
- if(test.split==TRUE){
- if(is.null(train.weight)) train.weight=rep(1,times=nrow(train))
- null.dev.train<-calc.dev(train$response, rep(mean(train$response),times=nrow(train)), train.weight, family="poisson")$deviance*nrow(train)
- dev.fit.train<-calc.dev(train$response, train.pred, train.weight, family="poisson")$deviance*nrow(train)
- dev.exp.train <- null.dev.train - dev.fit.train
- pct.dev.exp.train <- dev.exp.train/null.dev.train*100
- correlation.train<-cor(train$response,train.pred)
-
- jpeg(file=plotname)
- dev.contrib<-calc.dev(pois.data$pres.abs, pred, weight, family="poisson")$dev.cont
- par(mfrow=c(3,2))
- z<-sign(pred-pois.data$pres.abs)*dev.contrib
- z.range<-max(z)-min(z)
- z.lim<-c((min(z)-.1*z.range),(max(z)+.1*z.range))
- breaks<-quantile(z, probs = seq(0, .95,length=25))
- a<-outer(z,breaks,"<")
- res.mag<-apply(a,1,sum)
- plot(out$dat$ma$test.xy,col=beachcolours(heightrange=c(min(res.mag),max(res.mag)),sealevel=mean(res.mag),ncolours=length(table(res.mag)))[res.mag],cex=4,pch=19)
- x<-out$dat$ma$test.xy[,1]
- y<-out$dat$ma$test.xy[,2]
- a<-loess(z~x*y)
- x.lim<-rep(seq(from=min(out$dat$ma$test.xy[,1]),to=max(out$dat$ma$test.xy[,1]),length=100),each=100)
- y.lim<-rep(seq(from=min(out$dat$ma$test.xy[,2]),to=max(out$dat$ma$test.xy[,2]),length=100),times=100)
- z<-predict(a,newdata=cbind("x"=x.lim,"y"=y.lim))
- z[z>z.lim[2]]<-NA
- z[z<z.lim[1]]<-NA
- breaks<-quantile(na.omit(z), probs = seq(0, .95,length=25))
- a<-outer(z,breaks,"<")
- res.mag<-apply(a,1,sum)
- z<-matrix(data=z,ncol=100,nrow=100,byrow=TRUE)
- res.mag<-matrix(data=res.mag,ncol=100,nrow=100,byrow=TRUE)
- image(x=seq(from=min(x.lim),to=max(x.lim),length=100),y=seq(from=min(y.lim),to=max(y.lim),length=100),
- z=res.mag,
- col=beachcolours(heightrange=c(min(na.omit(res.mag)),max(na.omit(res.mag))),sealevel=mean(na.omit(res.mag)),
- ncolours=length(table(na.omit(res.mag)))),xlab="Latitude",ylab="Longitude",
- main="Smoothed deviance residuals over space")
-
- points(out$dat$ma$train.xy,pch=19,cex=1)
- #plot(unique(x.lim),apply(z,2,sum))
- #plot(unique(y.lim),apply(z,1,sum))
-
- mod.resids<-residuals(out$mods$final.mod,type="deviance")
- plot(pred,(pois.data$pres.abs-pred),xlab="Predicted Values",ylab="Residuals",main="Residuals vs Fitted")
- panel.smooth(pred,(pois.data$pres.abs-pred))
- plot(pred,sqrt(2*dev.contrib),ylab="sqrt(Std.deviance residuals)",xlab="Predicted Values",main="Scale Location")
- panel.smooth(pred,sqrt(2*dev.contrib))
- qqnorm((sqrt(2*dev.contrib)-mean(sqrt(2*dev.contrib))),ylab="Std.Deviance residuals")
- abline(0,1)
-
- graphics.off()
- return(list(null.dev=null.dev,dev.fit=dev.fit,dev.exp=dev.exp,pct.dev.exp=pct.dev.exp,correlation=correlation,
- null.dev.train=null.dev.train,dev.fit.train=dev.fit.train,dev.exp.train=dev.exp.train,pct.dev.exp.train=pct.dev.exp.train,correlation.train=correlation.train))
-
- }else{
- jpeg(file=plotname)
-
- dev.contrib<-calc.dev(pois.data$pres.abs, pred, weight, family="poisson")$dev.cont
- par(mfrow=c(3,2))
-
- dev.contrib<-calc.dev(pois.data$pres.abs, pred, weight, family="poisson")$dev.cont
- z<-sign(pred-pois.data$pres.abs)*dev.contrib
- breaks<-quantile(z, probs = seq(0, .95,length=25))
- a<-outer(z,breaks,"<")
- res.mag<-apply(a,1,sum)
- plot(out$dat$ma$train.xy,col=heat.colors(24)[res.mag],cex=4,pch=19)
- x<-out$dat$ma$train.xy[,1]
- y<-out$dat$ma$train.xy[,2]
- a<-loess(z~x*y)
- x.lim<-rep(seq(from=min(out$dat$ma$train.xy[,1]),to=max(out$dat$ma$train.xy[,1]),length=100),each=100)
- y.lim<-rep(seq(from=min(out$dat$ma$train.xy[,2]),to=max(out$dat$ma$train.xy[,2]),length=100),times=100)
- z<-predict(a,newdata=cbind("x"=x.lim,"y"=y.lim))
- breaks<-quantile(z, probs = seq(0, .95,length=25))
- a<-outer(z,breaks,"<")
- res.mag<-apply(a,1,sum)
- z<-matrix(data=z,ncol=100,nrow=100,byrow=TRUE)
- res.mag<-matrix(data=res.mag,ncol=100,nrow=100,byrow=TRUE)
-
- image(x=seq(from=min(x.lim),to=max(x.lim),length=100),y=seq(from=min(y.lim),to=max(y.lim),length=100),
- z=res.mag,
- col=beachcolours(heightrange=c(min(res.mag),max(res.mag)),sealevel=mean(res.mag),ncolours=length(table(res.mag))),xlab="Latitude",ylab="Longitude",
- main="Smoothed deviance residuals over space")
- points(out$dat$ma$train.xy,pch=19)
- #plot(unique(x.lim),apply(z,2,sum))
- #plot(unique(y.lim),apply(z,1,sum))
-
- mod.resids<-residuals(out$mods$final.mod,type="deviance")
- plot(pred,(pois.data$pres.abs-pred),xlab="Predicted Values",ylab="Residuals",main="Residuals vs Fitted")
- panel.smooth(pred,(pois.data$pres.abs-pred))
- plot(pred,sqrt(2*dev.contrib),ylab="sqrt(Std.deviance residuals)",xlab="Predicted Values",main="Scale Location")
- panel.smooth(pred,sqrt(2*dev.contrib))
- qqnorm((sqrt(2*dev.contrib)-mean(sqrt(2*dev.contrib))),ylab="Std.Deviance residuals")
- abline(0,1)
-
- graphics.off()
-
- capture.output(cat("\n\nEvaluation Statistics applied to test split:\n",
- "\n\t Correlation Coefficient : ",cor.test(pred,response)$estimate,
- "\n\t NULL Deviance : ",auc.output$null.dev,
- "\n\t Fit Deviance : ",auc.output$dev.fit,
- "\n\t Explained Deviance : ",auc.output$dev.exp,
- "\n\t Percent Deviance Explained : ",auc.output$pct.dev.exp,
- file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE))
-
- return(list(null.dev=null.dev,dev.fit=dev.fit,dev.exp=dev.exp,pct.dev.exp=pct.dev.exp,correlation=correlation))
- }
-}
-
-##############################################################################
-EvaluationStats<-function(out,thresh,train,train.pred,opt.methods=opt.methods){
- response<-out$dat$ma$ma.test[,1]
-
- if(out$input$model.source.file=="rf.r") {pred<-tweak.p(as.vector(predict(out$mods$final.mod,newdata=out$dat$ma$ma.test[,-1],type="prob")[,2]))
- modelname="Random Forest"
- }
-
- if(out$input$model.source.file=="mars.r") {pred<-mars.predict(out$mods$final.mod,out$dat$ma$ma.test)$prediction[,1]
- modelname="MARS"
- }
-
- if(out$input$model.source.file=="glm.r") {pred=glm.predict(out$mods$final.mod,out$dat$ma$ma.test)
- modelname="GLM"
- }
-
- if(out$input$model.source.file=="brt.r") {pred=predict.gbm(out$mods$final.mod,out$dat$ma$ma.test,out$mods$final.mod$target.trees,type="response")
- modelname="BRT"
- }
-
- ifelse(out$input$model.family!="poisson",
- auc.output<-make.auc.plot.jpg(out$dat$ma$ma.test,pred=pred,plotname=paste(out$dat$bname,"_auc_plot.jpg",sep=""),
- modelname=modelname,test.split=TRUE,thresh=thresh,train=train,train.pred,opt.methods=opt.methods,weight=out$dat$ma$test.weights,out=out),
- auc.output<-make.poisson.jpg(out$dat$ma$ma.test,pred=pred,plotname=paste(out$dat$bname,"_auc_plot.jpg",sep=""),
- modelname=modelname,test.split=TRUE,thresh=thresh,train=train,train.pred,weight=out$dat$ma$test.weights,out=out))
-
- out$mods$auc.output<-auc.output
-
-}
-
-"calibration" <-
- function(obs, preds, family = "binomial")
- {
- #
- # j elith/j leathwick 17th March 2005
- # calculates calibration statistics for either binomial or count data
- # but the family argument must be specified for the latter
- # a conditional test for the latter will catch most failures to specify
- # the family
- #
-
- if (family == "bernoulli") family <- "binomial"
- pred.range <- max(preds) - min(preds)
- if(pred.range > 1.2 & family == "binomial") {
- print(paste("range of response variable is ", round(pred.range, 2)), sep = "", quote = F)
- print("check family specification", quote = F)
- return()
- }
- if(family == "binomial") {
- pred <- preds + 1e-005
- pred[pred >= 1] <- 0.99999
- mod <- glm(obs ~ log((pred)/(1 - (pred))), family = binomial)
- lp <- log((pred)/(1 - (pred)))
- a0b1 <- glm(obs ~ offset(lp) - 1, family = binomial)
- miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
- ab1 <- glm(obs ~ offset(lp), family = binomial)
- miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
- miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
- }
- if(family == "poisson") {
- mod <- glm(obs ~ log(preds), family = poisson)
- lp <- log(preds)
- a0b1 <- glm(obs ~ offset(lp) - 1, family = poisson)
- miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
- ab1 <- glm(obs ~ offset(lp), family = poisson)
- miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
- miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
- }
- calibration.result <- c(mod$coef, miller1, miller2, miller3)
- names(calibration.result) <- c("intercept", "slope", "testa0b1", "testa0|b1", "testb1|a")
- return(calibration.result)
-}
-
-"calc.dev" <-
- function(obs.values, fitted.values, weights = rep(1,length(obs.values)), family="binomial", calc.mean = TRUE)
- {
- # j. leathwick/j. elith
- #
- # version 2.1 - 5th Sept 2005
- #
- # function to calculate deviance given two vectors of raw and fitted values
- # requires a family argument which is set to binomial by default
- #
- #
-
- if (length(obs.values) != length(fitted.values))
- stop("observations and predictions must be of equal length")
-
- y_i <- obs.values
-
- u_i <- fitted.values
-
- if (family == "binomial" | family == "bernoulli") {
-
- deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
- deviance <- -2 * sum(deviance.contribs * weights)
-
- }
-
- if (family == "poisson" | family == "Poisson") {
-
- deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
- deviance <- 2 * sum(deviance.contribs * weights)
-
- }
-
- if (family == "laplace") {
- deviance <- sum(abs(y_i - u_i))
- }
-
- if (family == "gaussian") {
- deviance <- sum((y_i - u_i) * (y_i - u_i))
- }
-
-
-
- if (calc.mean) deviance <- deviance/length(obs.values)
- dev=list(deviance=deviance,dev.cont=deviance.contribs)
- return(dev)
-
-}
-
-beachcolours<-function (heightrange, sealevel = 0, monochrome = FALSE, ncolours = if (monochrome) 16 else 64)
-{
-#this function was robbed from the spatstat library internals
- if (monochrome)
- return(grey(seq(0, 1, length = ncolours)))
- stopifnot(is.numeric(heightrange) && length(heightrange) ==
- 2)
- stopifnot(all(is.finite(heightrange)))
- depths <- heightrange[1]
- peaks <- heightrange[2]
- dv <- diff(heightrange)/(ncolours - 1)
- epsilon <- dv/2
- lowtide <- max(sealevel - epsilon, depths)
- hightide <- min(sealevel + epsilon, peaks)
- countbetween <- function(a, b, delta) {
- max(0, round((b - a)/delta))
- }
- nsea <- countbetween(depths, lowtide, dv)
- nbeach <- countbetween(lowtide, hightide, dv)
- nland <- countbetween(hightide, peaks, dv)
- colours <- character(0)
- if (nsea > 0)
- colours <- rev(rainbow(nsea, start = 3/6, end = 4/6))
- if (nbeach > 0)
- colours <- c(colours, rev(rainbow(nbeach, start = 3/12,
- end = 5/12)))
- if (nland > 0)
- colours <- c(colours, rev(rainbow(nland, start = 0, end = 1/6)))
- return(colours)
-}
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_BRT_pluggable.r b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_BRT_pluggable.r
deleted file mode 100644
index f336475..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_BRT_pluggable.r
+++ /dev/null
@@ -1,2505 +0,0 @@
-# A set of "pluggable" R functions for automated model fitting of boosted regression trees models to presence/absence data #
-#
-# Modified 12-2-09 to: remove categorical covariates from consideration if they only contain one level
-# ID factor variables based on "categorical" prefix and look for tifs in subdir
-# Give progress reports
-# write large output tif files in blocks to alleviate memory issues
-# various bug fixes
-#
-# Modified 3-4-09 to use a list object for passing of arguements and data
-#
-# Modified in early 2009 to incorporate new tools and methods as described in
-# Elith et al, 2008. The new algorithm:
-# 1. Subsets the data to a maximum of 500 used and 500 available to pick settings and
-# perform model selection.
-# 2. Fits a models using a range of learning rates to find a rate which produces an optimal number of ~1000 trees.
-# 3.
-# Modified 12-30-08 to use directories that don't end with a forward slash
-#
-# Modified 8-19-08 to include the creation of a image info table.
-# Modified 8-8-8 to modularize the model array input, and to include and xml output summary.
-# also added "debug.mode" to make debugging easier on my end.
-# Modified on 6-30-08 to avoid writing to directories other the 'output.dir' spec'd in the
-# command line arguements. If this arguement is not defined, output may still be written
-# to the input directories.
-# Modified on 6-27-08 to take in additional arguements for a file directory (containing
-# the .tif files used for prediction) and an output directory. Command line args are now
-# (note: ma=model array): 1. ma.name, 2. cov.list.name, 3. factor.list.name, 4. ma.dir,
-# 5. tif.dir, 6. output.dir. Also note that directories need to use forward slashes and end
-# with a forward slash.
-# modified on 6-24-08 to be 'pluggable'. The last 20 lines of code interpret command line
-# arguements and run the glm model.
-# modified on 6-23-08 to handle factor variables.
-# modified on 6-18-08 to remove MARS code.
-# modified on 6-18-08 to include new function to return covariate names from a model.
-# modified on 5/15/08 to fit both Logistic and MARS models
-
-
-# Libraries required to run this program #
-# PresenceAbsence - for ROC plots
-# XML - for XML i/o
-# rgdal - for geotiff i/o
-# gbm
-# gbmplus - not on CRAN, see elith et al or contact me.
-# survival - used by gbm library
-# splines - used by gbm library
-# lattice - used by gbm library
-# sp - used by rdgal library
-options(error=NULL)
-
-fit.brt.fct <- function(ma.name,tif.dir=NULL,output.dir=NULL,response.col="^response.binary",make.p.tif=T,make.binary.tif=T,
- simp.method="cross-validation",debug.mode=F,responseCurveForm="jpg",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
- learning.rate = NULL, bag.fraction = 0.5,
- prev.stratify = TRUE, model.family = "bernoulli",max.trees = 10000,tolerance.method = "auto",
- tolerance = 0.001,seed=NULL,opt.methods=2,save.model=TRUE,UnitTest=FALSE,MESS=FALSE){
-
-# Possibly to add later
-# offset = NULL, fold.vector = NULL, var.monotone = rep(0,length(gbm.x))
-
-# offset = NULL, # allows an offset to be specified
-# fold.vector = NULL, # allows a fold vector to be read in for CV with offsets,
-# tree.complexity = 1, # sets the complexity of individual trees
-# learning.rate = 0.01, # sets the weight applied to inidivudal trees
-# bag.fraction = 0.75, # sets the proportion of observations used in selecting variables
-# site.weights = rep(1, nrow(dat)), # allows varying weighting for sites
-# var.monotone = rep(0, length(gbm.x)), # restricts responses to individual predictors to monotone
-# n.folds = 10, # number of folds
-# prev.stratify = TRUE, # prevalence stratify the folds - only for p/a data
-# family = "bernoulli", # family - bernoulli (=binomial), poisson, laplace or gaussian
-# n.trees = 50, # number of initial trees to fit
-# step.size = n.trees, # numbers of trees to add at each cycle
-# max.trees = 10000, # max number of trees to fit before stopping
-# tolerance.method = "auto", # method to use in deciding to stop - "fixed" or "auto"
-# tolerance = 0.001, # tolerance value to use - if method == fixed is absolute,
-# seed=NULL # sets a seed for the algorithm, any inegeger is acceptable
-# opt.methods=2 # sets the method used for threshold optimization used in the
-# # the evaluation statistics module
-# save.model=FALSE # whether the model will be used to later produce tifs
-
- # This function fits a boosted regression tree model to presence-absence data.
- # written by Alan Swanson, Jan-March 2009
- # uses code modified from that published in Elith et al 2008
- # Maintained and edited by Marian Talbert September 2010-
- #
- # Arguements.
- # ma.name: is the name of a .csv file with a model array. full path must be included unless it is in the current
- # R working directory #
- # tif.dir: is the directory containing geotiffs for each covariate. only required if geotiffs output of the
- # response surface is requested # # cov.list.name: is the name of a text file with the names of covariates to be included in models (one per line).
- # output.dir: is the directory that output files will be stored in. if not given, files will go to the current working directory.
- # response.col: column number of the model array containing a binary 0/1 response. all other columns will be considered explanatory variables.
- # make.p.tif: T if a geotiff of the response surface is desired.
- # make.binary.tif: T if a geotiff of the response surface is desired.
- # simp.method: model simplification method. valid methods include: "cross-validation", "rel-inf", and "none". "cross-validation" uses the
- # methods of Elith et al, 2008 for removing covariates that don't contribute to the model. "rel-inf" simply removes covariates that contribute
- # less than 1%. cross-validation is very slow - it can add up to 10min to a run.
- # debug.mode: if T, output is directed to the console during the run. also, a pdf is generated which contains response curve plots and perspective plots
- # showing the effects of interactions deemed important. if F, output is diverted to a text file and the console is kept clear
- # except for final output of an xml file. in either case, a set of standard output files are created in the output directory.
- # tc: tree-complexity for brt fits. if specified, this sets the tree-complexity of the final model fit. A lower tree-complexity will be used for
- # model selection steps. if not set, this will be estimated loosely following the guidelines given by Elith et al, 2008.
- #
-
- # Value:
- # returns nothing but generates a number of output files in the directory
- # "output.dir" named above. These output files consist of:
- #
- # brt_output.txt: a text file with fairly detailed results of the final model.
- # brt_output.xml: an xml-formatted text file with results from the final model.
- # brt_response_curves.xml: an xml-formatted text file with response curves for
- # each covariate in the final model.
- # brt_prob_map.tif: a geotiff of the response surface
- # brt_bin_map.tif: a geotiff of the binary response surface. threhold is based on the roc curve at the point where sensitivity=specificity.
- # brt_log.txt: a file containing text output diverted from the console when debug.mode=F
- # brt_auc_plot.jpg: a jpg file of a ROC plot.
- # brt_response_curves.pdf: an pdf file with response curves for
- # each covariate in the final model and perspective plots showing the effect of interactions deemed significant.
- # only produced when debug.mode=T
- #
- # when debug.mode is true, these filenames will include a number in them so that they will not overwrite preexisting files. eg brt_1_output.txt.
- #
- times <- as.data.frame(matrix(NA,nrow=8,ncol=1,dimnames=list(c("start","read data","model tuning","model fit",
- "model summary","response curves","tif output","done"),c("time"))))
- times[1,1] <- unclass(Sys.time())
- t0 <- unclass(Sys.time())
-
- #simp.method <- match.arg(simp.method)
- out <- list(
- input=list(ma.name=ma.name,
- tif.dir=tif.dir,
- output.dir=output.dir,
- response.col=response.col,
- make.p.tif=make.p.tif,
- make.binary.tif=make.binary.tif,
- tc=tc,
- save.model=save.model,
- learning.rate=learning.rate,
- n.folds=n.folds,
- bag.fraction=bag.fraction,
- prev.stratify=prev.stratify,
- model.family=model.family,
- max.trees=max.trees,
- tolerance.method=tolerance.method,
- tolerance=tolerance,
- simp.method=simp.method,
- alpha=alpha,
- model.type="boosted regression tree",
- model.source.file=script.name,
- model.fitting.subset=c(n.pres=500,n.abs=500),
- run.time=paste(c(format(Sys.time(),"%Y-%m-%d"),format(Sys.time(),"%H:%M:%S")),collapse="T"),
- sig.test="relative influence",
- MESS=MESS),
- dat = list(missing.libs=NULL,
- output.dir=list(dname=NULL,exist=F,readable=F,writable=F),
- tif.dir=list(dname=NULL,exist=F,readable=F,writable=F),
- tif.ind=NULL,
- tif.names=NULL,
- bname=NULL,
- bad.factor.covs=NULL, # factorchange
- ma=list( status=c(exists=F,readable=F),
- dims=c(NA,NA),
- n.pres=c(all=NA,complete=NA,subset=NA,test=NA),
- n.abs=c(all=NA,complete=NA,subset=NA,test=NA),
- ratio=NA,
- resp.name=NULL,
- factor.levels=NA,
- used.covs=NULL,
- ma=NULL,
- train.weights=NULL,
- test.weights=NULL,
- train.xy=NULL,
- test.xy=NULL,
- ma.subset=NULL,
- weight.subset=NULL),
- ma.test=NULL),
- mods=list(parms=list(n.target.trees=1000,tc.full=tc,tc.sub=tc),
- lr.mod=NULL,
- simp.mod=NULL,
- final.mod=NULL,
- r.curves=NULL,
- tif.output=list(prob=NULL,bin=NULL),
- auc.output=NULL,
- interactions=NULL,
- summary=NULL),
- time=list(strt=unclass(Sys.time()),end=NULL),
- error.mssg=list(NULL),
- ec=0
- )
- if(!is.null(seed)) set.seed(seed)
- # load libaries #
-
- out <- check.libs(list("PresenceAbsence","rgdal","XML","sp","survival","lattice","raster","tcltk2","foreign","ade4","gbm"),out)
-
- # exit program now if there are missing libraries #
- if(!is.null(out$error.mssg[[1]])){
- cat(saveXML(brt.to.xml(out),indent=T),'\n')
- return()
- }
-
- if(is.na(match(simp.method,c("cross-validation","rel-inf","none")))){
- out$ec <- out$ec+1
- out$error.mssg[[out$ec]] <- "ERROR: arguement simp.method must be either cross-validation, rel-inf, or none"
- cat(saveXML(brt.to.xml(out),indent=T),'\n')
- return()
- }
-
- #if(simplify.brt==T) out$input$simp.method<-"cross-validation" else out$input$simp.method<-">1% rel. influence"
-
- # check output dir #
- out$dat$output.dir <- check.dir(output.dir)
- if(out$dat$output.dir$writable==F) {out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: output directory",output.dir,"is not writable")
- out$dat$output.dir$dname <- getwd()
- }
-
- # generate a filename for output #
- if(debug.mode==T){
- outfile <- paste(bname<-paste(out$dat$output.dir$dname,"/brt_",n<-1,sep=""),"_output.txt",sep="")
- while(file.access(outfile)==0) outfile<-paste(bname<-paste(out$dat$output.dir$dname,"/brt_",n<-n+1,sep=""),"_output.txt",sep="")
- capture.output(cat("temp"),file=outfile) # reserve the new basename #
- } else bname <- paste(out$dat$output.dir$dname,"/brt",sep="")
- out$dat$bname <- bname
-
- # sink console output to log file #
- if(!debug.mode) {sink(logname <- paste(bname,"_log.txt",sep=""));on.exit(sink)} else logname<-NULL
- options(warn=1)
-
- # check tif dir #
- if(!is.null(tif.dir)){
- out$dat$tif.dir <- check.dir(tif.dir)
- if(out$dat$tif.dir$readable==F & (out$input$make.binary.tif | out$input$make.p.tif)) {
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: tif directory",tif.dir,"is not readable")
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- cat(saveXML(brt.to.xml(out),indent=T),'\n')
- return()
- }
- }
-
- # find .tif files in tif dir #
-
- if(out$dat$tif.dir$readable) out$dat$tif.names <- list.files(out$dat$tif.dir$dname,pattern=".tif",recursive=T)
-
- # check for model array #
- out$input$ma.name <- check.dir(out$input$ma.name)$dname
- out <- read.ma(out)
- if(UnitTest==1) return(out)
- # exit program now if there are errors in the input data #
- if(!is.null(out$error.mssg[[1]])){
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- cat(saveXML(brt.to.xml(out),indent=T),'\n')
- return()
- }
-
- cat("\nbegin processing of model array:",out$input$ma.name,"\n")
- cat("\nfile basename set to:",out$dat$bname,"\n")
- if(debug.mode) assign("out",out,envir=.GlobalEnv)
- if(!debug.mode) {sink();cat("Progress:20%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("20%\n")} ### print time
- ##############################################################################################################
- # Begin model fitting #
- ##############################################################################################################
-
- # estimate optimal learning rate and tc # o
-
- if(out$input$model.family=="binomial") out$input$model.family="bernoulli"
- out <-est.lr(out)
- if(debug.mode) assign("out",out,envir=.GlobalEnv)
-
- # exit program now if lr estimation fails #
- if(!is.null(out$error.mssg[[1]])){
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- cat(saveXML(brt.to.xml(out),indent=T),'\n')
- return()}
-
- cat("\nfinished with learning rate estimation, lr=",out$mods$lr.mod$lr0,", t=",round(out$mods$lr.mod$t.elapsed,2),"sec\n")
- cat("\nfor final fit, lr=",out$mods$lr.mod$lr,"and tc=",out$mods$parms$tc.full,"\n");flush.console()
- if(!debug.mode) {sink();cat("Progress:30%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("30%\n")}
-
- if(out$input$simp.method=="cross-validation"){
- # remove variables with <1% relative influence and re-fit model
- print(debug.mode)
- t1 <- unclass(Sys.time())
- if(length(out$mods$lr.mod$good.cols)<=1) stop("BRT must have at least two independent variables")
- m0 <- gbm.step.fast(dat=out$dat$ma$ma.subset,gbm.x=out$mods$lr.mod $good.cols,gbm.y=1,family=out$input$model.family,
- n.trees = c(300,600,800,1000,1200,1500,1800),step.size=out$input$step.size,max.trees=out$input$max.trees,
- tolerance.method=out$input$tolerance.method,tolerance=out$input$tolerance, n.folds=out$input$n.folds,tree.complexity=out$mods$parms$tc.sub,
- learning.rate=out$mods$lr.mod$lr0,bag.fraction=out$input$bag.fraction,site.weights=out$dat$ma$weight.subset,autostop=T,debug.mode=F,silent=!debug.mode,
- plot.main=F,superfast=F)
- if(debug.mode) assign("m0",m0,envir=.GlobalEnv)
-
- t1b <- unclass(Sys.time())
- if(!debug.mode) {sink();cat("Progress:40%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("40%\n")}
- cat("\nfinished with trimmed model fitting, n.trees=",m0$target.trees,", t=",round(t1b-t1,2),"sec\n");flush.console()
- cat("\nbeginning model simplification - very slow...\n");flush.console()
- out$mods$simp.mod <- gbm.simplify(m0,n.folds=out$input$n.folds,plot=F,verbose=F,alpha=out$input$alpha) # this step is very slow #
- if(debug.mode) assign("out",out,envir=.GlobalEnv)
-
- out$mods$simp.mod$good.cols <- out$mods$simp.mod$pred.list[[length(out$mods$simp.mod$pred.list)]]
- out$mods$simp.mod$good.vars <- names(out$dat$ma$ma)[out$mods$simp.mod$good.cols]
- cat("\nfinished with model simplification, t=",round((unclass(Sys.time())-t1b)/60,2),"min\n");flush.console()
- if(!debug.mode) {sink();cat("Progress:50%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("50%\n")}
- }
-
- # fit final model #
- t2 <- unclass(Sys.time())
-
- if(out$mods$lr.mod$lr==0) out$mods$lr.mod$lr<-out$mods$lr.mod$lr0
- out$mods$final.mod <- gbm.step.fast(dat=out$dat$ma$ma,gbm.x=out$mods$simp.mod$good.cols,gbm.y = 1,family=out$input$model.family,
- n.trees = c(300,600,700,800,900,1000,1200,1500,1800,2200,2600,3000,3500,4000,4500,5000),n.folds=out$input$n.folds,
- tree.complexity=out$mods$parms$tc.full,learning.rate=out$mods$lr.mod$lr,bag.fraction=out$input$bag.fraction,site.weights=out$dat$ma$train.weights,
- autostop=T,debug.mode=F,silent=!debug.mode,plot.main=F,superfast=F)
-
-
-
- assign("out",out,envir=.GlobalEnv)
-
- t3 <- unclass(Sys.time())
- cat("\nfinished with final model fitting, n.trees=",out$mods$final.mod$target.trees,", t=",round(t3-t2,2),"sec\n\n\n");flush.console()
- if(!debug.mode) {sink();cat("Progress:60%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("60%\n")}
-
- ##############################################################################################################
- # Begin model output #
- ##############################################################################################################
-
- # Store .jpg ROC plot #
-
- # Generate and store text summary #
- y <- gbm.interactions(out$mods$final.mod)
- if(debug.mode) assign("out",out,envir=.GlobalEnv)
- if(class(y)!="try-error"){
- int <- y$rank.list;
- int<-int[int$p<.05,]
- int <- int[order(int$p),]
- int$p <- round(int$p,4)
- names(int) <- c("v1","name1","v2","name2","int.size","p-value")
- row.names(int)<-NULL
- if(nrow(int)>0) out$mods$interactions <- int else out$mods$interactions <- NULL
- } else {
- out$ec <-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: problem assessing interactions:",y)
- }
-
- model.summary <- summary(out$mods$final.mod,plotit=F)
- if(class(model.summary)=="try-error"){
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: can't generate summary of final model:",model.summary)
- cat(saveXML(brt.to.xml(out),indent=T),'\n')
- return()
- } else {
- out$mods$summary <- model.summary
- }
- if(debug.mode) assign("out",out,envir=.GlobalEnv)
-
-
-
- if(!is.null(out$dat$bad.factor.cols)){
- capture.output(cat("\nWarning: the following categorical response variables were removed from consideration\n",
- "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n"),
- file=paste(bname,"_output.txt",sep=""),append=T)
- cat("\nWarning: the following categorical response variables were removed from consideration\n",
- "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n\n")
- }
-
-
- txt0 <- paste("\nBoosted Regression Tree Modeling Results\n",out$input$run.time,"\n\n",
- "Data:\n",ma.name,"\n",
- "\n\tn(pres)=",out$dat$ma$n.pres[2],
- "\n\tn(abs)=",out$dat$ma$n.abs[2],
- "\n\tn covariates considered=",length(out$dat$ma$used.covs),
- "\n\n","Settings:\n",
- "\n\ttree complexity=",out$mods$parms$tc.full,
- "\n\tlearning rate=",round(out$mods$lr.mod$lr,4),
- "\n\tn(trees)=",out$mods$final.mod$target.trees,
- "\n\tmodel simplification=",out$input$simp.method,
- "\n\tn folds=",out$input$n.folds,
- "\n\tn covariates in final model=",nrow(out$mods$final.mod$contributions),
- "\n\ttotal time for model fitting=",round((unclass(Sys.time())-t0)/60,2),"min\n",sep="")
- txt1 <- "\nRelative influence of predictors in final model:\n\n"
- txt2 <- "\nImportant interactions in final model:\n\n"
-
- capture.output(cat(txt0),cat(txt1),print(out$mods$final.mod$contributions),cat(txt2),print(out$mods$interactions,row.names=F),file=paste(bname,"_output.txt",sep=""))
- cat(txt0);cat(txt1);print(out$mods$final.mod$contributions);cat(txt2);print(out$mods$interactions,row.names=F)
-
- if(out$input$model.family=="bernoulli"){
- auc.output <- make.auc.plot.jpg(out$dat$ma$ma,pred=predict.gbm(out$mods$final.mod,out$dat$ma$ma,
- out$mods$final.mod$target.trees,type="response"),plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="BRT",opt.methods=opt.methods,
- weight=out$dat$ma$train.weights,out=out)
-
- out$mods$auc.output<-auc.output
- }
- if(out$input$model.family=="poisson"){
- auc.output <- make.poisson.jpg(out$dat$ma$ma,pred=predict.gbm(out$mods$final.mod,out$dat$ma$ma,
- out$mods$final.mod$target.trees,type="response"),plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="BRT",
- weight=out$dat$ma$train.weights,out=out)
-
- out$mods$auc.output<-auc.output
- }
-
- if(!debug.mode) {sink();cat("Progress:70%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("70%\n")}
-
- # Response curves #
- if(is.null(responseCurveForm)){
- responseCurveForm<-0}
-
- if(debug.mode | responseCurveForm=="pdf"){
- nvar <- nrow(out$mods$final.mod$contributions)
- pcol <- min(ceiling(sqrt(nvar)),4)
- prow <- min(ceiling(nvar/pcol),3)
-
- pdf(paste(bname,"_response_curves.pdf",sep=""),width=11,height=8.5,onefile=T)
- par(oma=c(2,2,4,2))
- r.curves <- try(gbm.plot(out$mods$final.mod,plotit=T,plot.layout=c(prow,pcol)))
- if(class(r.curves)!="try-error") {out$mods$r.curves <- r.curves
- mtext(paste("BRT response curves for",basename(ma.name)),outer=T,side=3,cex=1.3)}
- par(mfrow=c(1,1))
- #for(i in 1:min(nrow(int),2)) gbm.perspec(fit,int$var1.index[i],int$var2.index[i])
- if(!is.null(out$mods$interactions)){
- for(i in 1:nrow(out$mods$interactions)) {gbm.perspec(out$mods$final.mod,out$mods$interactions$v1[i],out$mods$interactions$v2[i])
- mtext(paste("BRT interaction plots for",basename(ma.name)),outer=T,side=3,cex=1.5) }
- }
- graphics.off()
- } else {
- r.curves <- try(gbm.plot(out$mods$final.mod,plotit=F))
- if(class(r.curves)!="try-error") {out$mods$r.curves <- r.curves
- } else {
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: problem fitting response curves",r.curves)
- }
- }
- t4 <- unclass(Sys.time())
- cat("\nfinished with final model summarization, t=",round(t4-t3,2),"sec\n");flush.console()
- if(!debug.mode) {sink();cat("Progress:80%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("80%\n")}
-
- assign("out",out,envir=.GlobalEnv)
- # Make .tif of predictions #
-
- save.image(paste(output.dir,"modelWorkspace",sep="\\"))
- if(out$input$make.p.tif==T | out$input$make.binary.tif==T){
- cat("\nproducing prediction maps...","\n","\n");flush.console()
- mssg <- proc.tiff(model=out$mods$final.mod,vnames=as.character(out$mods$final.mod$contributions$var),
- tif.dir=out$dat$tif.dir$dname,filenames=out$dat$tif.ind,pred.fct=brt.predict,factor.levels=out$dat$ma$factor.levels,make.binary.tif=make.binary.tif,
- thresh=out$mods$auc.output$thresh,make.p.tif=make.p.tif,outfile.p=paste(out$dat$bname,"_prob_map.tif",sep=""),
- outfile.bin=paste(out$dat$bname,"_bin_map.tif",sep=""),tsize=50.0,NAval=-3000,logname=logname,out=out) #"brt.prob.map.tif"
-
- if(class(mssg)=="try-error" | mssg!=0){
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("Error producing prediction maps:",mssg)
- cat(saveXML(brt.to.xml(out),indent=T),'\n')
- return()
- } else {
- if(make.p.tif) out$mods$tif.output$prob <- paste(out$dat$bname,"_prob_map.tif",sep="")
- if(make.binary.tif) out$mods$tif.output$bin <- paste(out$dat$bname,"_bin_map.tif",sep="")
- t5 <- unclass(Sys.time())
- cat("\nfinished with prediction maps, t=",round(t5-t4,2),"sec\n");flush.console()
- }
- }
- if(!debug.mode) {sink();cat("Progress:90%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("90%\n")} ### print time
-
- # Evaluation Statistics on Test Data#
-
- if(!is.null(out$dat$ma$ma.test)) Eval.Stat<-EvaluationStats(out,thresh=auc.output$thresh,train=out$dat$ma$ma,train.pred=predict.gbm(out$mods$final.mod,out$dat$ma$ma,
- out$mods$final.mod$target.trees,type="response"),opt.methods)
-
-
-
- # Write summaries to xml #
- if(debug.mode) assign("out",out,envir=.GlobalEnv)
- doc <- brt.to.xml(out)
-
- cat(paste("\ntotal time=",round((unclass(Sys.time())-t0)/60,2),"min\n\n\n",sep=""))
- if(!debug.mode) {
- sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))
- cat("Progress:100%\n");flush.console() ### print time
-
- cat(saveXML(doc,indent=T),'\n')
- }
- capture.output(cat(saveXML(doc,indent=T)),file=paste(out$dat$bname,"_output.xml",sep=""))
- if(debug.mode) assign("fit",out$mods$final.mod,envir=.GlobalEnv)
- invisible(out)
-}
-
-brt.predict <- function(model,x) {
- # retrieve key items from the global environment #
- # make predictions from complete data only #
- #y <- rep(NA,nrow(x))
- #y[complete.cases(x)] <- predict.gbm(model, x[complete.cases(x),],model$target.trees,type="response")
-
- # make predictions from full data #
- y <- predict.gbm(model,x,model$target.trees,type="response")
- # encode missing values as -1.
- a<-complete.cases(x)
- y[!(a)]<- NaN
-
- # return predictions.
- return(y)
- }
-
-
-
-
-logit <- function(x) 1/(1+exp(-x))
-
-file_path_as_absolute <- function (x){
- if (!file.exists(epath <- path.expand(x)))
- stop(gettextf("file '%s' does not exist", x), domain = NA)
- cwd <- getwd()
- on.exit(setwd(cwd))
- if (file_test("-d", epath)) {
- setwd(epath)
- getwd()
- }
- else {
- setwd(dirname(epath))
- file.path(getwd(), basename(epath))
- }
-}
-#file_path_as_absolute(".")
-
-brt.to.xml <- function(out){
- require(XML)
- schema.http="http://www.w3.org/2001/XMLSchema-instance"
- schema.fname="file:/Users/isfs2/Desktop/Source/2008-04-09/src/gov/nasa/gsfc/quickmap/ModelBuilder/modelRun_output_v2.xsd"
- xml.out <- newXMLDoc()
- mr <- newXMLNode("modelRunOutput",doc=xml.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))#,parent=xml.out
- sm <- newXMLNode("singleModel",parent=mr)
- bg <- newXMLNode("background",parent=sm)
- newXMLNode("mdsName",out$input$ma.name,parent=bg)
- newXMLNode("runDate",out$input$run.time,parent=bg)
- lc <- newXMLNode("layersConsidered",parent=bg)#, parent = xml.out)
- kids <- lapply(paste(out$dat$tif.dir$dname,"/",out$dat$ma$used.covs,".tif",sep=""),function(x) newXMLNode("layer", x))
- addChildren(lc, kids)
- mo <- newXMLNode("modelOutput",parent=sm)
- newXMLNode("modelType",out$input$model.type,parent=mo)
- newXMLNode("modelSourceFile",out$input$model.source.file,parent=mo)
- newXMLNode("devianceExplained",out$mods$auc.output$pct_dev_exp,parent=mo,attrs=list(type="percentage"))
- if(!is.null(out$mods$summary)){
- newXMLNode("nativeOutput",paste(out$dat$bname,"_output.txt",sep=""),parent=mo)
- } else {
- newXMLNode("nativeOutput",NULL,parent=mo)
- }
- newXMLNode("binaryOutputFile",out$mods$tif.output[[2]],parent=mo)
- newXMLNode("probOutputFile",out$mods$tif.output[[1]],parent=mo)
- newXMLNode("auc",out$mods$auc.output$auc,parent=mo)
- newXMLNode("rocGraphic",out$mods$auc.output$plotname,parent=mo)
- newXMLNode("rocThresh",out$mods$auc.output$thresh,parent=mo)
- newXMLNode("modelDeviance",out$mods$auc.output$dev_fit,parent=mo)
- newXMLNode("nullDeviance",out$mods$auc.output$null_dev,parent=mo)
- if(is.null(out$mods$r.curves)) rc.name <- NULL else rc.name <- paste(out$dat$bname,"_response_curves.xml",sep="")
- newXMLNode("responsePlotsFile",rc.name,parent=mo)
- newXMLNode("significanceDescription",out$input$sig.test,parent=mo)
- mfp <- newXMLNode("modelFitParmas",parent=mo)
- newXMLNode("treeComplexity",out$input$tc,parent=mfp)
- newXMLNode("bagFraction",out$input$bag.fraction,parent=mfp)
- newXMLNode("simpMethod",out$input$simp.method,parent=mfp)
- newXMLNode("alpha",out$input$alpha,parent=mfp)
-
- sv <- newXMLNode("significantVariables",parent=mo)
- if(!is.null(out$mods$summary)) {
- t.table <- data.frame(significanceMeasurement=out$mods$summary$rel.inf,row.names=out$mods$summary$var)
- if(!is.null(out$mods$interactions)){
- int1 <- int2 <- out$mods$interactions
- int2$name1 <- int1$name2
- int2$name2 <- int1$name1
- int <- rbind(int1,int2)
- }
-
- for(i in 1:nrow(t.table)){
- x <- newXMLNode("sigVar",parent=sv)
- newXMLNode(name="name", row.names(t.table)[i],parent=x)
- kids <- lapply(1:ncol(t.table),function(j) newXMLNode(name=names(t.table)[j], t.table[i,j]))
- addChildren(x, kids)
- if(!is.null(out$mods$interactions)){
- ints <- c(1:nrow(int))[int$name1 %in% row.names(t.table)[i]]
- if(length(ints)>0){
- kids <- lapply(ints,function(j) newXMLNode(name="sigInteraction",attrs=list(name=as.character(int$name2)[j],size=int$int.size[j],p=int$"p-value"[j])))
- addChildren(x,kids)
- }
-
- }
- }
- }
-
- if(!is.null(out$mods$r.curves)){
- r.curves <- out$mods$r.curves
- factor.levels <- out$dat$ma$factor.levels
- rc.out <- newXMLDoc()
- root <- newXMLNode("responseCurves",doc=rc.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))
- for(i in 1:length(r.curves$names)){
- if(!is.na(f.index<-match(r.curves$names[i],names(factor.levels)))){
- vartype <- "factor"} else vartype="continuous"
- x <- newXMLNode("responseCurve",attrs=list(covariate=r.curves$names[i],type=vartype),parent=root)
- kids <- lapply(1:length(r.curves$preds[[i]]),function(j){
- newXMLNode(name="responsePt",parent=x,.children=list(
- newXMLNode(name="explanatory",as.character(r.curves$preds[[i]])[j]),
- newXMLNode(name="response",r.curves$resp[[i]][j])))})
- addChildren(x, kids)
- }
- saveXML(rc.out,rc.name,indent=T)
-
- }
- if(!is.null(out$error.mssg[[1]])) {
- kids <- lapply(out$error.mssg,function(j) newXMLNode(name="error",j))
- addChildren(mo,kids)
- }
- return(xml.out)
- }
-
-
-get.cov.names <- function(model){
- return(attr(terms(formula(model)),"term.labels"))
- }
-
-
-
-est.lr <- function(out){
- # this function estimates optimal number of trees at a variety of learning rates #
- # the learning rate that produces closest to 1000 trees is selected #
- # in addition, variables with >1% influence are identified by column number in
- # the original dataframe
- # written by AKS early 2009
- suppressMessages(require(gbm))
-
- t0 <- unclass(Sys.time())
-
- # set tree complexity for full-data run #
- a<-2.69; b<-0.0012174
- if(is.null(out$mods$parms$tc.full)) out$mods$parms$tc.full<-min(round(a+b*out$dat$ma$dims[1]),15) # this gives 3 for n=250
- if(is.null(out$mods$parms$tc.sub)){
- n <- out$dat$ma$n.abs[3]+out$dat$ma$n.pres[3] # this gives 3 for n=250
- if(is.na(n)) (n=length(out$dat$ma$weight.subset))
- out$mods$parms$tc.sub <- round(a+b*n)
- }
-
- cat("\n");cat("tree complexity set to",out$mods$parms$tc.sub,"\n")
-
- n.trees <- c(100,200,400,800,900,1000,1100,1200,1500,1800,2400)
- lrs <- c(.1,.06,.05,.04,.03,.02,.01,.005,.0025,.001,.0005,.0001)
- lr.out <- data.frame(lrs=lrs,max.trees=0)
- dat <- out$dat$ma$ma.subset
- gbm.y <- 1
- gbm.x <- 2:ncol(dat)
-
- max.trees <- 0
- i=1
-
- while(max.trees<800 & i<=nrow(lr.out)){
-
- tryCatch(gbm.fit <- gbm.step.fast(dat=dat,
- gbm.x = gbm.x,
- gbm.y = gbm.y,
- family = out$input$model.family,
- n.trees = n.trees,
- n.folds=out$input$n.folds,
- tree.complexity = out$mods$parms$tc.sub,
- learning.rate = lrs[i],
- bag.fraction = out$input$bag.fraction,
- site.weights=out$dat$ma$weight.subset,
- autostop=T,verbose=F,silent=T,plot.main=F),error=function(ex){cat("Error: learning rate estimation failed.\n");
- print(ex);
- stop();})
-
- if(class(gbm.fit)=="try-error"){
- out$ec <- out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: learning rate estimation failed:",gbm.fit)
- return(out)
- }
- lr.out$max.trees[i] <- max.trees <- gbm.fit$target.trees
- assign(paste("gbm.fit",i,sep="_"),gbm.fit)
- cat("lr =",lrs[i]," optimal n trees =",max.trees,"\n");flush.console()
- i<-i+1 #ifelse(max.trees<=200,i+2,i+1)
- }
- # pick lr that gives closest to 1000 trees #
-
- lr.out$i <- 1:nrow(lr.out)
- lr.out <- lr.out[lr.out$max.trees!=0,]
- ab<-coef(lm(max.trees~log(lrs),data=lr.out))
- tt <- out$dat$ma$ratio*800
- lr.full <- round(as.numeric(exp((tt-ab[1])/ab[2])),4)
- lr <- round(as.numeric(exp((1000-ab[1])/ab[2])),6)
- lr.out$abs <- abs(lr.out$max.trees-1000)
- lr.out$d.lr <- abs(lr.out$lrs-lr)
- lr.out <- lr.out[order(lr.out$abs,lr.out$d.lr),]
- lr0 <- lr.out$lrs[1]
- i <- lr.out$i[1]
- gbm.fit <- get(paste("gbm.fit",i,sep="_"))
- gbm.fit$gbm.call$dataframe <- as.character(substitute(dat))
- good.vars <- summary(gbm.fit,plotit=F)
- good.vars <- good.vars$var[good.vars$rel.inf>ifelse(out$input$simp.method!="none",1,0)]
- good.cols <- c(1:ncol(dat))[names(dat) %in% good.vars]
- out$mods$simp.mod <- list(good.cols=good.cols,good.vars=good.vars)
- out$mods$lr.mod <- list(tc=out$mods$parms$tc.sub,lr=lr.full,lr0=lr0,lr.out=lr.out,ab=ab,gbm.fit=gbm.fit,good.cols=good.cols,t.elapsed=c(unclass(Sys.time())-t0))
- if(!is.null(out$input$learning.rate)) {out$mods$lr.mod$lr0=out$input$learning.rate
- out$mods$lr.mod$lr=out$input$learning.rate
- }
- return(out)
- }
-
-
-check.dir <- function(dname){
- if(is.null(dname)) dname <- getwd()
- dname <- gsub("[\\]","/",dname)
- end.char <- substr(dname,nchar(dname),nchar(dname))
- if(end.char == "/") dname <- substr(dname,1,nchar(dname)-1)
- exist <- suppressWarnings(as.numeric(file.access(dname,mode=0))==0) # -1 if bad, 0 if ok #
- if(exist) dname <- file_path_as_absolute(dname)
- readable <- suppressWarnings(as.numeric(file.access(dname,mode=4))==0) # -1 if bad, 0 if ok #
- writable <- suppressWarnings(as.numeric(file.access(dname,mode=2))==0) # -1 if bad, 0 if ok #
- return(list(dname=dname,exist=exist,readable=readable,writable=writable))
- }
-
-
-
-get.image.info <- function(image.names){
- # this function creates a data.frame with summary image info for a set of images #
- require(rgdal)
- n.images <- length(image.names)
-
- full.names <- image.names
- out <- data.frame(image=full.names,available=rep(F,n.images),size=rep(NA,n.images),
- type=factor(rep("unk",n.images),levels=c("asc","envi","tif","unk")))
- out$type[grep(".tif",image.names)]<-"tif"
- out$type[grep(".asc",image.names)]<-"asc"
- for(i in 1:n.images){
- if(out$type[i]=="tif"){
- x <-try(GDAL.open(full.names[1],read.only=T))
- suppressMessages(try(GDAL.close(x)))
- if(class(x)!="try-error") out$available[i]<-T
- x<-try(file.info(full.names[i]))
- } else {
- x<-try(file.info(full.names[i]))
- if(!is.na(x$size)) out$available[i]<-T
- }
- if(out$available[i]==T){
- out$size[i]<-x$size
- if(out$type[i]=="unk"){
- # if extension not known, look for envi .hdr file in same directory #
- if(file.access(paste(file_path_sans_ext(full.names[i]),".hdr",sep=""))==0)
- out$type[i]<-"envi"
- }
- }
- }
- return(out)
-}
-
-gbm.step.fast <- function(
- dat, # the input dataframe
- gbm.x, # the predictors
- gbm.y, # and response
- offset = NULL, # allows an offset to be specified
- fold.vector = NULL, # allows a fold vector to be read in for CV with offsets,
- tree.complexity = 1, # sets the complexity of individual trees
- learning.rate = 0.01, # sets the weight applied to inidivudal trees
- bag.fraction = 0.75, # sets the proportion of observations used in selecting variables
- site.weights = rep(1, nrow(dat)), # allows varying weighting for sites
- var.monotone = rep(0, length(gbm.x)), # restricts responses to individual predictors to monotone
- n.folds = 10, # number of folds
- prev.stratify = TRUE, # prevalence stratify the folds - only for p/a data
- family = "bernoulli", # family - bernoulli (=binomial), poisson, laplace or gaussian
- n.trees = 50, # number of initial trees to fit
- step.size = n.trees, # numbers of trees to add at each cycle
- max.trees = 10000, # max number of trees to fit before stopping
- tolerance.method = "auto", # method to use in deciding to stop - "fixed" or "auto"
- tolerance = 0.001, # tolerance value to use - if method == fixed is absolute,
- # if auto is multiplier * total mean deviance
- keep.data = FALSE, # keep raw data in final model
- plot.main = TRUE, # plot hold-out deviance curve
- plot.folds = FALSE, # plot the individual folds as well
- verbose = TRUE, # control amount of screen reporting
- silent = FALSE, # to allow running with no output for simplifying model)
- keep.fold.models = FALSE, # keep the fold models from cross valiation
- keep.fold.vector = FALSE, # allows the vector defining fold membership to be kept
- keep.fold.fit = FALSE, # allows the predicted values for observations from CV to be kept
- autostop = FALSE, # setting autostop to T causes the tree fitting while loop to terminate
- # if the cv.loss value increases twice in a row (AKS).
-
- superfast=FALSE, # controls whether or not to compute final model when optimal n.trees differs from 1000 (AKS)
- ...) # allows for any additional plotting parameters
-{
-#
-# j. leathwick/j. elith - 19th September 2005
-#
-# version 2.9
-#
-# function to assess optimal no of boosting trees using k-fold cross validation
-#
-# implements the cross-validation procedure described on page 215 of
-# Hastie T, Tibshirani R, Friedman JH (2001) The Elements of Statistical Learning:
-# Data Mining, Inference, and Prediction Springer-Verlag, New York.
-#
-# divides the data into 10 subsets, with stratification by prevalence if required for pa data
-# then fits a gbm model of increasing complexity along the sequence from n.trees to n.trees + (n.steps * step.size)
-# calculating the residual deviance at each step along the way
-# after each fold processed, calculates the average holdout residual deviance and its standard error
-# then identifies the optimal number of trees as that at which the holdout deviance is minimised
-# and fits a model with this number of trees, returning it as a gbm model along with additional information
-# from the cv selection process
-#
-# updated 13/6/05 to accommodate weighting of sites
-#
-# updated 19/8/05 to increment all folds simultaneously, allowing the stopping rule
-# for the maxinum number of trees to be fitted to be imposed by the data,
-# rather than being fixed in advance
-#
-# updated 29/8/05 to return cv test statistics, and deviance as mean
-# time for analysis also returned via unclass(Sys.time())
-#
-# updated 5/9/05 to use external function calc.deviance
-# and to return cv test stats via predictions formed from fold models
-# with n.trees = target.trees
-#
-# updated 15/5/06 to calculate variance of fitted and predicted values across folds
-# these can be expected to approximate the variance of fitted values
-# as would be estimated for example by bootstrapping
-# as these will underestimate the true variance
-# they are corrected by multiplying by (n-1)2/n
-# where n is the number of folds
-#
-# updated 25/3/07 tp allow varying of bag fraction
-#
-# requires gbm library from Cran
-# requires roc and calibration scripts of J Elith
-# requires calc.deviance script of J Elith/J Leathwick
-#
-# updated 1/2/09 by aks:
-# now takes a vector arguement for n.trees: if n.trees is given as a (should be montonically
-# increasing) vector, then models with those # of trees are fit. if n.trees is a single number,
-# then the program works as default
-# there is also a provision for stopping the fitting of successive models IF the cv.loss.value increases
-# over two successive steps.
-
- require(gbm)
-
- if (silent) verbose <- FALSE
-
-# initiate timing call
-
- z1 <- unclass(Sys.time())
-
-# setup input data and assign to position one
-
- dataframe.name <- deparse(substitute(dat)) # get the dataframe name
-
- dat <- eval(dat)
- x.data <- eval(dat[, gbm.x]) #form the temporary datasets
- names(x.data) <- names(dat)[gbm.x]
- y.data <- eval(dat[, gbm.y])
- sp.name <- names(dat)[gbm.y]
- if (family == "bernoulli") prevalence <- mean(y.data)
-
- assign("x.data", x.data, env = globalenv()) #and assign them for later use
- assign("y.data", y.data, env = globalenv())
-
- offset.name <- deparse(substitute(offset)) # get the dataframe name
- offset = eval(offset)
- #print(summary(offset))
-
- n.cases <- nrow(dat)
- n.preds <- length(gbm.x)
-
- if (!silent) {
- cat("\n","\n");cat("GBM STEP - version 2.9","\n","\n") #AKS
- cat("Performing cross-validation optimization of a boosted regression tree model \n")#AKS
- cat("for",sp.name,"with dataframe",dataframe.name,"and using a family of",family,"\n\n")
- cat("Using",n.cases,"observations and",n.preds,"predictors \n\n")
- flush.console() #AKS
- }
-
-# set up the selector variable either with or without prevalence stratification
-
- if (is.null(fold.vector)) {
-
- if (prev.stratify & family == "bernoulli") {
- presence.mask <- dat[,gbm.y] == 1
- absence.mask <- dat[,gbm.y] == 0
- n.pres <- sum(presence.mask)
- n.abs <- sum(absence.mask)
-
-# create a vector of randomised numbers and feed into presences
- selector <- rep(0,n.cases)
- temp <- rep(seq(1, n.folds, by = 1), length = n.pres)
- temp <- temp[order(runif(n.pres, 1, 100))]
- selector[presence.mask] <- temp
-
-# and then do the same for absences
- temp <- rep(seq(1, n.folds, by = 1), length = n.abs)
- temp <- temp[order(runif(n.abs, 1, 100))]
- selector[absence.mask] <- temp
- }
-
- else { #otherwise make them random with respect to presence/absence
- selector <- rep(seq(1, n.folds, by = 1), length = n.cases)
- selector <- selector[order(runif(n.cases, 1, 100))]
- }
- }
- else {
- if (length(fold.vector) != n.cases) stop("supplied fold vector is of wrong length")
- cat("loading user-supplied fold vector \n\n")
- selector <- eval(fold.vector)
- }
-
-# set up the storage space for results
-
- pred.values <- rep(0, n.cases)
-
- cv.loss.matrix <- matrix(0, nrow = n.folds, ncol = 1)
- training.loss.matrix <- matrix(0, nrow = n.folds, ncol = 1)
- trees.fitted <- n.trees[1]
-
- model.list <- list(paste("model",c(1:n.folds),sep="")) # dummy list for the tree models
-
-# set up the initial call to gbm
-
- if (is.null(offset)) { #AKS (n.trees arg)
- gbm.call <- paste("gbm(y.subset~.,data=x.subset,n.trees=n.trees[1],interaction.depth=tree.complexity,shrinkage=learning.rate,bag.fraction=bag.fraction,weights=weight.subset,distribution=as.character(family),var.monotone=var.monotone,verbose=FALSE)",sep="")
- }
- else { #AKS (n.trees arg)
- gbm.call <- paste("gbm(y.subset~.+offset(offset.subset),data=x.subset,n.trees=n.trees[1],interaction.depth=tree.complexity,shrinkage=learning.rate,bag.fraction=bag.fraction,weights=weight.subset,distribution=as.character(family),var.monotone=var.monotone,verbose=FALSE)",sep="")
- }
-
-
- n.fitted <- n.trees[1] # AKS
-
-# calculate the total deviance
-
- y_i <- y.data
-
- u_i <- sum(y.data * site.weights) / sum(site.weights)
- u_i <- rep(u_i,length(y_i))
-
- total.deviance <- calc.deviance(y_i, u_i, weights = site.weights, family = family, calc.mean = FALSE)
-
- mean.total.deviance <- total.deviance/n.cases
-
- tolerance.test <- tolerance
-
- if (tolerance.method == "auto") {
- tolerance.test <- mean.total.deviance * tolerance
- }
-
-# now step through the folds setting up the initial call
-
- if (!silent){
-
- cat("creating",n.folds,"initial models of",n.trees,"trees","\n")
-
- if (prev.stratify & family == "bernoulli") {cat("\n");cat("folds are stratified by prevalence","\n","\n")#AKS
- } else {cat("\n","folds are unstratified","\n","\n")}
-
- cat ("total mean deviance = ",round(mean.total.deviance,4),"\n","\n")
-
- cat("tolerance is fixed at ",round(tolerance.test,4),"\n","\n")
- flush.console()#AKS
-
- if (tolerance.method != "fixed" & tolerance.method != "auto") {
- cat("invalid argument for tolerance method - should be auto or fixed","\n")
- return()}
- }
-
- if (verbose) cat("fitting initial model...","\n");flush.console()#AKS
-
- for (i in 1:n.folds) {
-
- model.mask <- selector != i #used to fit model on majority of data
- pred.mask <- selector == i #used to identify the with-held subset
-
- y.subset <- y.data[model.mask]
- x.subset <- x.data[model.mask,]
- weight.subset <- site.weights[model.mask]
-
- if (!is.null(offset)) {
- offset.subset <- offset[model.mask]
- }
- else {
- offset.subset <- NULL
- }
-
- model.list[[i]] <- eval(parse(text = gbm.call))
-
- fitted.values <- model.list[[i]]$fit #predict.gbm(model.list[[i]], x.subset, type = "response", n.trees = n.trees)
- if (!is.null(offset)) fitted.values <- fitted.values + offset[model.mask]
- if (family == "bernoulli") fitted.values <- exp(fitted.values)/(1 + exp(fitted.values))
- if (family == "poisson") fitted.values <- exp(fitted.values)
-
- pred.values[pred.mask] <- predict.gbm(model.list[[i]], x.data[pred.mask, ], n.trees = n.trees[1])
- if (!is.null(offset)) pred.values[pred.mask] <- pred.values[pred.mask] + offset[pred.mask]
- if (family == "bernoulli") pred.values[pred.mask] <- exp(pred.values[pred.mask])/(1 + exp(pred.values[pred.mask]))
- if (family == "poisson") pred.values[pred.mask] <- exp(pred.values[pred.mask])
-
-# calc training deviance
-
- y_i <- y.subset
- u_i <- fitted.values
- weight.fitted <- site.weights[model.mask]
- training.loss.matrix[i,1] <- calc.deviance(y_i, u_i, weight.fitted, family = family)
-
-# calc holdout deviance
-
- y_i <- y.data[pred.mask]
- u_i <- pred.values[pred.mask]
- weight.preds <- site.weights[pred.mask]
- cv.loss.matrix[i,1] <- calc.deviance(y_i, u_i, weight.preds, family = family)
-
- } # end of first loop
-
-# now process until the change in mean deviance is =< tolerance or max.trees is exceeded
-
- delta.deviance <- 1
-
- cv.loss.values <- apply(cv.loss.matrix,2,mean)
- if (verbose) cat("ntrees resid. dev.","\n")#AKS
- if (verbose) cat(n.fitted," ",round(cv.loss.values,4),"\n","\n")
-
- if (!silent) cat("")
- if (!silent) cat("now adding trees...","\n");flush.console()#AKS
-
- j <- 1
- k <- 2 #AKS
- stop.loop <- F #AKS
- if(length(n.trees>1)) max.trees <- n.trees[length(n.trees)] #AKS
-
- while (delta.deviance > tolerance.test & n.fitted < max.trees & stop.loop==F) { # beginning of inner loop
-
- # add a new column to the results matrice..
-
- training.loss.matrix <- cbind(training.loss.matrix,rep(0,n.folds))
- cv.loss.matrix <- cbind(cv.loss.matrix,rep(0,n.folds))
-
- if(length(n.trees>1)){ #AKS
- n.fitted <- n.trees[k] #AKS
- step.size <- n.trees[k]-n.trees[k-1]
- k <- k+1 #AKS
- } else { #AKS
- n.fitted <- n.fitted + step.size
- } #AKS
-
- trees.fitted <- c(trees.fitted,n.fitted)
-
- j <- j + 1
-
- for (i in 1:n.folds) {
-
- model.mask <- selector != i #used to fit model on majority of data
- pred.mask <- selector == i #used to identify the with-held subset
-
- y.subset <- y.data[model.mask]
- x.subset <- x.data[model.mask,]
- weight.subset <- site.weights[model.mask]
- if (!is.null(offset)) {
- offset.subset <- offset[model.mask]
- }
-
- model.list[[i]] <- gbm.more(model.list[[i]], weights = weight.subset, step.size)
-
- fitted.values <- model.list[[i]]$fit # predict.gbm(model.list[[i]],x.subset, type = "response", n.trees = n.fitted)
- if (!is.null(offset)) fitted.values <- fitted.values + offset[model.mask]
- if (family == "bernoulli") fitted.values <- exp(fitted.values)/(1 + exp(fitted.values))
- if (family == "poisson") fitted.values <- exp(fitted.values)
-
- pred.values[pred.mask] <- predict.gbm(model.list[[i]], x.data[pred.mask, ], n.trees = n.fitted)
- if (!is.null(offset)) pred.values[pred.mask] <- pred.values[pred.mask] + offset[pred.mask]
- if (family == "bernoulli") pred.values[pred.mask] <- exp(pred.values[pred.mask])/(1 + exp(pred.values[pred.mask]))
- if (family == "poisson") pred.values[pred.mask] <- exp(pred.values[pred.mask])
-
- # calculate training deviance
-
- y_i <- y.subset
- u_i <- fitted.values
- weight.fitted <- site.weights[model.mask]
- training.loss.matrix[i,j] <- calc.deviance(y_i, u_i, weight.fitted, family = family)
-
- # calc holdout deviance
-
- u_i <- pred.values[pred.mask]
- y_i <- y.data[pred.mask]
- weight.preds <- site.weights[pred.mask]
- cv.loss.matrix[i,j] <- calc.deviance(y_i, u_i, weight.preds, family = family)
-
- } # end of inner loop
-
- cv.loss.values <- apply(cv.loss.matrix,2,mean)
-
- if (j < 5 & autostop==F) { #AKS
- if (cv.loss.values[j] > cv.loss.values[j-1]) {
- if (!silent) cat("restart model with a smaller learning rate or smaller step size...")
- return()
- }
- }
-
- if (j >= 20) { #calculate stopping rule value
- test1 <- mean(cv.loss.values[(j-9):j])
- test2 <- mean(cv.loss.values[(j-19):(j-9)])
- delta.deviance <- test2 - test1
- }
-
- if (verbose) cat(n.fitted," ",round(cv.loss.values[j],4),"\n");flush.console()#AKS
- if(autostop==T & j>2){ # this if statement added by AKS
- if((cv.loss.values[j]>cv.loss.values[j-1])){# & (cv.loss.values[j-1]>cv.loss.values[j-2])){ # if deviance increases twice in a row
- stop.loop=T#n.fitted <- max.trees # by setting n.fitted to max.trees, the while loop will terminate.
- }
- }
-
-
-
- } # end of while loop
-
-# now begin process of calculating optimal number of trees
-
- training.loss.values <- apply(training.loss.matrix,2,mean)
-
- cv.loss.ses <- rep(0,length(cv.loss.values))
- cv.loss.ses <- sqrt(apply(cv.loss.matrix,2,var)) / sqrt(n.folds)
-
-# find the target holdout deviance
-
- y.bar <- min(cv.loss.values)
-
-# plot out the resulting curve of holdout deviance
-
- if (plot.main) {
-
- y.min <- min(cv.loss.values - cv.loss.ses) #je added multiplier 10/8/05
- y.max <- max(cv.loss.values + cv.loss.ses) #je added multiplier 10/8/05 }
-
- if (plot.folds) {
- y.min <- min(cv.loss.matrix)
- y.max <- max(cv.loss.matrix) }
-
- plot(trees.fitted, cv.loss.values, type = 'l', ylab = "holdout deviance",
- xlab = "no. of trees", ylim = c(y.min,y.max), ...)
- abline(h = y.bar, col = 2)
-
- lines(trees.fitted, cv.loss.values + cv.loss.ses, lty=2)
- lines(trees.fitted, cv.loss.values - cv.loss.ses, lty=2)
-
- if (plot.folds) {
- for (i in 1:n.folds) {
- lines(trees.fitted, cv.loss.matrix[i,],lty = 3)
- }
- }
- }
-
-# identify the optimal number of trees
-
- target.trees <- trees.fitted[match(TRUE,cv.loss.values == y.bar)]
- #cat("\n");cat("optimal n trees =",target.trees,"\n") #AKS
-
- if(plot.main) {
- abline(v = target.trees, col=3)
- title(paste(sp.name,", d - ",tree.complexity,", lr - ",learning.rate, sep=""))
- }
-
-# skip additional details on final model unless target.trees is close to 1000 (AKS)#
-if(abs(target.trees-1000) >= 600 & superfast==T){ # AKS
- return(list(target.trees=target.trees)) # AKS
- } else { # AKS
-
-
-# estimate the cv deviance and test statistics
-# includes estimates of the standard error of the fitted values added 2nd may 2005
-
- cv.deviance.stats <- rep(0, n.folds)
- cv.roc.stats <- rep(0, n.folds)
- cv.cor.stats <- rep(0, n.folds)
- cv.calibration.stats <- matrix(0, ncol=5, nrow = n.folds)
- if (family == "bernoulli") threshold.stats <- rep(0, n.folds)
-
- fitted.matrix <- matrix(NA, nrow = n.cases, ncol = n.folds) #used to calculate se's
- fold.fit <- rep(0,n.cases)
-
- for (i in 1:n.folds) {
-
- pred.mask <- selector == i #used to identify the with-held subset
- model.mask <- selector != i #used to fit model on majority of data
-
- fits <- predict.gbm(model.list[[i]], x.data[model.mask, ], n.trees = target.trees)
- if (!is.null(offset)) fits <- fits + offset[model.mask]
- if (family == "bernoulli") fits <- exp(fits)/(1 + exp(fits))
- if (family == "poisson") fits <- exp(fits)
- fitted.matrix[model.mask,i] <- fits
-
- fits <- predict.gbm(model.list[[i]], x.data[pred.mask, ], n.trees = target.trees)
- if (!is.null(offset)) fits <- fits + offset[pred.mask]
- fold.fit[pred.mask] <- fits # store the linear predictor values
- if (family == "bernoulli") fits <- exp(fits)/(1 + exp(fits))
- if (family == "poisson") fits <- exp(fits)
- fitted.matrix[pred.mask,i] <- fits
-
- y_i <- y.data[pred.mask]
- u_i <- fitted.matrix[pred.mask,i] #pred.values[pred.mask] ####
- weight.preds <- site.weights[pred.mask]
-
- cv.deviance.stats[i] <- calc.deviance(y_i, u_i, weight.preds, family = family)
-
- cv.cor.stats[i] <- cor(y_i,u_i)
-
- if (family == "bernoulli") {
- cv.roc.stats[i] <- roc(y_i,u_i)
- cv.calibration.stats[i,] <- calibration(y_i,u_i,"binomial")
- threshold.stats[i] <- approx(ppoints(u_i), sort(u_i,decreasing = T), prevalence)$y
- }
-
- if (family == "poisson") {
- cv.calibration.stats[i,] <- calibration(y_i,u_i,"poisson")
- }
- }
-
- fitted.vars <- apply(fitted.matrix,1, var, na.rm = TRUE)
-
- #now calculate the mean and se's for the folds
-
- cv.dev <- mean(cv.deviance.stats, na.rm = TRUE)
- cv.dev.se <- sqrt(var(cv.deviance.stats)) / sqrt(n.folds)
-
- cv.cor <- mean(cv.cor.stats, na.rm = TRUE)
- cv.cor.se <- sqrt(var(cv.cor.stats, use = "complete.obs")) / sqrt(n.folds)
-
- cv.roc <- 0.0
- cv.roc.se <- 0.0
-
- if (family == "bernoulli") {
- cv.roc <- mean(cv.roc.stats,na.rm=TRUE)
- cv.roc.se <- sqrt(var(cv.roc.stats, use = "complete.obs")) / sqrt(n.folds)
- cv.threshold <- mean(threshold.stats, na.rm = T)
- cv.threshold.se <- sqrt(var(threshold.stats, use = "complete.obs")) / sqrt(n.folds)
- }
-
- cv.calibration <- 0.0
- cv.calibration.se <- 0.0
-
- if (family == "poisson" | family == "bernoulli") {
- cv.calibration <- apply(cv.calibration.stats,2,mean)
- cv.calibration.se <- apply(cv.calibration.stats,2,var)
- cv.calibration.se <- sqrt(cv.calibration.se) / sqrt(n.folds) }
-
- #fit the final model
-
- if (is.null(offset)) {
- gbm.call <- paste("gbm(y.data~.,data=x.data,n.trees=target.trees,interaction.depth=tree.complexity,shrinkage=learning.rate,bag.fraction=bag.fraction,weights=site.weights,distribution=as.character(family),var.monotone=var.monotone,verbose=FALSE)",sep="")
- }
- else {
- gbm.call <- paste("gbm(y.data~.+ offset(offset),data=x.data,n.trees=target.trees,interaction.depth=tree.complexity,shrinkage=learning.rate,bag.fraction=bag.fraction,weights=site.weights,distribution=as.character(family),var.monotone=var.monotone,verbose=FALSE)",sep="")
- }
-
- if (!silent) cat("fitting final gbm model with a fixed number of ",target.trees," trees for ",sp.name,"\n")
-
- gbm.object <- eval(parse(text = gbm.call)) # AKS
-
- best.trees <- target.trees
-
-#extract fitted values and summary table
-
- gbm.summary <- summary(gbm.object,n.trees = target.trees, plotit = FALSE)
-
- fits <- predict.gbm(gbm.object,x.data,n.trees = target.trees)
- if (!is.null(offset)) fits <- fits + offset
- if (family == "bernoulli") fits <- exp(fits)/(1 + exp(fits))
- if (family == "poisson") fits <- exp(fits)
- fitted.values <- fits
-
- y_i <- y.data
- u_i <- fitted.values
- resid.deviance <- calc.deviance(y_i, u_i, weights = site.weights, family = family, calc.mean = FALSE)
-
- self.cor <- cor(y_i,u_i)
- self.calibration <- 0.0
- self.roc <- 0.0
-
- if (family == "bernoulli") { #do this manually as we need the residuals
- deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
- residuals <- sqrt(abs(deviance.contribs * 2))
- residuals <- ifelse((y_i - u_i) < 0, 0 - residuals, residuals)
- self.roc <- roc(y_i,u_i)
- self.calibration <- calibration(y_i,u_i,"binomial")
- }
-
- if (family == "poisson") { #do this manually as we need the residuals
- deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
- residuals <- sqrt(abs(deviance.contribs * 2))
- residuals <- ifelse((y_i - u_i) < 0, 0 - residuals, residuals)
- self.calibration <- calibration(y_i,u_i,"poisson")
- }
-
- if (family == "gaussian" | family == "laplace") {
- residuals <- y_i - u_i
- }
-
- mean.resid.deviance <- resid.deviance/n.cases
-
- z2 <- unclass(Sys.time())
- elapsed.time.minutes <- round((z2 - z1)/ 60,2) # calculate the total elapsed time
-
- if (verbose) {
- cat("\n")
- cat("mean total deviance =", round(mean.total.deviance,3),"\n")
- cat("mean residual deviance =", round(mean.resid.deviance,3),"\n","\n")
- cat("estimated cv deviance =", round(cv.dev,3),"; se =",
- round(cv.dev.se,3),"\n","\n")
- cat("training data correlation =",round(self.cor,3),"\n")
- cat("cv correlation = ",round(cv.cor,3),"; se =",round(cv.cor.se,3),"\n","\n")
- if (family == "bernoulli") {
- cat("training data ROC score =",round(self.roc,3),"\n")
- cat("cv ROC score =",round(cv.roc,3),"; se =",round(cv.roc.se,3),"\n","\n")
- }
- cat("elapsed time - ",round(elapsed.time.minutes,2),"minutes","\n")
- }
-
- if (n.fitted == max.trees & !silent) {
- cat("\n"," warning ","\n","\n")
- cat("maximum tree limit reached - results may not be optimal","\n")
- cat(" - refit with faster learning rate or increase maximum number of trees","\n")
-
-
- }
-
- # now assemble data to be returned
-
- gbm.detail <- list(dataframe = dataframe.name, gbm.x = gbm.x, predictor.names = names(x.data),
- gbm.y = gbm.y, response.name = sp.name, offset = offset.name, family = family, tree.complexity = tree.complexity,
- learning.rate = learning.rate, bag.fraction = bag.fraction, cv.folds = n.folds,
- prev.stratification = prev.stratify, max.fitted = n.fitted, n.trees = target.trees,
- best.trees = target.trees, train.fraction = 1.0, tolerance.method = tolerance.method,
- tolerance = tolerance, var.monotone = var.monotone, date = date(),
- elapsed.time.minutes = elapsed.time.minutes)
-
- training.stats <- list(null = total.deviance, mean.null = mean.total.deviance,
- resid = resid.deviance, mean.resid = mean.resid.deviance, correlation = self.cor,
- discrimination = self.roc, calibration = self.calibration)
-
- cv.stats <- list(deviance.mean = cv.dev, deviance.se = cv.dev.se,
- correlation.mean = cv.cor, correlation.se = cv.cor.se,
- discrimination.mean = cv.roc, discrimination.se = cv.roc.se,
- calibration.mean = cv.calibration, calibration.se = cv.calibration.se)
-
- if (family == "bernoulli") {
- cv.stats$cv.threshold <- cv.threshold
- cv.stats$cv.threshold.se <- cv.threshold.se
- }
-
- rm(x.data,y.data, envir = globalenv()) # finally, clean up the temporary dataframes
-
- # and assemble results for return
-
- gbm.object$gbm.call <- gbm.detail
- gbm.object$fitted <- fitted.values
- gbm.object$fitted.vars <- fitted.vars
- gbm.object$residuals <- residuals
- gbm.object$contributions <- gbm.summary
- gbm.object$self.statistics <- training.stats
- gbm.object$cv.statistics <- cv.stats
- gbm.object$weights <- site.weights
- gbm.object$trees.fitted <- trees.fitted
- gbm.object$training.loss.values <- training.loss.values
- gbm.object$cv.values <- cv.loss.values
- gbm.object$cv.loss.ses <- cv.loss.ses
- gbm.object$cv.loss.matrix <- cv.loss.matrix
- gbm.object$cv.roc.matrix <- cv.roc.stats
- gbm.object$target.trees <- target.trees
-
- if (keep.fold.models) gbm.object$fold.models <- model.list
- else gbm.object$fold.models <- NULL
-
- if (keep.fold.vector) gbm.object$fold.vector <- selector
- else gbm.object$fold.vector <- NULL
-
- if (keep.fold.fit) gbm.object$fold.fit <- fold.fit
- else gbm.object$fold.fit <- NULL
-
- return(gbm.object)
- } #end if statement
-}
-
-"gbm.plot" <-
-function(gbm.object, # a gbm object - could be one from gbm.step
- variable.no = 0, # the var to plot - if zero then plots all
- nt = gbm.object$n.trees, # how many trees to use
- smooth = FALSE, # should we add a smoothed version of the fitted function
- rug = T, # plot a rug of deciles
- n.plots = length(pred.names), # plot the first n most important preds
- common.scale = T, # use a common scale on the y axis
- write.title = T, # plot a title above the plot
- y.label = "fitted function", # the default y-axis label
- x.label = NULL, # the default x-axis label
- show.contrib = T, # show the contribution on the x axis
- plot.layout = c(3,4), # define the default layout for graphs on the page
- rug.side = 3, # which axis for rug plot? default (3) is top; bottom=1
- rug.lwd = 1, # line width for rug plots
- rug.tick = 0.03, # tick length for rug plots
- plotit=T, # AKS
- prob.scale=T, # AKS
- ... # other arguments to pass to the plotting
- # useful options include cex.axis, cex.lab, etc.
- )
-{
-# function to plot gbm response variables, with the option
-# of adding a smooth representation of the response if requested
-# additional options in this version allow for plotting on a common scale
-# note too that fitted functions are now centered by subtracting their mean
-#
-# version 2.9
-#
-# j. leathwick/j. elith - March 2007
-#
-
-require(gbm)
-
-
-gbm.call <- gbm.object$gbm.call
-gbm.x <- gbm.call$gbm.x
-pred.names <- gbm.call$predictor.names
-out.names <- rep("",length(pred.names))
-response.name <- gbm.call$response.name
-dataframe.name <- gbm.call$dataframe
-data <- eval.parent(parse(text = dataframe.name))
-
-max.plots <- plot.layout[1] * plot.layout[2]
-plot.count <- 0
-n.pages <- 1
-
-if (length(variable.no) > 1) {stop("only one response variable can be plotted at a time")}
-
-if (variable.no > 0) { #we are plotting all vars in rank order of contribution
- n.plots <- 1
- }
-
-max.vars <- length(gbm.object$contributions$var)
-if (n.plots > max.vars) {
- n.plots <- max.vars
- cat("warning - reducing no of plotted predictors to maximum available (",max.vars,")\n",sep="")
- }
-
-predictors <- list(rep(NA,n.plots)) # matrix(0,ncol=n.plots,nrow=100)
-responses <- list(rep(NA,n.plots)) # matrix(0,ncol=n.plots,nrow=100)
-
-for (j in c(1:n.plots)) { #cycle through the first time and get the range of the functions
- if (n.plots == 1) {
- k <- variable.no
- }
- else k <- match(gbm.object$contributions$var[j],pred.names)
-
- if (is.null(x.label)) var.name <- gbm.call$predictor.names[k]
- else var.name <- x.label
-
- pred.data <- data[,gbm.call$gbm.x[k]]
- out.names[j] <- names(data)[gbm.call$gbm.x[k]]
-
- response.matrix <- plot.gbm(gbm.object, i.var = k, n.trees = nt, return.grid = TRUE,...)
-
- predictors[[j]] <- response.matrix[,1]
- if (is.factor(data[,gbm.call$gbm.x[k]])) {
- predictors[[j]] <- factor(predictors[[j]],levels = levels(data[,gbm.call$gbm.x[k]]))
- }
- responses[[j]] <- response.matrix[,2] - mean(response.matrix[,2])
- if(prob.scale) responses[[j]] <- logit(responses[[j]])
-
- if(j == 1) {
- ymin = min(responses[[j]])
- ymax = max(responses[[j]])
- }
- else {
- ymin = min(ymin,min(responses[[j]]))
- ymax = max(ymax,max(responses[[j]]))
- }
- }
-
-# now do the actual plots
- if(plotit==T){
- for (j in c(1:n.plots)) {
-
- if (plot.count == max.plots) {
- plot.count = 0
- n.pages <- n.pages + 1
- }
-
- if (plot.count == 0) {
- #windows(width = 11, height = 8) #aks
- par(mfrow = plot.layout)
- }
-
- plot.count <- plot.count + 1
-
- if (n.plots == 1) {
- k <- match(pred.names[variable.no],gbm.object$contributions$var)
- if (show.contrib) {
- x.label <- paste(var.name," (",round(gbm.object$contributions[k,2],1),"%)",sep="")
- }
- }
- else {
- k <- match(gbm.object$contributions$var[j],pred.names)
- var.name <- gbm.call$predictor.names[k]
- if (show.contrib) {
- x.label <- paste(var.name," (",round(gbm.object$contributions[j,2],1),"%)",sep="")
- }
- else x.label <- var.name
- }
-
- if (common.scale) {
- plot(predictors[[j]],responses[[j]],ylim=c(ymin,ymax), type='l',
- xlab = x.label, ylab = y.label, ...)
- }
- else {
- plot(predictors[[j]],responses[[j]], type='l',
- xlab = x.label, ylab = y.label, ...)
- }
- if (smooth & is.vector(predictors[[j]])) {
- temp.lo <- loess(responses[[j]] ~ predictors[[j]], span = 0.3)
- lines(predictors[[j]],fitted(temp.lo), lty = 2, col = 2)
- }
- if (plot.count == 1) {
- if (write.title) {
- title(paste(response.name," - page ",n.pages,sep=""))
- }
- if (rug & is.vector(data[,gbm.call$gbm.x[k]])) {
- rug(quantile(data[,gbm.call$gbm.x[k]], probs = seq(0, 1, 0.1), na.rm = TRUE), side = rug.side, lwd = rug.lwd, ticksize = rug.tick)
- }
- }
- else {
- if (write.title & j == 1) {
- title(response.name)
- }
- if (rug & is.vector(data[,gbm.call$gbm.x[k]])) {
- rug(quantile(data[,gbm.call$gbm.x[k]], probs = seq(0, 1, 0.1), na.rm = TRUE), side = rug.side, lwd = rug.lwd, ticksize = rug.tick)
- }
- }
- }
- }
- return(invisible(list(names=out.names,preds=predictors,resp=responses)))
-}
-
-
-"gbm.perspec" <-
-function(gbm.object,
- x = 1, # the first variable to be plotted
- y = 2, # the second variable to be plotted
- pred.means = NULL, # allows specification of values for other variables
- x.label = NULL, # allows manual specification of the x label
- x.range = NULL, # manual range specification for the x variable
- y.label = NULL, # and y label
- y.range = NULL, # and the y
- z.range = NULL, # allows control of the vertical axis
- ticktype = "detailed",# specifiy detailed types - otherwise "simple"
- theta = 55, # rotation
- phi=40, # and elevation
- smooth = "none", # controls smoothing of the predicted surface
- mask = FALSE, # controls masking using a sample intensity model
- perspective = TRUE, # controls whether a contour or perspective plot is drawn
- verbose=F, # AKS
- ...) # allows the passing of additional arguments to plotting routine
- # useful options include shade, ltheta, lphi for controlling illumination
- # and cex for controlling text size - cex.axis and cex.lab have no effect
-{
-#
-# gbm.perspec version 2.9 April 2007
-# J Leathwick/J Elith
-#
-# takes a gbm boosted regression tree object produced by gbm.step and
-# plots a perspective plot showing predicted values for two predictors
-# as specified by number using x and y
-# values for all other variables are set at their mean by default
-# but values can be specified by giving a list consisting of the variable name
-# and its desired value, e.g., c(name1 = 12.2, name2 = 57.6)
-
- require(gbm)
-
-
-#get the boosting model details
-
- gbm.call <- gbm.object$gbm.call
- gbm.x <- gbm.call$gbm.x
- n.preds <- length(gbm.x)
- gbm.y <- gbm.call$gbm.y
- pred.names <- gbm.call$predictor.names
- family = gbm.call$family
-
- x.name <- gbm.call$predictor.names[x]
-
- if (is.null(x.label)) {
- x.label <- gbm.call$predictor.names[x]}
-
- y.name <- gbm.call$predictor.names[y]
-
- if (is.null(y.label)) {
- y.label <- gbm.call$predictor.names[y]}
-
- data <- eval.parent(parse(text=gbm.call$dataframe))[,gbm.x] #AKS
- n.trees <- gbm.call$best.trees
-
- if (is.null(x.range)) {
- if(!is.factor(data[,x]))
- x.var <- seq(min(data[,x],na.rm=T),max(data[,x],na.rm=T),length = 50)
- else x.var<- sort(unique(as.numeric(levels(data[,x]))))
- }
- else {x.var <- seq(x.range[1],x.range[2],length = 50)}
-
- if (is.null(y.range)) {
- if(!is.factor(data[,y]))
- y.var <- seq(min(data[,y],na.rm=T),max(data[,y],na.rm=T),length = 50)
- else y.var<- sort(unique(as.numeric(levels(data[,y]))))
- }
- else {y.var <- seq(y.range[1],y.range[2],length = 50)}
-
- pred.frame <- expand.grid(list(x.var,y.var))
- names(pred.frame) <- c(x.name,y.name)
-
- j <- 3
- for (i in 1:n.preds) {
- if (i != x & i != y) {
- if (is.vector(data[,i])) {
- m <- match(pred.names[i],names(pred.means))
- if (is.na(m)) {
- pred.frame[,j] <- mean(data[,i],na.rm=T)
- }
- else pred.frame[,j] <- pred.means[m]
- }
- if (is.factor(data[,i])) {
- m <- match(pred.names[i],names(pred.means))
- temp.table <- table(data[,i])
- if (is.na(m)) {
- pred.frame[,j] <- rep(names(temp.table)[2],2500)
- }
- else pred.frame[,j] <- pred.means[m]
- pred.frame[,j] <- factor(pred.frame[,j],levels=names(temp.table))
- }
- names(pred.frame)[j] <- pred.names[i]
- j <- j + 1
- }
- }
-#
-# form the prediction
-#
- prediction <- predict.gbm(gbm.object,pred.frame,n.trees = n.trees, type="response")
-
-# model smooth if required
-
- if (smooth == "model") {
- require(splines)
- pred.glm <- glm(prediction ~ ns(pred.frame[,1], df = 8) * ns(pred.frame[,2], df = 8), data=pred.frame,family=poisson)
- prediction <- fitted(pred.glm)
- }
-
-# report the maximum value and set up realistic ranges for z
-
- max.pred <- max(prediction)
- min.pred<-min(prediction)
- if(verbose) cat("maximum value = ",round(max.pred,2),"\n") #AKS
-
- if (is.null(z.range)) {
- if (family == "bernoulli") {
- z.range <- c(min.pred,max.pred)
- }
- else if (family == "poisson") {
- z.range <- c(0,max.pred * 1.1)
- }
- else {
- z.min <- min(data[,y],na.rm=T)
- z.max <- max(data[,y],na.rm=T)
- z.delta <- z.max - z.min
- z.range <- c(z.min - (1.1 * z.delta), z.max + (1.1 * z.delta))
- }
- }
-# form the matrix
-
- pred.matrix <- matrix(prediction,ncol=length(y.var),nrow=length(x.var))
-
-# kernel smooth if required
-
- if (smooth == "average") { #apply a 3 x 3 smoothing average
- pred.matrix.smooth <- pred.matrix
- for (i in 2:(length(x.var)-1)) {
- for (j in 2:(length(y.var)-1)) {
- pred.matrix.smooth[i,j] <- mean(pred.matrix[c((i-1):(i+1)),c((j-1):(j+1))])
- }
- }
- pred.matrix <- pred.matrix.smooth
- }
-
-# mask out values inside hyper-rectangle but outside of sample space
-
- if (mask) {
- mask.trees <- mask.object$gbm.call$best.trees
- point.prob <- predict.gbm(mask.object[[1]],pred.frame, n.trees = mask.trees, type="response")
- point.prob <- matrix(point.prob,ncol=50,nrow=50)
- pred.matrix[point.prob < 0.5] <- 0.0
- }
-#
-# and finally plot the result
-
- if (!perspective) {
- image(x = x.var, y = y.var, z = pred.matrix, zlim = z.range)
- }
- else {
- persp(x=x.var, y=y.var, z=pred.matrix, zlim= z.range, # input vars
- xlab = x.label, ylab = y.label, zlab = "fitted value", # labels
- theta=theta, phi=phi, r = sqrt(10), d = 3, # viewing pars
- ticktype = ticktype, mgp = c(4,1,0), ...) #
- }
-}
-
-"calibration" <-
-function(obs, preds, family = "binomial")
-{
-#
-# j elith/j leathwick 17th March 2005
-# calculates calibration statistics for either binomial or count data
-# but the family argument must be specified for the latter
-# a conditional test for the latter will catch most failures to specify
-# the family
-#
-
-if (family == "bernoulli") family <- "binomial"
-pred.range <- max(preds) - min(preds)
-if(pred.range > 1.2 & family == "binomial") {
-print(paste("range of response variable is ", round(pred.range, 2)), sep = "", quote = F)
-print("check family specification", quote = F)
-return()
-}
-if(family == "binomial") {
-pred <- preds + 1e-005
-pred[pred >= 1] <- 0.99999
-mod <- glm(obs ~ log((pred)/(1 - (pred))), family = binomial)
-lp <- log((pred)/(1 - (pred)))
-a0b1 <- glm(obs ~ offset(lp) - 1, family = binomial)
-miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
-ab1 <- glm(obs ~ offset(lp), family = binomial)
-miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
-miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
-}
-if(family == "poisson") {
-mod <- glm(obs ~ log(preds), family = poisson)
-lp <- log(preds)
-a0b1 <- glm(obs ~ offset(lp) - 1, family = poisson)
-miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
-ab1 <- glm(obs ~ offset(lp), family = poisson)
-miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
-miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
-}
-calibration.result <- c(mod$coef, miller1, miller2, miller3)
-names(calibration.result) <- c("intercept", "slope", "testa0b1", "testa0|b1", "testb1|a")
-return(calibration.result)
-}
-
-"roc" <-
-function (obsdat, preddat)
-{
-# code adapted from Ferrier, Pearce and Watson's code, by J.Elith
-#
-# see:
-# Hanley, J.A. & McNeil, B.J. (1982) The meaning and use of the area
-# under a Receiver Operating Characteristic (ROC) curve.
-# Radiology, 143, 29-36
-#
-# Pearce, J. & Ferrier, S. (2000) Evaluating the predictive performance
-# of habitat models developed using logistic regression.
-# Ecological Modelling, 133, 225-245.
-# this is the non-parametric calculation for area under the ROC curve,
-# using the fact that a MannWhitney U statistic is closely related to
-# the area
-#
- if (length(obsdat) != length(preddat))
- stop("obs and preds must be equal lengths")
- n.x <- length(obsdat[obsdat == 0])
- n.y <- length(obsdat[obsdat == 1])
- xy <- c(preddat[obsdat == 0], preddat[obsdat == 1])
- rnk <- rank(xy)
- wilc <- ((n.x * n.y) + ((n.x * (n.x + 1))/2) - sum(rnk[1:n.x]))/(n.x *
- n.y)
- return(round(wilc, 4))
-}
-
-"calc.deviance" <-
-function(obs.values, fitted.values, weights = rep(1,length(obs.values)), family="binomial", calc.mean = TRUE)
-{
-# j. leathwick/j. elith
-#
-# version 2.1 - 5th Sept 2005
-#
-# function to calculate deviance given two vectors of raw and fitted values
-# requires a family argument which is set to binomial by default
-#
-#
-
-if (length(obs.values) != length(fitted.values))
- stop("observations and predictions must be of equal length")
-
-y_i <- obs.values
-
-u_i <- fitted.values
-
-if (family == "binomial" | family == "bernoulli") {
-
- deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
- deviance <- -2 * sum(deviance.contribs * weights)
-
-}
-
-if (family == "poisson" | family == "Poisson") {
-
- deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
- deviance <- 2 * sum(deviance.contribs * weights)
-
-}
-
-if (family == "laplace") {
- deviance <- sum(abs(y_i - u_i))
- }
-
-if (family == "gaussian") {
- deviance <- sum((y_i - u_i) * (y_i - u_i))
- }
-
-
-
-if (calc.mean) deviance <- deviance/length(obs.values)
-
-return(deviance)
-
-}
-
-"gbm.interactions" <-
-function(gbm.object,
- use.weights = FALSE, # use weights for samples
- mask.object) # a gbm object describing sample intensity
-{
-#
-# gbm.interactions version 2.9
-#
-# j. leathwick, j. elith - May 2007
-#
-# functions assesses the magnitude of 2nd order interaction effects
-# in gbm models fitted with interaction depths greater than 1
-# this is achieved by:
-# 1. forming predictions on the linear scale for each predictor pair;
-# 2. fitting a linear model that relates these predictions to the predictor
-# pair, with the the predictors fitted as factors;
-# 3. calculating the mean value of the residuals, the magnitude of which
-# increases with the strength of any interaction effect;
-# 4. results are stored in an array;
-# 5. finally, the n most important interactions are identified,
-# where n is 25% of the number of interaction pairs;
-
- require(gbm)
-
- gbm.call <- gbm.object$gbm.call
- n.trees <- gbm.call$best.trees
- depth <- gbm.call$interaction.depth
- gbm.x <- gbm.call$gbm.x
- n.preds <- length(gbm.x)
- pred.names <- gbm.object$gbm.call$predictor.names
- cross.tab <- matrix(0,ncol=n.preds,nrow=n.preds)
- dimnames(cross.tab) <- list(pred.names,pred.names)
- int.p.table <- matrix(NA,ncol=n.preds,nrow=n.preds,dimnames=list(pred.names,pred.names))#AKS
-
- if (use.weights) mask.trees <- mask.object$gbm.call$best.trees
-
- #cat("gbm.interactions - version 2.9 \n") #aks
- #cat("Cross tabulating interactions for gbm model with ",n.preds," predictors","\n",sep="") #aks
-
- data <- eval.parent(parse(text=gbm.call$dataframe),n=1)[,gbm.x] #aks
-
- for (i in 1:(n.preds - 1)) { # step through the predictor set
- x.fac<-F
- if (is.vector(data[,i])) { # create a sequence through the range
- x.var <- seq(min(data[,i],na.rm=T),max(data[,i],na.rm=T),length = 20)
- x2 <- as.vector(tapply(x.var,rep(1:10,rep(2,10)),mean))
- } else { # otherwise set up simple factor variable
- x.var <- factor(names(table(data[,i])),levels = levels(data[,i]))
- x.fac<-T
- }
- x.length <- length(x.var)
-
- #cat(i,"\n") #aks
-
- for (j in (i+1):n.preds) { #create vector or factor data for second variable
- y.fac<-F
- if (is.vector(data[,j])) {
- y.var <- seq(min(data[,j],na.rm=T),max(data[,j],na.rm=T),length = 20)
- y2 <- as.vector(tapply(y.var,rep(1:10,rep(2,10)),mean))
-
- } else {
- y.var <- factor(names(table(data[,j])),levels = levels(data[,j]))
- y.fac<-T
- }
- y.length <- length(y.var)
-
-# and now make a temporary data frame
-
- pred.frame <- expand.grid(list(x.var,y.var))
- names(pred.frame) <- c(pred.names[i],pred.names[j])
-
- n <- 3 # and add the balance of the variables to it
-
- for (k in 1:n.preds) {
- if (k != i & k != j) {
- if (is.vector(data[,k])) { # either with the mean
- pred.frame[,n] <- mean(data[,k],na.rm=T)
- } else { # or the most common factor level
- temp.table <- sort(table(data[,k]),decreasing = TRUE)
- pred.frame[,n] <- rep(names(temp.table)[1],x.length * y.length)
- pred.frame[,n] <- as.factor(pred.frame[,n])
- }
- names(pred.frame)[n] <- pred.names[k]
- n <- n + 1
- }
- }
-#
-# form the prediction
-#
- prediction <- predict.gbm(gbm.object,pred.frame,n.trees = n.trees, type="link")
-
- if (use.weights) {
- point.prob <- predict.gbm(mask.object[[1]],pred.frame, n.trees = mask.trees, type="response")
- interaction.test.model <- lm(prediction ~ as.factor(pred.frame[,1]) + as.factor(pred.frame[,2]),
- weights = point.prob)
- }
-
- else {
-
- interaction.test.model <- lm(prediction ~ as.factor(pred.frame[,1]) + as.factor(pred.frame[,2]))
- }
- #cat("\n",i,names(data)[i],x.length,length(unique(data[,i]))," ",
- # j,names(data)[j],y.length,length(unique(data[,j])),dim(pred.frame));flush.console()
- #print(summary(data[,i]));print(summary(data[,j]))
- # check significance of interaction term in model that pools every 4 grid points #
- pred.frame<<-pred.frame
-
- if(x.fac==F | y.fac==F){ # case where at least one cov is not a factor
- if(x.fac==T) {x3 <- pred.frame[,1]
- } else { x3 <- rep(rep(x2,rep(2,10)),y.length) }
- if(y.fac==T) {y3 <- pred.frame[,1]
- } else { y3 <- rep(y2,rep(x.length*2,length(y2)))}
- int.p.table[i,j] <- anova(lm(prediction~as.factor(x3)*as.factor(y3)))[3,5] #aks
- }
-
-
- interaction.flag <- round(mean(resid(interaction.test.model)^2)*1000,2)
-
- cross.tab[i,j] <- interaction.flag
- } # end of j loop
- } # end of i loop
-
-# create an index of the values in descending order
-
- search.index <- ((n.preds^2) + 1) - rank(cross.tab, ties.method = "first")
-
- n.important <- max(2,round(0.1 * ((n.preds^2)/2),0))
- var1.names <- rep(" ",n.important)
- var1.index <- rep(0,n.important)
- var2.names <- rep(" ",n.important)
- var2.index <- rep(0,n.important)
- int.size <- rep(0,n.important)
- int.p <- rep(NA,n.important) #aks
-
- for (i in 1:n.important) {
-
- index.match <- match(i,search.index)
-
- j <- trunc(index.match/n.preds) + 1
- var1.index[i] <- j
- var1.names[i] <- pred.names[j]
-
- k <- index.match%%n.preds
- if (k > 0) { #only do this if k > 0 - otherwise we have all zeros from here on
- var2.index[i] <- k
- var2.names[i] <- pred.names[k]
-
- int.size[i] <- cross.tab[k,j]
- int.p[i] <- int.p.table[k,j] #aks
- }
-
- }
- rank.list <- data.frame(var1.index,var1.names,var2.index,var2.names,int.size,p=int.p)
- rank.list <- rank.list[complete.cases(rank.list),]
- return(list(rank.list = rank.list, interactions = cross.tab, gbm.call = gbm.object$gbm.call))
-}
-
-"gbm.simplify" <-
-function(gbm.object, # a gbm object describing sample intensity
- n.folds = 10, # number of times to repeat the analysis
- n.drops = "auto", # can be automatic or an integer specifying the number of drops to check
- alpha = 1, # controls stopping when n.drops = "auto"
- prev.stratify = TRUE, # use prevalence stratification in selecting evaluation data
- eval.data = NULL, # an independent evaluation data set - leave here for now
- plot = TRUE, # plot results
- verbose=F) # to suppress text output.
-{
-# function to simplify a brt model fitted using gbm.step
-#
-# version 2.9 - J. Leathwick/J. Elith - June 2007
-#
-# starts with an inital cross-validated model as produced by gbm.step
-# and then assesses the potential to remove predictors using k-fold cv
-# does this for each fold, removing the lowest contributing predictor,
-# and repeating this process for a set number of steps
-# after the removal of each predictor, the change in predictive deviance
-# is computed relative to that obtained when using all predictors
-# it returns a list containing the mean change in deviance and its se
-# as a function of the number of variables removed
-# having completed the cross validation, it then identifies the sequence
-# of variable to remove when using the full data set, testing this
-# up to the number of steps used in the cross-validation phase of the analysis
-# with results reported to the screen - it then returns
-# a table containing the order in which variables are to be removed
-# and a list of vectors, each of which specifies the predictor col numbers
-# in the original dataframe - the latter can be used as an argument to gbm.step
-# e.g., gbm.step(data = data, gbm.x = simplify.object$pred.list[[4]]...
-# would implement a new analysis with the original predictor set, minus its
-# four lowest contributing predictors
-#
-
-require(gbm)
-
-# first get the original analysis details..
-
- gbm.call <- gbm.object$gbm.call
- data <- eval.parent(parse(text=gbm.call$dataframe))
- n.cases <- nrow(data)
- gbm.x <- gbm.call$gbm.x
- gbm.y <- gbm.call$gbm.y
- family <- gbm.call$family
- lr <- gbm.call$learning.rate
- tc <- gbm.call$tree.complexity
- start.preds <- length(gbm.x)
- max.drops <- start.preds - 2
- response.name <- gbm.call$response.name
- predictor.names <- gbm.call$predictor.names
- n.trees <- gbm.call$best.trees
- pred.list <- list(initial = gbm.x)
- weights <- gbm.object$weights
-
- if (n.drops == "auto") auto.stop <- TRUE
-
- else auto.stop <- FALSE
-
-# take a copy of the original data and starting predictors
-
- orig.data <- data
- orig.gbm.x <- gbm.x
- verbose=TRUE
-# if (!is.null(eval.data)) independent.test <- TRUE
-# else independent.test <- FALSE
-
-# extract original performance statistics...
-
- original.deviance <- round(gbm.object$cv.statistics$deviance.mean,4)
- original.deviance.se <- round(gbm.object$cv.statistics$deviance.se,4)
-
- if(verbose){ #aks
- cat("\n");cat("gbm.simplify - version 2.9","\n\n")#AKS
- cat("simplifying gbm.step model for ",response.name," with ",start.preds," predictors",sep="")
- cat(" and ",n.cases," observations \n",sep="")
- cat("original deviance = ",original.deviance,"(",original.deviance.se,")\n\n",sep="")
- }
-
-# check that n.drops is less than n.preds - 2 and update if required
-
- if (auto.stop) {
- if(verbose) cat("variable removal will proceed until average change exceeds the original se\n\n") #aks
- n.drops <- 1 } else{
- if (n.drops > start.preds - 2) {
- if(verbose) cat("value of n.drops (",n.drops,") is greater than permitted","\n", #aks
- "resetting value to ",start.preds - 2,"\n\n",sep="")
- n.drops <- start.preds - 2
- } else {
- if(verbose) cat("a fixed number of",n.drops,"drops will be tested\n\n") #aks
- }
- }
- flush.console()#AKS
-
-
-# set up storage for results
-
- dev.results <- matrix(0, nrow = n.drops, ncol = n.folds)
- dimnames(dev.results) <- list(paste("drop.",1:n.drops,sep=""),
- paste("rep.",1:n.folds,sep=""))
-
- drop.count <- matrix(NA, nrow = start.preds, ncol = n.folds)
- dimnames(drop.count) <- list(predictor.names,paste("rep.",1:n.folds,sep=""))
-
- original.deviances <- rep(0,n.folds)
-
- model.list <- list(paste("model",c(1:n.folds),sep="")) # dummy list for the tree models
-
-# create gbm.fixed function call
-
- gbm.call.string <- paste("gbm.fixed(data=train.data,gbm.x=gbm.new.x,gbm.y=gbm.y,",sep="")
- gbm.call.string <- paste(gbm.call.string,"family=family,learning.rate=lr,tree.complexity=tc,",sep="")
- gbm.call.string <- paste(gbm.call.string,"n.trees = ",n.trees,", site.weights = weights.subset,verbose=FALSE)",sep="")
-
-# now set up the fold structure
-
- if (prev.stratify & family == "bernoulli") {
- presence.mask <- data[,gbm.y] == 1
- absence.mask <- data[,gbm.y] == 0
- n.pres <- sum(presence.mask)
- n.abs <- sum(absence.mask)
-
-# create a vector of randomised numbers and feed into presences
- selector <- rep(0,n.cases)
- temp <- rep(seq(1, n.folds, by = 1), length = n.pres)
- temp <- temp[order(runif(n.pres, 1, 100))]
- selector[presence.mask] <- temp
-
-# and then do the same for absences
- temp <- rep(seq(1, n.folds, by = 1), length = n.abs)
- temp <- temp[order(runif(n.abs, 1, 100))]
- selector[absence.mask] <- temp
- }
-
- else { #otherwise make them random with respect to presence/absence
- selector <- rep(seq(1, n.folds, by = 1), length = n.cases)
- selector <- selector[order(runif(n.cases, 1, 100))]
- }
-
-# now start by creating the intial models for each fold
-
- if(verbose) cat("creating initial models");flush.console()#AKS
-
- gbm.new.x <- orig.gbm.x
-
- for (i in 1:n.folds) {
-
-# create the training and prediction folds
-
- train.data <- orig.data[selector!=i,]
- weights.subset <- weights[selector != i]
- eval.data <- orig.data[selector==i,]
-
- model.list[[i]] <- eval(parse(text=gbm.call.string)) # create a fixed size object
-
-# now make predictions to the withheld fold
-
- u_i <- eval.data[,gbm.y]
- y_i <- predict.gbm(model.list[[i]], eval.data, n.trees, "response")
-
- original.deviances[i] <- round(calc.deviance(u_i,y_i, family = family, calc.mean = TRUE),4)
- if(verbose) cat(".");flush.console()#AKS
- } # end of creating initial models
- if(verbose) {cat("\n");cat("done \n\n")} #aks
- n.steps <- 1
-
- while (n.steps <= n.drops & n.steps <= max.drops) {
-
- if(verbose) cat("dropping predictor",n.steps,"\n");flush.console()#AKS
-
- for (i in 1:n.folds) {
-
-# get the right data
-
- train.data <- orig.data[selector!=i,]
- eval.data <- orig.data[selector==i,]
- weights.subset <- weights[selector != i]
-
-# get the current model details
-
- gbm.x <- model.list[[i]]$gbm.call$gbm.x
- n.preds <- length(gbm.x)
- these.pred.names <- model.list[[i]]$gbm.call$predictor.names
- contributions <- model.list[[i]]$contributions
-
-# get the index number in pred.names of the last variable in the contribution table
-
- last.variable <- match(as.character(contributions[n.preds,1]),these.pred.names)
- gbm.new.x <- gbm.x[-last.variable]
-
-# and keep a record of what has been dropped
-
- last.variable <- match(as.character(contributions[n.preds,1]),predictor.names)
- drop.count[last.variable,i] <- n.steps
-
- model.list[[i]] <- eval(parse(text=gbm.call.string)) # create a fixed size object
-
- u_i <- eval.data[,gbm.y]
- y_i <- predict.gbm(model.list[[i]],eval.data,n.trees,"response")
-
- deviance <- round(calc.deviance(u_i,y_i, family = family, calc.mean = TRUE),4)
-
-# calculate difference between intial and new model by subtracting new from old because we want to minimise deviance
-
- dev.results[n.steps,i] <- round(deviance - original.deviances[i] ,4)
-
- }
-
- if (auto.stop){ # check to see if delta mean is less than original deviance error estimate
-
- delta.mean <- mean(dev.results[n.steps,])
-
- if (delta.mean < (alpha * original.deviance.se)) {
- n.drops <- n.drops + 1
- dev.results <- rbind(dev.results, rep(0,n.folds))
- }
- }
- n.steps <- n.steps + 1
- }
-
-# now label the deviance matrix
-
- dimnames(dev.results) <- list(paste("drop.",1:n.drops,sep=""),
- paste("rep.",1:n.folds,sep=""))
-
-# calculate mean changes in deviance and their se
-
- mean.delta <- apply(dev.results,1,mean)
- se.delta <- sqrt(apply(dev.results,1,var))/sqrt(n.folds)
-
-###########################
-
- if (plot) {
- y.max <- 1.5 * max(mean.delta + se.delta)
- y.min <- 1.5 * min(mean.delta - se.delta)
- plot(seq(0,n.drops),c(0,mean.delta),xlab="variables removed",
- ylab = "change in predictive deviance",type='l',ylim=c(y.min,y.max))
- lines(seq(0,n.drops),c(0,mean.delta) + c(0,se.delta),lty = 2)
- lines(seq(0,n.drops),c(0,mean.delta) - c(0,se.delta),lty = 2)
- abline(h = 0 , lty = 2, col = 3)
- min.y <- min(c(0,mean.delta))
- min.pos <- match(min.y,c(0,mean.delta)) - 1 # subtract one because now zero base
- abline(v = min.pos, lty = 3, col = 2)
- abline(h = original.deviance.se, lty = 2, col = 2)
- title(paste("RFE deviance - ",response.name," - folds = ",n.folds,sep=""))
- }
-
-# and do a final backwards drop sequence from the original model
-
- if(verbose) cat("\nnow processing final dropping of variables with full data \n\n") #aks
-
- gbm.call.string <- paste("gbm.fixed(data=orig.data,gbm.x=gbm.new.x,gbm.y=gbm.y,",sep="")
- gbm.call.string <- paste(gbm.call.string,"family=family,learning.rate=lr,tree.complexity=tc,",sep="")
- gbm.call.string <- paste(gbm.call.string,"n.trees = ",n.trees,", site.weights = weights,verbose=FALSE)",sep="")
-
- n.steps <- n.steps - 1 #decrement by one to reverse last increment in prev loop
-
- final.model <- gbm.object # restore the original model and data
- train.data <- orig.data
-
-# and set up storage
-
- final.drops <- matrix(NA, nrow = start.preds, ncol = 1)
- dimnames(final.drops) <- list(predictor.names,"step")
-
- for (i in 1:n.steps) {
-
-# get the current model details
-
- gbm.x <- final.model$gbm.call$gbm.x
- n.preds <- length(gbm.x)
- these.pred.names <- final.model$gbm.call$predictor.names
- contributions <- final.model$contributions
-
- if(verbose) cat(i,"-",as.character(contributions[n.preds,1]),"\n");flush.console()#AKS
-
-# get the index number in pred.names of the last variable in the contribution table
-
- last.variable <- match(as.character(contributions[n.preds,1]),these.pred.names)
- gbm.new.x <- gbm.x[-last.variable]
-
-# and keep a record of what has been dropped
-
- last.variable <- match(as.character(contributions[n.preds,1]),predictor.names)
- final.drops[last.variable] <- i
-
- final.model <- eval(parse(text=gbm.call.string)) # create a fixed size object
-
- }
-
-#and then the corresponding numbers
-
- removal.list <- dimnames(final.drops)[[1]]
- removal.list <- removal.list[order(final.drops)]
- removal.list <- removal.list[1:n.drops]
-
- removal.numbers <- rep(0,n.steps)
-
-# construct predictor lists to faciliate final model fitting
-
- for (i in 1:n.steps) {
- removal.numbers[i] <- match(removal.list[i],predictor.names)
- pred.list[[i]] <- orig.gbm.x[0-removal.numbers[1:i]]
- names(pred.list)[i] <- paste("preds.",i,sep="")
- }
-
- deviance.summary <- data.frame(mean = round(mean.delta,4), se = round(se.delta,4))
-
- final.drops <- data.frame("preds" = dimnames(final.drops)[[1]][order(final.drops)],
- "order" = final.drops[order(final.drops)])
-
- return(list(deviance.summary = deviance.summary,
- deviance.matrix = dev.results, drop.count = drop.count,
- final.drops = final.drops, pred.list = pred.list,
- gbm.call = gbm.call))
-
-}
-
-"gbm.fixed" <-
-function (data, # the input dataframe
- gbm.x, # indices of the predictors in the input dataframe
- gbm.y, # index of the response in the input dataframe
- tree.complexity = 1, # the tree depth - sometimes referred to as interaction depth
- site.weights = rep(1, nrow(data)), # by default set equal
- verbose = TRUE, # to control reporting
- learning.rate = 0.001, # controls speed of the gradient descent
- n.trees = 2000, # default number of trees
- train.fraction = 1,
- bag.fraction = 0.5, # varies random sample size for each new tree
- family = "bernoulli", # can be any of bernoulli, poisson, gaussian, laplace - note quotes
- keep.data = FALSE, # keep original data
- var.monotone = rep(0, length(gbm.x)) # constrain to positive (1) or negative monontone (-1)
- )
-{
-#
-# j leathwick, j elith - 6th May 2007
-#
-# version 2.9 - developed in R 2.0
-#
-# calculates a gradient boosting (gbm)object with a fixed number of trees
-# with the number of trees identified using gbm.step or some other procedure
-#
-# mostly used as a utility function, e.g., when being called by gbm.simplify
-#
-# takes as input a dataset and args selecting x and y variables, learning rate and tree complexity
-#
-# updated 13/6/05 to accommodate weighting of sites when calculating total and residual deviance
-#
-# updated 10/8/05 to correct how site.weights are returned
-#
-# requires gbm
-#
-#
- require(gbm)
-
-# setup input data and assign to position one
-
- dataframe.name <- deparse(substitute(data)) # get the dataframe name
-
- if(length(gbm.x)<=1) stop("Only one predictor remains in backward selection\nplease select more predictors")
- x.data <- eval(data[, gbm.x]) #form the temporary datasets
- names(x.data) <- names(data)[gbm.x]
- y.data <- eval(data[, gbm.y])
- sp.name <- names(data)[gbm.y]
-
-
- assign("x.data", x.data, pos = 1) #and assign them for later use
- assign("y.data", y.data, pos = 1)
-
-#fit the gbm model
-
- z1 <- unclass(Sys.time())
-
- gbm.call <- paste("gbm(y.data ~ .,n.trees = n.trees, data=x.data, verbose = F, interaction.depth = tree.complexity,
- weights = site.weights, shrinkage = learning.rate, distribution = as.character(family),
- var.monotone = var.monotone, bag.fraction = bag.fraction, keep.data = keep.data)", sep="")
-
- if (verbose) {
- print(paste("fitting gbm model with a fixed number of ",n.trees," trees for ",sp.name,sep=""),quote=FALSE) }
-
- gbm.object <- eval(parse(text = gbm.call))
-
- best.trees <- n.trees
-
-#extract fitted values and summary table
-
- fitted.values <- predict.gbm(gbm.object,x.data,n.trees = n.trees,type="response")
- gbm.summary <- summary(gbm.object,n.trees = n.trees, plotit = FALSE)
-
- y_i <- y.data
- u_i <- fitted.values
-
- if (family == "poisson") {
- deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
- resid.deviance <- 2 * sum(deviance.contribs * site.weights)
- residuals <- sqrt(abs(deviance.contribs * 2))
- residuals <- ifelse((y_i - u_i) < 0, 0 - residuals, residuals)
-
- u_i <- sum(y.data * site.weights) / sum(site.weights)
- deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
- total.deviance <- 2 * sum(deviance.contribs * site.weights)
- }
-
- if (family == "bernoulli") {
- deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
- resid.deviance <- -2 * sum(deviance.contribs * site.weights)
- residuals <- sqrt(abs(deviance.contribs * 2))
- residuals <- ifelse((y_i - u_i) < 0, 0 - residuals, residuals)
-
- u_i <- sum(y.data * site.weights) / sum(site.weights)
- deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
- total.deviance <- -2 * sum(deviance.contribs * site.weights)
- }
-
- if (family == "laplace") {
- resid.deviance <- sum(abs(y_i - u_i))
- residuals <- y_i - u_i
- u_i <- mean(y.data)
- total.deviance <- sum(abs(y_i - u_i))
- }
-
- if (family == "gaussian") {
- resid.deviance <- sum((y_i - u_i) * (y_i - u_i))
- residuals <- y_i - u_i
- u_i <- mean(y.data)
- total.deviance <- sum((y_i - u_i) * (y_i - u_i))
- }
-
- if (verbose) {
- print(paste("total deviance = ",round(total.deviance,2),sep=""),quote=F)
- print(paste("residual deviance = ",round(resid.deviance,2),sep=""),quote=F)}
-
-# now assemble data to be returned
-
- z2 <- unclass(Sys.time())
- elapsed.time.minutes <- round((z2 - z1)/ 60,2) #calculate the total elapsed time
-
- gbm.detail <- list(dataframe = dataframe.name, gbm.x = gbm.x, predictor.names = names(x.data),
- gbm.y = gbm.y, reponse.name = names(y.data), family = family, tree.complexity = tree.complexity,
- learning.rate = learning.rate, bag.fraction = bag.fraction, cv.folds = 0, n.trees = n.trees, best.trees = best.trees,
- train.fraction = train.fraction, var.monotone = var.monotone, date = date(), elapsed.time.minutes = elapsed.time.minutes)
-
- gbm.object$gbm.call <- gbm.detail
- gbm.object$fitted <- fitted.values
- gbm.object$residuals <- residuals
- gbm.object$contributions <- gbm.summary
- gbm.object$self.statistics <- list(null.deviance = total.deviance, resid.deviance = resid.deviance)
- gbm.object$weights <- site.weights
-
- rm(x.data,y.data, pos=1) #finally, clean up the temporary dataframes
-
- return(gbm.object)
-}
-
-
-make.p.tif=T
-make.binary.tif=T
-
-tc=NULL
-n.folds=3
-alpha=1
-
-learning.rate = NULL
-bag.fraction = 0.5
-prev.stratify = TRUE
-max.trees = 10000
-tolerance.method = "auto"
-tolerance = 0.001
-seed=NULL
-opt.methods=2
-save.model=TRUE
-MESS=FALSE
-# Interpret command line argurments #
-# Make Function Call #
-Args <- commandArgs(trailingOnly=FALSE)
-
- for (i in 1:length(Args)){
- if(Args[i]=="-f") ScriptPath<-Args[i+1]
- }
-
- for (arg in Args) {
- argSplit <- strsplit(arg, "=")
- argSplit[[1]][1]
- argSplit[[1]][2]
- if(argSplit[[1]][1]=="c") csv <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="o") output <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mpt") make.p.tif <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mbt") make.binary.tif <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="tc") tc <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="nf") n.folds <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="alp") alpha <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="lr") learning.rate <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="bf") bag.fraction <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="ps") prev.stratify <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mt") max.trees <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="om") opt.methods <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="seed") seed <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="savm") save.model <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="tolm") tolerance.method <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="tol") tolerance <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mes") MESS <- argSplit[[1]][2]
-
- }
- print(csv)
- print(output)
- print(responseCol)
-
-ScriptPath<-dirname(ScriptPath)
-source(paste(ScriptPath,"LoadRequiredCode.r",sep="\\"))
-
-
-alpha<-as.numeric(alpha)
-make.p.tif<-as.logical(make.p.tif)
-make.binary.tif<-as.logical(make.binary.tif)
-prev.stratify<-as.logical(prev.stratify)
-save.model<-make.p.tif | make.binary.tif
-opt.methods<-as.numeric(opt.methods)
-MESS<-as.logical(MESS)
-
- fit.brt.fct(ma.name=csv,
- tif.dir=NULL,
- output.dir=output,
- response.col=responseCol,
- make.p.tif=make.p.tif,make.binary.tif=make.binary.tif,
- simp.method="cross-validation",debug.mode=F,responseCurveForm="pdf",tc=tc,n.folds=n.folds,alpha=alpha,script.name="brt.r",
- learning.rate =learning.rate, bag.fraction = bag.fraction,prev.stratify = prev.stratify,max.trees = max.trees,seed=seed,
- save.model=save.model,opt.methods=opt.methods,MESS=MESS)
-
-
-
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_GLM_pluggable.r b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_GLM_pluggable.r
deleted file mode 100644
index a472b6d..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_GLM_pluggable.r
+++ /dev/null
@@ -1,775 +0,0 @@
-# A set of "pluggable" R functions for automated model fitting of glm models to presence/absence data #
-#
-# Modified 12-2-09 to: remove categorical covariates from consideration if they only contain one level
-# ID factor variables based on "categorical" prefix and look for tifs in subdir
-# Give progress reports
-# write large output tif files in blocks to alleviate memory issues
-# various bug fixes
-#
-#
-# Modified 3-4-09 to use a list object for passing of arguements and data
-#
-
-
-# Libraries required to run this program #
-# PresenceAbsence - for ROC plots
-# XML - for XML i/o
-# rgdal - for geotiff i/o
-# sp - used by rdgal library
-# raster for geotiff o
-options(error=NULL)
-
-fit.glm.fct <- function(ma.name,tif.dir=NULL,output.dir=NULL,response.col="^response.binary",make.p.tif=T,make.binary.tif=T,
- simp.method="AIC",responseCurveForm=NULL,debug.mode=F,model.family="binomial",script.name="glm.r",opt.methods=2,save.model=TRUE,UnitTest=FALSE,MESS=FALSE){
- # This function fits a stepwise GLM model to presence-absence data.
- # written by Alan Swanson, 2008-2009
- ## Maintained and edited by Marian Talbert September 2010-
- # Arguements.
- # ma.name: is the name of a .csv file with a model array. full path must be included unless it is in the current
- # R working directory #
- # tif.dir: is the directory containing geotiffs for each covariate. only required if geotiffs output of the
- # response surface is requested # # cov.list.name: is the name of a text file with the names of covariates to be included in models (one per line).
- # output.dir: is the directory that output files will be stored in. if not given, files will go to the current working directory.
- # response.col: column number of the model array containing a binary 0/1 response. all other columns will be considered explanatory variables.
- # make.p.tif: T if a geotiff of the response surface is desired.
- # make.binary.tif: T if a geotiff of the response surface is desired.
- # simp.method: model simplification method. valid methods include: "AIC" and "BIC".
- # debug.mode: if T, output is directed to the console during the run. also, a pdf is generated which contains response curve plots and perspective plots
- # showing the effects of interactions deemed important. if F, output is diverted to a text file and the console is kept clear
- # except for final output of an xml file. in either case, a set of standard output files are created in the output directory.
- #
-
- # Value:
- # returns nothing but generates a number of output files in the directory
- # "output.dir" named above. These output files consist of:
- #
- # glm_output.txt: a text file with fairly detailed results of the final model.
- # glm_output.xml: an xml-formatted text file with results from the final model.
- # glm_response_curves.xml: an xml-formatted text file with response curves for
- # each covariate in the final model.
- # glm_prob_map.tif: a geotiff of the response surface
- # glm_bin_map.tif: a geotiff of the binary response surface. threhold is based on the roc curve at the point where sensitivity=specificity.
- # glm_log.txt: a file containing text output diverted from the console when debug.mode=F
- # glm_auc_plot.jpg: a jpg file of a ROC plot.
- # glm_response_curves.pdf: an pdf file with response curves for
- # each covariate in the final model and perspective plots showing the effect of interactions deemed significant.
- # only produced when debug.mode=T
- # seed=NULL # sets a seed for the algorithm, any inegeger is acceptable
- # opt.methods=2 # sets the method used for threshold optimization used in the
- # # the evaluation statistics module
- # save.model=FALSE # whether the model will be used to later produce tifs
- #
- # when debug.mode is true, these filenames will include a number in them so that they will not overwrite preexisting files. eg brt_1_output.txt.
- #
- times <- as.data.frame(matrix(NA,nrow=7,ncol=1,dimnames=list(c("start","read data","model fit",
- "model summary","response curves","tif output","done"),c("time"))))
- times[1,1] <- unclass(Sys.time())
- t0 <- unclass(Sys.time())
- #simp.method <- match.arg(simp.method)
- out <- list(
- input=list(ma.name=ma.name,
- tif.dir=tif.dir,
- output.dir=output.dir,
- response.col=response.col,
- make.p.tif=make.p.tif,
- model.family=model.family,
- make.binary.tif=make.binary.tif,
- simp.method=simp.method,
- model.type="stepwise glm",
- model.source.file=script.name,
- model.fitting.subset=NULL,
- save.model=save.model,
- run.time=paste(c(format(Sys.time(),"%Y-%m-%d"),format(Sys.time(),"%H:%M:%S")),collapse="T"),
- sig.test="t-test p-value",
- MESS=MESS),
- dat = list(missing.libs=NULL,
- output.dir=list(dname=NULL,exist=F,readable=F,writable=F),
- tif.dir=list(dname=NULL,exist=F,readable=F,writable=F),
- tiff.ind=NULL,
- tif.names=NULL,
- bname=NULL,
- bad.factor.covs=NULL, # factorchange
- ma=list( status=c(exists=F,readable=F),
- dims=c(NA,NA),
- resp.name=NULL,
- factor.levels=NA,
- used.covs=NULL,
- ma=NULL,
- train.weights=NULL,
- test.weights=NULL,
- train.xy=NULL,
- test.xy=NULL,
- ma.subset=NULL
- ),
- ma.test=NULL),
- mods=list(final.mod=NULL,
- r.curves=NULL,
- tif.output=list(prob=NULL,bin=NULL),
- auc.output=NULL,
- interactions=NULL, # not used #
- summary=NULL),
- time=list(strt=unclass(Sys.time()),end=NULL),
- error.mssg=list(NULL),
- ec=0 # error count #
- )
- # load libaries #
- out <- check.libs(list("PresenceAbsence","rgdal","XML","sp","survival","tools","raster","tcltk2","foreign","ade4"),out)
-
- # exit program now if there are missing libraries #
- if(!is.null(out$error.mssg[[1]])){
- cat(saveXML(glm.to.xml(out),indent=T),'\n')
- return()
- }
-
- if(is.na(match(simp.method,c("AIC","BIC")))){
- return()
- }
-
- # check output dir #
-
- out$dat$output.dir <- check.dir(output.dir)
- if(out$dat$output.dir$writable==F) {out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: output directory",output.dir,"is not writable")
- out$dat$output.dir$dname <- getwd()
- }
-
- # generate a filename for output #
- if(debug.mode==T){ #paste(bname,"_summary.txt",sep="")
- outfile <- paste(bname<-paste(out$dat$output.dir$dname,"/glm_",n<-1,sep=""),"_output.txt",sep="")
- while(file.access(outfile)==0) outfile<-paste(bname<-paste(out$dat$output.dir$dname,"/glm_",n<-n+1,sep=""),"_output.txt",sep="")
- capture.output(cat("temp"),file=outfile) # reserve the new basename #
- } else bname <- paste(out$dat$output.dir$dname,"/glm",sep="")
- out$dat$bname <- bname
-
- # sink console output to log file #
- if(!debug.mode) {sink(logname <- paste(bname,"_log.txt",sep=""));on.exit(sink)} else logname<-NULL
- options(warn=1)
-
- # check tif dir #
- if(!is.null(tif.dir)){
- out$dat$tif.dir <- check.dir(tif.dir)
- if(out$dat$tif.dir$readable==F & (out$input$make.binary.tif | out$input$make.p.tif)) {
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: tif directory",tif.dir,"is not readable")
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- cat(saveXML(brt.to.xml(out),indent=T),'\n')
- return()
- }
- }
-
-
- # find .tif files in tif dir #
-
- if(out$dat$tif.dir$readable) out$dat$tif.names <- list.files(out$dat$tif.dir$dname,pattern=".tif",recursive=T)
-
- # check for model array #
- out$input$ma.name <- check.dir(out$input$ma.name)$dname
- if(UnitTest!=FALSE) options(warn=2)
- out <- read.ma(out)
- if(UnitTest==1) return(out)
-
- if(!is.null(out$error.mssg[[1]])){
- if(!debug.mode) {sink();on.exit();unlink(logname)}
- cat(saveXML(glm.to.xml(out),indent=T),'\n')
- return()
- }
- #allowing site weights
-
- times[2,1] <- unclass(Sys.time())
- if(!debug.mode) {sink();cat("Progress:20%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("20%\n")} ### print time
- cat("\nbegin processing of model array:",out$input$ma.name,"\n")
- cat("\nfile basename set to:",out$dat$bname,"\n")
- if(debug.mode) assign("out",out,envir=.GlobalEnv)
-
-
-
-
- ##############################################################################################################
- # Begin model fitting #
- ##############################################################################################################
-
- # Fit null GLM and run stepwise, then print results #
- cat("\n","Fitting stepwise GLM","\n")
- flush.console()
- penalty <- if(out$input$simp.method=="AIC") 2 else log(nrow(out$dat$ma$ma))
- scope.glm <- list(lower=as.formula(paste(out$dat$ma$resp.name,"~1")),
- upper=as.formula(paste(out$dat$ma$resp.name,"~",paste(out$dat$ma$used.covs,collapse='+'))))
-
- mymodel.glm.step <- step(glm(as.formula(paste(out$dat$ma$resp.name,"~1")),family=out$input$model.family,data=out$dat$ma$ma,weights=out$dat$ma$train.weights,na.action="na.exclude"),
- direction='both',scope=scope.glm,trace=0,k=penalty)
-
- out$mods$final.mod <- mymodel.glm.step
-
- out$dat$ma$used.covs <- attr(terms(formula(out$mods$final.mod)),"term.labels")
- #assign("out",out,envir=.GlobalEnv)
- t3 <- unclass(Sys.time())
- cat("\n","Finished with stepwise GLM","\n")
- cat("Summary of Model:","\n")
- print(out$mods$summary <- summary(mymodel.glm.step))
- if(!is.null(out$dat$bad.factor.cols)){
- cat("\nWarning: the following categorical response variables were removed from consideration\n",
- "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n\n")
- }
- flush.console()
-
- flush.console()
- times[3,1] <- unclass(Sys.time())
- if(!debug.mode) {sink();cat("Progress:40%\n");flush.console();sink(logname,append=T)} else cat("40%\n")
-
- #r<-residuals(out$mods$final.mod, "deviance")
-
- if(length(coef(out$mods$final.mod))==1) stop("Null model was selected. \nEvaluation metrics and plots will not be produced")
-
- ##############################################################################################################
- # Begin model output #
- ##############################################################################################################
-
- # Store .jpg ROC plot #
- txt0 <- paste("Generalized Linear Results\n",out$input$run.time,"\n\n","Data:\n\t ",ma.name,"\n\t ","n(pres)=",
- out$dat$ma$n.pres[2],"\n\t n(abs)=",out$dat$ma$n.abs[2],"\n\t number of covariates considered=",(length(names(out$dat$ma$ma))-1),
- "\n\n","Settings:\n","\n\t model family=",out$input$model.family,
- "\n\n","Results:\n\t ","number covariates in final model=",length(out$dat$ma$used.covs),
- "\n\t total time for model fitting=",round((unclass(Sys.time())-t0)/60,2),"min\n",sep="")
-
- capture.output(cat(txt0),file=paste(bname,"_output.txt",sep=""))
-
- capture.output(out$mods$summary,file=paste(bname,"_output.txt",sep=""),append=TRUE)
- if(!is.null(out$dat$bad.factor.cols)){
- capture.output(cat("\nWarning: the following categorical response variables were removed from consideration\n",
- "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n"),
- file=paste(bname,"_output.txt",sep=""),append=T)
- }
-
-
- auc.output <- make.auc.plot.jpg(out$dat$ma$ma,pred=predict(mymodel.glm.step,type='response'),plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="GLM",opt.methods=opt.methods,
- weight=out$dat$ma$train.weights,out=out)
-
- out$mods$auc.output<-auc.output
-
- # if(out$input$model.family=="poisson"){
- # auc.output <- make.poisson.jpg(out$dat$ma$ma,pred=predict(mymodel.glm.step,type='response'),
- # plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="BRT",
- # weight=out$dat$ma$train.weights,out=out)
-
- # out$mods$auc.output<-auc.output
- # }
-
- # out$mods$auc.output<-auc.output
-
-
-
-
- times[4,1] <- unclass(Sys.time())
- if(!debug.mode) {sink();cat("Progress:70%\n");flush.console();sink(logname,append=T)} else cat("70%\n")
-
- # Response curves #
-
-if(is.null(responseCurveForm)){
-responseCurveForm<-0}
-
-if(debug.mode | responseCurveForm=="pdf"){
- nvar <- length(coef(out$mods$final.mod))-1
- pcol <- min(ceiling(sqrt(nvar)),4)
- prow <- min(ceiling(nvar/pcol),3)
-
- pdf(paste(bname,"_response_curves.pdf",sep=""),width=11,height=8.5,onefile=T)
- par(oma=c(2,2,4,2),mfrow=c(prow,pcol))
- r.curves <-my.termplot(out$mods$final.mod,plot.it=T)
- mtext(paste("GLM response curves for",basename(ma.name)),outer=T,side=3,cex=1.3)
- par(mfrow=c(1,1))
- graphics.off()
- } else r.curves<-try(my.termplot(out$mods$final.mod,plot.it=F))
-
-
- if(class(r.curves)!="try-error") {
- out$mods$r.curves <- r.curves
- } else {
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: problem fitting response curves",r.curves)
- }
-
-
- t4 <- unclass(Sys.time())
- cat("\nfinished with final model summarization, t=",round(t4-t3,2),"sec\n");flush.console()
- times[5,1] <- unclass(Sys.time())
- if(!debug.mode) {sink();cat("Progress:80%\n");flush.console();sink(logname,append=T)} else cat("80%\n")
-
-
- ##############################################################################################################
- # Make .tif of predictions #
- ##############################################################################################################
- out$mods$final.mod$contributions$var<-attr(terms(formula(out$mods$final.mod)),"term.labels")
- assign("out",out,envir=.GlobalEnv)
-
- save.image(paste(output.dir,"modelWorkspace",sep="\\"))
- if(out$input$make.p.tif==T | out$input$make.binary.tif==T){
- if((n.var <- length(coef(out$mods$final.mod)))<2){
- mssg <- "Error producing geotiff output: null model selected by stepwise procedure - pointless to make maps"
- class(mssg)<-"try-error"
- } else {
- cat("\nproducing prediction maps...","\n","\n");flush.console()
- mssg <- proc.tiff(model=out$mods$final.mod,vnames=attr(terms(formula(out$mods$final.mod)),"term.labels"),
- tif.dir=out$dat$tif.dir$dname,filenames=out$dat$tif.ind,pred.fct=glm.predict,factor.levels=out$dat$ma$factor.levels,make.binary.tif=make.binary.tif,
- thresh=out$mods$auc.output$thresh,make.p.tif=make.p.tif,outfile.p=paste(out$dat$bname,"_prob_map.tif",sep=""),
- outfile.bin=paste(out$dat$bname,"_bin_map.tif",sep=""),tsize=50,NAval=-3000,fnames=out$dat$tif.names,logname=logname,out=out) #"brt.prob.map.tif"
- }
- # model=out$mods$final.mod;vnames=attr(terms(formula(out$mods$final.mod)),"term.labels");
-# tif.dir=out$dat$tif.dir$dname;pred.fct=glm.predict;factor.levels=out$dat$ma$factor.levels;make.binary.tif=make.binary.tif;
-# thresh=out$mods$auc.output$thresh;make.p.tif=make.p.tif;outfile.p=paste(out$dat$bname,"_prob_map.tif",sep="");
-# outfile.bin=paste(out$dat$bname,"_bin_map.tif",sep="");tsize=50;NAval=-3000;fnames=out$dat$tif.names
- if(class(mssg)=="try-error"){
- if(!debug.mode) {sink();on.exit();unlink(logname)}
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("Error producing prediction maps:",mssg)
- cat(saveXML(glm.to.xml(out),indent=T),'\n')
- return()
- } else {
- if(make.p.tif) out$mods$tif.output$prob <- paste(out$dat$bname,"_prob_map.tif",sep="")
- if(make.binary.tif) out$mods$tif.output$bin <- paste(out$dat$bname,"_bin_map.tif",sep="")
- t5 <- unclass(Sys.time())
- cat("\nfinished with prediction maps, t=",round(t5-t4,2),"sec\n");flush.console()
- }
- }
- times[6,1] <- unclass(Sys.time())
- if(!debug.mode) {sink();cat("Progress:90%\n");flush.console();sink(logname,append=T)} else cat("90%\n")
-
- # Evaluation Statistics on Test Data#
-
- if(!is.null(out$dat$ma$ma.test)) Eval.Stat<-EvaluationStats(out,thresh=auc.output$thresh,train=out$dat$ma$ma,
- train.pred=predict(mymodel.glm.step,type="response"),opt.methods)
-
-
- # Write summaries to xml #
- assign("out",out,envir=.GlobalEnv)
- doc <- glm.to.xml(out)
-
- #cat(paste("\ntotal time=",round((unclass(Sys.time())-t0)/60,2),"min\n\n\n",sep=""))
- if(!debug.mode) {
- sink();on.exit();unlink(logname)
- cat("Progress:100%\n");flush.console()
- cat(saveXML(doc,indent=T),'\n')
- flush.console()
- } else {cat("100%\n")}
- capture.output(cat(saveXML(doc,indent=T)),file=paste(out$dat$bname,"_output.xml",sep=""))
- assign("fit",out$mods$final.mod,envir=.GlobalEnv)
- times[7,1] <- unclass(Sys.time())
-
- times$net <- times$time - times$time[1]
- times$pct <- round(times$net/times$net[7]*100,2)
- times$process <- c(0,times$time[-1]-times$time[-7])
- times$ppcnt <- round(times$process/times$net[7]*100,2)
- write.csv(times,paste(bname,"times.csv",sep="_"))
- invisible(out)
-}
-
-glm.predict <- function(model,x) {
- # retrieve key items from the global environment #
- # make predictionss.
-
- y <- as.vector(predict(model,x,type="response"))
-
- # encode missing values as -1.
- y[is.na(y)]<- NaN
-
- # return predictions.
- return(y)
- }
-
-logit <- function(x) 1/(1+exp(-x))
-
-
-file_path_as_absolute <- function (x){
- if (!file.exists(epath <- path.expand(x)))
- stop(gettextf("file '%s' does not exist", x), domain = NA)
- cwd <- getwd()
- on.exit(setwd(cwd))
- if (file_test("-d", epath)) {
- setwd(epath)
- getwd()
- }
- else {
- setwd(dirname(epath))
- file.path(getwd(), basename(epath))
- }
-}
-#file_path_as_absolute(".")
-
-glm.to.xml <- function(out){
- require(XML)
- schema.http="http://www.w3.org/2001/XMLSchema-instance"
- schema.fname="file:/Users/isfs2/Desktop/Source/2008-04-09/src/gov/nasa/gsfc/quickmap/ModelBuilder/modelRun_output_v2.xsd"
- xml.out <- newXMLDoc()
- mr <- newXMLNode("modelRunOutput",doc=xml.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))#,parent=xml.out
- sm <- newXMLNode("singleModel",parent=mr)
- bg <- newXMLNode("background",parent=sm)
- newXMLNode("mdsName",out$input$ma.name,parent=bg)
- newXMLNode("runDate",out$input$run.time,parent=bg)
- lc <- newXMLNode("layersConsidered",parent=bg)#, parent = xml.out)
- kids <- lapply(paste(out$dat$tif.dir$dname,"/",out$dat$tif.names,sep=""),function(x) newXMLNode("layer", x))
- addChildren(lc, kids)
- mo <- newXMLNode("modelOutput",parent=sm)
- newXMLNode("modelType",out$input$model.type,parent=mo)
- newXMLNode("modelSourceFile",out$input$model.source.file,parent=mo)
- newXMLNode("devianceExplained",out$mods$auc.output$pct_dev_exp,parent=mo,attrs=list(type="percentage"))
- newXMLNode("nativeOutput",paste(out$dat$bname,"_output.txt",sep=""),parent=mo)
- newXMLNode("binaryOutputFile",out$mods$tif.output[[2]],parent=mo)
- newXMLNode("probOutputFile",out$mods$tif.output[[1]],parent=mo)
- newXMLNode("auc",out$mods$auc.output$auc,parent=mo)
- newXMLNode("rocGraphic",out$mods$auc.output$plotname,parent=mo)
- newXMLNode("rocThresh",out$mods$auc.output$thresh,parent=mo)
- newXMLNode("modelDeviance",out$mods$auc.output$dev_fit,parent=mo)
- newXMLNode("nullDeviance",out$mods$auc.output$null_dev,parent=mo)
- if(is.null(out$mods$r.curves)) rc.name <- NULL else rc.name <- paste(out$dat$bname,"_response_curves.xml",sep="")
- newXMLNode("responsePlotsFile",rc.name,parent=mo)
- newXMLNode("significanceDescription",out$input$sig.test,parent=mo)
- mfp <- newXMLNode("modelFitParmas",parent=mo)
- newXMLNode("simpMethod",out$input$model.type,parent=mfp)
- newXMLNode("simpCriteria",out$input$simp.method,parent=mfp)
-
- sv <- newXMLNode("significantVariables",parent=mo)
- if(!is.null(out$mods$summary)) {
- t.table <- out$mods$summary$coefficients
- t.table <- t.table[order(t.table[,4]),]
- dimnames(t.table)[[2]] <- c("coefficient","standardError","testStatistic","significanceMeasurement")
- t.table <- as.data.frame(t.table)
- for(i in 1:nrow(t.table)){
- x <- newXMLNode("sigVar",parent=sv)
- newXMLNode(name="name", row.names(t.table)[i],parent=x)
- kids <- lapply(1:ncol(t.table),function(j) newXMLNode(name=names(t.table)[j], t.table[i,j]))
- addChildren(x, kids)
- }
- }
-
- if(!is.null(out$mods$r.curves)){
- r.curves <- out$mods$r.curves
- factor.levels <- out$dat$ma$factor.levels
- rc.out <- newXMLDoc()
- root <- newXMLNode("responseCurves",doc=rc.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))
- for(i in 1:length(r.curves$names)){
- if(!is.na(f.index<-match(r.curves$names[i],names(factor.levels)))){
- vartype <- "factor"} else vartype="continuous"
- x <- newXMLNode("responseCurve",attrs=list(covariate=r.curves$names[i],type=vartype),parent=root)
- kids <- lapply(1:length(r.curves$preds[[i]]),function(j){
- newXMLNode(name="responsePt",parent=x,.children=list(
- newXMLNode(name="explanatory",as.character(r.curves$preds[[i]])[j]),
- newXMLNode(name="response",r.curves$resp[[i]][j])))})
- addChildren(x,kids)
- }
- saveXML(rc.out,rc.name,indent=T)
-
- } else { rc.name<-NULL }
- if(!is.null(out$error.mssg[[1]])) {
- kids <- lapply(out$error.mssg,function(j) newXMLNode(name="error",j))
- addChildren(mo,kids)
- }
- return(xml.out)
- }
-
-
-get.cov.names <- function(model){
- return(attr(terms(formula(model)),"term.labels"))
- }
-
-
-check.dir <- function(dname){
- if(is.null(dname)) dname <- getwd()
- dname <- gsub("[\\]","/",dname)
- end.char <- substr(dname,nchar(dname),nchar(dname))
- if(end.char == "/") dname <- substr(dname,1,nchar(dname)-1)
- exist <- suppressWarnings(as.numeric(file.access(dname,mode=0))==0) # -1 if bad, 0 if ok #
- if(exist) dname <- file_path_as_absolute(dname)
- readable <- suppressWarnings(as.numeric(file.access(dname,mode=4))==0) # -1 if bad, 0 if ok #
- writable <- suppressWarnings(as.numeric(file.access(dname,mode=2))==0) # -1 if bad, 0 if ok #
- return(list(dname=dname,exist=exist,readable=readable,writable=writable))
- }
-
-
-get.image.info <- function(image.names){
- # this function creates a data.frame with summary image info for a set of images #
- require(rgdal)
- require(tools)
- n.images <- length(image.names)
-
- full.names <- image.names
- out <- data.frame(image=full.names,available=rep(F,n.images),size=rep(NA,n.images),
- type=factor(rep("unk",n.images),levels=c("asc","envi","tif","unk")))
- out$type[grep(".tif",image.names)]<-"tif"
- out$type[grep(".asc",image.names)]<-"asc"
- for(i in 1:n.images){
- if(out$type[i]=="tif"){
- x <-try(GDAL.open(full.names[1],read.only=T))
- suppressMessages(try(GDAL.close(x)))
- if(class(x)!="try-error") out$available[i]<-T
- x<-try(file.info(full.names[i]))
- } else {
- x<-try(file.info(full.names[i]))
- if(!is.na(x$size)) out$available[i]<-T
- }
- if(out$available[i]==T){
- out$size[i]<-x$size
- if(out$type[i]=="unk"){
- # if extension not known, look for envi .hdr file in same directory #
- if(file.access(paste(file_path_sans_ext(full.names[i]),".hdr",sep=""))==0)
- out$type[i]<-"envi"
- }
- }
- }
- return(out)
-}
-
-#make.r.curves.glm <- function(model){
-# tms <- as.matrix(predict(model,type="terms"))
-# mf <- model.frame(model)
-# preds <- list()
-# response <- list()
-# p.names <- colnames(tms)
-# is.fac <- sapply(p.names, function(i) is.factor(mf[, i]))
-# for(i in 1:length(p.names)){
-# if(is.fac[i]){
-# ff <- mf[, p.names[i]]
-# if (!is.null(model$na.action)) ff <- naresid(model$na.action,ff)
-# xx <- as.numeric(ff)
-# ll <- levels(ff)
-# out <- rep(NA,length(ll))
-# for (j in seq_along(ll)) {
-# ww <- which(ff == ll[j])[1]
-# out[j]<-tms[ww,i]
-# #out[j]<-tms[ff==ll[j],i][1]
-# }
-#
-# }
-#
-#
-#
-#data = NULL; envir = environment(formula(model));
-# partial.resid = FALSE; rug = FALSE; terms = NULL; se = FALSE;
-# xlabs = NULL; ylabs = NULL; main = NULL; col.term = 2; lwd.term = 1.5;
-# col.se = "orange"; lty.se = 2; lwd.se = 1; col.res = "gray";
-# cex = 1; pch = par("pch"); col.smth = "darkred"; lty.smth = 2;
-# span.smth = 2/3; ask = dev.interactive() && nb.fig < n.tms;
-# use.factor.levels = TRUE; smooth = NULL; ylim = "common";plot.it=F;
-#terms="yell_250m_evi_16landcovermap_4ag05"
-my.termplot <- function (model, data = NULL, envir = environment(formula(model)),
- partial.resid = FALSE, rug = FALSE, terms = NULL, se = FALSE,
- xlabs = NULL, ylabs = NULL, main = NULL, col.term = 2, lwd.term = 1.5,
- col.se = "orange", lty.se = 2, lwd.se = 1, col.res = "gray",
- cex = 1, pch = 1, col.smth = "darkred", lty.smth = 2,
- span.smth = 2/3, ask = dev.interactive() && nb.fig < n.tms,
- use.factor.levels = TRUE, smooth = NULL, ylim = "common",plot.it=F,
- ...)
-{ # this function is borrowed from the stats library #
-
- which.terms <- terms
- terms <- if (is.null(terms))
- predict(model, type = "terms", se.fit = se)
- else predict(model, type = "terms", se.fit = se, terms = terms)
- n.tms <- ncol(tms <- as.matrix(if (se)
- terms$fit
- else terms))
- mf <- model.frame(model)
- if (is.null(data))
- data <- eval(model$call$data, envir)
- if (is.null(data))
- data <- mf
- if (NROW(tms) < NROW(data)) {
- use.rows <- match(rownames(tms), rownames(data))
- }
- else use.rows <- NULL
- nmt <- colnames(tms)
- cn <- parse(text = nmt)
- if (!is.null(smooth))
- smooth <- match.fun(smooth)
- if (is.null(ylabs))
- ylabs <- paste("Partial for", nmt)
- if (is.null(main))
- main <- ""
- else if (is.logical(main))
- main <- if (main)
- deparse(model$call, 500)
- else ""
- else if (!is.character(main))
- stop("'main' must be TRUE, FALSE, NULL or character (vector).")
- main <- rep(main, length.out = n.tms)
- pf <- envir
- carrier <- function(term) {
- if (length(term) > 1)
- carrier(term[[2]])
- else eval(term, data, enclos = pf)
- }
- carrier.name <- function(term) {
- if (length(term) > 1)
- carrier.name(term[[2]])
- else as.character(term)
- }
- if (is.null(xlabs))
- xlabs <- unlist(lapply(cn, carrier.name))
- if (partial.resid || !is.null(smooth)) {
- pres <- residuals(model, "partial")
- if (!is.null(which.terms))
- pres <- pres[, which.terms, drop = FALSE]
- }
- is.fac <- sapply(nmt, function(i) is.factor(mf[, i]))
- se.lines <- function(x, iy, i, ff = 2) {
- tt <- ff * terms$se.fit[iy, i]
- lines(x, tms[iy, i] + tt, lty = lty.se, lwd = lwd.se,
- col = col.se)
- lines(x, tms[iy, i] - tt, lty = lty.se, lwd = lwd.se,
- col = col.se)
- }
- if(plot.it) nb.fig <- prod(par("mfcol"))
- if (ask & plot.it) {
- oask <- devAskNewPage(TRUE)
- on.exit(devAskNewPage(oask))
- }
- ylims <- ylim
- if (identical(ylims, "common")) {
- ylims <- if (!se)
- range(tms, na.rm = TRUE)
- else range(tms + 1.05 * 2 * terms$se.fit, tms - 1.05 *
- 2 * terms$se.fit, na.rm = TRUE)
- if (partial.resid)
- ylims <- range(ylims, pres, na.rm = TRUE)
- if (rug)
- ylims[1] <- ylims[1] - 0.07 * diff(ylims)
- }
- preds <- list()
- response <- list()
- p.names <- xlabs
- for (i in 1:n.tms) {
- if (identical(ylim, "free")) {
- ylims <- range(tms[, i], na.rm = TRUE)
- if (se)
- ylims <- range(ylims, tms[, i] + 1.05 * 2 * terms$se.fit[,
- i], tms[, i] - 1.05 * 2 * terms$se.fit[, i],
- na.rm = TRUE)
- if (partial.resid)
- ylims <- range(ylims, pres[, i], na.rm = TRUE)
- if (rug)
- ylims[1] <- ylims[1] - 0.07 * diff(ylims)
- }
- if (is.fac[i]) {
- ff <- mf[, nmt[i]]
- if (!is.null(model$na.action))
- ff <- naresid(model$na.action, ff)
- preds[[i]] <- ll <- levels(ff)
- xlims <- range(seq_along(ll)) + c(-0.5, 0.5)
- xx <- as.numeric(ff)
- response[[i]]<-rep(NA,length(ll))
- if (rug) {
- xlims[1] <- xlims[1] - 0.07 * diff(xlims)
- xlims[2] <- xlims[2] + 0.03 * diff(xlims)
- }
-
- if(plot.it){
- plot(1, 0, type = "n", xlab = xlabs[i], ylab = ylabs[i],
- xlim = xlims, ylim = ylims, main = main[i], xaxt = "n",
- ...)
- if (use.factor.levels)
- axis(1, at = seq_along(ll), labels = ll, ...)
- else axis(1)
- for (j in seq_along(ll)) {
- ww <- which(ff == ll[j])[c(1, 1)]
- jf <- j + c(-0.4, 0.4)
- lines(jf, response[[i]][j]<-tms[ww, i], col = col.term, lwd = lwd.term,...)
- if (se) se.lines(jf, iy = ww, i = i)
- }
- } else {
- for (j in seq_along(ll)) {
- ww <- which(ff == ll[j])[c(1, 1)]
- response[[i]][j]<-tms[ww, i]
- }
- }
- }
- else {
- xx <- carrier(cn[[i]])
- if (!is.null(use.rows))
- xx <- xx[use.rows]
- xlims <- range(xx, na.rm = TRUE)
- if (rug)
- xlims[1] <- xlims[1] - 0.07 * diff(xlims)
-
- response[[i]]<- logit(seq(min(tms[,i]),max(tms[,i]),length=100)) #aks
- preds[[i]]<-seq(min(xx),max(xx),length=100) #aks
- if(plot.it){
- oo <- order(xx)
- plot(xx[oo], logit(tms[oo, i]), type = "l", xlab = xlabs[i],
- ylab = ylabs[i], xlim = xlims, ylim = logit(ylims),
- main = main[i], col = col.term, lwd = lwd.term,
- ...)
- if (se)
- se.lines(xx[oo], iy = oo, i = i)
- }
- }
- if(plot.it){
- if (partial.resid) {
- if (!is.fac[i] && !is.null(smooth)) {
- smooth(xx, pres[, i], lty = lty.smth, cex = cex,
- pch = pch, col = col.res, col.smooth = col.smth,
- span = span.smth)
- }
- else points(xx, pres[, i], cex = cex, pch = pch,
- col = col.res)
- }
- if (rug) {
- n <- length(xx)
- lines(rep.int(jitter(xx), rep.int(3, n)), rep.int(ylims[1] +
- c(0, 0.05, NA) * diff(ylims), n))
- if (partial.resid)
- lines(rep.int(xlims[1] + c(0, 0.05, NA) * diff(xlims),
- n), rep.int(pres[, i], rep.int(3, n)))
- }
- }
- }
- invisible(list(names=p.names,preds=preds,resp=response))
-}
-
-
-# Interpret command line argurments #
-# Make Function Call #
- # Interpret command line argurments #
-# Make Function Call #
-make.p.tif=T
-make.binary.tif=T
-simp.method="AIC"
-opt.methods=2
-save.model=FALSE
-MESS=FALSE
-
-Args <- commandArgs(trailingOnly=FALSE)
-
- for (i in 1:length(Args)){
- if(Args[i]=="-f") ScriptPath<-Args[i+1]
- }
-
- print(Args)
- for (arg in Args) {
- argSplit <- strsplit(arg, "=")
- argSplit[[1]][1]
- argSplit[[1]][2]
- if(argSplit[[1]][1]=="c") csv <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="o") output <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mpt") make.p.tif <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mbt") make.binary.tif <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="om") opt.methods <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="savm") save.model <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="sm") simp.method <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mes") MESS <- argSplit[[1]][2]
- }
- print(csv)
- print(output)
- print(responseCol)
-
-ScriptPath<-dirname(ScriptPath)
-source(paste(ScriptPath,"LoadRequiredCode.r",sep="\\"))
-
-make.p.tif<-as.logical(make.p.tif)
-make.binary.tif<-as.logical(make.binary.tif)
-save.model<-make.p.tif | make.binary.tif
-opt.methods<-as.numeric(opt.methods)
-MESS<-as.logical(MESS)
-
- fit.glm.fct(ma.name=csv,
- tif.dir=NULL,output.dir=output,
- response.col=responseCol,make.p.tif=make.p.tif,make.binary.tif=make.binary.tif,
- simp.method=simp.method,debug.mode=F,responseCurveForm="pdf",script.name="glm.r",opt.methods=opt.methods,save.model=save.model,MESS=MESS)
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_MARS_pluggable.r b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_MARS_pluggable.r
deleted file mode 100644
index 914906f..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_MARS_pluggable.r
+++ /dev/null
@@ -1,1697 +0,0 @@
-# A set of "pluggable" R functions for automated model fitting of glm models to presence/absence data #
-#
-# Modified 12-2-09 to: remove categorical covariates from consideration if they only contain one level
-# ID factor variables based on "categorical" prefix and look for tifs in subdir
-# Give progress reports
-# write large output tif files in blocks to alleviate memory issues
-# various bug fixes
-#
-#
-# Modified 3-4-09 to use a list object for passing of arguements and data
-#
-
-
-# Libraries required to run this program #
-# PresenceAbsence - for ROC plots
-# XML - for XML i/o
-# rgdal - for geotiff i/o
-# sp - used by rdgal library
-# raster for geotiff o
-options(error=NULL)
-
-fit.mars.fct <- function(ma.name,tif.dir=NULL,output.dir=NULL,response.col="^response.binary",make.p.tif=T,make.binary.tif=T,
- mars.degree=1,mars.penalty=2,responseCurveForm=NULL,debug.mode=T,script.name="mars.r",opt.methods=2,save.model=TRUE,UnitTest=FALSE,MESS=FALSE){
- # This function fits a stepwise GLM model to presence-absence data.
- # written by Alan Swanson, 2008-2009
- # # Maintained and edited by Marian Talbert September 2010-
- # Arguements.
- # ma.name: is the name of a .csv file with a model array. full path must be included unless it is in the current
- # R working directory # THIS FILE CAN NOW INCLUDE AN OPTIONAL COLUMN OF SITE WEIGHTS WHICH MUST BE LABELED "site.weights"
- # tif.dir: is the directory containing geotiffs for each covariate. only required if geotiffs output of the
- # response surface is requested # # cov.list.name: is the name of a text file with the names of covariates to be included in models (one per line).
- # output.dir: is the directory that output files will be stored in. if not given, files will go to the current working directory.
- # response.col: column number of the model array containing a binary 0/1 response. all other columns will be considered explanatory variables.
- # make.p.tif: T if a geotiff of the response surface is desired.
- # make.binary.tif: T if a geotiff of the response surface is desired.
- # simp.method: model simplification method. valid methods include: "AIC" and "BIC". NOT CURRENTLY FUNCTIONAL
- # debug.mode: if T, output is directed to the console during the run. also, a pdf is generated which contains response curve plots and perspective plots
- # showing the effects of interactions deemed important. if F, output is diverted to a text file and the console is kept clear
- # except for final output of an xml file. in either case, a set of standard output files are created in the output directory.
- #
-
- # Value:
- # returns nothing but generates a number of output files in the directory
- # "output.dir" named above. These output files consist of:
- #
- # glm_output.txt: a text file with fairly detailed results of the final model.
- # glm_output.xml: an xml-formatted text file with results from the final model.
- # glm_response_curves.xml: an xml-formatted text file with response curves for
- # each covariate in the final model.
- # glm_prob_map.tif: a geotiff of the response surface
- # glm_bin_map.tif: a geotiff of the binary response surface. threhold is based on the roc curve at the point where sensitivity=specificity.
- # glm_log.txt: a file containing text output diverted from the console when debug.mode=F
- # glm_auc_plot.jpg: a jpg file of a ROC plot.
- # glm_response_curves.pdf: an pdf file with response curves for
- # each covariate in the final model and perspective plots showing the effect of interactions deemed significant.
- # only produced when debug.mode=T
- # # seed=NULL # sets a seed for the algorithm, any inegeger is acceptable
- # opt.methods=2 # sets the method used for threshold optimization used in the
- # # the evaluation statistics module
- # save.model=FALSE # whether the model will be used to later produce tifs
- # when debug.mode is true, these filenames will include a number in them so that they will not overwrite preexisting files. eg brt_1_output.txt.
- #
- times <- as.data.frame(matrix(NA,nrow=7,ncol=1,dimnames=list(c("start","read data","model fit",
- "model summary","response curves","tif output","done"),c("time"))))
- times[1,1] <- unclass(Sys.time())
- t0 <- unclass(Sys.time())
- #simp.method <- match.arg(simp.method)
-
- out <- list(
- input=list(ma.name=ma.name,
- tif.dir=tif.dir,
- output.dir=output.dir,
- response.col=response.col,
- make.p.tif=make.p.tif,
- make.binary.tif=make.binary.tif,
- site.weights=NULL,
- save.model=save.model,
- mars.degree=mars.degree,
- mars.penalty=mars.penalty,
- model.type="stepwise with pruning",
- model.source.file=script.name,
- model.fitting.subset=NULL, # not used.
- model.family="binomial",
- run.time=paste(c(format(Sys.time(),"%Y-%m-%d"),format(Sys.time(),"%H:%M:%S")),collapse="T"),
- sig.test="chi-squared anova p-value",
- MESS=MESS),
- dat = list(missing.libs=NULL,
- output.dir=list(dname=NULL,exist=F,readable=F,writable=F),
- tif.dir=list(dname=NULL,exist=F,readable=F,writable=F),
- tif.ind=NULL,
- tif.names=NULL,
- bname=NULL,
- bad.factor.covs=NULL, # factorchange
- ma=list( status=c(exists=F,readable=F),
- dims=c(NA,NA),
- n.pres=c(all=NA,complete=NA,subset=NA),
- n.abs=c(all=NA,complete=NA,subset=NA),
- ratio=NA,
- resp.name=NULL,
- train.weights=NULL,
- test.weights=NULL,
- train.xy=NULL,
- test.xy=NULL,
- factor.levels=NA,
- used.covs=NULL,
- ma=NULL,
- ma.subset=NULL,
- ma.test=NULL)),
- mods=list(final.mod=NULL,
- r.curves=NULL,
- tif.output=list(prob=NULL,bin=NULL),
- auc.output=NULL,
- interactions=NULL, # not used #
- summary=NULL),
- time=list(strt=unclass(Sys.time()),end=NULL),
- error.mssg=list(NULL),
- ec=0 # error count #
- )
-
- # load libaries #
- out <- check.libs(list("PresenceAbsence","rgdal","XML","sp","survival","mda","raster","tcltk2","foreign","ade4"),out)
-
- # exit program now if there are missing libraries #
- if(!is.null(out$error.mssg[[1]])){
- cat(saveXML(mars.to.xml(out),indent=T),'\n')
- return()
- }
-
- # check output dir #
- out$dat$output.dir <- check.dir(output.dir)
- if(out$dat$output.dir$writable==F) {out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: output directory",output.dir,"is not writable")
- out$dat$output.dir$dname <- getwd()
- }
-
- # generate a filename for output #
- if(debug.mode==T){
- outfile <- paste(bname<-paste(out$dat$output.dir$dname,"/mars_",n<-1,sep=""),"_output.txt",sep="")
- while(file.access(outfile)==0) outfile<-paste(bname<-paste(out$dat$output.dir$dname,"/mars_",n<-n+1,sep=""),"_output.txt",sep="")
- capture.output(cat("temp"),file=outfile) # reserve the new basename #
- } else bname<-paste(out$dat$output.dir$dname,"/mars",sep="")
- out$dat$bname <- bname
-
- # sink console output to log file #
- if(!debug.mode) {sink(logname <- paste(bname,"_log.txt",sep=""));on.exit(sink)} else logname<-NULL
- options(warn=1)
-
- # check tif dir #
- # check tif dir #
- if(!is.null(tif.dir)){
- out$dat$tif.dir <- check.dir(tif.dir)
- if(out$dat$tif.dir$readable==F & (out$input$make.binary.tif | out$input$make.p.tif)) {
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: tif directory",tif.dir,"is not readable")
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- cat(saveXML(brt.to.xml(out),indent=T),'\n')
- return()
- }
- }
-
-
- # find .tif files in tif dir #
- if(out$dat$tif.dir$readable) out$dat$tif.names <- list.files(out$dat$tif.dir$dname,pattern=".tif",recursive=T)
-
- # check for model array #
- out$input$ma.name <- check.dir(out$input$ma.name)$dname
-
- if(UnitTest!=FALSE) options(warn=2)
- out <- read.ma(out)
- if(UnitTest==1) return(out)
-
- # exit program now if there are errors in the input data #
- if(!is.null(out$error.mssg[[1]])){
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- cat(saveXML(mars.to.xml(out),indent=T),'\n')
- return()
- }
-
- cat("\nbegin processing of model array:",out$input$ma.name,"\n")
- cat("\nfile basename set to:",out$dat$bname,"\n")
- assign("out",out,envir=.GlobalEnv)
- if(!debug.mode) {sink();cat("Progress:20%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("20%\n")} ### print time
- ##############################################################################################################
- # Begin model fitting #
- ##############################################################################################################
-
- # Fit null GLM and run stepwise, then print results #
- cat("\n","Fitting MARS model","\n")
- flush.console()
-
- fit <- mars.glm(data=out$dat$ma$ma, mars.x=c(2:ncol(out$dat$ma$ma)), mars.y=1, mars.degree=out$input$mars.degree, family=out$input$model.family,
- site.weights=out$dat$ma$train.weights, penalty=out$input$mars.penalty)
-
- out$mods$final.mod <- fit
-
- out$mods$final.mod$contributions$var<-names(out$dat$ma$ma)[-1]
-
- assign("out",out,envir=.GlobalEnv)
- t3 <- unclass(Sys.time())
- fit_contribs <- try(mars.contribs(fit))
- if(class(fit_contribs)=="try-error"){
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]]<- paste("Error summarizing MARS model:",fit_contribs)
- cat(saveXML(mars.to.xml(out),indent=T),'\n')
- return()
- }
-
- x<-fit_contribs$deviance.table
- x <- x[x[,2]!=0,]
- x <- x[order(x[,4]),]
- row.names(x) <- x[,1]
- x$df <- -1*x$df
- x <- x[,-1]
-
- txt0 <- paste("\nMARS Model Results\n","\n","Data:\n",ma.name,"\n","\n\t n(pres)=",
- out$dat$ma$n.pres[2],"\n\t n(abs)=",out$dat$ma$n.abs[2],"\n\t n covariates considered=",length(out$dat$ma$used.covs),
- "\n",
- "\n total time for model fitting=",round((unclass(Sys.time())-t0)/60,2),"min\n",sep="")
-
- capture.output(cat(txt0),file=paste(bname,"_output.txt",sep=""))
-
- cat("\n","Finished with MARS","\n")
- cat("Summary of Model:","\n")
- print(out$mods$summary <- x)
- if(!is.null(out$dat$bad.factor.cols)){
- cat("\nWarning: the following categorical response variables were removed from consideration\n",
- "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n\n")
- }
- cat("\n","Storing output...","\n","\n")
- #flush.console()
- capture.output(cat("\n\nSummary of Model:\n"),file=paste(bname,"_output.txt",sep=""),append=TRUE)
- capture.output(print(out$mods$summary),file=paste(bname,"_output.txt",sep=""),append=TRUE)
- if(!is.null(out$dat$bad.factor.cols)){
- capture.output(cat("\nWarning: the following categorical response variables were removed from consideration\n",
- "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n"),
- file=paste(bname,"_output.txt",sep=""),append=T)
- }
-
- if(!debug.mode) {sink();cat("Progress:40%\n");flush.console();sink(logname,append=T)} else cat("40%\n")
-
-
- ##############################################################################################################
- # Begin model output #
- ##############################################################################################################
-
- # Store .jpg ROC plot #
- auc.output <- make.auc.plot.jpg(out$dat$ma$ma,pred=mars.predict(fit,out$dat$ma$ma)$prediction[,1],
- plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="MARS",opt.methods=opt.methods,
- weight=out$dat$ma$train.weights,out=out)
- out$mods$auc.output<-auc.output
-
- if(!debug.mode) {sink();cat("Progress:70%\n");flush.console();sink(logname,append=T)} else cat("70%\n")
-
- # Response curves #
-
- if(is.null(responseCurveForm)){
- responseCurveForm<-0}
-
- if(debug.mode | responseCurveForm=="pdf"){
- nvar <- nrow(out$mods$summary)
- pcol <- min(ceiling(sqrt(nvar)),4)
- prow <- min(ceiling(nvar/pcol),3)
- r.curves <- try(mars.plot(fit,plot.layout=c(prow,pcol),file.name=paste(bname,"_response_curves.pdf",sep="")))
-
- } else r.curves<-try(mars.plot(fit,plot.it=F))
-
- if(class(r.curves)!="try-error") {
- out$mods$r.curves <- r.curves
- } else {
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: problem fitting response curves",r.curves)
- }
-
- pred.fct<-pred.mars
-
- assign("out",out,envir=.GlobalEnv)
-
- save.image(paste(output.dir,"modelWorkspace",sep="\\"))
- t4 <- unclass(Sys.time())
- cat("\nfinished with final model summarization, t=",round(t4-t3,2),"sec\n");flush.console()
- if(!debug.mode) {sink();cat("Progress:80%\n");flush.console();sink(logname,append=T)} else cat("70%\n")
- # Make .tif of predictions #
-
- if(out$input$make.p.tif==T | out$input$make.binary.tif==T){
- if((n.var <- nrow(out$mods$summary))<1){
- mssg <- "Error producing geotiff output: null model selected by stepwise procedure - pointless to make maps"
- class(mssg)<-"try-error"
- } else {
- cat("\nproducing prediction maps...","\n","\n");flush.console()
- mssg <- try(proc.tiff(model=out$mods$final.mod,vnames=names(out$dat$ma$ma)[-1],
- tif.dir=out$dat$tif.dir$dname,filenames=out$dat$tif.ind,pred.fct=pred.mars,factor.levels=out$dat$ma$factor.levels,make.binary.tif=make.binary.tif,
- thresh=out$mods$auc.output$thresh,make.p.tif=make.p.tif,outfile.p=paste(out$dat$bname,"_prob_map.tif",sep=""),
- outfile.bin=paste(out$dat$bname,"_bin_map.tif",sep=""),tsize=50.0,NAval=-3000,
- fnames=out$dat$tif.names,logname=logname,out=out)) #"brt.prob.map.tif"
- }
-
- if(class(mssg)=="try-error"){
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("Error producing prediction maps:",mssg)
- cat(saveXML(mars.to.xml(out),indent=T),'\n')
- return()
- } else {
- if(make.p.tif) out$mods$tif.output$prob <- paste(out$dat$bname,"_prob_map.tif",sep="")
- if(make.binary.tif) out$mods$tif.output$bin <- paste(out$dat$bname,"_bin_map.tif",sep="")
- t5 <- unclass(Sys.time())
- cat("\nfinished with prediction maps, t=",round(t5-t4,2),"sec\n");flush.console()
- }
- }
- if(!debug.mode) {sink();cat("Progress:90%\n");flush.console();sink(logname,append=T)} else cat("90%\n")
-
- # Evaluation Statistics on Test Data#
-
- if(!is.null(out$dat$ma$ma.test)) Eval.Stat<-EvaluationStats(out,thresh=auc.output$thresh,train=out$dat$ma$ma,
- train.pred=mars.predict(fit,out$dat$ma$ma)$prediction[,1],opt.methods)
-
-
-
- # Write summaries to xml #
- if(debug.mode) assign("out",out,envir=.GlobalEnv)
- doc <- mars.to.xml(out)
-
- cat(paste("\ntotal time=",round((unclass(Sys.time())-t0)/60,2),"min\n\n\n",sep=""))
- if(!debug.mode) {
- sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))
- cat("Progress:100%\n");flush.console()
- #cat(saveXML(doc,indent=T),'\n')
- } else #unlink(outfile)
- capture.output(cat(saveXML(doc,indent=T)),file=paste(out$dat$bname,"_output.xml",sep=""))
- if(debug.mode) assign("fit",out$mods$final.mod,envir=.GlobalEnv)
- invisible(out)
- }
-################################################################################
-########### End fit.mars.fct ####################################
-
-pred.mars <- function(model,x) {
- # retrieve key items from the global environment #
- # make predictionss.
- y <- rep(NA,nrow(x))
- y[complete.cases(x)] <- as.vector(mars.predict(model,x[complete.cases(x),])$prediction[,1])
-
-#if(sum(is.na(x))/dim(x)[2]!=sum(is.na(y)))
-#h<-is.na(x)
-#h<-apply(h,1,sum)
-#h=h/35
-#f<-is.na(y)
-#which((h-f)!=0,arr.ind=TRUE)
-#b<-cbind(x[which((h-f)!=0,arr.ind=TRUE),],y[which((h-f)!=0,arr.ind=TRUE)])
-
-#which(is.na(y)
- # encode missing values as -1.
- y[is.na(y)]<- NaN
-
- # return predictions.
- return(y)
- }
-
-logit <- function(x) 1/(1+exp(-x))
-
-file_path_as_absolute <- function (x){
- if (!file.exists(epath <- path.expand(x)))
- stop(gettextf("file '%s' does not exist", x), domain = NA)
- cwd <- getwd()
- on.exit(setwd(cwd))
- if (file_test("-d", epath)) {
- setwd(epath)
- getwd()
- }
- else {
- setwd(dirname(epath))
- file.path(getwd(), basename(epath))
- }
-}
-#file_path_as_absolute(".")
-
-mars.to.xml <- function(out){
- require(XML)
- schema.http="http://www.w3.org/2001/XMLSchema-instance"
- schema.fname="file:/Users/isfs2/Desktop/Source/2008-04-09/src/gov/nasa/gsfc/quickmap/ModelBuilder/modelRun_output_v2.xsd"
- xml.out <- newXMLDoc()
- mr <- newXMLNode("modelRunOutput",doc=xml.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))#,parent=xml.out
- sm <- newXMLNode("singleModel",parent=mr)
- bg <- newXMLNode("background",parent=sm)
- newXMLNode("mdsName",out$input$ma.name,parent=bg)
- newXMLNode("runDate",out$input$run.time,parent=bg)
- lc <- newXMLNode("layersConsidered",parent=bg)#, parent = xml.out)
- kids <- lapply(paste(out$dat$tif.dir$dname,"/",out$dat$tif.names,sep=""),function(x) newXMLNode("layer", x))
- addChildren(lc, kids)
- mo <- newXMLNode("modelOutput",parent=sm)
- newXMLNode("modelType",out$input$model.type,parent=mo)
- newXMLNode("modelSourceFile",out$input$model.source.file,parent=mo)
- newXMLNode("devianceExplained",out$mods$auc.output$pct_dev_exp,parent=mo,attrs=list(type="percentage"))
- newXMLNode("nativeOutput",paste(out$dat$bname,"_output.txt",sep=""),parent=mo)
- newXMLNode("binaryOutputFile",out$mods$tif.output[[2]],parent=mo)
- newXMLNode("probOutputFile",out$mods$tif.output[[1]],parent=mo)
- newXMLNode("auc",out$mods$auc.output$auc,parent=mo)
- newXMLNode("rocGraphic",out$mods$auc.output$plotname,parent=mo)
- newXMLNode("rocThresh",out$mods$auc.output$thresh,parent=mo)
- newXMLNode("modelDeviance",out$mods$auc.output$dev_fit,parent=mo)
- newXMLNode("nullDeviance",out$mods$auc.output$null_dev,parent=mo)
- if(is.null(out$mods$r.curves)) rc.name <- NULL else rc.name <- paste(out$dat$bname,"_response_curves.xml",sep="")
- newXMLNode("responsePlotsFile",rc.name,parent=mo)
- newXMLNode("significanceDescription",out$input$sig.test,parent=mo)
- mfp <- newXMLNode("modelFitParmas",parent=mo)
- newXMLNode("marsDegree",out$input$mars.degree,parent=mfp)
- newXMLNode("marsPenalty",out$input$mars.penalty,parent=mfp)
-
- sv <- newXMLNode("significantVariables",parent=mo)
- if(!is.null(out$mods$summary)) {
- t.table <- out$mods$summary#$coefficients
- names(t.table)[3]<-"significanceMeasurement"
- for(i in 1:nrow(t.table)){
- x <- newXMLNode("sigVar",parent=sv)
- newXMLNode(name="name", row.names(t.table)[i],parent=x)
- kids <- lapply(1:ncol(t.table),function(j) newXMLNode(name=names(t.table)[j], t.table[i,j]))
- addChildren(x, kids)
- }
- }
-
- if(!is.null(out$mods$r.curves)){
- r.curves <- out$mods$r.curves
- factor.levels <- out$dat$ma$factor.levels
- rc.out <- newXMLDoc()
- root <- newXMLNode("responseCurves",doc=rc.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))
- for(i in 1:length(r.curves$names)){
- if(!is.na(f.index<-match(r.curves$names[i],names(factor.levels)))){
- vartype <- "factor"} else vartype="continuous"
- x <- newXMLNode("responseCurve",attrs=list(covariate=r.curves$names[i],type=vartype),parent=root)
- kids <- lapply(1:length(r.curves$preds[[i]]),function(j){
- newXMLNode(name="responsePt",parent=x,.children=list(
- newXMLNode(name="explanatory",as.character(r.curves$preds[[i]])[j]),
- newXMLNode(name="response",r.curves$resp[[i]][j])))})
- addChildren(x, kids)
- }
- saveXML(rc.out,rc.name,indent=T)
-
- }
- if(!is.null(out$error.mssg[[1]])) {
- kids <- lapply(out$error.mssg,function(j) newXMLNode(name="error",j))
- addChildren(mo,kids)
- }
- return(xml.out)
- }
-
-
-get.cov.names <- function(model){
- return(attr(terms(formula(model)),"term.labels"))
- }
-
-
-check.dir <- function(dname){
- if(is.null(dname)) dname <- getwd()
- dname <- gsub("[\\]","/",dname)
- end.char <- substr(dname,nchar(dname),nchar(dname))
- if(end.char == "/") dname <- substr(dname,1,nchar(dname)-1)
- exist <- suppressWarnings(as.numeric(file.access(dname,mode=0))==0) # -1 if bad, 0 if ok #
- if(exist) dname <- file_path_as_absolute(dname)
- readable <- suppressWarnings(as.numeric(file.access(dname,mode=4))==0) # -1 if bad, 0 if ok #
- writable <- suppressWarnings(as.numeric(file.access(dname,mode=2))==0) # -1 if bad, 0 if ok #
- return(list(dname=dname,exist=exist,readable=readable,writable=writable))
- }
-
-
-get.image.info <- function(image.names){
- # this function creates a data.frame with summary image info for a set of images #
- require(rgdal)
- n.images <- length(image.names)
-
- full.names <- image.names
- out <- data.frame(image=full.names,available=rep(F,n.images),size=rep(NA,n.images),
- type=factor(rep("unk",n.images),levels=c("asc","envi","tif","unk")))
- out$type[grep(".tif",image.names)]<-"tif"
- out$type[grep(".asc",image.names)]<-"asc"
- for(i in 1:n.images){
- if(out$type[i]=="tif"){
- x <-try(GDAL.open(full.names[1],read.only=T))
- suppressMessages(try(GDAL.close(x)))
- if(class(x)!="try-error") out$available[i]<-T
- x<-try(file.info(full.names[i]))
- } else {
- x<-try(file.info(full.names[i]))
- if(!is.na(x$size)) out$available[i]<-T
- }
- if(out$available[i]==T){
- out$size[i]<-x$size
- if(out$type[i]=="unk"){
- # if extension not known, look for envi .hdr file in same directory #
- if(file.access(paste(file_path_sans_ext(full.names[i]),".hdr",sep=""))==0)
- out$type[i]<-"envi"
- }
- }
- }
- return(out)
-}
-
-###########################################################################################
-# The following functions are from Elith et al.
-###########################################################################################
-
-"calc.deviance" <-
-function(obs.values, fitted.values, weights = rep(1,length(obs.values)), family=family, calc.mean = TRUE)
-{
-# j. leathwick/j. elith
-#
-# version 2.1 - 5th Sept 2005
-#
-# function to calculate deviance given two vectors of raw and fitted values
-# requires a family argument which is set to binomial by default
-#
-#
-
-if (length(obs.values) != length(fitted.values))
- stop("observations and predictions must be of equal length")
-
-y_i <- obs.values
-
-u_i <- fitted.values
-
-if (family == "binomial" | family == "bernoulli") {
-
- deviance.contribs <- (y_i * log(u_i)) + ((1-y_i) * log(1 - u_i))
- deviance <- -2 * sum(deviance.contribs * weights)
-
-}
-
-if (family == "poisson" | family == "Poisson") {
-
- deviance.contribs <- ifelse(y_i == 0, 0, (y_i * log(y_i/u_i))) - (y_i - u_i)
- deviance <- 2 * sum(deviance.contribs * weights)
-
-}
-
-if (family == "laplace") {
- deviance <- sum(abs(y_i - u_i))
- }
-
-if (family == "gaussian") {
- deviance <- sum((y_i - u_i) * (y_i - u_i))
- }
-
-
-
-if (calc.mean) deviance <- deviance/length(obs.values)
-
-return(deviance)
-
-}
-
-"calibration" <-
-function(obs, preds, family = family)
-{
-#
-# j elith/j leathwick 17th March 2005
-# calculates calibration statistics for either binomial or count data
-# but the family argument must be specified for the latter
-# a conditional test for the latter will catch most failures to specify
-# the family
-#
-
-if (family == "bernoulli") family <- "binomial"
-pred.range <- max(preds) - min(preds)
-if(pred.range > 1.2 & family == "binomial") {
-print(paste("range of response variable is ", round(pred.range, 2)), sep = "", quote = F)
-print("check family specification", quote = F)
-return()
-}
-if(family == "binomial") {
-pred <- preds + 1e-005
-pred[pred >= 1] <- 0.99999
-mod <- glm(obs ~ log((pred)/(1 - (pred))), family = binomial)
-lp <- log((pred)/(1 - (pred)))
-a0b1 <- glm(obs ~ offset(lp) - 1, family = binomial)
-miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
-ab1 <- glm(obs ~ offset(lp), family = binomial)
-miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
-miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
-}
-if(family == "poisson") {
-mod <- glm(obs ~ log(preds), family = poisson)
-lp <- log(preds)
-a0b1 <- glm(obs ~ offset(lp) - 1, family = poisson)
-miller1 <- 1 - pchisq(a0b1$deviance - mod$deviance, 2)
-ab1 <- glm(obs ~ offset(lp), family = poisson)
-miller2 <- 1 - pchisq(a0b1$deviance - ab1$deviance, 1)
-miller3 <- 1 - pchisq(ab1$deviance - mod$deviance, 1)
-}
-calibration.result <- c(mod$coef, miller1, miller2, miller3)
-names(calibration.result) <- c("intercept", "slope", "testa0b1", "testa0|b1", "testb1|a")
-return(calibration.result)
-}
-
-"mars.contribs" <-
-function (mars.glm.object,sp.no = 1, verbose = TRUE)
-{
-
-# j leathwick/j elith August 2006
-#
-# version 3.1 - developed in R 2.3.1 using mda 0.3-1
-#
-# takes a mars/glm model and uses the updated mars export table
-# stored as the second list item from mars.binomial
-# assessing the contribution of the fitted functions,
-# amalgamating terms for variables as required
-#
-# amended 29/9/04 to pass original mars model details
-# and to return f-statistics
-#
-# amended 7th January to accommodate any glm model family
-#
-# modified 050609 by aks to output a numeric deviance table #
-
- mars.detail <- mars.glm.object$mars.call
- pred.names <- mars.detail$predictor.base.names #get the names from the original data
- n.preds <- length(pred.names)
-
- spp.names <- mars.detail$y.names
- family <- mars.detail$family
-
- m.table <- mars.glm.object$mars.table[-1,]
- m.table$names1 <- as.character(m.table$names1) #convert from a factor
-
- x.data <- as.data.frame(eval(mars.glm.object$basis.functions))
- y.data <- as.data.frame(eval(mars.glm.object$y.values))
-
- assign("x.data", x.data, pos = 1)
- assign("y.data", y.data, pos = 1)
- assign("sp.no", sp.no, pos = 1)
-
- glm.model <- glm(y.data[,sp.no] ~ .,data = x.data,family = family)
-
- print(paste("performing backwards drops for mars/glm model for",
- spp.names[sp.no]),quote=F)
-
- n.bfs <- length(m.table[,1])
-
- delta.deviance <- rep(0,n.preds)
- df <- rep(0,n.preds)
- signif <- rep(0,n.preds)
-
- for (i in 1:n.preds) { #start at two because first line is the constant
-
- # look for variable names in the table matching those in the var list
-
- var.nos <- grep(as.character(pred.names[i]),m.table$names1)
-
- #drop.list stores numbers of basis functions to be dropped
- if (length(var.nos) > 0) {
- drop.list <- 0 - var.nos
- x.data.new <- x.data[,drop.list]
- assign("x.data.new",x.data.new,pos=1)
-
- if (verbose) {
- print(paste("Dropping ",pred.names[i],"...",sep=""),
- quote=FALSE)
- }
- x.data.new<-as.data.frame(x.data.new)
- if(dim(x.data.new)[2]==0){
- new.model <- glm(y.data[,sp.no] ~ 1, family = family)
- }else new.model <- glm(y.data[,sp.no] ~ ., data=x.data.new, family = family)
-
- comparison <- anova(glm.model,new.model,test="Chisq")
-
- df[i] <- comparison[2,3]
- delta.deviance[i] <- zapsmall(comparison[2,4],4)
- signif[i] <- zapsmall(comparison[2,5],6)
- }
-
- }
-
- rm(x.data,y.data,sp.no,pos=1) # tidy up temporary files
-
- #deviance.table <- as.data.frame(cbind(pred.names,delta.deviance,df,signif))
- #names(deviance.table) <- c("variable","delta_dev","deg. free.","p-value")
- deviance.table <- data.frame(variable=pred.names,delta_dev=delta.deviance,df=df,p_value=signif)#aks
- return(list(mars.call=mars.detail,deviance.table=deviance.table))
-}
-
-"mars.cv" <-
-function (mars.glm.object, nk = 10, sp.no = 1, prev.stratify = F)
-{
-#
-# j. leathwick/j. elith - August 2006
-#
-# version 3.1 - developed in R 2.3.1 using mda 0.3-1
-#
-# function to perform k-fold cross validation
-# with full model perturbation for each subset
-#
-# requires mda library from Cran
-# requires functions mw and calibration
-#
-# takes a mars/glm object produced by mars.glm
-# and first assesses the full model, and then
-# randomly subsets the dataset into nk folds and drops
-# each subset in turn, fitting on remaining data
-# and predicting for withheld data
-#
-# caters for both single species and community models via the argument sp.no
-# for the first, sp.no can be left on its default of 1
-# for community models, sp.no can be varied from 1 to n.spp
-#
-# modified 29/9/04 to
-# 1. return mars analysis details for audit trail
-# 2. calculate roc and calibration on subsets as well as full data
-# returning the mean and se of the ROC scores
-# and the mean calibration statistics
-#
-# modified 8/10/04 to add prevalence stratification
-# modified 7th January to test for binomial family and return if not
-#
-# updated 15th March to cater for both binomial and poisson families
-#
-# updated 16th June 2005 to calculate residual deviance
-#
-
- data <- mars.glm.object$mars.call$dataframe #get the dataframe name
- dataframe.name <- deparse(substitute(data))
-
- data <- as.data.frame(eval(parse(text=data))) #and now the data
- n.cases <- nrow(data)
-
- mars.call <- mars.glm.object$mars.call #and the mars call details
- mars.x <- mars.call$mars.x
- mars.y <- mars.call$mars.y
- mars.degree <- mars.call$degree
- mars.penalty <- mars.call$penalty
- family <- mars.call$family
- site.weights <- eval(mars.glm.object$weights$site.weights)
-
- n.spp <- length(mars.y)
-
- if (sp.no > n.spp) {
- print(paste("the value specified for sp.no of",sp.no),quote=F)
- print(paste("exceeds the total number of species, which is ",n.spp),quote=F)
- return()
- }
-
- xdat <- as.data.frame(data[,mars.x])
- xdat <- mars.new.dataframe(xdat)[[1]]
- ydat <- mars.glm.object$y.values[,sp.no]
- target.sp <- names(data)[mars.y[sp.no]]
-
- if (prev.stratify) {
- presence.mask <- ydat == 1
- absence.mask <- ydat == 0
- n.pres <- sum(presence.mask)
- n.abs <- sum(absence.mask)
- }
-
- print(paste("Calculating ROC and calibration from full model for",target.sp),quote=F)
-
- u_i <- mars.glm.object$fitted.values[,sp.no]
- y_i <- ydat
-
- if (family == "binomial") {
- full.resid.deviance <- calc.deviance(y_i,u_i, weights = site.weights, family="binomial")
- full.test <- roc(y_i, u_i)
- full.calib <- calibration(y_i, u_i)
- }
-
- if (family=="poisson") {
- full.resid.deviance <- calc.deviance(y_i,u_i, weights = site.weights, family="poisson")
- full.test <- cor(y_i, u_i)
- full.calib <- calibration(y_i, u_i, family = "poisson")
- }
-
-# set up for results storage
-
- subset.test <- rep(0,nk)
- subset.calib <- as.data.frame(matrix(0,ncol=5,nrow=nk))
- names(subset.calib) <- c("intercept","slope","test1","test2","test3")
- subset.resid.deviance <- rep(0,nk)
-
-# now setup for withholding random subsets
-
- pred.values <- rep(0, n.cases)
- fitted.values <- rep(0, n.cases)
-
- if (prev.stratify) {
-
- selector <- rep(0,n.cases)
-
-#create a vector of randomised numbers and feed into presences
-
- temp <- rep(seq(1, nk, by = 1), length = n.pres)
- temp <- temp[order(runif(n.pres, 1, 100))]
- selector[presence.mask] <- temp
-
-# and then do the same for absences
-
- temp <- rep(seq(1, nk, by = 1), length = n.abs)
- temp <- temp[order(runif(n.abs, 1, 100))]
- selector[absence.mask] <- temp
-
- }
- else { #otherwise make them random with respect to presence/absence
-
- selector <- rep(seq(1, nk, by = 1), length = n.cases)
- selector <- selector[order(runif(n.cases, 1, 100))]
- }
-
- print("", quote = FALSE)
- print("Creating predictions for subsets...", quote = F)
-
- for (i in 1:nk) {
- cat(i," ")
- model.mask <- selector != i #used to fit model on majority of data
- pred.mask <- selector == i #used to identify the with-held subset
- assign("species.subset", ydat[model.mask], pos = 1)
- assign("predictor.subset", xdat[model.mask, ], pos = 1)
-
- # fit new mars model
-
- mars.object <- mars(y = species.subset, x = predictor.subset,
- degree = mars.degree, penalty = mars.penalty)
-
- # and extract basis functions
-
- n.bfs <- length(mars.object$selected.terms)
- bf.data <- as.data.frame(mars.object$x)
- names(bf.data) <- paste("bf",1:n.bfs,sep="")
- assign("bf.data", bf.data, pos=1)
-
- # then fit a binomial model to them
-
- mars.binomial <- glm(species.subset ~ .,data=bf.data[,-1], family= family, maxit = 100)
-
- pred.basis.functions <- as.data.frame(mda:::model.matrix.mars(mars.object,
- xdat[pred.mask, ]))
-
- #now name the bfs to match the approach used in mars.binomial
-
- names(pred.basis.functions) <- paste("bf",1:n.bfs,sep="")
-
- # and form predictions for them and evaluate performance
-
- fitted.values[pred.mask] <- predict(mars.binomial,
- pred.basis.functions, type = "response")
-
- y_i <- ydat[pred.mask]
- u_i <- fitted.values[pred.mask]
- weights.subset <- site.weights[pred.mask]
-
- if (family == "binomial") {
- subset.resid.deviance[i] <- calc.deviance(y_i,u_i,weights = weights.subset, family="binomial")
- subset.test[i] <- roc(y_i,u_i)
- subset.calib[i,] <- calibration(y_i, u_i)
- }
-
- if (family=="poisson"){
- subset.resid.deviance[i] <- calc.deviance(y_i,u_i,weights = weights.subset, family="poisson")
- subset.test[i] <- cor(y_i, u_i)
- subset.calib[i,] <- calibration(y_i, u_i, family = family)
- }
- }
-
- cat("","\n")
-
-# tidy up temporary files
-
- rm(species.subset,predictor.subset,bf.data,pos=1)
-
-# and assemble results for return
-
-# mars.detail <- list(dataframe = dataframe.name,
-# x = mars.x, x.names = names(xdat),
-# y = mars.y, y.names = names(data)[mars.y],
-# target.sp = target.sp, degree=mars.degree, penalty = mars.penalty, family = family)
-
- y_i <- ydat
- u_i <- fitted.values
-
- if (family=="binomial") {
- cv.resid.deviance <- calc.deviance(y_i,u_i,weights = site.weights, family="binomial")
- cv.test <- roc(y_i, u_i)
- cv.calib <- calibration(y_i, u_i)
- }
-
- if (family=="poisson"){
- cv.resid.deviance <- calc.deviance(y_i,u_i,weights = site.weights, family="poisson")
- cv.test <- cor(y_i, u_i)
- cv.calib <- calibration(y_i, u_i, family = "poisson")
- }
-
- subset.test.mean <- mean(subset.test)
- subset.test.se <- sqrt(var(subset.test))/sqrt(nk)
-
- subset.test <- list(test.scores = subset.test, subset.test.mean = subset.test.mean,
- subset.test.se = subset.test.se)
-
- subset.calib.mean <- apply(subset.calib[,c(1:2)],2,mean)
- names(subset.calib.mean) <- names(subset.calib)[c(1:2)] #mean only of parameters
-
- subset.calib <- list(subset.calib = subset.calib,
- subset.calib.mean = subset.calib.mean)
-
- subset.deviance.mean <- mean(subset.resid.deviance)
- subset.deviance.se <- sqrt(var(subset.resid.deviance))/sqrt(nk)
-
- subset.deviance <- list(subset.deviances = subset.resid.deviance, subset.deviance.mean = subset.deviance.mean,
- subset.deviance.se = subset.deviance.se)
-
- return(list(mars.call = mars.call, full.resid.deviance = full.resid.deviance,
- full.test = full.test, full.calib = full.calib, pooled.deviance = cv.resid.deviance, pooled.test = cv.test,
- pooled.calib = cv.calib,subset.deviance = subset.deviance, subset.test = subset.test, subset.calib = subset.calib))
-}
-
-"mars.export" <-
-function (object,lineage)
-{
-#
-# j leathwick/j elith August 2006
-#
-# takes a mars model fitted using library mda
-# and extracts the basis functions and their
-# coefficients, returning them as a table
-# caters for models with degree up to 2
-#
-# version 3.1 - developed in R 2.3.1 using mda 0.3-1
-
- which <- object$selected.terms
- nterms <- length(which)
- nspp <- ncol(eval(object$call$y))
- dir <- object$factor
- cut <- object$cuts
- var.names <- dimnames(object$factor)[[2]]
- p <- length(var.names)
- coefs <- as.data.frame(object$coefficients)
- names(coefs) <- names(eval(object$call$y))
-
-# setup storage for results
-
- names1 <- rep("null", length = nterms)
- types1 <- rep("null", length = nterms)
- levels1 <- rep("null", length = nterms)
- signs1 <- rep(0, length = nterms)
- cuts1 <- rep(0, length = nterms)
-
- names2 <- rep("null", length = nterms)
- types2 <- rep("null", length = nterms)
- levels2 <- rep("null", length = nterms)
- signs2 <- rep(0, length = nterms)
- cuts2 <- rep(0, length = nterms)
- names1[1] <- "constant"
- signs1[1] <- 1
-
-# now cycle through the terms
-if(nterms>1){
- for (i in seq(2, nterms)) {
- j <- which[i]
- term.count = 1
- for (k in 1:p) {
- if (dir[j, k] != 0) {
- if (term.count == 1) {
- n <- match(var.names[k],lineage$full.name)
- names1[i] <- lineage$base.name[n] #var.names[k]
- types1[i] <- lineage$type[n]
- levels1[i] <- lineage$level[n]
- signs1[i] <- dir[j, k]
- cuts1[i] <- cut[j, k]
- term.count <- term.count + 1
- }
- else {
- names2[i] <- var.names[k]
- n <- match(var.names[k],lineage$full.name)
- names2[i] <- lineage$base.name[n] #var.names[k]
- types2[i] <- lineage$type[n]
- levels2[i] <- lineage$level[n]
- signs2[i] <- dir[j, k]
- cuts2[i] <- cut[j, k]
- }
- }
- }
- }
- }
- mars.export.table <- data.frame(names1, types1, levels1, signs1, cuts1,
- names2, types2, levels2, signs2, cuts2, coefs)
-
- return(mars.export.table)
-}
-
-"mars.glm" <-
-function (data, # the input data frame
- mars.x, # column numbers of the predictors
- mars.y, # column number(s) of the response variable(s)
- mars.degree = 1, # level of interactions - 1 = zero, 2 = 1st order, etc
- site.weights = rep(1, nrow(data)), # one weight per site
- spp.weights = rep(1,length(mars.y)), # one wieght per species
- penalty = 2, # the default penaly for a mars model
- family =family) # the family for the glm model
-{
-#
-# j leathwick, j elith - August 2006
-#
-# version 3.1 - developed in R 2.3.1 using mda 0.3-1
-#
-# calculates a mars/glm object in which basis functions are calculated
-# using an initial mars model with single or multiple responses
-# data for individual species are then fitted as glms using the
-# common set of mars basis functions with results returned as a list
-#
-# takes as input a dataset and args selecting x and y variables, and degree of interaction
-# along with site and species weights, the CV penalty, and the glm family argument
-# the latter would normally be one of "binomial" or "poisson" - "gaussian" could be used
-# but in this case the model shouldn't differ from that fitted using mars on its own
-#
-# requires mda and leathwick/elith's mars.export
-#
-# modified 3/11/04 to store information on glm phase convergence
-# and with number of iterations raised to 100 to encourage convergence for low prevalence species
-# modified 4/11/04 to accommodate observation weights in both mars and glm steps
-# modified 12/04 to accommodate non-binomial families
-# modified 11/05 to accommodate factor variables
-# these are done as 0/1 dummy variables in a new dataframe
-# created using mars.new.dataframe
-
- require(mda)
-
- n.spp <- length(mars.y)
-
-# setup input data and assign to position one
-
- dataframe.name <- deparse(substitute(data)) # get the dataframe name
-
- xdat <- as.data.frame(eval(data[, mars.x])) #form the temporary datasets
- predictor.base.names <- names(xdat)
-
-# create the new dataframe with dummy vars for factor predictors
- xdat <- mars.new.dataframe(xdat)
- lineage <- xdat[[2]] # tracks which variables have had dummy's created
- xdat <- xdat[[1]]
- predictor.dummy.names <- names(xdat)
-
- ydat <- as.data.frame(eval(data[, mars.y]))
- names(ydat) <- names(data)[mars.y]
-
- assign("xdat", xdat, pos = 1) #and assign them for later use
- assign("ydat", ydat, pos = 1)
-
-# create storage space for glm model results
-
- n.cases <- nrow(xdat)
-
- fitted.values <- matrix(0,ncol = n.spp, nrow = n.cases)
- model.residuals <- matrix(0,ncol = n.spp, nrow = n.cases)
- null.deviances <- rep(0,n.spp)
- residual.deviances <- rep(0,n.spp)
- null.dfs <- rep(0,n.spp)
- residual.dfs <- rep(0,n.spp)
- converged <- rep(TRUE,n.spp)
-
-# fit the mars model and extract the basis functions
-
- cat("fitting initial mars model for",n.spp,"responses","\n")
- cat("followed by a glm model with a family of",family,"\n")
-
- mars.object <- mars(x = xdat, y = ydat, degree = mars.degree, w = site.weights,
- wp = spp.weights, penalty = penalty)
- if(length(mars.object$coefficients)==1) stop("MARS has fit the null model (intercept only) \n new predictors are required")
- bf.data <- as.data.frame(eval(mars.object$x))
- n.bfs <- ncol(bf.data)
- bf.names <- paste("bf", 1:n.bfs, sep = "")
- names(bf.data) <- bf.names
- bf.data <- as.data.frame(bf.data[,-1])
-
- m.table <- as.data.frame(mars.export(mars.object,lineage))
- names(m.table)[(10 + 1):(10 + n.spp)] <- names(ydat)
-
- p.values <- matrix(0, ncol = n.spp, nrow = n.bfs)
- rownames(p.values) <- paste("bf", 1:n.bfs, sep = "")
- colnames(p.values) <- names(ydat)
-
-# now cycle through the species fitting glm models
-
- cat("fitting glms for individual responses","\n")
-
- for (i in 1:n.spp) {
-
- cat(names(ydat)[i],"\n")
- model.glm <- glm(ydat[, i] ~ ., data = bf.data, weights = site.weights,
- family = family, maxit = 100)
-
-# update the coefficients and other results
-
- # then match names and insert as appropriate
- m.table[ , i + 10] <- 0 # set all values to zero
- m.table[ , i + 10] <- model.glm$coefficients # update all the constant
- sum.table <- summary(model.glm)$coefficients
- p.values[,i] <- sum.table[,4]
- fitted.values[,i] <- model.glm$fitted
- model.residuals[,i] <- resid(model.glm)
- null.deviances[i] <- model.glm$null.deviance
- residual.deviances[i] <- model.glm$deviance
- null.dfs[i] <- model.glm$df.null
- residual.dfs[i] <- model.glm$df.residual
- converged[i] <- model.glm$converged
- }
-
-# now assemble data to be returned
-
- fitted.values <- as.data.frame(fitted.values)
- names(fitted.values) <- names(ydat)
-
- model.residuals <- as.data.frame(model.residuals)
- names(model.residuals) <- names(ydat)
-
- deviances <- data.frame(names(ydat),null.deviances,null.dfs,residual.deviances,residual.dfs,converged)
- names(deviances) <- c("species","null.dev","null.df","resid.dev","resid.df","converged")
-
- weights = list(site.weights = site.weights, spp.weights = spp.weights)
-
- mars.detail <- list(dataframe = dataframe.name, mars.x = mars.x,
- predictor.base.names = predictor.base.names, predictor.dummy.names = predictor.dummy.names,
- mars.y = mars.y, y.names = names(ydat), degree=mars.degree, penalty = penalty,
- family = family)
-
- rm(xdat,ydat,pos=1) #finally, clean up the temporary dataframes
-
- return(list(mars.table = m.table, basis.functions = bf.data, y.values = ydat,
- fitted.values = fitted.values, residuals = model.residuals, weights = weights, deviances = deviances,
- p.values = p.values, mars.call = mars.detail,mars.object=mars.object))
-}
-
-"mars.new.dataframe" <-
-function (input.data)
-{
-#
-# j leathwick, j elith - August 2006
-#
-# version 3.1 - developed in R 2.3.1 using mda 0.3-1
-#
-# takes an input data frame and checks for factor variables
-# converting these to dummy variables, one each for each factor level
-# returning it for use with mars.glm so that factor vars can be included
-# in a mars analysis
-#
-
- if (!is.data.frame(input.data)) {
- print("input data must be a dataframe..",quote = FALSE)
- return()
- }
-
- n <- 1
- for (i in 1:ncol(input.data)) { #first transfer the vector variables
- if (is.vector(input.data[,i])) {
- if (n == 1) {
- output.data <- as.data.frame(input.data[,i])
- names.list <- names(input.data)[i]
- var.type <- "vector"
- factor.level <- "na"
- }
- else {
- output.data[,n] <- input.data[,i]
- names.list <- c(names.list,names(input.data)[i])
- var.type <- c(var.type,"vector")
- factor.level <- c(factor.level,"na")
- }
- names(output.data)[n] <- names(input.data)[i]
- n <- n + 1
- }
- }
-
- for (i in 1:ncol(input.data)) { # and then the factor variables
- if (is.factor(input.data[,i])) {
- temp.table <- summary(input.data[,i])
- for (j in 1:length(temp.table)) {
- names.list <- c(names.list,names(input.data)[i])
- var.type <- c(var.type,"factor")
- factor.level <- c(factor.level,names(temp.table)[j])
- output.data[,n] <- ifelse(input.data[,i] == names(temp.table)[j],1,0)
- names(output.data)[n] <- paste(names(input.data)[i],".",names(temp.table)[j],sep="")
- n <- n + 1
- }
- }
- }
-
- lineage <- data.frame(names(output.data),names.list,var.type,factor.level)
- for (i in 1:4) lineage[,i] <- as.character(lineage[,i])
- names(lineage) <- c("full.name","base.name","type","level")
-
- return(list(dataframe = output.data, lineage = lineage))
-}
-
-"mars.plot" <-
-function (mars.glm.object, #the input mars object
- sp.no = 0, # the species number for multi-response models
- plot.rug=T, # plot a rug of deciles
- plot.layout = c(3,4), # the plot layout to use
- file.name = NA, # giving a file name will send results to a pdf
- plot.it=T) # option for making curves but no plots (aks)
-{
-
-# j leathwick/j elith August 2006
-#
-# version 3.1 - developed in R 2.3.1 using mda 0.3-1
-#
-# requires mars.export of leathwick/elith
-#
-# takes a mars or mars/glm model and either
-# creates a mars export table (vanilla mars object)
-# and works from this or uses the updated mars export table
-# stored as the first list item from mars.binomial
-# plotting out the fitted functions, amalgamating terms
-# for variables and naming the pages as required
-#
-# caters for multispecies mars models by successively plotting
-# all species unless a value other than zero is given for sp.no
-#
-# modified by aks 050609 to only open one plot window and use the record=T option.
-
- max.plots <- plot.layout[1] * plot.layout[2]
- if(plot.it){ #aks
- if (is.na(file.name)) {
- use.windows = TRUE
- windows(width = 11, height = 8, record=T) #AKS
- par(mfrow = plot.layout) #AKS
- }
- else {
- use.windows = FALSE
- pdf(file=file.name,width = 11, height=8)
- par(mfrow = plot.layout) #AKS
- }
- } else use.windows = FALSE
-
- if (class(mars.glm.object) == "mars") { #then we have a mars object
- mars.binomial = FALSE
- model <- mars.glm.object
- xdat <- eval(model$call$x)
- Y <- as.data.frame(eval(model$call$y))
- n.env <- ncol(xdat)
- m.table <- mars.export(mars.glm.object)
- }
- else {
- mars.binomial = TRUE
-
- dat <- mars.glm.object$mars.call$dataframe
- mars.x <- mars.glm.object$mars.call$mars.x
- xdat <- as.data.frame(eval(parse(text=dat)))
- xdat <- xdat[,mars.x]
-
- m.table <- mars.glm.object[[1]]
-
- }
-
- n.bfs <- length(m.table[,1])
- n.spp <- length(m.table[1,]) - 10
- r.curves <- list(names=NULL,preds=list(),resp=list()) #aks
- spp.names <- names(m.table)[(10+1):(10+n.spp)]
-
- if (sp.no == 0) {
- wanted.species <- seq(1:n.spp)
- }
- else {
- wanted.species <- sp.no
- }
-
- xrange <- matrix(0,nrow = 2,ncol = ncol(xdat))
- factor.filter <- rep(FALSE,ncol(xdat))
- for (i in 1:ncol(xdat)) factor.filter[i] <- is.vector(xdat[,i])
-
- if(sum(factor.filter>1)) {
- xrange[,factor.filter] <- sapply(xdat[,factor.filter], range)
- } else xrange[,factor.filter]<-range(xdat[,factor.filter])
-
- for (i in wanted.species) {
- n.pages <- 1
- plotit <- rep(TRUE, n.bfs)
- print(paste("plotting responses for ",spp.names[i]),quote=F)
- nplots <- 0
- cntr <- 1 #aks
- for (j in 2:n.bfs) {
- if (m.table$names2[j] == "null") {
- if (plotit[j]) {
- varno <- pmatch(as.character(m.table$names1[j]),
- names(xdat))
- if (factor.filter[varno]) {
- Xi <- seq(xrange[1, varno], xrange[2, varno],
- length = 100)
- bf <- pmax(0, m.table$signs1[j] * (Xi - m.table$cuts1[j]))
- bf <- bf * m.table[j, i + 10]
- bf <- bf - mean(bf)
- }
- else {
- factor.table <- as.data.frame(table(xdat[,varno]))
- names(factor.table) <- c("levels","coefficients")
- factor.table$coefficients <- 0
- level.no <- match(m.table$levels1[j],factor.table$levels)
- factor.table$coefficients[level.no] <- m.table[j, i + 10]
- }
- if (j < n.bfs) {
- for (k in ((j + 1):n.bfs)) {
- if (m.table$names1[j] == m.table$names1[k] & m.table$names2[k] == "null") {
- if (factor.filter[varno]) {
- bf.add <- pmax(0, m.table$signs1[k] *
- (Xi - m.table$cuts1[k]))
- bf.add <- bf.add * m.table[k, i + 10]
- bf <- bf + bf.add
- }
- else {
- level.no <- match(m.table$levels1[k],factor.table$levels)
- factor.table$coefficients[level.no] <- m.table[k, i + 10]
- }
- plotit[k] <- FALSE
- }
- }
- }
- #if (nplots == 0) { #AKS
-# if (use.windows) windows(width = 11, height = 8)
-# par(mfrow = plot.layout)
-# }
- if (factor.filter[varno]) {
- if(plot.it) plot(Xi, bf, type = "l", xlab = names(xdat)[varno], ylab = "response") #aks
- if (plot.rug & plot.it) rug(quantile(xdat[,varno], probs = seq(0, 1, 0.1), na.rm = FALSE))
- r.curves$preds[[cntr]] <- Xi #aks
- r.curves$resp[[cntr]] <- bf #aks
- }
- else {
- if(plot.it) plot(factor.table$levels, factor.table$coefficients, xlab = names(xdat)[varno]) #aks
- r.curves$preds[[cntr]] <- factor.table$levels #aks
- r.curves$resp[[cntr]] <- factor.table$coefficients #aks
-
- }
- r.curves$names <- c(r.curves$names,names(xdat)[varno]) #aks
- cntr <- cntr + 1 #aks
- nplots = nplots + 1
- plotit[j] <- FALSE
- }
- }
- else { # case where there is an interaction #
- if (plotit[j]) {
- varno1 <- pmatch(as.character(m.table$names1[j]), names(xdat))
- X1 <- seq(xrange[1, varno1], xrange[2, varno1], length = 20)
- bf1 <- pmax(0, m.table$signs1[j] * (X1 - m.table$cuts1[j]))
- varno2 <- pmatch(as.character(m.table$names2[j]), names(xdat))
- X2 <- seq(xrange[1, varno2], xrange[2, varno2], length = 20)
- bf2 <- pmax(0, m.table$signs2[j] * (X2 - m.table$cuts2[j]))
- if(factor.filter[varno1] & factor.filter[varno2]){ #aks
- zmat <- bf1 %o% bf2
- zmat <- zmat * m.table[j, i + 10]
- if (j < n.bfs) {
- for (k in ((j + 1):n.bfs)) {
- if (m.table$names1[j] == m.table$names1[k] & m.table$names2[j] == m.table$names2[k]) {
- bf1 <- pmax(0, m.table$signs1[k] * (X1 - m.table$cuts1[k]))
- bf2 <- pmax(0, m.table$signs2[j] * (X2 - m.table$cuts2[j]))
- zmat2 <- bf1 %o% bf2
- zmat2 <- zmat2 * m.table[j, i + 10]
- zmat = zmat + zmat2
- plotit[k] <- FALSE
- }
- }
- }
- #if (nplots == 0) { #AKS
- # if (use.windows) windows(width = 11, height = 8)
- # par(mfrow = plot.layout)
- # }
- if(plot.it){
- persp(x = X1, y = X2, z = zmat, xlab = names(xdat)[varno1],
- ylab = names(xdat)[varno2], theta = 45, phi = 25) }
- r.curves$preds[[cntr]] <- X1 #aks
- r.curves$resp[[cntr]] <- apply(zmat,1,mean,na.rm=T) #aks
- nplots = nplots + 1
- } else {
- r.curves$preds[[cntr]] <- NA #aks
- r.curves$resp[[cntr]] <- NA #aks
-
- }
- r.curves$names <- c(r.curves$names,names(xdat)[varno]) #aks
- cntr <- cntr + 1 #aks
- }
- }
- if (nplots == 1 & plot.it) {
- title(paste(spp.names[i], " - page ", n.pages, sep = ""))
- }
- if (nplots == max.plots) {
- nplots = 0
- n.pages <- n.pages + 1
- }
- }
- }
- if (!use.windows & plot.it) dev.off()
- invisible(r.curves) #aks
-}
-
-"mars.plot.fits" <-
-function(mars.glm.object, # the input mars object
- sp.no = 0, # allows selection of individual spp for multiresponse models
- mask.presence = FALSE, # plots out just presence records
- use.factor = FALSE, # draws plots as factors for faster printing
- plot.layout = c(4,2), # the default plot layout
- file.name = NA) # allows plotting to a pdf file
-{
-#
-# j leathwick, j elith - August 2006
-#
-# version 3.1 - developed in R 2.3.1 using mda 0.3-1
-#
-# to plot distribution of fitted values in relation to ydat from mars or other p/a models
-# allows masking out of absences to enable focus on sites with high predicted values
-# fitted values = those from model; raw.values = original y values
-# label = text species name; ydat = predictor dataset
-# mask.presence forces function to only plot fitted values for presences
-# use.factor forces to use quicker printing box and whisker plot
-# file.name routes to a pdf file of this name
-#
-
- max.plots <- plot.layout[1] * plot.layout[2]
-
- if (is.na(file.name)) { #setup for windows or file output
- use.windows = TRUE
- }
- else {
- pdf(file.name, width=8, height = 11)
- par(mfrow = plot.layout)
- par(cex = 0.5)
- use.windows = FALSE
- }
-
- dat <- mars.glm.object$mars.call$dataframe #get the dataframe name
- dat <- as.data.frame(eval(parse(text=dat))) #and now the data
-
- n.cases <- nrow(dat)
-
- mars.call <- mars.glm.object$mars.call #and the mars call details
- mars.x <- mars.call$mars.x
- mars.y <- mars.call$mars.y
- family <- mars.call$family
-
- xdat <- as.data.frame(dat[,mars.x])
- ydat <- as.data.frame(dat[,mars.y])
-
- n.spp <- ncol(ydat)
- n.preds <- ncol(xdat)
-
- fitted.values <- mars.glm.object$fitted.values
-
- pred.names <- names(dat)[mars.x]
- spp.names <- names(dat)[mars.y]
-
- if (sp.no == 0) {
- wanted.species <- seq(1:n.spp)
- }
- else {
- wanted.species <- sp.no
- }
-
- for (i in wanted.species) {
-
- if (mask.presence) {
- mask <- ydat[,i] == 1 }
- else {
- mask <- rep(TRUE, length = n.cases)
- }
-
- robust.max.fit <- approx(ppoints(fitted.values[mask,i]), sort(fitted.values[mask,i]), 0.99) #find 99%ile value
- nplots <- 0
-
- for (j in 1:n.preds) {
- if (use.windows & nplots == 0) {
- windows(width = 8, height = 11)
- par(mfrow = plot.layout)
- par(cex = 0.5)
- }
- nplots <- nplots + 1
- if (is.vector(xdat[,j])) wt.mean <- mean((xdat[mask, j] * fitted.values[mask, i]^5)/mean(fitted.values[mask, i]^5))
- else wt.mean <- 0
- if (use.factor) {
- temp <- factor(cut(xdat[mask, j], breaks = 12))
- if (family == "binomial") {
- plot(temp, fitted.values[mask,i], xlab = pred.names[j], ylab = "fitted values", ylim = c(0, 1))
- }
- else {
- plot(temp, fitted.values[mask,i], xlab = pred.names[j], ylab = "fitted values")}
- }
- else {
- if (family == "binomial") {
- plot(xdat[mask, j], fitted.values[mask,i], xlab = pred.names[j], ylab = "fitted values",
- ylim = c(0, 1))
- }
- else {
- plot(xdat[mask, j], fitted.values[mask,i], xlab = pred.names[j], ylab = "fitted values")
- }
- }
- abline(h = (0.333 * robust.max.fit$y), lty = 2.)
- if (nplots == 1) {
- title(paste(spp.names[i], ", wtm = ", zapsmall(wt.mean, 4.)))}
- else {
- title(paste("wtm = ", zapsmall(wt.mean, 4.)))}
- nplots <- ifelse(nplots == max.plots, 0, nplots)
- }
- }
- if (!use.windows) dev.off()
-}
-
-"mars.predict" <-
-function (mars.glm.object,new.data)
-{
-#
-# j leathwick, j elith - August 2006
-#
-# version 3.1 - developed in R 2.3.1 using mda 0.3-1
-#
-# calculates a mars/glm object in which basis functions are calculated
-# using an initial mars model with single or multiple responses
-# data for individual species are then fitted as glms using the
-# common set of mars basis functions with results returned as a list
-#
-# takes as input a dataset and args selecting x and y variables, and degree of interaction
-# along with site and species weights, the CV penalty, and the glm family argument
-# the latter would normally be one of "binomial" or "poisson" - "gaussian" could be used
-# but in this case the model shouldn't differ from that fitted using mars on its own
-#
-# naming problem for dataframes fixed - je - 15/12/06
-#
-# requires mda and leathwick/elith's mars.export
-#
- require(mda)
-
-# first recreate both the original mars model and the glm model
-
-# setup input data and create original temporary data
-
- dataframe.name <- mars.glm.object$mars.call$dataframe # get the dataframe name
- mars.x <- mars.glm.object$mars.call$mars.x
- mars.y <- mars.glm.object$mars.call$mars.y
- n.spp <- length(mars.y)
- family <- mars.glm.object$mars.call$family
- mars.degree <- mars.glm.object$mars.call$degree
- penalty <- mars.glm.object$mars.call$penalty
- site.weights <- mars.glm.object$weights[[1]]
- spp.weights <- mars.glm.object$weights[[2]]
-
- print("creating original data frame...",quote=FALSE)
-
- base.data <- as.data.frame(eval.parent(parse(text = dataframe.name))) #aks
-
- x.temp <- eval(base.data[, mars.x]) #form the temporary datasets
- base.names <- names(x.temp)
-
- xdat <- mars.new.dataframe(x.temp)[[1]]
-
- ydat <- as.data.frame(base.data[, mars.y])
- names(ydat) <- names(base.data)[mars.y]
-
- assign("xdat", xdat, pos = 1) #and assign them for later use
- assign("ydat", ydat, pos = 1)
-
-# now create the temporary dataframe for the new data
-
- print("checking variable matching with new data",quote = FALSE)
-
- new.names <- names(new.data)
-
- for (i in 1:length(base.names)) {
-
- name <- base.names[i]
-
- if (!(name %in% new.names)) {
- print(paste("Variable ",name," missing from new data",sep=""),quote = FALSE) #aks
- return()
- }
- }
-
- print("and creating temporary dataframe for new data...",quote=FALSE)
-
- selector <- match(names(x.temp),names(new.data))
-
- pred.dat <- mars.new.dataframe(new.data[,selector])[[1]]
-
- assign("pred.dat", pred.dat, pos = 1) #and assign them for later use
-
-# fit the mars model and extract the basis functions
-
- print(paste("re-fitting initial mars model for",n.spp,"responses"),quote = FALSE)
- print(paste("using glm family of",family),quote = FALSE)
-
- #mars.fit <- mars(x = xdat, y = ydat, degree = mars.degree, w = site.weights,
- # wp = spp.weights, penalty = penalty)
-
- mars.fit <- mars.glm.object$mars.object #AKS
-
- old.bf.data <- as.data.frame(eval(mars.fit$x))
- n.bfs <- ncol(old.bf.data)
- bf.names <- paste("bf", 1:n.bfs, sep = "")
- old.bf.data <- as.data.frame(old.bf.data[,-1])
- names(old.bf.data) <- bf.names[-1]
-
- new.bf.data <- as.data.frame(mda:::model.matrix.mars(mars.fit,pred.dat))
- new.bf.data <- as.data.frame(new.bf.data[,-1])
- names(new.bf.data) <- bf.names[-1]
-
-# now cycle through the species fitting glm models
-
- print("fitting glms for individual responses", quote = F)
-
- prediction <- as.data.frame(matrix(0, ncol = n.spp, nrow = nrow(pred.dat)))
- names(prediction) <- names(ydat)
- standard.errors <- as.data.frame(matrix(0, ncol = n.spp, nrow = nrow(pred.dat)))
- names(standard.errors) <- names(ydat)
-
- for (i in 1:n.spp) {
-
- print(names(ydat)[i], quote = FALSE)
- model.glm <- glm(ydat[, i] ~ ., data = old.bf.data, weights = site.weights,
- family = family, maxit = 100)
- temp <- predict.glm(model.glm,new.bf.data,type="response",se.fit=TRUE)
- prediction[,i] <- temp[[1]]
- standard.errors[,i] <- temp[[2]]
-
- }
-
- return(list("prediction"=prediction,"ses"=standard.errors))
-}
-
-"roc" <-
-function (obsdat, preddat)
-{
-# code adapted from Ferrier, Pearce and Watson's code, by J.Elith
-#
-# see:
-# Hanley, J.A. & McNeil, B.J. (1982) The meaning and use of the area
-# under a Receiver Operating Characteristic (ROC) curve.
-# Radiology, 143, 29-36
-#
-# Pearce, J. & Ferrier, S. (2000) Evaluating the predictive performance
-# of habitat models developed using logistic regression.
-# Ecological Modelling, 133, 225-245.
-# this is the non-parametric calculation for area under the ROC curve,
-# using the fact that a MannWhitney U statistic is closely related to
-# the area
-#
- if (length(obsdat) != length(preddat))
- stop("obs and preds must be equal lengths")
- n.x <- length(obsdat[obsdat == 0])
- n.y <- length(obsdat[obsdat == 1])
- xy <- c(preddat[obsdat == 0], preddat[obsdat == 1])
- rnk <- rank(xy)
- wilc <- ((n.x * n.y) + ((n.x * (n.x + 1))/2) - sum(rnk[1:n.x]))/(n.x *
- n.y)
- return(round(wilc, 4))
-}
-
-
-
-#set defaults
-make.p.tif=T
-make.binary.tif=T
-mars.degree=1
-mars.penalty=2
-script.name="mars.r"
-opt.methods=2
-save.model=TRUE
-MESS=FALSE
-
-# Interpret command line argurments #
-# Make Function Call #
-Args <- commandArgs(trailingOnly=FALSE)
-
- for (i in 1:length(Args)){
- if(Args[i]=="-f") ScriptPath<-Args[i+1]
- }
-
- print(Args)
- for (arg in Args) {
- argSplit <- strsplit(arg, "=")
- argSplit[[1]][1]
- argSplit[[1]][2]
- if(argSplit[[1]][1]=="c") csv <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="o") output <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mpt") make.p.tif <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mbt") make.binary.tif <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="deg") mars.degree <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="pen") mars.penalty <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="om") opt.methods <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="savm") save.model <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mes") MESS <- argSplit[[1]][2]
- }
- print(csv)
- print(output)
- print(responseCol)
-
-ScriptPath<-dirname(ScriptPath)
-source(paste(ScriptPath,"LoadRequiredCode.r",sep="\\"))
-print(ScriptPath)
-
-make.p.tif<-as.logical(make.p.tif)
-make.binary.tif<-as.logical(make.binary.tif)
-save.model<-make.p.tif | make.binary.tif
-opt.methods<-as.numeric(opt.methods)
-MESS<-as.logical(MESS)
-
-fit.mars.fct(ma.name=csv,
- tif.dir=NULL,output.dir=output,
- response.col=responseCol,make.p.tif=make.p.tif,make.binary.tif=make.binary.tif,
- mars.degree=mars.degree,mars.penalty=mars.penalty,debug.mode=F,responseCurveForm="pdf",
- script.name="mars.r",save.model=save.model,opt.methods=as.numeric(opt.methods),MESS=MESS)
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_RF_pluggable.r b/contrib/sahm/pySAHM/Resources/R_Modules/FIT_RF_pluggable.r
deleted file mode 100644
index d6015cc..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/FIT_RF_pluggable.r
+++ /dev/null
@@ -1,649 +0,0 @@
-# A set of R functions for automated model fitting of random forest models to presence/absence data #
-#
-# Modified 12-2-09 to: remove categorical covariates from consideration if they only contain one level
-# ID factor variables based on "categorical" prefix and look for tifs in subdir
-# Give progress reports
-# write large output tif files in blocks to alleviate memory issues
-# various bug fixes
-#
-# Adapted from existing pluggable BRT and GLM modules in April 2009 by Alan Swanson
-
-
-# Libraries required to run this program #
-# PresenceAbsence - for ROC plots
-# XML - for XML i/o
-# rgdal - for geotiff i/o
-# RandomForest - duh
-# sp - used by rdgal library
-
-options(error=NULL)
-
-fit.rf.fct <- function(ma.name,tif.dir=NULL,output.dir=NULL,response.col="^response.binary",make.p.tif=T,make.binary.tif=T,
- debug.mode=F,responseCurveForm="pdf",xtest=NULL,ytest=NULL,n.trees=1000,mtry=NULL, samp.replace=FALSE, sampsize=NULL,nodesize=NULL,maxnodes=NULL,importance=FALSE,
- localImp=FALSE,nPerm=1,proximity=NULL,oob.prox=proximity,norm.votes=TRUE,do.trace=FALSE,keep.forest=NULL,keep.inbag=FALSE, make.r.curves=T,
- seed=NULL,script.name="rf.r",opt.methods=2,save.model=TRUE,UnitTest=FALSE,MESS=FALSE){
- # This function fits a boosted regression tree model to presence-absence data.
- # written by Alan Swanson, Jan-March 2009
- # uses code modified from that published in Elith et al 2008
- # # Maintained and edited by Marian Talbert September 2010-
- # Arguements.
- # ma.name: is the name of a .csv file with a model array. full path must be included unless it is in the current
- # R working directory #
- # tif.dir: is the directory containing geotiffs for each covariate. only required if geotiffs output of the
- # response surface is requested # # cov.list.name: is the name of a text file with the names of covariates to be included in models (one per line).
- # output.dir: is the directory that output files will be stored in. if not given, files will go to the current working directory.
- # response.col: column number of the model array containing a binary 0/1 response. all other columns will be considered explanatory variables.
- # make.p.tif: T if a geotiff of the response surface is desired.
- # make.binary.tif: T if a geotiff of the response surface is desired.
- # simp.method: model simplification method. valid methods include: "cross-validation", "rel-inf", and "none". "cross-validation" uses the
- # methods of Elith et al, 2008 for removing covariates that don't contribute to the model. "rel-inf" simply removes covariates that contribute
- # less than 1%. cross-validation is very slow - it can add up to 10min to a run.
- # debug.mode: if T, output is directed to the console during the run. also, a pdf is generated which contains response curve plots and perspective plots
- # showing the effects of interactions deemed important. if F, output is diverted to a text file and the console is kept clear
- # except for final output of an xml file. in either case, a set of standard output files are created in the output directory.
- # tc: tree-complexity for brt fits. if specified, this sets the tree-complexity of the final model fit. A lower tree-complexity will be used for
- # model selection steps. if not set, this will be estimated loosely following the guidelines given by Elith et al, 2008.
- #
-
- # Value:
- # returns nothing but generates a number of output files in the directory
- # "output.dir" named above. These output files consist of:
- #
- # brt_output.txt: a text file with fairly detailed results of the final model.
- # brt_output.xml: an xml-formatted text file with results from the final model.
- # brt_response_curves.xml: an xml-formatted text file with response curves for
- # each covariate in the final model.
- # brt_prob_map.tif: a geotiff of the response surface
- # brt_bin_map.tif: a geotiff of the binary response surface. threhold is based on the roc curve at the point where sensitivity=specificity.
- # brt_log.txt: a file containing text output diverted from the console when debug.mode=F
- # brt_auc_plot.jpg: a jpg file of a ROC plot.
- # brt_response_curves.pdf: an pdf file with response curves for
- # each covariate in the final model and perspective plots showing the effect of interactions deemed significant.
- # only produced when debug.mode=T
- # seed=NULL # sets a seed for the algorithm, any inegeger is acceptable
- # opt.methods=2 # sets the method used for threshold optimization used in the
- # # the evaluation statistics module
- # save.model=FALSE # whether the model will be used to later produce tifs
- #
- # when debug.mode is true, these filenames will include a number in them so that they will not overwrite preexisting files. eg brt_1_output.txt.
- #
- times <- as.data.frame(matrix(NA,nrow=8,ncol=1,dimnames=list(c("start","read data","model tuning","model fit",
- "model summary","response curves","tif output","done"),c("time"))))
- times[1,1] <- unclass(Sys.time())
- t0 <- unclass(Sys.time())
- #simp.method <- match.arg(simp.method)
- out <- list(
- input=list(ma.name=ma.name,
- tif.dir=tif.dir,
- output.dir=output.dir,
- response.col=response.col,
- save.model=save.model,
- xtest=xtest,
- ytest=ytest,
- n.trees=n.trees,
- mtry=mtry,
- samp.replace=samp.replace,
- sampsize=sampsize,
- nodesize=nodesize,
- maxnodes=maxnodes,
- importance=importance,
- localImp=localImp,
- nPerm=nPerm,
- proximity=proximity,
- oob.prox=oob.prox,
- norm.votes=norm.votes,
- do.trace=do.trace,
- keep.forest=keep.forest,
- keep.inbag=keep.inbag,
- make.p.tif=make.p.tif,
- make.binary.tif=make.binary.tif,
- model.type="random forest regression tree",
- model.source.file=script.name,
- model.fitting.subset=c(n.pres=50,n.abs=50),#subset used for response curves
- run.time=paste(c(format(Sys.time(),"%Y-%m-%d"),format(Sys.time(),"%H:%M:%S")),collapse="T"),
- sig.test="mean decrease in accuracy",
- MESS=MESS),
- dat = list(missing.libs=NULL,
- output.dir=list(dname=NULL,exist=F,readable=F,writable=F),
- tif.dir=list(dname=NULL,exist=F,readable=F,writable=F),
- tif.ind=NULL,
- tif.names=NULL,
- bname=NULL,
- bad.factor.covs=NULL, # factorchange
- ma=list( status=c(exists=F,readable=F),
- dims=c(NA,NA),
- n.pres=c(all=NA,complete=NA,subset=NA),
- n.abs=c(all=NA,complete=NA,subset=NA),
- ratio=NA,
- resp.name=NULL,
- factor.levels=NULL,
- used.covs=NULL,
- ma=NULL,
- ma.subset=NULL,
- train.xy=NULL,
- test.xy=NULL,
- site.weights=NULL),
- ma.test=NULL),
- mods=list(parms=list(n.trees=n.trees,mtry=NULL),
- full.mod=NULL,
- simp.mod=NULL,
- final.mod=NULL,
- r.curves=NULL,
- tif.output=list(prob=NULL,bin=NULL),
- auc.output=NULL,
- interactions=NULL,
- summary=NULL),
- time=list(strt=unclass(Sys.time()),end=NULL),
- error.mssg=list(NULL),
- ec=0
- )
-
- if(!is.null(seed)) set.seed(seed)
- #if(simplify.brt==T) out$input$simp.method<-"cross-validation" else out$input$simp.method<-">1% rel. influence"
- # load libaries #
- out <- check.libs(list("randomForest","PresenceAbsence","rgdal","XML","sp","raster","tcltk2","foreign","ade4"),out)
-
- # exit program now if there are missing libraries #
- if(!is.null(out$error.mssg[[1]])){
- cat(saveXML(rf.to.xml(out),indent=T),'\n')
- return()
- }
-
- # check output dir #
- out$dat$output.dir <- check.dir(output.dir)
- if(out$dat$output.dir$writable==F) {out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: output directory",output.dir,"is not writable")
- out$dat$output.dir$dname <- getwd()
-
- }
-
- # generate a filename for output #
- if(debug.mode==T){
- outfile <- paste(bname<-paste(out$dat$output.dir$dname,"/rf_",n<-1,sep=""),"_output.txt",sep="")
- while(file.access(outfile)==0) outfile<-paste(bname<-paste(out$dat$output.dir$dname,"/rf_",n<-n+1,sep=""),"_output.txt",sep="")
- capture.output(cat("temp"),file=outfile) # reserve the new basename #
- } else bname <- paste(out$dat$output.dir$dname,"/rf",sep="")
- out$dat$bname <- bname
-
- # sink console output to log file #
- if(!debug.mode) {sink(logname <- paste(bname,"_log.txt",sep=""));on.exit(sink)} else logname<-NULL
- #options(warn=1)
-
- # check tif dir #
- # check tif dir #
- if(!is.null(tif.dir)){
- out$dat$tif.dir <- check.dir(tif.dir)
- if(out$dat$tif.dir$readable==F & (out$input$make.binary.tif | out$input$make.p.tif)) {
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: tif directory",tif.dir,"is not readable")
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- cat(saveXML(brt.to.xml(out),indent=T),'\n')
- return()
- }
- }
-
-
- # find .tif files in tif dir #
- if(out$dat$tif.dir$readable) out$dat$tif.names <- list.files(out$dat$tif.dir$dname,pattern=".tif",recursive=T)
-
- # check for model array #
- out$input$ma.name <- check.dir(out$input$ma.name)$dname
- if(UnitTest!=FALSE) options(warn=2)
- out <- read.ma(out)
- if(UnitTest==1) return(out)
- # exit program now if there are errors in the input data #
- if(!is.null(out$error.mssg[[1]])){
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- cat(saveXML(rf.to.xml(out),indent=T),'\n')
- return()
- }
- t1 <- unclass(Sys.time())
- cat("\ndone processing data, t=",round(t1-t0,1),"sec\n")
- cat("\nbegin processing of model array:",out$input$ma.name,"\n")
- cat("\nfile basename set to:",out$dat$bname,"\n")
- if(debug.mode) flush.console()
-
- if(!debug.mode) {sink();cat("Progress:20%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("20%\n")} ### print time
-
- ##############################################################################################################
- # Begin model fitting #
- ##############################################################################################################
-
-
- # tune the mtry parameter - this controls the number of covariates randomly subset for each split #
- cat("\ntuning mtry parameter\n")
-
- x=out$dat$ma$ma[,-1]
- y=factor(out$dat$ma$ma[,1])
- if(is.null(mtry)){
- mtry <- try(tuneRF(x=out$dat$ma$ma[,-1],y=factor(out$dat$ma$ma[,1]),mtryStart=3,importance=TRUE,ntreeTry=100,
- replace=FALSE, doBest=F, plot=F),silent=T)
- mtry <- try(mtry[mtry[,2]==min(mtry[,2]),1][1])
- t2 <- unclass(Sys.time())
- if(!debug.mode) {sink();cat("Progress:30%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("30%\n")}
-
- cat("\ndone tuning random forest parameters, t=",round(t2-t1,1),"sec\n")
- }
-
- cat("\nnow fitting full random forest model using mtry=",mtry,"\n")
- if(debug.mode) flush.console()
-
- rf.full <- randomForest(x=out$dat$ma$ma[,-1],y=factor(out$dat$ma$ma[,1]),xtest=xtest,ytest=ytest,importance=TRUE, ntree=n.trees,
- mtry=mtry,replace=samp.replace,sampsize=ifelse(is.null(sampsize),(ifelse(samp.replace,nrow(x),ceiling(.632*nrow(x)))),sampsize),
- nodesize=ifelse(is.null(nodesize),(if (!is.null(y) && !is.factor(y)) 5 else 1),nodesize),maxnodes=maxnodes,
- localImp=localImp, nPerm=nPerm, keep.forest=ifelse(is.null(keep.forest),!is.null(y) && is.null(xtest),keep.forest),
- corr.bias=corr.bias, keep.inbag=keep.inbag)
-
- out$mods$parms$mtry<-mtry
- out$mods$final.mod <- rf.full
-
- t3 <- unclass(Sys.time())
- if(!debug.mode) {sink();cat("Progress:40%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("40%\n")} ### print time
-
- cat("\nfinished fitting full model, t=",round(t2-t1,1),"sec\nnow computing output stats...\n")
- if(debug.mode) flush.console()
-
- ##############################################################################################################
- # Begin model output #
- ##############################################################################################################
-
- # ROC plot #
-
- model.summary <- try(importance(out$mods$final.mod),silent=T)
- if(class(model.summary)=="try-error"){
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: can't generate summary of final model:",model.summary)
- cat(saveXML(rf.to.xml(out),indent=T),'\n')
- return()
- } else {
- model.summary<-model.summary[order(model.summary[,3],decreasing=T),]
- out$mods$summary <- model.summary
- }
-
- txt0 <- paste("Random Forest Modeling Results\n",out$input$run.time,"\n\n",
- "Data:\n\t",ma.name,
- "\n\tn(pres)=",out$dat$ma$n.pres[2],
- "\n\tn(abs)=",out$dat$ma$n.abs[2],
- "\n\tn covariates considered=",length(out$dat$ma$used.covs),
- "\n\n","Settings:",
- "\n\tn covariates considered at each split =",out$mods$parms$mtry,
- "\n\tn trees=",out$mods$parms$n.tree,
- "\n\ttotal time for model fitting=",round((unclass(Sys.time())-t0)/60,2),"min\n",sep="")
- txt1 <- "\nRelative performance of predictors in final model:\n\n"
- txt2 <- "\nDefault summary of random forest fit:\n"
- capture.output(cat(txt0),cat(txt1),print(round(model.summary,4)),cat(txt2),print(out$mods$final.mod),file=paste(bname,"_output.txt",sep=""))
- cat(txt0);cat(txt1);print(round(model.summary,4));cat(txt2);print(out$mods$final.mod);cat("\n\n")
- if(!is.null(out$dat$bad.factor.cols)){
- capture.output(cat("\nWarning: the following categorical response variables were removed from consideration\n",
- "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n"),
- file=paste(bname,"_output.txt",sep=""),append=T)
- cat("\nWarning: the following categorical response variables were removed from consideration\n",
- "because they had only one level:",paste(out$dat$bad.factor.cols,collapse=","),"\n\n")
- }
-
- auc.output <- make.auc.plot.jpg(out$dat$ma$ma,pred=tweak.p(as.vector(predict(out$mods$final.mod,type="prob")[,2])),
- plotname=paste(bname,"_auc_plot.jpg",sep=""),modelname="RF",opt.methods=opt.methods,weight=rep(1,times=dim(out$dat$ma$ma)[1]),out=out)
-
- if(class(auc.output)=="try-error"){
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("Error making ROC plot:",auc.output)
- } else { out$mods$auc.output<-auc.output}
-
-
- #assign("out",out,envir=.GlobalEnv)
-
- # Text summary #
-
-
- if(!debug.mode) {sink();cat("Progress:70%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("60%\n")} ### print time
-
- if(debug.mode) flush.console()
-
- # Response curves #
- t4 <- unclass(Sys.time())
- if(make.r.curves){
-
- r.curves <- list(names=row.names(out$mods$summary),preds=list(),resp=list())
- inc <- 10/length(r.curves$names)
- assign("r.curves",r.curves,envir=.GlobalEnv)
-
- if(is.null(responseCurveForm)){
- responseCurveForm<-0}
-
- if(debug.mode | responseCurveForm=="pdf"){
- nvar <- nrow(out$mods$summary)
- pcol <- min(ceiling(sqrt(nvar)),4)
- prow <- min(ceiling(nvar/pcol),3)
- pdf(paste(bname,"_response_curves.pdf",sep=""),width=11,height=8.5,onefile=T)
- par(oma=c(2,2,4,2),mfrow=c(prow,pcol))
- }
- for(i in 1:length(r.curves$names)){
- assign("i",i,envir=.GlobalEnv)
-
- x<-try(partialPlot(out$mods$final.mod,out$dat$ma$ma.subset,r.curves$names[i],n.pt=50,plot=T,main="",
- xlab=r.curves$names[i]))
- if(class(x)=="try-error"){
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))} else graphics.off()
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("ERROR: can't generate response curves:",x)
- cat(saveXML(rf.to.xml(out),indent=T),'\n')
- return()
- } else {
- r.curves$preds[[i]] <- x$x
- r.curves$resp[[i]] <- x$y
- }
- if(!debug.mode) {sink();cat(paste("Progress:",round(70+i*inc,1),"%\n",sep=""));flush.console();sink(logname,append=T)} else {cat("\n");cat(paste(round(70+i*inc,1),"%\n",sep=""))} ### print time
- }
- if(debug.mode) graphics.off()
- out$mods$r.curves <- r.curves
- }
-
- t5 <- unclass(Sys.time())
- #if(!debug.mode) {sink();cat("80%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("80%\n")} ### print time
- cat("\nfinished with response curves, t=",round(t5-t4,2),"sec\n")
- if(debug.mode) flush.console()
-
- # Make .tif of predictions #
- out$mods$final.mod$contributions$var<-as.character(row.names(out$mods$summary))
-
- assign("out",out,envir=.GlobalEnv)
- save.image(paste(output.dir,"modelWorkspace",sep="\\"))
- if(out$input$make.p.tif==T | out$input$make.binary.tif==T){
- cat("\nproducing prediction maps...","\n","\n");flush.console()
- mssg <- try(proc.tiff(model=out$mods$final.mod,vnames=as.character(row.names(out$mods$summary)),
- tif.dir=out$dat$tif.dir$dname,filenames=out$dat$tif.ind,pred.fct=rf.predict,factor.levels=out$dat$ma$factor.levels,make.binary.tif=make.binary.tif,
- thresh=out$mods$auc.output$thresh,make.p.tif=make.p.tif,outfile.p=paste(out$dat$bname,"_prob_map.tif",sep=""),
- outfile.bin=paste(out$dat$bname,"_bin_map.tif",sep=""),tsize=50.0,NAval=-3000,fnames=out$dat$tif.names,logname=logname,out=out),silent=T) #"brt.prob.map.tif"
-
- if(class(mssg)=="try-error" | mssg!=0){
- if(!debug.mode) {sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))}
- out$ec<-out$ec+1
- out$error.mssg[[out$ec]] <- paste("Error producing prediction maps:",mssg)
- cat(saveXML(rf.to.xml(out),indent=T),'\n')
- return()
- } else {
- if(make.p.tif) out$mods$tif.output$prob <- paste(out$dat$bname,"_prob_map.tif",sep="")
- if(make.binary.tif) out$mods$tif.output$bin <- paste(out$dat$bname,"_bin_map.tif",sep="")
- t5 <- unclass(Sys.time())
- cat("\nfinished with prediction maps, t=",round(t5-t4,2),"sec\n");flush.console()
- }
- }
- if(!debug.mode) {sink();cat("Progress:90%\n");flush.console();sink(logname,append=T)} else {cat("\n");cat("90%\n")} ### print time
-
- # Evaluation Statistics on Test Data#
-
- if(!is.null(out$dat$ma$ma.test)) Eval.Stat<-EvaluationStats(out,thresh=auc.output$thresh,train=out$dat$ma$ma,
- train.pred=tweak.p(as.vector(predict(out$mods$final.mod,type="prob")[,2])),opt.methods)
-
-
-
-
- # Write summaries to xml #
- assign("out",out,envir=.GlobalEnv)
- doc <- rf.to.xml(out)
-
- cat(paste("\ntotal time=",round((unclass(Sys.time())-t0)/60,2),"min\n\n\n",sep=""))
- if(!debug.mode) {
- sink();on.exit();unlink(paste(bname,"_log.txt",sep=""))
- cat("Progress:100%\n");flush.console()
- cat(saveXML(doc,indent=T),'\n')
- }
- capture.output(cat(saveXML(doc,indent=T)),file=paste(out$dat$bname,"_output.xml",sep=""))
- assign("fit",out$mods$final.mod,envir=.GlobalEnv)
- invisible(out)
-}
-
-rf.predict <- function(model,x) {
- # retrieve key items from the global environment #
- # make predictions from complete data only #
- y <- rep(NA,nrow(x))
- y[complete.cases(x)] <- as.vector(predict(model,newdata=x[complete.cases(x),],type="prob")[,2])
-
- # make predictions from full data #
-
- # encode missing values as -1.
- y[is.na(y)]<- NaN
-
- # return predictions.
- return(y)
- }
-
-logit <- function(x) 1/(1+exp(-x))
-
-file_path_as_absolute <- function (x){
- if (!file.exists(epath <- path.expand(x)))
- stop(gettextf("file '%s' does not exist", x), domain = NA)
- cwd <- getwd()
- on.exit(setwd(cwd))
- if (file_test("-d", epath)) {
- setwd(epath)
- getwd()
- }
- else {
- setwd(dirname(epath))
- file.path(getwd(), basename(epath))
- }
-}
-#file_path_as_absolute(".")
-
-rf.to.xml <- function(out){
- require(XML)
- schema.http="http://www.w3.org/2001/XMLSchema-instance"
- schema.fname="file:/Users/isfs2/Desktop/Source/2008-04-09/src/gov/nasa/gsfc/quickmap/ModelBuilder/modelRun_output_v2.xsd"
- xml.out <- newXMLDoc()
- mr <- newXMLNode("modelRunOutput",doc=xml.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))#,parent=xml.out
- sm <- newXMLNode("singleModel",parent=mr)
- bg <- newXMLNode("background",parent=sm)
- newXMLNode("mdsName",out$input$ma.name,parent=bg)
- newXMLNode("runDate",out$input$run.time,parent=bg)
- lc <- newXMLNode("layersConsidered",parent=bg)#, parent = xml.out)
- kids <- lapply(paste(out$dat$tif.dir$dname,"/",out$dat$tif.names,sep=""),function(x) newXMLNode("layer", x))
- addChildren(lc, kids)
- mo <- newXMLNode("modelOutput",parent=sm)
- newXMLNode("modelType",out$input$model.type,parent=mo)
- newXMLNode("modelSourceFile",out$input$model.source.file,parent=mo)
- newXMLNode("devianceExplained",out$mods$auc.output$pct_dev_exp,parent=mo,attrs=list(type="percentage"))
- newXMLNode("nativeOutput",paste(out$dat$bname,"_output.txt",sep=""),parent=mo)
- newXMLNode("binaryOutputFile",out$mods$tif.output[[2]],parent=mo)
- newXMLNode("probOutputFile",out$mods$tif.output[[1]],parent=mo)
- newXMLNode("auc",out$mods$auc.output$auc,parent=mo)
- newXMLNode("rocGraphic",out$mods$auc.output$plotname,parent=mo)
- newXMLNode("rocThresh",out$mods$auc.output$thresh,parent=mo)
- newXMLNode("modelDeviance",out$mods$auc.output$dev_fit,parent=mo)
- newXMLNode("nullDeviance",out$mods$auc.output$null_dev,parent=mo)
- if(is.null(out$mods$r.curves)) rc.name <- NULL else rc.name <- paste(out$dat$bname,"_response_curves.xml",sep="")
- newXMLNode("responsePlotsFile",rc.name,parent=mo)
- newXMLNode("significanceDescription",out$input$sig.test,parent=mo)
- mfp <- newXMLNode("modelFitParmas",parent=mo)
- newXMLNode("nTrees",out$mods$parms$n.tree,parent=mfp)
- newXMLNode("mTry",out$mods$parms$mtry,parent=mfp)
-
- sv <- newXMLNode("significantVariables",parent=mo)
- if(!is.null(out$mods$summary)) {
- t.table <- data.frame(significanceMeasurement=out$mods$summary[,3],row.names=row.names(out$mods$summary))
- for(i in 1:nrow(t.table)){
- x <- newXMLNode("sigVar",parent=sv)
- newXMLNode(name="name", row.names(t.table)[i],parent=x)
- kids <- lapply(1:ncol(t.table),function(j) newXMLNode(name=names(t.table)[j], t.table[i,j]))
- addChildren(x, kids)
- }
- }
- if(!is.null(out$mods$r.curves)){
- r.curves <- out$mods$r.curves
- rc.out <- newXMLDoc()
- root <- newXMLNode("responseCurves",doc=rc.out,namespaceDefinitions=c(xsi=schema.http,noNamespaceSchemaLocation=schema.fname))
- for(i in 1:length(r.curves$names)){
- vartype <- ifelse(class(r.curves$preds[[i]])=="character","factor","continuous")
- x <- newXMLNode("responseCurve",attrs=list(covariate=r.curves$names[i],type=vartype),parent=root)
- kids <- lapply(1:length(r.curves$preds[[i]]),function(j){
- newXMLNode(name="responsePt",parent=x,.children=list(
- newXMLNode(name="explanatory",r.curves$preds[[i]][j]),
- newXMLNode(name="response",r.curves$resp[[i]][j])))})
- addChildren(x, kids)
- }
- saveXML(rc.out,rc.name,indent=T)
- }
- if(!is.null(out$error.mssg[[1]])) {
- kids <- lapply(out$error.mssg,function(j) newXMLNode(name="error",j))
- addChildren(mo,kids)
- }
- return(xml.out)
- }
-
-
-get.cov.names <- function(model){
- return(attr(terms(formula(model)),"term.labels"))
- }
-
-check.dir <- function(dname){
- if(is.null(dname)) dname <- getwd()
- dname <- gsub("[\\]","/",dname)
- end.char <- substr(dname,nchar(dname),nchar(dname))
- if(end.char == "/") dname <- substr(dname,1,nchar(dname)-1)
- exist <- suppressWarnings(as.numeric(file.access(dname,mode=0))==0) # -1 if bad, 0 if ok #
- if(exist) dname <- file_path_as_absolute(dname)
- readable <- suppressWarnings(as.numeric(file.access(dname,mode=4))==0) # -1 if bad, 0 if ok #
- writable <- suppressWarnings(as.numeric(file.access(dname,mode=2))==0) # -1 if bad, 0 if ok #
- return(list(dname=dname,exist=exist,readable=readable,writable=writable))
- }
-
-
-get.image.info <- function(image.names){
- # this function creates a data.frame with summary image info for a set of images #
- require(rgdal)
- n.images <- length(image.names)
-
- full.names <- image.names
- out <- data.frame(image=full.names,available=rep(F,n.images),size=rep(NA,n.images),
- type=factor(rep("unk",n.images),levels=c("asc","envi","tif","unk")))
- out$type[grep(".tif",image.names)]<-"tif"
- out$type[grep(".asc",image.names)]<-"asc"
- for(i in 1:n.images){
- if(out$type[i]=="tif"){
- x <-try(GDAL.open(full.names[1],read.only=T),silent=T)
- suppressMessages(try(GDAL.close(x),silent=T))
- if(class(x)!="try-error") out$available[i]<-T
- x<-try(file.info(full.names[i]))
- } else {
- x<-try(file.info(full.names[i]))
- if(!is.na(x$size)) out$available[i]<-T
- }
- if(out$available[i]==T){
- out$size[i]<-x$size
- if(out$type[i]=="unk"){
- # if extension not known, look for envi .hdr file in same directory #
- if(file.access(paste(file_path_sans_ext(full.names[i]),".hdr",sep=""))==0)
- out$type[i]<-"envi"
- }
- }
- }
- return(out)
-}
-
-tweak.p <- function(p){
- p[p==1]<-max(p[p<1])
- p[p==0]<-min(p[p>0])
- return(p)
- }
-
-
-#
-
- # Interpret command line argurments #
-# Make Function Call #
-#Set defaults for optional commands
-make.p.tif=T
-make.binary.tif=T
-responseCurveForm="pdf"
-xtest=NULL
-ytest=NULL
-n.trees=1000
-mtry=NULL
-samp.replace=FALSE
-sampsize=NULL
-nodesize=NULL
-maxnodes=NULL
-importance=FALSE
-localImp=FALSE
-nPerm=1
-proximity=NULL
-oob.prox=proximity
-norm.votes=TRUE
-do.trace=FALSE
-keep.forest=NULL
-keep.inbag=FALSE
-make.r.curves=T
-seed=NULL
-opt.methods=2
-save.model=TRUE
-seed=NULL
-MESS=FALSE
-
-Args <- commandArgs(trailingOnly=FALSE)
-
- for (i in 1:length(Args)){
- if(Args[i]=="-f") ScriptPath<-Args[i+1]
- }
-
- for (arg in Args) {
- argSplit <- strsplit(arg, "=")
- argSplit[[1]][1]
- argSplit[[1]][2]
- if(argSplit[[1]][1]=="c") csv <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="o") output <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mpt") make.p.tif <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mbt") make.binary.tif <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="xtst") xtest <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="ytst") ytest <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="ntree") n.trees <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mtry") mtry <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="sampR") samp.replace <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="sampS") sampsize <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="nodeS") nodesize <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="maxN") maxnodes <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="impt") importance <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="locImp") localImp <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="nPerm") nPerm <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="prox") proximity <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="oopp") oop.prox <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="NVot") norm.votes <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="Trce") do.trace <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="kf") keep.forest <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="Kbag") keep.inbag <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="curves") make.r.curves <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="om") opt.methods <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="savm") save.model <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="mes") MESS <- argSplit[[1]][2]
-
- }
- print(csv)
- print(output)
- print(responseCol)
-
-make.p.tif<-as.logical(make.p.tif)
-make.binary.tif<-as.logical(make.binary.tif)
-samp.replace<-as.logical(samp.replace)
-importance<-as.logical(importance)
-localImp<-as.logical(localImp)
-norm.votes<-as.logical(norm.votes)
-do.trace<-as.logical(do.trace)
-keep.inbag<-as.logical(keep.inbag)
-make.r.curves<-as.logical(make.r.curves)
-save.model<-make.p.tif | make.binary.tif
-n.trees<-as.numeric(n.trees)
-opt.methods<-as.numeric(opt.methods)
-ScriptPath<-dirname(ScriptPath)
-MESS<-as.logical(MESS)
-
-source(paste(ScriptPath,"LoadRequiredCode.r",sep="\\"))
-
-fit.rf.fct(ma.name=csv,tif.dir=NULL,output.dir=output,response.col=responseCol,make.p.tif=make.p.tif,make.binary.tif=make.binary.tif,
- debug.mode=F,responseCurveForm="pdf",xtest=xtest,ytest=ytest,n.trees=n.trees,mtry=mtry,samp.replace=samp.replace, sampsize=sampsize,
- nodesize=nodesize,maxnodes=maxnodes,importance=importance,
- localImp=localImp,nPerm=nPerm,proximity=proximity,oob.prox=oob.prox,norm.votes=norm.votes,do.trace=do.trace,keep.forest=keep.forest,
- keep.inbag=keep.inbag,make.r.curves=make.r.curves,
- seed=seed,script.name="rf.r",opt.methods=opt.methods,save.model=save.model,MESS=MESS)
-
-
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/FunctionCall.r b/contrib/sahm/pySAHM/Resources/R_Modules/FunctionCall.r
deleted file mode 100644
index 4787464..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/FunctionCall.r
+++ /dev/null
@@ -1,87 +0,0 @@
-setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
-source("FIT_BRT_pluggable.r")
-source("FIT_MARS_pluggable.r")
-source("FIT_RF_pluggable.r")
-source("FIT_GLM_pluggable.r")
-
-source("EvaluationStats.r")
-source("TestTrainRocPlot.r")
-source("PredictModel.r")
-source("read.ma.r")
-source("proc.tiff.r")
-
-# Curr
-#trace(proc.tiff,browser)
-#options(error=expression(if(interactive()) recover() else dump.calls()))
-#options(error=NULL)
-
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
- rc="ResponseBinary"
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
- fit.brt.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=F,make.binary.tif=F,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL,opt.methods=1,seed=1,save.model=TRUE)
-
-PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-
-#Now testing to make sure this code works with no test training split
-ma.name<-"H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\ModelOutputCheck\\NewInput.csv"
-ma.name="C:\\VisTrails\\mtalbert_20110406T093111\\sahm4h5b1t.mds"
-
-ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv"
-fit.brt.fct(ma.name=ma.name,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
-
-
-#this is the GLM_pluggable1.r under NewMDSBuilder (Works with new vistrails format)
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110510T100421\\TestTrainingSplit_1.csv"
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
-rc="responseCount"
-
- fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col=rc,make.p.tif=T,make.binary.tif=T,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
-
-
-#Mars check Works with new vistrails format
- fit.mars.fct(ma.name=ma.name,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
-
-
-fit.rf.fct(ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv",
- tif.dir=NULL,
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- debug.mode=T,n.trees=1000,ma.test=NULL,make.r.curves=T,script.name="glm.r")
-
-
-
-#this one does not subset paths set up in the old way works with old sahm as well as for
-fit.brt.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
-tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
-response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,ma.test=NULL,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
-
-
-fit.mars.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
- tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
-
-fit.glm.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
- tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",ma.test=NULL,script.name="glm.r")
-
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/LoadRequiredCode.r b/contrib/sahm/pySAHM/Resources/R_Modules/LoadRequiredCode.r
deleted file mode 100644
index 9518b44..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/LoadRequiredCode.r
+++ /dev/null
@@ -1,16 +0,0 @@
-#source(paste(ScriptPath,"EvaluationStats.r",sep="\\"))
-source(paste(ScriptPath,"TestTrainRocPlot.r",sep="\\"))
-source(paste(ScriptPath,"read.ma.r",sep="\\"))
-source(paste(ScriptPath,"proc.tiff.r",sep="\\"))
-source(paste(ScriptPath,"check.libs.r",sep="\\"))
-source(paste(ScriptPath,"modalDialog.r",sep="\\"))
-#replace EvaluationStats with
-source(paste(ScriptPath,"make.auc.r",sep="\\"))
-#source(paste(ScriptPath,"make.poisson.plot.r",sep="\\"))
-#source(paste(ScriptPath,"make.auc.plot.r",sep="\\"))
-source(paste(ScriptPath,"EvalStats.r",sep="\\"))
-source(paste(ScriptPath,"EvalStatsHelperFcts.r",sep="\\"))
-source(paste(ScriptPath,"AppendOut.r",sep="\\"))
-source(paste(ScriptPath,"ResidualImage.r",sep="\\"))
-source(paste(ScriptPath,"Pred.Surface.r",sep="\\"))
-#Fit.Mars
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore.r b/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore.r
deleted file mode 100644
index 92b945b..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore.r
+++ /dev/null
@@ -1,435 +0,0 @@
-Pairs.Explore<-function(num.plots=5,min.cor=.7,input.file,output.file,response.col="ResponseBinary",cors.w.highest=FALSE,pres=TRUE,absn=TRUE,bgd=TRUE,Debug=FALSE){
-
-
- #num.plots=plots per page of display
- #min.cor=the minimum correlation to be included in determining which set of predictors to display
- #input.file=a csv assumed to have the new vistrails form with the first several rows specifiying where to find tiffs
- # and which columns to include in analysis
- #output.file=...
- #response.col=name of response column to be removed and used elsewhere
- #modifications
- #5/10/2011 altered to handle count data as well presence absence.
- #any counts higher than or equal to 1 are set to be presence though I might consider
- #adding the option to have a threshold set instead of using just presence/absence
-
-
- absn<-as.logical(absn)
- pres<-as.logical(pres)
- bgd<-as.logical(bgd)
- cors.w.highest<-as.logical(cors.w.highest)
-
- #Read input data and remove any columns to be excluded
- dat<-read.csv(input.file,skip=3,header=FALSE)
-
- hl<-readLines(input.file,1)
- hl=strsplit(hl,',')
- colnames(dat) = hl[[1]]
-
- tif.info<-readLines(input.file,3)
- tif.info<-strsplit(tif.info,',')
- include<-(as.numeric(tif.info[[2]]))
-
- #Remove coordinates, response column, site.weights
- #before exploring predictor relationship
- rm.cols <- as.vector(na.omit(c(match("x",tolower(names(dat))),match("y",tolower(names(dat))),
- match("site.weights",tolower(names(dat))),match(tolower(response.col),tolower(names(dat))),match("Split",names(dat)))))
-
- #remove testing split
- if(!is.na(match("Split",names(dat)))) dat<-dat[-c(which(dat$Split=="test"),arr.ind=TRUE),]
-
- include[is.na(include)]<-0
- rm.cols<-unique(c(rm.cols,which(include==0,arr.ind=TRUE)))
- response<-dat[,match(tolower(response.col),tolower(names(dat)))]
-
- dat<-dat[order(response),]
- response<-response[order(response)]
-
- #for the purpose of the pairs plot, taking all counts greater than 1 and setting them equal to presence
- #this is never exported
- if(response.col=="responseCount") {response[response>=1]<-1
- }
-
- #remove any of pres absn or bgd that aren't desired
- temp<-c(0,1,-9999)
- temp<-temp[c(absn,pres,bgd)]
- dat<-dat[response%in%temp,]
- response<-response[response%in%temp]
-
-
- if(sum(response==-9999)>1000){
- s<-sample(which(response==-9999,arr.ind=TRUE),size=(sum(response==-9999)-1000))
- dat<-dat[-c(s),]
- response<-response[-c(s)]
- }
-
- if (response.col=="responseCount") {
- TrueResponse<-dat[,match(tolower(response.col),tolower(names(dat)))]
- } else TrueResponse<-response
-
- #now remove all columns except predictors
- dat<-dat[-rm.cols]
- dat[dat==-9999]<-NA
- response<-response[complete.cases(dat)]
- TrueResponse<-TrueResponse[complete.cases(dat)]
- dat<-dat[complete.cases(dat),]
-
-
- #dat<-dat[1:2000,]
- #Remove columns with only one unique value
- varr <- function(x) var(x,na.rm=TRUE)
-
- dat<-try(dat[,as.vector(apply(dat,2,varr)==0)!=1],silent=TRUE)
- if(class(dat)=="try-error") stop("mds file contains nonnumeric columns please remove and continue")
- #record correlations for later plots
-
- cmat<-cor(dat,use="pairwise.complete.obs")
- smat<-cor(dat,method="spearman",use="pairwise.complete.obs")
- if(dim(dat)[1]<2000){
- kmat<-cor(dat,method="kendall",use="pairwise.complete.obs")}
- else {s<-sample(seq(1:dim(dat)[1]),size=2000,replace=FALSE)
- kmat<-cor(dat[s,],method="kendall",use="pairwise.complete.obs")
- }
-
- cmat=pmax(abs(cmat),abs(smat),abs(kmat),na.rm=TRUE)
-
- High.cor<-sort(apply(abs(cmat)>min.cor,2,sum)-1,decreasing=TRUE)
-
- #take the top num.plots to put in the pairs plot or if the looking at a single
- #predictor and other predictors it's correlated with, take the top num.plots-1
- #of those with which it is correlated
- {if(cors.w.highest==FALSE){
- HighToPlot<-dat[,match(names(High.cor),names(dat))[1:min(num.plots,length(High.cor))]]
- }else{
- #take the column of the correlation matrix corresponding to the
- #predictor with the higest number of total correlations record the names
- #of the predictors that are correlated with this one predictor
- temp<-cmat[rownames(cmat)==names(High.cor[1]),]
- CorWHigh<-temp[abs(cmat[,colnames(cmat)==names(High.cor[1])])>min.cor]
-
- #record counts of total number of correlations with all predictors for those
- #predictors that are highly correlated with the Highest predictor
- High.cor<-sort(High.cor[names(CorWHigh)],decreasing=TRUE)
- HighToPlot<-dat[,match(names(High.cor),names(dat))[1:min(num.plots,length(High.cor))]]
- }}
- cor.hightoplot<-abs(cor(HighToPlot,use="pairwise.complete.obs"))
- diag(cor.hightoplot)<-0
- cor.range<-c(quantile(as.vector(cor.hightoplot),probs=c(0,.5,.7,.85)),1)
-
- ## put histograms on the diagonal
- panel.hist <- function(x, ...)
- {
- usr <- par("usr"); on.exit(par(usr))
- par(usr = c(usr[1:2], 0, 1.5) )
- h <- hist(x, plot = FALSE)
- breaks <- h$breaks; nB <- length(breaks)
- y <- h$counts; y <- y/max(y)
- rect(breaks[-nB], 0, breaks[-1], y, col="steelblue", ...)
-
- }
-
-
- ## put (absolute) correlations on the upper panels,
- ## with size proportional to the correlations.
- panel.cor <- function(x, y, digits=2, prefix="", cor.range,cex.cor, ...)
- {
- a<-colors()
- usr <- par("usr"); on.exit(par(usr))
- par(usr = c(0, 1, 0, 1))
- r <- abs(cor(x, y,use="pairwise.complete.obs"))
- spear<-abs(cor(x,y,method="spearman",use="pairwise.complete.obs"))
- ken<- abs(cor(x,y,method="kendall",use="pairwise.complete.obs"))
- all.cor<-max(r,spear,ken)
- #range.seq<-seq(from=cor.range[1],to=cor.range[2],length=20)
- if(all.cor>=cor.range[4]){
- rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
- a[59])} else if(all.cor>=cor.range[3]){
- rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
- a[76])} else if(all.cor>=cor.range[2]){
- rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
- a[382])}
- r<-max(all.cor)
- cex.cor=3
- txt <- format(c(r, 0.123456789), digits=digits)[1]
- txt <- paste(prefix, txt, sep="")
- #if(missing(cex.cor)) cex.cor <- 1.2/strwidth(txt)
-
- txt2=""
- if(max(all.cor)>cor.range[2]){
- if(spear==max(all.cor) && spear!=cor(x,y,use="pairwise.complete.obs")) {txt2 <- " s"
- } else if(ken==max(all.cor) && ken!=cor(x,y,use="pairwise.complete.obs")){
- txt2 <-" k"
- }
-
- }
- text(0.5, 0.5, txt, cex = .7+cex.cor * (r-min(cor.range))/(max(cor.range)-min(cor.range)))
- text(.9,.1,txt2,cex=1.5)
- }
-
-# #Find a new unique file name (one in the desired directory that hasn't yet been used)
-# outfile <- paste(output.dir,"Predictor_Correlation.pdf",sep="\\")
-# while(file.access(outfile)==0) outfile<-paste(output.dir,"Predictor_Correlation.pdf",sep="\\")
-#
-# options(warn=-1)
-# pdf(outfile,width=11,height=9,onefile=T)
-# MyPairs(HighToPlot,cor.range=cor.range,my.labels=(as.vector(High.cor)[1:num.plots]),
-# lower.panel=panel.smooth,diag.panel=panel.hist, upper.panel=panel.cor,pch=21,bg = c("red","steelblue")[as.factor(response)],col.smooth = "red")
-# graphics.off()
-# options(warn=0)
-#
-# }
-
-
- #Find a new unique file name (one in the desired directory that hasn't yet been used)
-
- options(warn=-1)
- if(Debug==FALSE) jpeg(output.file,width=1000,height=1000,pointsize=13)
- MyPairs(cbind(TrueResponse,HighToPlot),cor.range=cor.range,my.labels=(as.vector(High.cor)[1:num.plots]),
- lower.panel=panel.smooth,diag.panel=panel.hist, upper.panel=panel.cor,pch=21,bg = c("green","red","yellow")[factor(response,levels=c(0,1,-9999))],col.smooth = "red")
-
- if(Debug==FALSE) graphics.off()
- options(warn=0)
-
- }
-
-MyPairs<-function (x,my.labels,labels, panel = points, ..., lower.panel = panel,
- upper.panel = panel, diag.panel = NULL, text.panel = textPanel,
- label.pos = 0.5 + has.diag/3, cex.labels = NULL, font.labels = 1,
- row1attop = TRUE, gap = 1,Toplabs=NULL)
-{
- response<-x[,1]
- response[response==-9999]<-0
- x<-x[,2:dim(x)[2]]
-
- textPanel <- function(x = 0.5, y = 0.5, txt, cex, font) text(x,
- y, txt, cex = cex, font = font)
- localAxis <- function(side, x, y, xpd, bg, col = NULL, main,
- oma, ...) {
- if (side%%2 == 1)
- Axis(x, side = side, xpd = NA, ...)
- else Axis(y, side = side, xpd = NA, ...)
- }
- localPlot <- function(..., main, oma, font.main, cex.main) plot(...)
- localLowerPanel <- function(..., main, oma, font.main, cex.main) lower.panel(...)
- localUpperPanel <- function(..., main, oma, font.main, cex.main) upper.panel(...)
- localDiagPanel <- function(..., main, oma, font.main, cex.main) diag.panel(...)
- dots <- list(...)
- nmdots <- names(dots)
- if (!is.matrix(x)) {
- x <- as.data.frame(x)
- for (i in seq_along(names(x))) {
- if (is.factor(x[[i]]) || is.logical(x[[i]]))
- x[[i]] <- as.numeric(x[[i]])
- if (!is.numeric(unclass(x[[i]])))
- stop("non-numeric argument to 'pairs'")
- }
- } else if (!is.numeric(x))
- stop("non-numeric argument to 'pairs'")
- panel <- match.fun(panel)
- if ((has.lower <- !is.null(lower.panel)) && !missing(lower.panel))
- lower.panel <- match.fun(lower.panel)
- if ((has.upper <- !is.null(upper.panel)) && !missing(upper.panel))
- upper.panel <- match.fun(upper.panel)
- if ((has.diag <- !is.null(diag.panel)) && !missing(diag.panel))
- diag.panel <- match.fun(diag.panel)
- if (row1attop) {
- tmp <- lower.panel
- lower.panel <- upper.panel
- upper.panel <- tmp
- tmp <- has.lower
- has.lower <- has.upper
- has.upper <- tmp
- }
- nc <- ncol(x)
- if (nc < 2)
- stop("only one column in the argument to 'pairs'")
- has.labs <- TRUE
- if (missing(labels)) {
- labels <- colnames(x)
- if (is.null(labels))
- labels <- paste("var", 1L:nc)
- }
- else if (is.null(labels))
- has.labs <- FALSE
- oma <- if ("oma" %in% nmdots)
- dots$oma
- else NULL
- main <- if ("main" %in% nmdots)
- dots$main
- else NULL
- if (is.null(oma)) {
- oma <- c(4, 4, 4, 4)
- if (!is.null(main))
- oma[3L] <- 6
- }
-
- nCol<-ifelse(length(unique(response))>1,nc+1,nc)
- j.start<-ifelse(length(unique(response))>1,0,1)
- opar <- par(mfrow = c(nc, nCol), mar = rep.int(gap/2, 4), oma = oma)
- on.exit(par(opar))
- for (i in if (row1attop)
- 1L:(nc)
- else nc:1L) for (j in j.start:(nc)) {
-
-
- if(i==1){ par(mar = c(gap/2,gap/2,gap,gap/2)) #top row add extra room at top
- if(j==0){
- par(mar = c(gap/2,gap,gap,gap)) #top left corner room at top and on right
- localPlot(x[, i],response, xlab = "", ylab = "", axes = FALSE,
- type="n",...)
- }else if(j==1) {par(mar = c(gap/2,gap,gap,gap/2)) #extra room on left and topfor second plot top row
- localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
- type="n",...)} else {
- par(mar = c(gap/2,gap/2,gap,gap/2)) #all other top row plots need extra room at top only
- localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
- type="n",...)
- }}else { par(mar = rep.int(gap/2, 4))
- if(j==0){ par(mar = c(gap/2,gap,gap/2,gap)) #left column needs extra room on right only
- localPlot(x[, i],response, xlab = "", ylab = "", axes = FALSE,
- type="n",...)
- }else if(j==1){ par(mar = c(gap/2,gap,gap/2,gap/2)) #second column needs extra room on left so labels fit
- localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
- type="n",...)
- }else localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
- type="n",...)}
- if(j==0) {
- if(i==1) par(mar=c(gap/2,gap,gap,gap))
- else par(mar = c(gap/2,gap,gap/2,gap))
-
- if(i==1) title(main="Response",line=.04,cex.main=1.5)
-
- box()
- my.lab<-paste("cor=",round(max(abs(cor(x[,(i)],response,use="pairwise.complete.obs")),abs(cor(x[,(i)],response,method="spearman",use="pairwise.complete.obs")),
- abs(cor(x[,(i)],response,method="kendall",use="pairwise.complete.obs"))),digits=2),sep="")
-
- #panel smooth doesn't work for two reasons: one, the response is binary and it requires more than two unique values
- #second I don't think it can use weights which is necessary with an overwhelming amount of background points so that presnce points
- #can't be viewed
- #panel.smooth(as.vector(x[, (i)]), as.vector(jitter(response,factor=.1)),weights=
- # c(rep(table(response)[2]/table(response)[1],times=table(response)[1]),rep(1,times=table(response)[2])),...)
-
- if(length(unique(response))>2) panel.smooth(as.vector(x[, (i)]), as.vector(response),...)
- else my.panel.smooth(as.vector(x[, (i)]), as.vector(response),weights=
- c(rep(table(response)[2]/table(response)[1],times=table(response)[1]),rep(1,times=table(response)[2])),...)
-
- title(ylab=paste("cor=",round(max(abs(cor(x[,(i)],response,use="pairwise.complete.obs")),
- abs(cor(x[,(i)],response,method="spearman",use="pairwise.complete.obs")),abs(cor(x[,(i)],response,method="kendall",use="pairwise.complete.obs"))),digits=2),
- sep=""),line=.02,cex.lab=1.5)
- #,y=.85,x=max(x[,(i)])-.2*diff(range(x[,(i)])),cex=1.5)
-
- } else{
- if (i == j || (i < j && has.lower) || (i > j && has.upper)) {
- box()
- if(i==1) title(main=paste("Total Cor=",my.labels[j],sep=""),line=.04,cex.main=1.5)
- #if (i == 1 && (!(j%%2) || !has.upper || !has.lower))
- # localAxis(1 + 2 * row1attop, x[, j], x[, i],
- # ...)
- if (i == nc)
- localAxis(3 - 2 * row1attop, x[, j], x[, i],
- ...)
- if (j == 1 && (i!=1 || !has.upper || !has.lower))
- localAxis(2, x[, j], x[, i], ...)
- #if (j == nc && (i%%2 || !has.upper || !has.lower))
- # localAxis(4, x[, j], x[, i], ...)
- mfg <- par("mfg")
- if (i == j) {
- if (has.diag)
- localDiagPanel(as.vector(x[, i]),...)
- if (has.labs) {
- par(usr = c(0, 1, 0, 1))
- if (is.null(cex.labels)) {
- l.wid <- strwidth(labels, "user")
- cex.labels <- max(0.8, min(2, 0.9/max(l.wid)))
- }
-
- text.panel(0.5, label.pos, labels[i], cex = cex.labels,
- font = font.labels)
- }
- }
-
- else if (i < j)
- if(length(unique(x[,i])>2)){
- localLowerPanel(as.vector(x[, j]), as.vector(x[,
- i]), ...) } else {
- my.panel.smooth(as.vector(x[, j]),as.vector(x[,i]))
- }
-
- else localUpperPanel(as.vector(x[, j]), as.vector(x[,
- i]), ...)
- if (any(par("mfg") != mfg))
- stop("the 'panel' function made a new plot")
- }
- else par(new = FALSE)
- }}
- if (!is.null(main)) {
- font.main <- if ("font.main" %in% nmdots)
- dots$font.main
- else par("font.main")
- cex.main <- if ("cex.main" %in% nmdots)
- dots$cex.main
- else par("cex.main")
- mtext(main, 3, 3, TRUE, 0.5, cex = cex.main, font = font.main)
- }
- invisible(NULL)
-}
-
-
-my.panel.smooth<-function (x, y, col = par("col"), bg = NA, pch = par("pch"),
- cex = 1, col.smooth = "red", span = 2/3, iter = 3, weights=rep(1,times=length(y)), ...)
-{
- o<-order(x)
- points(x, y, pch = pch, col = col, bg = bg, cex = cex)
- ok <- is.finite(x) & is.finite(y)
- if (any(ok) && length(unique(x))>3)
- lines(lowess(x[o],y[o],iter=0),col="red")
- #lines(smooth.spline(x,w=weights,jitter(y,amount=(max(y)-min(y))/100),nknots=min(length(unique(x)),4)),col="red")
-
-}
-
-
-Args <- commandArgs(T)
- print(Args)
- #assign default values
- num.plots <- 10
- min.cor <- .7
- responseCol <- "ResponseBinary"
- cors.w.highest <- FALSE
- pres=TRUE
- absn=TRUE
- bgd=TRUE
- #replace the defaults with passed values
- for (arg in Args) {
- argSplit <- strsplit(arg, "=")
- argSplit[[1]][1]
- argSplit[[1]][2]
- if(argSplit[[1]][1]=="p") num.plots <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="m") min.cor <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="o") output.file <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="i") infile <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="core") cors.w.highest <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="pres") pres <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="absn") absn <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="bgd") bgd <- argSplit[[1]][2]
- }
-
- print(num.plots)
- print(min.cor)
- print(output.file)
- print (infile)
- print(responseCol)
- print(cors.w.highest)
- print(pres)
- print(absn)
- print(bgd)
-
- #Run the Pairs Explore function with these parameters
- Pairs.Explore(num.plots=num.plots,
- min.cor=min.cor,
- input.file=infile,
- output.file=output.file,
- response.col=responseCol,
- cors.w.highest=cors.w.highest,
- pres,
- absn,
- bgd)
-
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore2.r b/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore2.r
deleted file mode 100644
index 156e158..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/PairsExplore2.r
+++ /dev/null
@@ -1,430 +0,0 @@
-Pairs.Explore<-function(num.plots=5,min.cor=.7,input.file,output.file,response.col="ResponseBinary",cors.w.highest=FALSE,pres=TRUE,absn=TRUE,bgd=TRUE,Debug=FALSE){
-
-
- #num.plots=plots per page of display
- #min.cor=the minimum correlation to be included in determining which set of predictors to display
- #input.file=a csv assumed to have the new vistrails form with the first several rows specifiying where to find tiffs
- # and which columns to include in analysis
- #output.file=...
- #response.col=name of response column to be removed and used elsewhere
- #modifications
- #5/10/2011 altered to handle count data as well presence absence.
- #any counts higher than or equal to 1 are set to be presence though I might consider
- #adding the option to have a threshold set instead of using just presence/absence
-
-
- absn<-as.logical(absn)
- pres<-as.logical(pres)
- bgd<-as.logical(bgd)
- cors.w.highest<-as.logical(cors.w.highest)
-
- #Read input data and remove any columns to be excluded
- dat<-read.csv(input.file,skip=3,header=FALSE)
-
- hl<-readLines(input.file,1)
- hl=strsplit(hl,',')
- colnames(dat) = hl[[1]]
-
- tif.info<-readLines(input.file,3)
- tif.info<-strsplit(tif.info,',')
- include<-(as.numeric(tif.info[[2]]))
-
- #Remove coordinates, response column, site.weights
- #before exploring predictor relationship
- rm.cols <- as.vector(na.omit(c(match("x",tolower(names(dat))),match("y",tolower(names(dat))),
- match("site.weights",tolower(names(dat))),match(tolower(response.col),tolower(names(dat))),match("Split",names(dat)))))
-
- #remove testing split
- if(!is.na(match("Split",names(dat)))) dat<-dat[-c(which(dat$Split=="test"),arr.ind=TRUE),]
-
- include[is.na(include)]<-0
- rm.cols<-unique(c(rm.cols,which(include==0,arr.ind=TRUE)))
- response<-dat[,match(tolower(response.col),tolower(names(dat)))]
-
- dat<-dat[order(response),]
- response<-response[order(response)]
-
- #for the purpose of the pairs plot, taking all counts greater than 1 and setting them equal to presence
- #this is never exported
- if(response.col=="responseCount") {response[response>=1]<-1
- }
-
- #remove any of pres absn or bgd that aren't desired
- temp<-c(0,1,-9999)
- temp<-temp[c(absn,pres,bgd)]
- dat<-dat[response%in%temp,]
- response<-response[response%in%temp]
-
-
- if(sum(response==-9999)>1000){
- s<-sample(which(response==-9999,arr.ind=TRUE),size=(sum(response==-9999)-1000))
- dat<-dat[-c(s),]
- response<-response[-c(s)]
- }
-
- if (response.col=="responseCount") {
- TrueResponse<-dat[,match(tolower(response.col),tolower(names(dat)))]
- } else TrueResponse<-response
-
- #now remove all columns except predictors
- dat<-dat[-rm.cols]
- dat[dat==-9999]<-NA
- #dat<-dat[1:2000,]
- #Remove columns with only one unique value
- varr <- function(x) var(x,na.rm=TRUE)
-
- dat<-try(dat[,as.vector(apply(dat,2,varr)==0)!=1],silent=TRUE)
- if(class(dat)=="try-error") stop("mds file contains nonnumeric columns please remove and continue")
- #record correlations for later plots
-
- cmat<-cor(dat,use="pairwise.complete.obs")
- smat<-cor(dat,method="spearman",use="pairwise.complete.obs")
- if(dim(dat)[1]<2000){
- kmat<-cor(dat,method="kendall",use="pairwise.complete.obs")}
- else {s<-sample(seq(1:dim(dat)[1]),size=2000,replace=FALSE)
- kmat<-cor(dat[s,],method="kendall",use="pairwise.complete.obs")
- }
-
- cmat=pmax(abs(cmat),abs(smat),abs(kmat),na.rm=TRUE)
-
- High.cor<-sort(apply(abs(cmat)>min.cor,2,sum)-1,decreasing=TRUE)
-
- #take the top num.plots to put in the pairs plot or if the looking at a single
- #predictor and other predictors it's correlated with, take the top num.plots-1
- #of those with which it is correlated
- {if(cors.w.highest==FALSE){
- HighToPlot<-dat[,match(names(High.cor),names(dat))[1:min(num.plots,length(High.cor))]]
- }else{
- #take the column of the correlation matrix corresponding to the
- #predictor with the higest number of total correlations record the names
- #of the predictors that are correlated with this one predictor
- temp<-cmat[rownames(cmat)==names(High.cor[1]),]
- CorWHigh<-temp[abs(cmat[,colnames(cmat)==names(High.cor[1])])>min.cor]
-
- #record counts of total number of correlations with all predictors for those
- #predictors that are highly correlated with the Highest predictor
- High.cor<-sort(High.cor[names(CorWHigh)],decreasing=TRUE)
- HighToPlot<-dat[,match(names(High.cor),names(dat))[1:min(num.plots,length(High.cor))]]
- }}
- cor.hightoplot<-abs(cor(HighToPlot,use="pairwise.complete.obs"))
- diag(cor.hightoplot)<-0
- cor.range<-c(quantile(as.vector(cor.hightoplot),probs=c(0,.5,.7,.85)),1)
-
- ## put histograms on the diagonal
- panel.hist <- function(x, ...)
- {
- usr <- par("usr"); on.exit(par(usr))
- par(usr = c(usr[1:2], 0, 1.5) )
- h <- hist(x, plot = FALSE)
- breaks <- h$breaks; nB <- length(breaks)
- y <- h$counts; y <- y/max(y)
- rect(breaks[-nB], 0, breaks[-1], y, col="steelblue", ...)
-
- }
-
-
- ## put (absolute) correlations on the upper panels,
- ## with size proportional to the correlations.
- panel.cor <- function(x, y, digits=2, prefix="", cor.range,cex.cor, ...)
- {
- a<-colors()
- usr <- par("usr"); on.exit(par(usr))
- par(usr = c(0, 1, 0, 1))
- r <- abs(cor(x, y,use="pairwise.complete.obs"))
- spear<-abs(cor(x,y,method="spearman",use="pairwise.complete.obs"))
- ken<- abs(cor(x,y,method="kendall",use="pairwise.complete.obs"))
- all.cor<-max(r,spear,ken)
- #range.seq<-seq(from=cor.range[1],to=cor.range[2],length=20)
- if(all.cor>=cor.range[4]){
- rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
- a[59])} else if(all.cor>=cor.range[3]){
- rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
- a[76])} else if(all.cor>=cor.range[2]){
- rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col =
- a[382])}
- r<-max(all.cor)
- cex.cor=3
- txt <- format(c(r, 0.123456789), digits=digits)[1]
- txt <- paste(prefix, txt, sep="")
- #if(missing(cex.cor)) cex.cor <- 1.2/strwidth(txt)
-
- txt2=""
- if(max(all.cor)>cor.range[2]){
- if(spear==max(all.cor) && spear!=cor(x,y,use="pairwise.complete.obs")) {txt2 <- " s"
- } else if(ken==max(all.cor) && ken!=cor(x,y,use="pairwise.complete.obs")){
- txt2 <-" k"
- }
-
- }
- text(0.5, 0.5, txt, cex = .7+cex.cor * (r-min(cor.range))/(max(cor.range)-min(cor.range)))
- text(.9,.1,txt2,cex=1.5)
- }
-
-# #Find a new unique file name (one in the desired directory that hasn't yet been used)
-# outfile <- paste(output.dir,"Predictor_Correlation.pdf",sep="\\")
-# while(file.access(outfile)==0) outfile<-paste(output.dir,"Predictor_Correlation.pdf",sep="\\")
-#
-# options(warn=-1)
-# pdf(outfile,width=11,height=9,onefile=T)
-# MyPairs(HighToPlot,cor.range=cor.range,my.labels=(as.vector(High.cor)[1:num.plots]),
-# lower.panel=panel.smooth,diag.panel=panel.hist, upper.panel=panel.cor,pch=21,bg = c("red","steelblue")[as.factor(response)],col.smooth = "red")
-# graphics.off()
-# options(warn=0)
-#
-# }
-
-
- #Find a new unique file name (one in the desired directory that hasn't yet been used)
-
- options(warn=-1)
- if(Debug==FALSE) jpeg(output.file,width=1000,height=1000,pointsize=13)
- MyPairs(cbind(TrueResponse,HighToPlot),cor.range=cor.range,my.labels=(as.vector(High.cor)[1:num.plots]),
- lower.panel=panel.smooth,diag.panel=panel.hist, upper.panel=panel.cor,pch=21,bg = c("green","red","yellow")[factor(response,levels=c(0,1,-9999))],col.smooth = "red")
-
- if(Debug==FALSE) graphics.off()
- options(warn=0)
-
- }
-
-MyPairs<-function (x,my.labels,labels, panel = points, ..., lower.panel = panel,
- upper.panel = panel, diag.panel = NULL, text.panel = textPanel,
- label.pos = 0.5 + has.diag/3, cex.labels = NULL, font.labels = 1,
- row1attop = TRUE, gap = 1,Toplabs=NULL)
-{
- response<-x[,1]
- response[response==-9999]<-0
- x<-x[,2:dim(x)[2]]
-
- textPanel <- function(x = 0.5, y = 0.5, txt, cex, font) text(x,
- y, txt, cex = cex, font = font)
- localAxis <- function(side, x, y, xpd, bg, col = NULL, main,
- oma, ...) {
- if (side%%2 == 1)
- Axis(x, side = side, xpd = NA, ...)
- else Axis(y, side = side, xpd = NA, ...)
- }
- localPlot <- function(..., main, oma, font.main, cex.main) plot(...)
- localLowerPanel <- function(..., main, oma, font.main, cex.main) lower.panel(...)
- localUpperPanel <- function(..., main, oma, font.main, cex.main) upper.panel(...)
- localDiagPanel <- function(..., main, oma, font.main, cex.main) diag.panel(...)
- dots <- list(...)
- nmdots <- names(dots)
- if (!is.matrix(x)) {
- x <- as.data.frame(x)
- for (i in seq_along(names(x))) {
- if (is.factor(x[[i]]) || is.logical(x[[i]]))
- x[[i]] <- as.numeric(x[[i]])
- if (!is.numeric(unclass(x[[i]])))
- stop("non-numeric argument to 'pairs'")
- }
- } else if (!is.numeric(x))
- stop("non-numeric argument to 'pairs'")
- panel <- match.fun(panel)
- if ((has.lower <- !is.null(lower.panel)) && !missing(lower.panel))
- lower.panel <- match.fun(lower.panel)
- if ((has.upper <- !is.null(upper.panel)) && !missing(upper.panel))
- upper.panel <- match.fun(upper.panel)
- if ((has.diag <- !is.null(diag.panel)) && !missing(diag.panel))
- diag.panel <- match.fun(diag.panel)
- if (row1attop) {
- tmp <- lower.panel
- lower.panel <- upper.panel
- upper.panel <- tmp
- tmp <- has.lower
- has.lower <- has.upper
- has.upper <- tmp
- }
- nc <- ncol(x)
- if (nc < 2)
- stop("only one column in the argument to 'pairs'")
- has.labs <- TRUE
- if (missing(labels)) {
- labels <- colnames(x)
- if (is.null(labels))
- labels <- paste("var", 1L:nc)
- }
- else if (is.null(labels))
- has.labs <- FALSE
- oma <- if ("oma" %in% nmdots)
- dots$oma
- else NULL
- main <- if ("main" %in% nmdots)
- dots$main
- else NULL
- if (is.null(oma)) {
- oma <- c(4, 4, 4, 4)
- if (!is.null(main))
- oma[3L] <- 6
- }
-
- nCol<-ifelse(length(unique(response))>1,nc+1,nc)
- j.start<-ifelse(length(unique(response))>1,0,1)
- opar <- par(mfrow = c(nc, nCol), mar = rep.int(gap/2, 4), oma = oma)
- on.exit(par(opar))
- for (i in if (row1attop)
- 1L:(nc)
- else nc:1L) for (j in j.start:(nc)) {
-
-
- if(i==1){ par(mar = c(gap/2,gap/2,gap,gap/2)) #top row add extra room at top
- if(j==0){
- par(mar = c(gap/2,gap,gap,gap)) #top left corner room at top and on right
- localPlot(x[, i],response, xlab = "", ylab = "", axes = FALSE,
- type="n",...)
- }else if(j==1) {par(mar = c(gap/2,gap,gap,gap/2)) #extra room on left and topfor second plot top row
- localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
- type="n",...)} else {
- par(mar = c(gap/2,gap/2,gap,gap/2)) #all other top row plots need extra room at top only
- localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
- type="n",...)
- }}else { par(mar = rep.int(gap/2, 4))
- if(j==0){ par(mar = c(gap/2,gap,gap/2,gap)) #left column needs extra room on right only
- localPlot(x[, i],response, xlab = "", ylab = "", axes = FALSE,
- type="n",...)
- }else if(j==1){ par(mar = c(gap/2,gap,gap/2,gap/2)) #second column needs extra room on left so labels fit
- localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
- type="n",...)
- }else localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE,
- type="n",...)}
- if(j==0) {
- if(i==1) par(mar=c(gap/2,gap,gap,gap))
- else par(mar = c(gap/2,gap,gap/2,gap))
-
- if(i==1) title(main="Response",line=.04,cex.main=1.5)
-
- box()
- my.lab<-paste("cor=",round(max(abs(cor(x[,(i)],response,use="pairwise.complete.obs")),abs(cor(x[,(i)],response,method="spearman",use="pairwise.complete.obs")),
- abs(cor(x[,(i)],response,method="kendall",use="pairwise.complete.obs"))),digits=2),sep="")
-
- #panel smooth doesn't work for two reasons: one, the response is binary and it requires more than two unique values
- #second I don't think it can use weights which is necessary with an overwhelming amount of background points so that presnce points
- #can't be viewed
- #panel.smooth(as.vector(x[, (i)]), as.vector(jitter(response,factor=.1)),weights=
- # c(rep(table(response)[2]/table(response)[1],times=table(response)[1]),rep(1,times=table(response)[2])),...)
-
- if(length(unique(response))>2) panel.smooth(as.vector(x[, (i)]), as.vector(response),...)
- else my.panel.smooth(as.vector(x[, (i)]), as.vector(response),weights=
- c(rep(table(response)[2]/table(response)[1],times=table(response)[1]),rep(1,times=table(response)[2])),...)
-
- title(ylab=paste("cor=",round(max(abs(cor(x[,(i)],response,use="pairwise.complete.obs")),
- abs(cor(x[,(i)],response,method="spearman",use="pairwise.complete.obs")),abs(cor(x[,(i)],response,method="kendall",use="pairwise.complete.obs"))),digits=2),
- sep=""),line=.02,cex.lab=1.5)
- #,y=.85,x=max(x[,(i)])-.2*diff(range(x[,(i)])),cex=1.5)
-
- } else{
- if (i == j || (i < j && has.lower) || (i > j && has.upper)) {
- box()
- if(i==1) title(main=paste("Total Cor=",my.labels[j],sep=""),line=.04,cex.main=1.5)
- #if (i == 1 && (!(j%%2) || !has.upper || !has.lower))
- # localAxis(1 + 2 * row1attop, x[, j], x[, i],
- # ...)
- if (i == nc)
- localAxis(3 - 2 * row1attop, x[, j], x[, i],
- ...)
- if (j == 1 && (i!=1 || !has.upper || !has.lower))
- localAxis(2, x[, j], x[, i], ...)
- #if (j == nc && (i%%2 || !has.upper || !has.lower))
- # localAxis(4, x[, j], x[, i], ...)
- mfg <- par("mfg")
- if (i == j) {
- if (has.diag)
- localDiagPanel(as.vector(x[, i]),...)
- if (has.labs) {
- par(usr = c(0, 1, 0, 1))
- if (is.null(cex.labels)) {
- l.wid <- strwidth(labels, "user")
- cex.labels <- max(0.8, min(2, 0.9/max(l.wid)))
- }
-
- text.panel(0.5, label.pos, labels[i], cex = cex.labels,
- font = font.labels)
- }
- }
-
- else if (i < j)
- if(length(unique(x[,i])>2)){
- localLowerPanel(as.vector(x[, j]), as.vector(x[,
- i]), ...) } else {
- my.panel.smooth(as.vector(x[, j]),as.vector(x[,i]))
- }
-
- else localUpperPanel(as.vector(x[, j]), as.vector(x[,
- i]), ...)
- if (any(par("mfg") != mfg))
- stop("the 'panel' function made a new plot")
- }
- else par(new = FALSE)
- }}
- if (!is.null(main)) {
- font.main <- if ("font.main" %in% nmdots)
- dots$font.main
- else par("font.main")
- cex.main <- if ("cex.main" %in% nmdots)
- dots$cex.main
- else par("cex.main")
- mtext(main, 3, 3, TRUE, 0.5, cex = cex.main, font = font.main)
- }
- invisible(NULL)
-}
-
-
-my.panel.smooth<-function (x, y, col = par("col"), bg = NA, pch = par("pch"),
- cex = 1, col.smooth = "red", span = 2/3, iter = 3, weights=rep(1,times=length(y)), ...)
-{
- o<-order(x)
- points(x, y, pch = pch, col = col, bg = bg, cex = cex)
- ok <- is.finite(x) & is.finite(y)
- if (any(ok) && length(unique(x))>3)
- lines(lowess(x[o],y[o],iter=0),col="red")
- #lines(smooth.spline(x,w=weights,jitter(y,amount=(max(y)-min(y))/100),nknots=min(length(unique(x)),4)),col="red")
-
-}
-
-
-Args <- commandArgs(T)
- print(Args)
- #assign default values
- num.plots <- 10
- min.cor <- .7
- responseCol <- "ResponseBinary"
- cors.w.highest <- FALSE
- pres=TRUE
- absn=TRUE
- bgd=TRUE
- #replace the defaults with passed values
- for (arg in Args) {
- argSplit <- strsplit(arg, "=")
- argSplit[[1]][1]
- argSplit[[1]][2]
- if(argSplit[[1]][1]=="p") num.plots <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="m") min.cor <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="o") output.file <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="i") infile <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="core") cors.w.highest <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="pres") pres <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="absn") absn <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="bgd") bgd <- argSplit[[1]][2]
- }
-
- print(num.plots)
- print(min.cor)
- print(output.file)
- print (infile)
- print(responseCol)
- print(cors.w.highest)
- print(pres)
- print(absn)
- print(bgd)
-
- #Run the Pairs Explore function with these parameters
- Pairs.Explore(num.plots=num.plots,
- min.cor=min.cor,
- input.file=infile,
- output.file=output.file,
- response.col=responseCol,
- cors.w.highest=cors.w.highest,
- pres,
- absn,
- bgd)
-
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Pred.Surface.r b/contrib/sahm/pySAHM/Resources/R_Modules/Pred.Surface.r
deleted file mode 100644
index a138e82..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Pred.Surface.r
+++ /dev/null
@@ -1,54 +0,0 @@
-Pred.Surface<-function(object, model, filename="", na.rm=TRUE,NAval) {
- predrast <- raster(object)
- filename <- trim(filename)
- firstrow <- 1
- firstcol <- 1
- ncols <- ncol(predrast)
- lyrnames <- layerNames(object)
- xylyrnames <- c('x', 'y', lyrnames)
- v <- matrix(NA, ncol=nrow(predrast), nrow=ncol(predrast))
- na.rm <- FALSE
- tr <- blockSize(predrast, n=nlayers(object)+3)
- ablock <- 1:(ncol(object) * tr$nrows[1])
- napred <- rep(NA, ncol(predrast)*tr$nrows[1])
- predrast <- writeStart(predrast, filename=filename,overwrite=TRUE)
- ############################################################
- for (i in 1:tr$n) {
- if (i==tr$n) {
- ablock <- 1:(ncol(object) * tr$nrows[i])
- napred <- rep(NA, ncol(predrast) * tr$nrows[i])
- }
- rr <- firstrow + tr$row[i] - 1
- p <- xyFromCell(predrast, ablock + (tr$row[i]-1) * ncol(predrast))
- p <- na.omit(p)
- blockvals <- data.frame(x=p[,1], y=p[,2])
- if (na.rm) {
- blockvals <- na.omit(blockvals)
- }
- if (nrow(blockvals) == 0 ) {
- predv <- napred
- } else {
-
- predv <- predict(model, blockvals)
- predv[is.na(predv)]<-NAval
- }
- if (na.rm) {
- naind <- as.vector(attr(blockvals, "na.action"))
- if (!is.null(naind)) {
- p <- napred
- p[-naind] <- predv
- predv <- p
- rm(p)
- }
- }
-
- # to change factor to numeric; should keep track of this to return a factor type RasterLayer
- predv = as.numeric(predv)
- predrast <- writeValues(predrast, predv, tr$row[i])
- NAvalue(predrast)<-NAval
- }
- predrast <- writeStop(predrast)
- a<-readGDAL(predrast at file@name)
- writeGDAL(a,predrast at file@name, drivername = "GTiff",setStatistics=TRUE,mvFlag=NAval)
- return(predrast)
- }
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/PredictModel.r b/contrib/sahm/pySAHM/Resources/R_Modules/PredictModel.r
deleted file mode 100644
index 69383fe..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/PredictModel.r
+++ /dev/null
@@ -1,331 +0,0 @@
-PredictModel<-function(workspace=NULL,new.tifs=NULL,out.dir=NULL,thresh=NULL,make.btif=NULL,make.ptif=NULL){
-
-#This functions separates the step of model fit from producing probability or binary surfaces
-#the default is to read in a workspace and make predictions using the original tiffs supplied
-#but if an mds with new tiff directories are supplied, the function will instead use these
-#options are available for setting the threshold
-#and true and false for whether to make binary or prob.tif
-
-#my stuff to delete
-#workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\")
-#new.tifs<-out$input$ma.name
-#end delete
-
- load(workspace)
-
- if(!is.null(new.tifs)){
-
- ma.name <- new.tifs
- #get the paths off of the new mds file
- tif.info<-readLines(ma.name,3)
- tif.info<-strsplit(tif.info,',')
- include<-(as.numeric(tif.info[[2]]))
- paths<-as.character(tif.info[[3]])
-
- paths<-paths[paths!=""]
- #this line needs to be changed eventually to deal with locations of model fit covaries from different models
- if(out$input$model.source.file=="brt.r") {model.covs<-levels(summary(out$mods$final.mod,plotit=FALSE)[,1])
- pred.fct=brt.predict
- }
-
- ma.cols <- match(model.covs,sub(".tif","",basename(paths)))
- paths<-paths[ma.cols]
- #checking that all tifs are present
- if(any(is.na(ma.cols))){
-
- stop("ERROR: the following geotiff(s) are missing in ",
- tif.dir,": ",paste(ma.names[-r.col][is.na(ma.cols)],collapse=" ,"),sep="")
- }
- #checking that we have read access to all tiffs
- if(sum(file.access(paths),mode=0)!=0){
- stop("ERROR: the following geotiff(s) are missing : ",
- paths[(file.access(paths)!=0),][1],sep="")
-
- }
- out$dat$tif.ind<-paths
- }
-
- if(out$input$model.source.file=="rf.r") {
- pred.fct=rf.predict
- library(randomForest)
- }
- if(out$input$model.source.file=="mars.r") {
- pred.fct=pred.mars
- library(mda)
- }
- if(out$input$model.source.file=="glm.r") pred.fct=glm.predict
- if(out$input$model.source.file=="brt.r") {
- pred.fct=brt.predict
- library(gbm)
- }
-
- if(!is.null(thresh))out$mods$auc.output$thresh<-thresh
- if(!is.null(make.btif)) make.binary.tif<-make.btif
- if(!is.null(make.ptif)) make.p.tif<-make.ptif
-
-
- assign("Pred.Surface",Pred.Surface,envir=.GlobalEnv)
- mssg <- proc.tiff(model=out$mods$final.mod,vnames=as.character(out$mods$final.mod$contributions$var),
- tif.dir=out$dat$tif.dir$dname,filenames=out$dat$tif.ind,pred.fct=pred.fct,factor.levels=out$dat$ma$factor.levels,make.binary.tif=make.binary.tif,
- thresh=out$mods$auc.output$thresh,make.p.tif=make.p.tif,outfile.p=paste(out.dir,"prob_map.tif",sep="\\"),
- outfile.bin=paste(out.dir,"bin_map.tif",sep="\\"),tsize=50.0,NAval=-3000,logname=logname,out=out)
-
-
-}
-
-brt.predict <- function(model,x) {
- # retrieve key items from the global environment #
- # make predictions from complete data only #
- #y <- rep(NA,nrow(x))
- #y[complete.cases(x)] <- predict.gbm(model, x[complete.cases(x),],model$target.trees,type="response")
-
- # make predictions from full data #
- y <- predict.gbm(model,x,model$target.trees,type="response")
- # encode missing values as -1.
- a<-complete.cases(x)
- y[!(a)]<- NaN
-
- # return predictions.
- return(y)
- }
-
-pred.mars <- function(model,x) {
- # retrieve key items from the global environment #
- # make predictionss.
- y <- rep(NA,nrow(x))
- y[complete.cases(x)] <- as.vector(mars.predict(model,x[complete.cases(x),])$prediction[,1])
-
-#if(sum(is.na(x))/dim(x)[2]!=sum(is.na(y)))
-#h<-is.na(x)
-#h<-apply(h,1,sum)
-#h=h/35
-#f<-is.na(y)
-#which((h-f)!=0,arr.ind=TRUE)
-#b<-cbind(x[which((h-f)!=0,arr.ind=TRUE),],y[which((h-f)!=0,arr.ind=TRUE)])
-
-#which(is.na(y)
- # encode missing values as -1.
- y[is.na(y)]<- NaN
-
- # return predictions.
- return(y)
- }
-
-glm.predict <- function(model,x) {
- # retrieve key items from the global environment #
- # make predictionss.
-
- y <- as.vector(predict(model,x,type="response"))
-
- # encode missing values as -1.
- y[is.na(y)]<- NaN
-
- # return predictions.
- return(y)
- }
-
-"mars.predict" <-
-function (mars.glm.object,new.data)
-{
-#
-# j leathwick, j elith - August 2006
-#
-# version 3.1 - developed in R 2.3.1 using mda 0.3-1
-#
-# calculates a mars/glm object in which basis functions are calculated
-# using an initial mars model with single or multiple responses
-# data for individual species are then fitted as glms using the
-# common set of mars basis functions with results returned as a list
-#
-# takes as input a dataset and args selecting x and y variables, and degree of interaction
-# along with site and species weights, the CV penalty, and the glm family argument
-# the latter would normally be one of "binomial" or "poisson" - "gaussian" could be used
-# but in this case the model shouldn't differ from that fitted using mars on its own
-#
-# naming problem for dataframes fixed - je - 15/12/06
-#
-# requires mda and leathwick/elith's mars.export
-#
- require(mda)
-
-# first recreate both the original mars model and the glm model
-
-# setup input data and create original temporary data
-
- dataframe.name <- mars.glm.object$mars.call$dataframe # get the dataframe name
- mars.x <- mars.glm.object$mars.call$mars.x
- mars.y <- mars.glm.object$mars.call$mars.y
- n.spp <- length(mars.y)
- family <- mars.glm.object$mars.call$family
- mars.degree <- mars.glm.object$mars.call$degree
- penalty <- mars.glm.object$mars.call$penalty
- site.weights <- mars.glm.object$weights[[1]]
- spp.weights <- mars.glm.object$weights[[2]]
-
- print("creating original data frame...",quote=FALSE)
-
- base.data <- as.data.frame(eval.parent(parse(text = dataframe.name),n=3)) #aks
-
- x.temp <- eval(base.data[, mars.x]) #form the temporary datasets
- base.names <- names(x.temp)
-
- xdat <- mars.new.dataframe(x.temp)[[1]]
-
- ydat <- as.data.frame(base.data[, mars.y])
- names(ydat) <- names(base.data)[mars.y]
-
- assign("xdat", xdat, pos = 1) #and assign them for later use
- assign("ydat", ydat, pos = 1)
-
-# now create the temporary dataframe for the new data
-
- print("checking variable matching with new data",quote = FALSE)
-
- new.names <- names(new.data)
-
- for (i in 1:length(base.names)) {
-
- name <- base.names[i]
-
- if (!(name %in% new.names)) {
- print(paste("Variable ",name," missing from new data",sep=""),quote = FALSE) #aks
- return()
- }
- }
-
- print("and creating temporary dataframe for new data...",quote=FALSE)
-
- selector <- match(names(x.temp),names(new.data))
-
- pred.dat <- mars.new.dataframe(new.data[,selector])[[1]]
-
- assign("pred.dat", pred.dat, pos = 1) #and assign them for later use
-
-# fit the mars model and extract the basis functions
-
- print(paste("re-fitting initial mars model for",n.spp,"responses"),quote = FALSE)
- print(paste("using glm family of",family),quote = FALSE)
-
- #mars.fit <- mars(x = xdat, y = ydat, degree = mars.degree, w = site.weights,
- # wp = spp.weights, penalty = penalty)
-
- mars.fit <- mars.glm.object$mars.object #AKS
-
- old.bf.data <- as.data.frame(eval(mars.fit$x))
- n.bfs <- ncol(old.bf.data)
- bf.names <- paste("bf", 1:n.bfs, sep = "")
- old.bf.data <- as.data.frame(old.bf.data[,-1])
- names(old.bf.data) <- bf.names[-1]
-
- new.bf.data <- as.data.frame(mda:::model.matrix.mars(mars.fit,pred.dat))
- new.bf.data <- as.data.frame(new.bf.data[,-1])
- names(new.bf.data) <- bf.names[-1]
-
-# now cycle through the species fitting glm models
-
- print("fitting glms for individual responses", quote = F)
-
- prediction <- as.data.frame(matrix(0, ncol = n.spp, nrow = nrow(pred.dat)))
- names(prediction) <- names(ydat)
- standard.errors <- as.data.frame(matrix(0, ncol = n.spp, nrow = nrow(pred.dat)))
- names(standard.errors) <- names(ydat)
-
- for (i in 1:n.spp) {
-
- print(names(ydat)[i], quote = FALSE)
- model.glm <- glm(ydat[, i] ~ ., data = old.bf.data, weights = site.weights,
- family = family, maxit = 100)
- temp <- predict.glm(model.glm,new.bf.data,type="response",se.fit=TRUE)
- prediction[,i] <- temp[[1]]
- standard.errors[,i] <- temp[[2]]
-
- }
-
- return(list("prediction"=prediction,"ses"=standard.errors))
-}
-
-"mars.new.dataframe" <-
-function (input.data)
-{
-#
-# j leathwick, j elith - August 2006
-#
-# version 3.1 - developed in R 2.3.1 using mda 0.3-1
-#
-# takes an input data frame and checks for factor variables
-# converting these to dummy variables, one each for each factor level
-# returning it for use with mars.glm so that factor vars can be included
-# in a mars analysis
-#
-
- if (!is.data.frame(input.data)) {
- print("input data must be a dataframe..",quote = FALSE)
- return()
- }
-
- n <- 1
- for (i in 1:ncol(input.data)) { #first transfer the vector variables
- if (is.vector(input.data[,i])) {
- if (n == 1) {
- output.data <- as.data.frame(input.data[,i])
- names.list <- names(input.data)[i]
- var.type <- "vector"
- factor.level <- "na"
- }
- else {
- output.data[,n] <- input.data[,i]
- names.list <- c(names.list,names(input.data)[i])
- var.type <- c(var.type,"vector")
- factor.level <- c(factor.level,"na")
- }
- names(output.data)[n] <- names(input.data)[i]
- n <- n + 1
- }
- }
-
- for (i in 1:ncol(input.data)) { # and then the factor variables
- if (is.factor(input.data[,i])) {
- temp.table <- summary(input.data[,i])
- for (j in 1:length(temp.table)) {
- names.list <- c(names.list,names(input.data)[i])
- var.type <- c(var.type,"factor")
- factor.level <- c(factor.level,names(temp.table)[j])
- output.data[,n] <- ifelse(input.data[,i] == names(temp.table)[j],1,0)
- names(output.data)[n] <- paste(names(input.data)[i],".",names(temp.table)[j],sep="")
- n <- n + 1
- }
- }
- }
-
- lineage <- data.frame(names(output.data),names.list,var.type,factor.level)
- for (i in 1:4) lineage[,i] <- as.character(lineage[,i])
- names(lineage) <- c("full.name","base.name","type","level")
-
- return(list(dataframe = output.data, lineage = lineage))
-}
-
-
-
-
-
-new.tifs=NULL
-# Interpret command line argurments #
-# Make Function Call #
-Args <- commandArgs(trailingOnly=FALSE)
-
- for (i in 1:length(Args)){
- if(Args[i]=="-f") ScriptPath<-Args[i+1]
- }
-
- for (arg in Args) {
- argSplit <- strsplit(arg, "=")
- argSplit[[1]][1]
- argSplit[[1]][2]
- if(argSplit[[1]][1]=="ws") ws <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="new.tifs") new.tifs <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="o") out.dir <- argSplit[[1]][2]
- }
-
-PredictModel(workspace=ws,new.tifs=new.tifs,out.dir=out.dir)
-
-
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/ResidualImage.r b/contrib/sahm/pySAHM/Resources/R_Modules/ResidualImage.r
deleted file mode 100644
index 2d0104d..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/ResidualImage.r
+++ /dev/null
@@ -1,42 +0,0 @@
-resid.image<-function(dev.contrib,pred,raw.dat,x,y,model.type,file.name,out){
- z<-sign(pred-raw.dat)*dev.contrib
- a<-loess(z~x*y)
- x.lim<-rep(seq(from=min(out$dat$ma$train.xy[,1]),to=max(out$dat$ma$train.xy[,1]),length=100),each=100)
- y.lim<-rep(seq(from=min(out$dat$ma$train.xy[,2]),to=max(out$dat$ma$train.xy[,2]),length=100),times=100)
- z<-predict(a,newdata=cbind("x"=x.lim,"y"=y.lim))
- x.lim<-seq(from=min(out$dat$ma$train.xy[,1]),to=max(out$dat$ma$train.xy[,1]),length=100)
- y.lim<-seq(from=min(out$dat$ma$train.xy[,2]),to=max(out$dat$ma$train.xy[,2]),length=100)
- z<-matrix(data=z,ncol=100,nrow=100,byrow=TRUE)
- # browser()
- ########################################### experiment
- # if(out$input$make.binary.tif==TRUE | out$input$make.p.tif==TRUE){
- # out$dat$tif.ind[1]
- # RasterInfo=raster(out$dat$tif.ind[1])
- # gi <- GDALinfo(out$dat$tif.ind[1])
- # dims <- as.vector(gi)[1:2]
- # ps <- as.vector(gi)[6:7]
- # ll <- as.vector(gi)[4:5]
- # pref<-attr(gi,"projection")
-
-
- # }
-
-
- ##########################################################
- jpeg(file=paste(file.name,"resid.plot.jpg",sep="/"))
- par(oma=c(3,3,3,3))
- layout(matrix(data=c(1,2), nrow=1, ncol=2), widths=c(4,1), heights=c(1,1))
- image(z,x=x.lim,y=y.lim,col=beachcolours(heightrange=c(min(z),max(z)),sealevel=0,ncolours=length(table(z))),
- main="Spatial pattern of deviance residuals\n(magnitude and sign)",xlab="X coordinate",ylab="Y coordinate")
- points(x,y,cex=.5)
- #image(x=c(1,2),y=sort(unique(z)),z=matrix(data=cbind(rep(sort(unique(z)),times=2)),ncol=2),col=beachcolours(heightrange=c(min(z),max(z)),sealevel=0,ncolours=length(table(z))))
- par(mar = c(3,2.5,2.5,2))
- colrange<-seq(from=min(z),to=max(z),length=100)
- image(1,colrange,
- matrix(data=colrange, ncol=length(colrange),nrow=1),
- col=beachcolours(heightrange=c(min(z),max(z)),sealevel=0,ncolours=length(colrange)),
- xlab="",ylab="",
- xaxt="n")
- graphics.off()
- return(a)
- }
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/RunMaxEnt.jar b/contrib/sahm/pySAHM/Resources/R_Modules/RunMaxEnt.jar
deleted file mode 100644
index 45a9faf..0000000
Binary files a/contrib/sahm/pySAHM/Resources/R_Modules/RunMaxEnt.jar and /dev/null differ
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainRocPlot.r b/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainRocPlot.r
deleted file mode 100644
index 7e79c14..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainRocPlot.r
+++ /dev/null
@@ -1,372 +0,0 @@
-TestTrainRocPlot<-function (DATA, threshold = 101, find.auc = TRUE, which.model = (1:(ncol(DATA) -
- 2)), na.rm = FALSE, xlab = "1-Specificity (false positives)",
- ylab = "Sensitivity (true positives)", main = "ROC Plot",
- model.names = NULL, color = NULL, line.type = NULL, lwd = 1,
- mark = 0, mark.numbers = TRUE, mark.color = NULL, opt.thresholds = NULL,
- opt.methods = NULL, req.sens, req.spec, obs.prev = NULL,
- smoothing = 1, add.legend = TRUE, legend.text = model.names,
- legend.cex = 0.8, add.opt.legend = TRUE, opt.legend.text = NULL,
- opt.legend.cex = 0.7, counter.diagonal = FALSE, pch = NULL,
- FPC, FNC, cost.line = FALSE,add.roc=FALSE)
-{
- if (is.data.frame(DATA) == FALSE) {
- if (is.matrix(DATA) == TRUE) {
- DATA <- as.data.frame(DATA)
- }
- else {
- stop("'DATA' must be either data frame or matrix")
- }
- }
- OBS <- DATA[, 2]
- if (length(OBS[OBS == 0]) == 0) {
- stop("no observed absences in dataset, therefore specificity does not",
- "exist, and modeling, much less Area Under the Curve, is not very",
- "meaningful")
- }
- if (length(OBS[OBS == 1]) == 0) {
- stop("no observed presences in dataset, therefore sensitivity does not",
- "exist, and modeling, much less Area Under the Curve, is not very",
- "meaningful")
- }
- if (is.logical(find.auc) == FALSE) {
- stop("'find.auc' must be of logical type")
- }
- if (is.logical(na.rm) == FALSE) {
- stop("'na.rm' must be of logical type")
- }
- if (is.logical(mark.numbers) == FALSE) {
- stop("'mark.numbers' must be of logical type!")
- }
- if (is.logical(add.legend) == FALSE) {
- stop("'add.legend' must be of logical type!")
- }
- if (is.logical(add.opt.legend) == FALSE) {
- stop("'add.opt.legend' must be of logical type")
- }
- if (is.logical(counter.diagonal) == FALSE) {
- stop("'counter.diagonal' must be of logical type")
- }
- if (length(smoothing) != 1) {
- stop("'smoothing' must be a single number greater than or equal to 1")
- }
- else {
- if (is.numeric(smoothing) == FALSE) {
- stop("'smoothing' must be a single number greater than or equal to 1")
- }
- else {
- if (smoothing < 1) {
- stop("'smoothing' must be a single number greater than or equal to 1")
- }
- }
- }
- if (sum(is.na(DATA)) > 0) {
- if (na.rm == TRUE) {
- NA.rows <- apply(is.na(DATA), 1, sum)
- warning(length(NA.rows[NA.rows > 0]), " rows ignored due to NA values")
- DATA <- DATA[NA.rows == 0, ]
- }
- else {
- return(NA)
- }
- }
- DATA[DATA[, 2] > 0, 2] <- 1
- N.models <- ncol(DATA) - 2
- if (is.null(obs.prev) == TRUE) {
- obs.prev <- sum(DATA[, 2])/nrow(DATA)
- }
- if (obs.prev < 0 || obs.prev > 1) {
- stop("'obs.prev' must be a number between zero and one")
- }
- if (obs.prev == 0) {
- warning("because your observed prevalence was zero, results may be strange")
- }
- if (obs.prev == 1) {
- warning("because your observed prevalence was one, results may be strange")
- }
- if (min(which.model) < 1 || sum(round(which.model) != which.model) !=
- 0) {
- stop("values in 'which.model' must be positive integers")
- }
- if (max(which.model) > N.models) {
- stop("values in 'which.model' must not be greater than number of models in 'DATA'!")
- }
- if (is.null(model.names) == TRUE) {
- model.names <- if (is.null(names(DATA)) == FALSE) {
- names(DATA)[-c(1, 2)]
- }
- else {
- paste("Model", 1:N.models)
- }
- }
- if (N.models != length(model.names) && (length(which.model) !=
- 1 || length(model.names) != 1)) {
- stop("If 'model.names' is specified it must either be a single name, or a vector",
- "of the same length as the number of model predictions in 'DATA'")
- }
- if (is.null(legend.text) == TRUE) {
- legend.text <- model.names
- }
- if (length(legend.text) != N.models) {
- stop("'opt.legend.text' must be of same length as 'opt.methods'")
- }
- DATA <- DATA[, c(1, 2, which.model + 2)]
- if (length(model.names) != 1) {
- model.names <- model.names[which.model]
- }
- if (length(legend.text) != 1) {
- legend.text <- legend.text[which.model]
- }
- N.dat <- ncol(DATA) - 2
- if (is.null(obs.prev) == TRUE) {
- obs.prev <- sum(DATA[, 2])/nrow(DATA)
- }
- if (obs.prev < 0 || obs.prev > 1) {
- stop("'obs.prev' must be a number between zero and one")
- }
- mark <- matrix(mark, length(mark), N.dat)
- if (!is.null(opt.methods) && is.null(opt.thresholds)) {
- opt.thresholds <- TRUE
- }
- if (is.null(opt.methods) && is.null(opt.thresholds)) {
- opt.thresholds <- FALSE
- }
- if (is.null(opt.methods)) {
- opt.methods <- c(1, 2, 4)
- }
- if (is.logical(opt.thresholds) == TRUE) {
- if (opt.thresholds == TRUE) {
- POSSIBLE.meth <- c("Default", "Sens=Spec", "MaxSens+Spec",
- "MaxKappa", "MaxPCC", "PredPrev=Obs", "ObsPrev",
- "MeanProb", "MinROCdist", "ReqSens", "ReqSpec",
- "Cost")
- N.meth <- length(opt.methods)
- if (is.numeric(opt.methods) == TRUE) {
- if (sum(opt.methods %in% (1:length(POSSIBLE.meth))) !=
- N.meth) {
- stop("invalid optimization method")
- }
- else {
- opt.methods <- POSSIBLE.meth[opt.methods]
- }
- }
- if (sum(opt.methods %in% POSSIBLE.meth) != N.meth) {
- stop("invalid optimization method")
- }
- if (is.null(opt.legend.text) == TRUE) {
- opt.legend.text <- opt.methods
- }
- if (length(opt.legend.text) != N.meth) {
- stop("'opt.legend.text' must be of same length as 'opt.methods'")
- }
- if ("ReqSens" %in% opt.methods) {
- if (missing(req.sens)) {
- warning("req.sens defaults to 0.85")
- req.sens <- 0.85
- }
- }
- if ("ReqSpec" %in% opt.methods) {
- if (missing(req.spec)) {
- warning("req.spec defaults to 0.85")
- req.spec <- 0.85
- }
- }
- if ("Cost" %in% opt.methods) {
- if (missing(FPC) || missing(FNC)) {
- warning("costs assumed to be equal")
- FPC <- 1
- FNC <- 1
- }
- if (FPC <= 0 || FNC <= 0) {
- stop("costs must be positive")
- }
- if (is.logical(cost.line) == FALSE) {
- stop("'cost.line' must be of logical type")
- }
- if (!"Cost" %in% opt.methods) {
- cost.line <- FALSE
- }
- }
- mark <- optimal.thresholds(DATA = DATA, threshold = threshold,
- model.names = model.names, na.rm = na.rm, opt.methods = opt.methods,
- req.sens = req.sens, req.spec = req.spec, obs.prev = obs.prev,
- smoothing = smoothing, FPC = FPC, FNC = FNC)[,
- -1, drop = FALSE]
- if (is.null(pch) == TRUE) {
- pch <- c(1, 5, 2, 16, 15, 17, 8, 6, 9, 12, 4,
- 7)[match(opt.methods, POSSIBLE.meth)]
- }
- else {
- pch <- rep(pch, length(opt.methods))[1:length(opt.methods)]
- }
- }
- }
- if (is.logical(opt.thresholds) == FALSE) {
- if (!is.numeric(opt.thresholds)) {
- stop("'opt.thresholds' must be 'TRUE', 'FALSE', or numeric")
- }
- if (min(opt.thresholds) < 0) {
- stop("'opt.thresholds' can not be negative")
- }
- if (max(opt.thresholds) > 1) {
- if (N.thr == 1 && round(opt.thresholds) == opt.thresholds) {
- opt.thresholds <- seq(length = opt.thresholds,
- from = 0, to = 1)
- N.thr <- length(opt.thresholds)
- }
- else {
- stop("non-interger, non-logical 'opt.thresholds' greater than 1")
- }
- }
- N.opt.thresh <- length(opt.thresholds)
- if (is.null(opt.legend.text)) {
- opt.legend.text <- rep("threshold", N.opt.thresh)
- }
- if (length(opt.legend.text) != N.opt.thresh) {
- stop("length of 'opt.legend.text' does not match number of specified thresholds")
- }
- if (is.null(pch)) {
- pch <- 1:N.opt.thresh
- }
- if (length(pch) != N.opt.thresh) {
- stop("length of 'pch' does not match number of specified thresholds")
- }
- mark <- matrix(opt.thresholds, length(opt.thresholds),
- N.dat)
- opt.thresholds = TRUE
- }
- if (is.null(pch) == TRUE) {
- pch <- 16
- }
- if (is.null(color) == TRUE) {
- colors <- rep(1, N.dat)
- if (is.null(line.type) == TRUE) {
- line.type <- (1:N.dat) + 1
- }
- }
- else {
- if (is.logical(color) == TRUE) {
- if (color == FALSE) {
- colors <- rep(1, N.dat)
- if (is.null(line.type) == TRUE) {
- line.type <- (1:N.dat) + 1
- }
- }
- else {
- colors <- (1:N.dat) + 1
- lwd <- 2 * lwd
- if (is.null(line.type) == TRUE) {
- line.type <- rep(1, N.dat)
- }
- }
- }
- else {
- colors <- rep(color, N.dat)[1:N.dat]
- lwd <- 2 * lwd
- if (is.null(line.type) == TRUE) {
- line.type <- rep(1, N.dat)
- }
- }
- }
- if (is.null(mark.color) == TRUE) {
- mark.colors <- colors
- }
- else {
- if (is.logical(mark.color) == TRUE) {
- if (mark.color == FALSE) {
- mark.colors <- rep(1, N.dat)
- }
- else {
- mark.colors <- (1:N.dat) + 1
- }
- }
- else {
- mark.colors <- rep(mark.color, N.dat)[1:N.dat]
- }
- }
- if (is.null(line.type) == FALSE) {
- if (is.logical(line.type) == TRUE) {
- if (line.type == FALSE) {
- line.type <- rep(1, N.dat)
- }
- else {
- line.type <- (1:N.dat) + 1
- }
- }
- else {
- line.type <- rep(line.type, N.dat)[1:N.dat]
- }
- }
- op <- par(pty = "s")
- if(add.roc==FALSE){
- plot(c(0, 1), c(0, 1), type = "n", xlab = xlab, ylab = ylab,
- main = main)}
- lines(c(0, 1), c(0, 1), col = "lightgray")
- if (counter.diagonal == TRUE) {
- abline(a = 1, b = -1, col = "lightgray")
- }
- for (dat in 1:N.dat) {
- Model.dat <- roc.plot.calculate(DATA = DATA, threshold = threshold,
- which.model = dat)
- lines(x = (1 - Model.dat$specificity), y = Model.dat$sensitivity,
- lty = line.type[dat], lwd = lwd, col = colors[dat])
- if (max(mark) != 0) {
- Mark.dat <- roc.plot.calculate(DATA = DATA, threshold = mark[,
- dat], which.model = dat)
- Mark.pretty <- round(Mark.dat$threshold, 2)
- Mark.pretty.char <- as.character(Mark.pretty)
- Mark.pretty.char[Mark.pretty == 0] <- "0.00"
- Mark.pretty.char[Mark.pretty == 1] <- "1.00"
- Mark.pretty.char[nchar(Mark.pretty.char) == 3] <- paste(Mark.pretty.char[nchar(Mark.pretty.char) ==
- 3], "0", sep = "")
- if(add.roc==FALSE){
- points(x = (1 - Mark.dat$specificity), y = Mark.dat$sensitivity,
- cex = 2, pch = pch, col = mark.colors[dat])
- if (mark.numbers == TRUE) {
- text(x = (1 - Mark.dat$specificity), y = Mark.dat$sensitivity -
- 0.03, labels = Mark.pretty.char, pos = 4, col = mark.colors[dat])
- }}
- }
- if (cost.line == TRUE) {
- tag <- match("Cost", opt.methods)
- sl <- (FPC/FNC) * (1 - obs.prev)/obs.prev
- if (obs.prev == 0) {
- obs.prev <- 1e-06
- }
- abline(a = Mark.dat$sensitivity[tag] - ((1 - Mark.dat$specificity[tag]) *
- sl), b = sl, col = mark.colors[dat], lty = 3)
- }
- }
- inset <- c(0.02, 0.02)
- if (opt.thresholds == TRUE && add.opt.legend == TRUE) {
- if (N.dat == 1) {
- opt.legend.names <- paste(Mark.pretty.char, opt.legend.text)
- }
- else {
- opt.legend.names <- opt.legend.text
- }
- leg.loc <- legend(x = "bottomright", inset = inset, pt.cex = 1,
- legend = opt.legend.names, pch = pch, bg = "white",
- cex = opt.legend.cex)
- inset <- c(0.02, leg.loc$rect$top + 0.05)
- }
- if (add.legend == TRUE) {
- legend.names <- legend.text
- if (find.auc == TRUE) {
- AUC <- rep(0, N.dat)
- for (dat in 1:N.dat) {
- AUC[dat] <- auc(DATA = DATA, which.model = dat)$AUC
- }
- AUC.pretty <- round(AUC, 2)
- AUC.pretty.char <- as.character(AUC.pretty)
- AUC.pretty.char[AUC.pretty == 0] <- "0.00"
- AUC.pretty.char[AUC.pretty == 1] <- "1.00"
- AUC.pretty.char[nchar(AUC.pretty.char) == 3] <- paste(AUC.pretty.char[nchar(AUC.pretty.char) ==
- 3], "0", sep = "")
- legend.names <- paste(AUC.pretty.char, legend.text)
- }
- legend(x = "bottomright", inset = inset, legend = legend.names,
- lty = line.type, col = colors, title = "AUC:", cex = legend.cex,
- lwd = lwd, bg = "white")
- }
- par(op)
-}
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainSplit.r b/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainSplit.r
deleted file mode 100644
index d2564ea..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/TestTrainSplit.r
+++ /dev/null
@@ -1,188 +0,0 @@
- TestTrainSplit<-function(input.file,output.file,response.col="ResponseBinary",trainProp=.7,RatioPresAbs=NULL){
-
-#Description:
-#this code takes as input an mds file with the first line being the predictor or
-#response name, the second line an indicator of predictors to include and the
-#third line being paths where tif files can be found. An output file and a
-#response column must also be specified. Given a training proportion, a new
-#column is created indicating whether each observation should be assigned to the
-#test or training split with the correct proportion.
-#trainProp=#obs to be assigned to training split/total sample size
-#his will be balanced with respect to the response in that the training
-#proportion will be matched as close as possible for each level of the response.
-#An optional parameter, RatioPresAbs, can be used to specify if there is a certain
-#ratio of presence to absence points that should be used this ensures the given
-#ratio for all data used in both the test and train split. For categorical data,
-#all responses greater than or equal to 1 will be used to meet this ratio.
-#This option reduces the sample size as some data must be thrown away to meet
-#the constraint of having the desired proportion. Background points are ignored
-#by this module (they are read in, written out, but not assigned to either the
-#test or training split). Output is written to a csv that can be used by the
-#SAHM R modules.
-
-#Written by Marian Talbert 3/23/2011
-#Modified 5/10/2011 to handle count data
-
-
-
- if(trainProp<=0 | trainProp>1) stop("Train Proportion (trainProp) must be a number between 0 and 1 excluding 0")
- if(!is.null(RatioPresAbs)) {
- if(RatioPresAbs<=0) stop("The ratio of presence to absence (RatioPresAbs) must be a \ngreater than 0")}
-
- #Read input data and remove any columns to be excluded
- dat.in<-read.csv(input.file,header=FALSE,as.is=TRUE)
- dat<-as.data.frame(dat.in[4:dim(dat.in)[1],])
- names(dat)<-dat.in[1,]
-
- response<-dat[,match(tolower(response.col),tolower(names(dat)))]
-
- if(sum(as.numeric(response)==0)==0 && !is.null(RatioPresAbs)) stop("The ratio of presence to absence cannot be set with only presence data")
-
- #Ignoring background data that might be present in the mds
-
- bg.dat<-dat[response==-9999,]
-
- if(dim(bg.dat)[1]!=0){
- dat<-dat[-c(which(response==-9999,arr.ind=TRUE)),]
- dat.in<-dat.in[-c(which(response==-9999,arr.ind=TRUE)+3),]
- response<-response[-c(which(response==-9999,arr.ind=TRUE))]
- bg.dat$TrainSplit=""
- }
-
- temp<-if(!is.null(RatioPresAbs))(sum(response>=1)/sum(response==0)==RatioPresAbs)
- if(is.null(temp)) temp<-FALSE
- if(is.null(RatioPresAbs)| temp){
- #Randomly sample presesce absence or counts as close to the size of the training proportion as possible
-
- #iterate through each unique response and randomly assign the trainProp to be in the training split
- TrainSplit<-numeric()
- for(i in sort(as.numeric(unique(response)))){
- TrainSplit<-c(TrainSplit,sample(which(response==i,arr.ind=TRUE),size=round(sum(response==i)*trainProp)))
- }
-
-
- #Take everything not in the training set for the test set
- TestSplit=which(!(seq(1:length(response)))%in%TrainSplit,arr.ind=TRUE)
-
- dat$TrainSplit[seq(1:length(response))%in%TrainSplit]<-"train"
- dat$TrainSplit[seq(1:length(response))%in%TestSplit]<-"test"
-
- #inserting data must be done in 3 steps because dat.in isn't a proper dataframe in that
- #not all elements in a column are of the same type
- dat.in<-dat.in[c(1:3,rownames(dat)),] #removing rows that weren't selected for the test train split
- dat.in[4:(dim(dat.in)[1]),(dim(dat.in)[2]+1)]<-dat$TrainSplit
- dat.in[c(1,3),(dim(dat.in)[2])]<-c("Split","")
- dat.in[2,(dim(dat.in)[2])]<-1
-
-
- } else { #now considering if there is a desired ratio of presence to absence points
- if(sum(response>=1)/sum(response==0)>=RatioPresAbs){
-
- #first determine how many presence points to remove
- TotToRmv<-(sum(response>=1)-RatioPresAbs*sum(response==0))
- # if(TotToRmv/sum(response>=1)>.5) {
- # warning("******************************************\n**** Over 50% of the
- # presence points were removed to meet the desired ratio of presence to absence \n******************************************")}
- #determine the number of each count to remove weighted by the reponse and then remove these
- EachToRmv<-round(TotToRmv*table(response[response!=0])/sum(response!=0))
- ByCount<-split(cbind(which(response!=0,arr.ind=TRUE)),f=response[response!=0])
-
- #sampling one from a vector of size 1 actually samples a sequence from 1 to the value in the vector
- #so correcting this here
- sam<-function(x,size){if(length(x)==1 & size==1) return(x)
- else sample(x=x,size=size)}
-
- RmvIndx<-as.vector(unlist(mapply(sam,x=ByCount,size=EachToRmv)))
- KeepIndx<-seq(1:length(response))[-c(RmvIndx)]
- Response<-response[KeepIndx]
- names(Response)<-KeepIndx
-
- #now break these into a train an test split while
- TrainSplit<-numeric()
-
- for(i in sort(as.numeric(unique(Response)))){
- TrainSplit<-c(TrainSplit,sample(names(Response[Response==i]),size=round(sum(Response==i)*trainProp)))
- }
- TrainSplit<-as.numeric(TrainSplit)
- #Take everything not in the training set or in the remove list for the test set
- TestSplit<-seq(from=1,to=length(response))[-c(c(TrainSplit,RmvIndx))]
-
- dat$TrainSplit[seq(1:length(response))%in%TrainSplit]<-"train"
- dat$TrainSplit[seq(1:length(response))%in%TestSplit]<-"test"
-
-
- }
-
- if(sum(response>=1)/sum(response==0)<RatioPresAbs){
- browser()
- #first ballance all responses greater than 1
- TrainSplit<-numeric()
- for(i in sort(as.numeric(unique(response[response!=0])))){
- TrainSplit<-c(TrainSplit,sample(which(response==i,arr.ind=TRUE),size=round(sum(response==i)*trainProp)))
- }
- # if((sum(response==0)-sum(response>=1)/RatioPresAbs)/sum(response==0)>.5) {
- # warning("******************************************\n**** Over 50% of the
- # absence points were removed to meet the desired ratio of presence to absence \n******************************************")}
- #now sampling the right number of absence points for the train split
- TrainSplit<-c(TrainSplit,sample(which(response==0,arr.ind=TRUE),size=round(sum(response>=1)*(1/RatioPresAbs)*trainProp)))
-
- #Take everything not in the training set for the test set
- TestSplit=which(!(seq(1:length(response)))%in%TrainSplit,arr.ind=TRUE)
-
- #now sample some points to remove so we have the correct proportion
- temp<-sample(which(TestSplit%in%which(response==0,arr.ind=TRUE),arr.ind=TRUE),
- size=round(sum(TestSplit%in%which(response==0,arr.ind=TRUE))-(1-trainProp)*sum(response>=1)*(1/RatioPresAbs)))
- TestSplit<-TestSplit[-c(temp)]
-
- dat$TrainSplit[seq(1:length(response))%in%TrainSplit]<-"train"
- dat$TrainSplit[seq(1:length(response))%in%TestSplit]<-"test"
-
- }
-
- dat<-dat[c(TrainSplit,TestSplit),]
-
- dat.in<-dat.in[c(1:3,rownames(dat)),] #removing rows that weren't selected for the test train split
- dat.in[4:(dim(dat.in)[1]),(dim(dat.in)[2]+1)]<-dat$TrainSplit
- dat.in[c(1,3),(dim(dat.in)[2])]<-c("Split","")
- dat.in[2,(dim(dat.in)[2])]<-1
-
-
- }
-
- if(dim(bg.dat)[1]!=0) {
- names(bg.dat)<-names(dat.in)
- dat.in<-rbind(dat.in,bg.dat)}
-
- #write output files for R modules
- write.table(dat.in,file=output.file,row.names=FALSE,col.names=FALSE,sep=",",quote=FALSE)
-
-
- }
-
-
- #Reading in command line arguments
- Args <- commandArgs(T)
- print(Args)
- #assign default values
-
- responseCol <- "responseBinary"
- trainProp=.7
- RatioPresAbs=NULL
- #replace the defaults with passed values
- for (arg in Args) {
- argSplit <- strsplit(arg, "=")
- argSplit[[1]][1]
- argSplit[[1]][2]
- if(argSplit[[1]][1]=="p") trainProp <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="m") RatioPresAbs <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="o") output.file <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="i") infil <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
- }
-
- RatioResAbs<-as.numeric(RatioPresAbs)
- trainProp<-as.numeric(trainProp)
-
- #Run the Test training split with these parameters
- TestTrainSplit(input.file=infil,output.file=output.file,response.col=responseCol,
- trainProp=trainProp,RatioPresAbs=RatioPresAbs)
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/CallPairsPlot.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/CallPairsPlot.r
deleted file mode 100644
index 608b7f3..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/CallPairsPlot.r
+++ /dev/null
@@ -1,114 +0,0 @@
-#Running R from the command line
-#input.file="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv"
- #output.dir<-"H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck\\"
- #response.col= "ResponseBinary"
- #min.cor<-.7
- #num.plots<-10
-source("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules\\PairsExplore.r")
-
-
-
-num.plots <- 10
- min.cor <- .7
- responseCol <- "responseCount"
- cors.w.highest <- FALSE
- pres=FALSE
- absn=TRUE
- bgd=TRUE
- #infile="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110510T100421\\TestTrainingSplit_1.csv"
- infile="I:\\NPS_NPMP_data\\ModelingSession_June\\EAME_MDS.csv"
- output.file="H:\\Desktop\\SAHM\\Output\\PairsPlot\\pairPres.jpg"
- Pairs.Explore(num.plots=num.plots,
- min.cor=min.cor,
- input.file=infile,
- output.file=output.file,
- response.col=responseCol,
- pres=TRUE,
- absn=TRUE,
- bgd=TRUE,
- Debug=TRUE)
-
-#binary
-input.file="C:\\VisTrails\\EAMEBinTT.csv"
-input.file="C:\\VisTrails\\DICKBinTT.csv"
-input.file="C:\\VisTrails\\HESPBinTT.csv"
-input.file="C:\\VisTrails\\GRSPBinTT.csv"
-responseCol="responseBinary"
-input.file="I:\\SpeciesData\\kudzu\\July2011\\MergedDataset_1.csv"
-#list.files("I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110725T102358")
-Pairs.Explore(num.plots=num.plots,
- min.cor=min.cor,
- input.file=input.file,
- output.file=output.file,
- response.col=responseCol,
- pres=TRUE,
- absn=TRUE,
- bgd=TRUE,
- Debug=TRUE)
-
-
-#count
-input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\EAME_MDS.csv"
-input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\DICK_MDS.csv"
-input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\HESP_MDS.csv"
-input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\GRSP_MDS.csv"
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T083827\\MergedDataset_1.csv"
-
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T114212\\MergedDataset_1.csv"
-responseCol="responseBinary"
-Pairs.Explore(num.plots=num.plots,
- min.cor=min.cor,
- input.file=input.file,
- output.file=output.file,
- response.col=responseCol,
- pres=TRUE,
- absn=TRUE,
- bgd=TRUE,
- Debug=TRUE)
-
-print(getwd())
-source_pathname = get("PairsExplore",envir = parent.frame())
-source_dirname = dirname(source_pathname )
-setwd(source_dirname)
-print(getwd())
-
-
-frame_files <- lapply(sys.frames(), function(x) x$ofile)
-frame_files <- Filter(Negate(is.null), frame_files)
-PATH <- dirname(frame_files[[length(frame_files)]])
-
-
-as.double.foo <- function(x)
-{
- str(sys.calls())
- print(sys.frames())
- print(sys.parents())
- print(sys.frame(-1)); print(parent.frame())
- x
-}
-t2 <- function(x) as.double(x)
-a <- structure(pi, class = "foo")
-t2(a)
-
-library(R.utils)
-print(getAbsolutePath("Pairs.Explore"))
-
-
-Pairs.Explore(num.plots=10,min.cor=.7,input.file="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv",
-output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck\\",
-response.col="ResponseBinary",cors.w.highest=TRUE)
-
-# The BRT Function
-C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\pySAHM\Resources\R_Modules\FIT_BRT_pluggable.r --args c=I:\VisTrails\WorkingFiles\workspace\GYA_demo\test.csv o=C:\temp rc=ResponseBinary
-
-
-C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f H:\Desktop\SAHM\Rcode\PredictorSelection\PairsExplore2.r --args p=10 m=.7 o=H:\Desktop\SAHM\Rcode\ExposingModelParameters\PDFCheck\ i="I:\VisTrails\WorkingFiles\workspace\GYA_demo\test.csv" rc="ResponseBinary" core=TRUE
-
-
-
-if(argSplit[[1]][1]=="p") num.plots <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="m") min.cor <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="o") output.dir <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="i") input.file <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="rc") responseCol <- argSplit[[1]][2]
- if(argSplit[[1]][1]=="core") cors.w.higest <- argSplit[[1]][2]
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Debugging.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Debugging.r
deleted file mode 100644
index 5ae306d..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Debugging.r
+++ /dev/null
@@ -1,173 +0,0 @@
-setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
-source("FIT_BRT_pluggable.r")
-source("FIT_MARS_pluggable.r")
-source("FIT_RF_pluggable.r")
-source("FIT_GLM_pluggable.r")
-
-source("EvaluationStats.r")
-source("TestTrainRocPlot.r")
-source("read.ma.r")
-source("proc.tiff.r")
-source("PredictModel.r")
-
-# Currently testing to see if models work with
-# * new test train split
-# * separation of model fit from prediction
-# * working with count data
-# * producing correct evaluation metrics
-#Future testing will include testing that factor columns are handled correctly
-#trace(proc.tiff,browser)
-#options(error=expression(if(interactive()) recover() else dump.calls()))
-#options(error=NULL)
-#trace(proc.tiff,browser)
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
-output.dir="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\brtoutput_1"
-rc="responseBinary"
-PredictModel(workspace="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T130214\\brtoutput_1\\modelWorkspace",out.dir="C:\\VisTrails")
-PredictModel(workspace="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T130214\\brtoutput_1\\modelWorkspace",out.dir="C:\\VisTrails\\mtalbert_20110505T161105",make.btif=TRUE,make.ptif=TRUE)
-#######################################################
-## BRT TESTING
-
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
- rc="ResponseBinary"
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
-
-#this file does have a test training split
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110602T155823\\MergedDataset_1.csv"
- rc="responseCount"
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T095017\\MergedDataset_2.csv"
-output.dir="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T095017\\brtoutput_1"
-rc="responseBinary"
-
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T134303\\TestTrainingSplit_1.csv"
-output.dir="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T134303\\marsoutput_3"
-rc="responseBinary"
-
-fit.mars.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",model.family="binomial",script.name="mars.r")
-
-fit.brt.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, max.trees = NULL,opt.methods=1,seed=1,save.model=TRUE)
-
-source("FIT_MARS_pluggable.r")
-PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-#########################################################
-## MARS TESTING
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
-
- #this input file does not have a test training split
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
- rc="ResponseBinary"
-
- #this file does have a test training split
- input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
- rc="responseBinary"
-
-fit.mars.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- mars.degree=1,mars.penalty=2,debug.mode=F,responseCurveForm="pdf",model.family="binomial",script.name="mars.r")
-
-PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-#########################################################
-## GLM TESTING
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
- rc="ResponseBinary"
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
-
-#this file does have a test training split
- input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
- rc="responseBinary"
-
-fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
-
-PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-########################################################
-## RANDOM FOREST TESTING
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
- rc="ResponseBinary"
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
-
-#this file does have a test training split
- input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
- rc="responseBinary"
-
-fit.rf.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- debug.mode=T,n.trees=1000)
-
-PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-
-#Now testing to make sure this code works with no test training split
-ma.name<-"H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\ModelOutputCheck\\NewInput.csv"
-ma.name="C:\\VisTrails\\mtalbert_20110406T093111\\sahm4h5b1t.mds"
-
-ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv"
-fit.brt.fct(ma.name=ma.name,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
-
-
-#this is the GLM_pluggable1.r under NewMDSBuilder (Works with new vistrails format)
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110510T100421\\TestTrainingSplit_1.csv"
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
-rc="responseCount"
-
- fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col=rc,make.p.tif=T,make.binary.tif=T,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
-
-
-#Mars check Works with new vistrails format
- fit.mars.fct(ma.name=ma.name,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
-
-
-fit.rf.fct(ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv",
- tif.dir=NULL,
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- debug.mode=T,n.trees=1000,ma.test=NULL,make.r.curves=T,script.name="glm.r")
-
-
-
-#this one does not subset paths set up in the old way works with old sahm as well as for
-fit.brt.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
-tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
-response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,ma.test=NULL,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
-
-
-fit.mars.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
- tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
-
-fit.glm.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
- tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",ma.test=NULL,script.name="glm.r")
-
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Dickessel.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Dickessel.r
deleted file mode 100644
index fc80871..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/Dickessel.r
+++ /dev/null
@@ -1,231 +0,0 @@
- setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
-source("FIT_BRT_pluggable.r")
-source("FIT_MARS_pluggable.r")
-source("FIT_RF_pluggable.r")
-source("FIT_GLM_pluggable.r")
-
-source("EvaluationStats.r")
-source("TestTrainRocPlot.r")
-source("read.ma.r")
-source("proc.tiff.r")
-source("PredictModel.r")
-
-# Currently testing to see if models work with
-# * new test train split
-# * separation of model fit from prediction
-# * working with count data
-# * producing correct evaluation metrics
-#Future testing will include testing that factor columns are handled correctly
-#trace(proc.tiff,browser)
-#options(error=expression(if(interactive()) recover() else dump.calls()))
-#options(error=NULL)
-#trace(proc.tiff,browser)
-#################################################################################
-## Testing the code with some dickessel data
-
- ## EAME
- input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\EAME_MDS.csv"
- rc="responseCount"
- output.dir="C:\\VisTrails\\EAMENoTestTrain"
-
-## DICK
- input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\DICK_MDS.csv"
- rc="responseCount"
- output.dir="C:\\VisTrails\\DICKNoTestTrain"
-
-## HESP
- input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\HESP_MDS.csv"
- rc="responseCount"
- output.dir="C:\\VisTrails\\HESPNoTestTrain"
-
- ## GRSP
- input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\GRSP_MDS.csv"
- rc="responseCount"
- output.dir="C:\\VisTrails\\GRSPNoTestTrain"
-
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110623T104642\\SelectPredictorsLayers_second_1.csv"
-fit.brt.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "binomial", opt.methods=1,seed=1,save.model=FALSE)
-
-# No Predictions here
-# PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r",model.family="binomial",save.model=FALSE)
-
- #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
- fit.mars.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",model.family="poisson",script.name="mars.r",save.model=FALSE)
-
- #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-
-
-#######################################################
-### Now with a test/train split
-#################################################
-## GRSP
-input.file="C:\\VisTrails\\GRSP_TestTrain.csv"
- rc="responseCount"
- output.dir="C:\\VisTrails\\GRSPTest"
-
-
-input.file="C:\\VisTrails\\HESP_TestTrain.csv"
- rc="responseCount"
- output.dir="C:\\VisTrails\\HESPTest"
-
-input.file="C:\\VisTrails\\EAME_TestTrain.csv"
- rc="responseCount"
- output.dir="C:\\VisTrails\\EAMETest"
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T083717\\TestTrainingSplit_1"
- rc="responseCount"
- output.dir="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T083717"
-
-############################################################
-### Testing with binary data
-
- ## EAME
- input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\EAME_MDS_binary.csv"
- rc="responseBinary"
- output.dir="C:\\VisTrails\\EAMEBin"
-
-## DICK
- input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\DICK_MDS_binary.csv"
- rc="responseBinary"
- output.dir="C:\\VisTrails\\DICKBin"
-
-## HESP
- input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\HESP_MDS_binary.csv"
- rc="responseBinary"
- output.dir="C:\\VisTrails\\HESPBin"
-
- ## GRSP
- input.file="I:\\NPS_NPMP_data\\ModelingSession_June\\GRSP_MDS_binary.csv"
- rc="responseBinary"
- output.dir="C:\\VisTrails\\GRSPBin"
-
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T083717\\TestTrainingSplit_1.csv"
- rc="responseCount"
- output.dir="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T083717"
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T113117\\TestTrainingSplit_1.csv"
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110622T113117\\MergedDataset_2.csv"
-fit.brt.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "binomial", opt.methods=1,seed=1,save.model=FALSE)
-
-# No Predictions here
-# PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r",model.family="binomial",save.model=FALSE)
-
- #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
- fit.mars.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",model.family="binomial",script.name="mars.r",save.model=FALSE)
-
- #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-fit.rf.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- debug.mode=T,n.trees=1000,save.model=FALSE)
-
-
-###################################################################################
-## testing with binary with a test train split
- ## EAME
- input.file="C:\\VisTrails\\EAMEBinTT.csv"
- rc="responseBinary"
- output.dir="C:\\VisTrails\\EAMEBinTT"
-
-## DICK
- input.file="C:\\VisTrails\\DICKBinTT.csv"
- rc="responseBinary"
- output.dir="C:\\VisTrails\\DICKBinTT"
-
-## HESP
- input.file="C:\\VisTrails\\HESPBinTT.csv"
- rc="responseBinary"
- output.dir="C:\\VisTrails\\HESPBinTT"
-
- ## GRSP
- input.file="C:\\VisTrails\\GRSPBinTT.csv"
- rc=r"responseBinary"
- output.dir="C:\\VisTrails\\GRSPBinTT"
-
-fit.brt.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "binomial", opt.methods=1,seed=1,save.model=FALSE)
-
-# No Predictions here
-# PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r",model.family="binomial",save.model=FALSE)
-
- #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
- fit.mars.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",model.family="binomial",script.name="mars.r",save.model=FALSE)
-
- #PredictModel(workspace=paste("C:\\VisTrails\\EAMENoTestTrain","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-fit.rf.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- debug.mode=T,n.trees=1000,save.model=FALSE)
-
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T083827\\MergedDataset_1.csv"
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T112620\\TestTrainingSplit_1.csv"
-
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T114212\\MergedDataset_1.csv"
-
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T115847\\TestTrainingSplit_2.csv"
- rc="responseBinary"
-output.dir="C:\\VisTrails"
-
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T134656\\TestTrainingSplit_1.csv"
-rc="responseCount"
-fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=T,make.binary.tif=T,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r",model.family="binomial",save.model=FALSE)
-
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\talbertc_20110621T114212\\MergedDataset_1.csv"
-fit.brt.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "binomial", opt.methods=1,seed=1,save.model=FALSE)
-
-
-C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\pySAHM\Resources\R_Modules\FIT_RF_pluggable.r --args mbt=FALSE mpt=FALSE c=N:\Active\FORT_RAM\VisTrails\workspace\dignizio_20110616T162343\TestTrainingSplit_4.csv o=N:\Active\FORT_RAM\VisTrails\workspace\dignizio_20110616T162343\rfoutput_7 rc=responseBinary
-C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\pySAHM\Resources\R_Modules\PairsExplore.r --args i=N:\Active\FORT_RAM\VisTrails\workspace\talbertc_20110621T083827\MergedDataset_1.csv o=N:\Active\FORT_RAM\VisTrails\workspace\talbertc_20110621T083827\PredictorCorrelation_second_1.jpg m=0.7 rc=responseBinary pres=TRUE absn=TRUE bgd=TRUE
-C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\pySAHM\Resources\R_Modules\FIT_BRT_pluggable.r --args c=N:\Active\FORT_RAM\VisTrails\workspace\talbertc_20110621T105356\TestTrainingSplit_1.csv o=N:\Active\FORT_RAM\VisTrails\workspace\talbertc_20110621T105356\brtoutput_1 rc=responseBinary
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/QuickDebug.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/QuickDebug.r
deleted file mode 100644
index cc1b157..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/QuickDebug.r
+++ /dev/null
@@ -1,75 +0,0 @@
-setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
-setwd("I:\\VisTrails\\Central_VisTrailsInstall\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
-source("FIT_BRT_pluggable.r")
-source("FIT_MARS_pluggable.r")
-source("FIT_RF_pluggable.r")
-source("FIT_GLM_pluggable.r")
-
-source("EvaluationStats.r")
-source("TestTrainRocPlot.r")
-source("read.maNew.r")
-source("proc.tiff.r")
-source("PredictModel.r")
-source("PredictModel.r")
-source("modalDialog.R")
-source("check.libs.r")
-options(error=expression(if(interactive()) recover() else dump.calls()))
-options(error=NULL)
-trace(proc.tiff,browser)
-
-list.files()
-#Testing Compile Output on data with no test train and with a test train
-
-
-input.file="N:/Active/FORT_RAM/VisTrails/workspace/mtalbert_20110817T104421/MergedDataset_1.csv"
-#input.file="N:/Active/FORT_RAM/VisTrails/workspace/mtalbert_20110817T104421/MergedDatasetTestTrain_1.csv"
-
-#No test training split
-
-#this one has a test training split
-
-output.dir="C:\\temp\\SAHMDebugJunk\\BRTOut1"
-rc="responseBinary"
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110824T133049\\CovariateCorrelationOutputMDS_anothertry.csv"
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110825T130119\\CovariateCorrelationOutputMDS_anothertry2.csv"
-#input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110824T133049\\CovariateCorrelationOutputMDS_anothertry2.csv"
-
-##RF
- fit.rf.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- debug.mode=T,n.trees=1000,opt.methods=5)
-
- PredictModel(workspace=paste(output.dir,"modelWorkspace",sep="\\"),out.dir=output.dir)
-
-##BRT
- fit.brt.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, max.trees = NULL,opt.methods=2,seed=1,save.model=TRUE)
-
- PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-##MARS
- fit.mars.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- mars.degree=1,mars.penalty=2,debug.mode=F,responseCurveForm="pdf",script.name="mars.r")
-
- PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-##GLM
- fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
-
- PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-
-## Command line
-C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall_debug\vistrails\packages\sahm\pySAHM\Resources\R_Modules\FIT_MARS_pluggable.r --args c=I:\VisTrails\WorkingFiles\workspace\talbertc_20110824T133049\CovariateCorrelationOutputMDS_anothertry2.csv o=I:\VisTrails\WorkingFiles\workspace\talbertc_20110824T133049\marsoutput_4 rc=responseBinary
-C:\R-2.12.1\bin\i386\Rterm.exe --vanilla -f I:\VisTrails\Central_VisTrailsInstall\vistrails\packages\sahm\pySAHM\Resources\R_Modules\FIT_RF_pluggable.r --args c=I:\VisTrails\WorkingFiles\workspace\talbertc_20110825T130119\CovariateCorrelationOutputMDS_anothertry2.csv o=I:\VisTrails\WorkingFiles\workspace\talbertc_20110825T130119\rfoutput_1 rc=responseBinary
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTestTrainSplit.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTestTrainSplit.r
deleted file mode 100644
index 5263aef..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTestTrainSplit.r
+++ /dev/null
@@ -1,171 +0,0 @@
-### This file runs the TestTrainSplit and checks that all ratios end up being what they should if RatioPresAbs is set at an extreme value
-### an excessive number of values are deleted and ratios and be drastically off might want to include future error checking
-setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
-source("TestTrainSplit.r")
-
-input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSetNullModelTest.csv"
-output.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSetNullSplit.csv"
-
-input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSetIncludeTest.csv"
-output.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSetIncludeSplit.csv"
-
-input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
-output.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSplitTest.csv"
-
-input.file="N:/Active/FORT_RAM/VisTrails/workspace/mtalbert_20110817T104421/MergedDataset_1.csv"
-input.file="I:/VisTrails/WorkingFiles/workspace/morisettej_20110810T153126/CovariateCorrelationOutputMDS_anothertry.csv"
-output.file="N:/Active/FORT_RAM/VisTrails/workspace/mtalbert_20110817T104421/MergedDatasetTestTrain_1.csv"
-response.col="ResponseBinary"
-
-## Running the code
-TestTrainSplit(input.file,output.file,response.col=response.col,trainProp=.7) #tried also with .8, and no RatioPresAb
-
-## Running some tests on the output
-input.file<-output.file
-dat<-read.csv(input.file,skip=3,header=FALSE)
-
- hl<-readLines(input.file,1)
- hl=strsplit(hl,',')
- colnames(dat) = hl[[1]]
-
- tif.info<-readLines(input.file,3)
- tif.info<-strsplit(tif.info,',')
- include<-(as.numeric(tif.info[[2]]))
-
-# checking that trainProp is correct
-ta<-table(dat$Split,dat$responseBinary)
-ta
-#if there are background points, remove them here
-ta<-ta[-1,]
-ta<-ta[,-1]
-
-#checking that the trainProp was ballanced for each count all of these
-#should be approximately equal to the trainProp this works less well for
-#smaller sample sizes
-ta[2,]/(ta[1,]+ta[2,])
-
-#checks trainProp is correct
-sum(ta[2,])/sum(ta)
-sum(ta[1,])/sum(ta)
-
-#checking ratio of presence to absence should equal RatioPresAbs
-sum(ta[1,2:dim(ta)[2]])/ta[1,1]
-sum(ta[2,2:dim(ta)[2]])/ta[2,1]
-
-#######################################################
-#### testing looking at an mds with counts case 1. appears to be working###########
-input.file<-"H:\\Desktop\\SAHM\\Data\\ChangeFamilyData\\MergedDataSet_1.csv"
-output.file<-"H:\\Desktop\\SAHM\\Output\\TestTrainSplit\\testtrain.mds"
-TestTrainSplit(input.file,output.file,response.col="ResponseCount",trainProp=.7,RatioPresAbs=.9)
-
-input.file<-output.file
-dat<-read.csv(input.file,skip=3,header=FALSE)
-
- hl<-readLines(input.file,1)
- hl=strsplit(hl,',')
- colnames(dat) = hl[[1]]
-
- tif.info<-readLines(input.file,3)
- tif.info<-strsplit(tif.info,',')
- include<-(as.numeric(tif.info[[2]]))
-
-# checking that trainProp is correct
-ta<-table(dat$Split,dat$responseCount)
-ta
-
-#if there are background points, remove them here
-ta<-ta[-1,]
-ta<-ta[,-1]
-
-#checking that the trainProp was ballanced for each count all of these
-#should be approximately equal to the trainProp this works less well for
-#smaller sample sizes
-ta[2,]/(ta[1,]+ta[2,])
-
-#checks trainProp is correct
-sum(ta[2,])/sum(ta)
-sum(ta[1,])/sum(ta)
-
-#checking ratio of presence to absence should equal RatioPresAbs
-sum(ta[1,2:dim(ta)[2]])/ta[1,1]
-sum(ta[2,2:dim(ta)[2]])/ta[2,1]
-
-
-#######################################################
-#### testing looking at an mds with counts case 2. Looks like this is working too###########
-input.file<-"H:\\Desktop\\SAHM\\Data\\ChangeFamilyData\\MergedDataSet_1.csv"
-output.file<-"H:\\Desktop\\SAHM\\Output\\TestTrainSplit\\testtrain.mds"
-TestTrainSplit(input.file,output.file,response.col="ResponseCount",trainProp=.7,RatioPresAbs=.4)
-
-input.file<-output.file
-dat<-read.csv(input.file,skip=3,header=FALSE)
-
- hl<-readLines(input.file,1)
- hl=strsplit(hl,',')
- colnames(dat) = hl[[1]]
-
- tif.info<-readLines(input.file,3)
- tif.info<-strsplit(tif.info,',')
- include<-(as.numeric(tif.info[[2]]))
-
-# checking that trainProp is correct
-ta<-table(dat$Split,dat$responseCount)
-ta
-
-#if there are background points, remove them here
-ta<-ta[-1,]
-ta<-ta[,-1]
-
-#checking that the trainProp was ballanced for each count all of these
-#should be approximately equal to the trainProp this works less well for
-#smaller sample sizes
-ta[2,]/(ta[1,]+ta[2,])
-
-
-#checks trainProp is correct
-sum(ta[2,])/sum(ta)
-sum(ta[1,])/sum(ta)
-
-#checking ratio of presence to absence should equal RatioPresAbs for both the test and train split
-sum(ta[1,2:dim(ta)[2]])/ta[1,1]
-sum(ta[2,2:dim(ta)[2]])/ta[2,1]
-
-
-#######################################################
-#### testing looking at an mds with counts case 3. Without a RatioPresAbs###########
-input.file<-"H:\\Desktop\\SAHM\\Data\\ChangeFamilyData\\MergedDataSet_1.csv"
-output.file<-"H:\\Desktop\\SAHM\\Output\\TestTrainSplit\\testtrain.mds"
-TestTrainSplit(input.file,output.file,response.col="ResponseCount",trainProp=.7)
-
-input.file<-output.file
-dat<-read.csv(input.file,skip=3,header=FALSE)
-
- hl<-readLines(input.file,1)
- hl=strsplit(hl,',')
- colnames(dat) = hl[[1]]
-
- tif.info<-readLines(input.file,3)
- tif.info<-strsplit(tif.info,',')
- include<-(as.numeric(tif.info[[2]]))
-
-# checking that trainProp is correct
-ta<-table(dat$Split,dat$responseCount)
-ta
-
-#if there are background points, remove them here
-ta<-ta[-1,]
-ta<-ta[,-1]
-
-#checking that the trainProp was ballanced for each count all of these
-#should be approximately equal to the trainProp this works less well for
-#smaller sample sizes
-ta[2,]/(ta[1,]+ta[2,])
-
-
-#checks trainProp is correct
-sum(ta[2,])/sum(ta)
-sum(ta[1,])/sum(ta)
-
-#checking ratio of presence to absence should equal RatioPresAbs for both the test and train split
-sum(ta[1,2:dim(ta)[2]])/ta[1,1]
-sum(ta[2,2:dim(ta)[2]])/ta[2,1]
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTests.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTests.r
deleted file mode 100644
index 7aba394..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/RunTests.r
+++ /dev/null
@@ -1,173 +0,0 @@
-setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
-source("FIT_BRT_pluggable.r")
-source("FIT_MARS_pluggable.r")
-source("FIT_RF_pluggable.r")
-source("FIT_GLM_pluggable.r")
-source("EvaluationStats.r")
-source("TestTrainRocPlot.r")
-source("read.ma.r")
-source("proc.tiff.r")
-source("PredictModel.r")
-source("PairsExplore.r")
-
-# Currently testing to see if models work with
-# * new test train split
-# * separation of model fit from prediction
-# * working with count data
-# * producing correct evaluation metrics
-#Future testing will include testing that factor columns are handled correctly
-
-
-#################################################################
-## Current test files
-input.file<-vector()
-input.file[1]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullModelTest.csv"
-input.file[2]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullSplit.csv"
-input.file[3]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetIncludeTest.csv"
-input.file[4]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetIncludeSplit.csv"
-input.file[5]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSet_1.csv"
-input.file[6]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSplitTest.csv"
-input.file[7]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullModelTest2.csv"
-output.file<-sub("851/","851/TestOutput/",input.file)
-output.file<-sub(".csv",".jpg",output.file)
-
-#######################################################
-Debug=FALSE
-rc="ResponseBinary"
-output.dir="C:/VisTrails/mtalbert_20110504T132851/TestOutput"
-
-#BRT TEST LIST
- brt.list<-list()
- #this is the default scenario
- brt.list[[1]]<-list(make.p.tif=TRUE,
- make.binary.tif=TRUE,
- tc=NULL,
- n.folds=3,
- alpha=1,
- learning.rate=NULL,
- bag.fraction=.5,
- model.family="\"bernoulli\"",
- prev.stratify=TRUE,
- max.trees=10000,
- opt.methods=2,
- seed=NULL,
- tolerance.method="\"auto\"",
- tolerance=.001,
- debug.mode=FALSE)
- #setting up some alternative scenarios
- brt.list[[2]]<-brt.list[[1]]
- brt.list[[2]]$learning.rate=.002
-
- brt.list[[3]]<-brt.list[[1]]
- brt.list[[3]]$bag.fraction=1
- brt.list[[3]]$opt.methods=4
-
- #which datasets to test with the given set of parameters
- brt.use.list<-list()
- brt.use.list[[1]]<-c(3,4,5)
- brt.use.list[[2]]<-c(5,6,7)
- brt.use.list[[3]]<-c(3)
-
-#MARS TEST LIST
- mars.list<-list()
- #this is the default scenario
- mars.list[[1]]<-list(make.p.tif=T,
- make.binary.tif=T,
- mars.degree=1,
- mars.penalty=2,
- model.family="\"binomial\"",
- script.name="\"mars.r\"",
- opt.methods=2,
- save.model=TRUE,
- debug.mode=FALSE)
- #setting up some alternative scenarios
- mars.list[[2]]<-mars.list[[1]]
- mars.list[[2]]$mars.degree=2
-
- mars.list[[3]]<-mars.list[[1]]
- mars.list[[3]]$mars.penalty=3
- mars.list[[3]]$opt.methods=4
-
- #which datasets to test with the given set of parameters
- mars.use.list<-list()
- mars.use.list[[1]]<-c(3)
- mars.use.list[[2]]<-c(2,5,6,7)
- mars.use.list[[3]]<-c(3,4)
-
-#GLM TEST LIST
- glm.list<-list()
- #this is the default scenario
- glm.list[[1]]<-list(make.p.tif=TRUE,
- make.binary.tif=TRUE,
- simp.method="\"AIC\"",
- model.family="\"binomial\"",
- opt.methods=2,
- save.model=FALSE,
- debug.mode=FALSE)
- #setting up some alternative scenarios
- glm.list[[2]]<-glm.list[[1]]
- glm.list[[2]]$simp.method="\"BIC\""
-
- glm.list[[3]]<-glm.list[[1]]
- glm.list[[3]]$opt.methods=4
-
- #which datasets to test with the given set of parameters
- glm.use.list<-list()
- glm.use.list[[1]]<-c(1,3)
- glm.use.list[[2]]<-c(2,5,6,7)
- glm.use.list[[3]]<-c(1,2,3,4)
-
-#RF TEST LIST
- rf.list<-list()
- #this is the default scenario
- rf.list[[1]]<-list(make.p.tif=T,
- make.binary.tif=T,
- responseCurveForm="\"pdf\"",
- xtest=NULL,
- ytest=NULL,
- n.trees=1000,
- mtry=NULL,
- samp.replace=FALSE,
- sampsize=NULL,
- nodesize=NULL,
- maxnodes=NULL,
- importance=FALSE,
- localImp=FALSE,
- nPerm=1,
- proximity=NULL,
- oob.prox=proximity,
- norm.votes=TRUE,
- do.trace=FALSE,
- keep.forest=NULL,
- keep.inbag=FALSE,
- make.r.curves=T,
- seed=NULL,
- opt.methods=2,
- save.model=TRUE,
- seed=NULL)
- #setting up some alternative scenarios
- rf.list[[2]]<-rf.list[[1]]
- rf.list[[2]]$samp.replace=TRUE
-
- rf.list[[3]]<-rf.list[[1]]
- rf.list[[3]]$opt.methods=4
- rf.list[[3]]$seed=5
-
- rf.list[[4]]<-rf.list[[1]]
- rf.list[[4]]$opt.methods=4
- rf.list[[4]]$seed=5
-
- #which datasets to test with the given set of parameters
- rf.use.list<-list()
- rf.use.list[[1]]<-c(1,3)
- rf.use.list[[2]]<-c(2,5,6,7)
- rf.use.list[[3]]<-c(3,4)
- rf.use.list[[4]]<-c(3,4)
-
-
-parameter.list<-list(brt.list=brt.list,brt.use.list=brt.use.list,mars.list=mars.list,mars.use.list=mars.use.list,
- glm.list=glm.list,glm.use.list=glm.use.list,rf.list=rf.list,rf.use.list=rf.use.list)
-
-Out<-TestFunction(input.file,parameter.list,Debug,rc,output.dir)
-
-
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/SyntheticData.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/SyntheticData.r
deleted file mode 100644
index 48f73f1..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/SyntheticData.r
+++ /dev/null
@@ -1,78 +0,0 @@
-library(raster)
-slopedeg<-raster("C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\slopedeg.tif")
-bio_4<-raster("C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\bio_4_wgs84.tif")
-bio_12<-raster("C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\bio_12_wgs84.tif")
-bio_7<-raster("C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\bio_7_wgs84.tif")
-
-#putting bio_4 on a 0 to 1 range
-temp<-as.matrix(log(bio_4))
-b4<-(log(bio_4)-min(temp))/max(temp-min(temp))
-
-#putting bio_7 on a 0 to 1 range
-temp<-as.matrix(2^bio_7)
-b7<-(2^bio_7-min(temp))/max(temp-min(temp))
-
-#putting slopedeg on a 0 to 1 range
-temp<-as.matrix(slopedeg)
-sld<-(slopedeg-min(temp))/max(temp-min(temp))
-
-#making bio_12 discrete
-temp<-as.matrix(bio_12)
-qan<-quantile(temp,probs=c(.25,.5,.75))
-b12<-.25+.25*(bio_12>=qan[1])+.25*(bio_12>qan[2])+.25*(bio_12>qan[3])
-writeRaster(b12, filename="C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\Cat12_wgs84.tif")
-
-
-#for binomal data
-myFct<-.5*b4*b7+.25*sld+.25*b12+.18
-m<-as.matrix(myFct)
-xcoord<-sample(dim(m)[1],size=200)
-ycoord<-sample(dim(m)[2],size=200)
-cells<-cbind(xcoord,ycoord)
-cellNumbs<-cellFromRowCol(myFct,xcoord,ycoord)
-
-writeRaster(myFct, filename="C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\BinomialSurface.tif")
-
-value<-extract(myFct,cellNumbs)
-responseBinary<-rbinom(length(value),1,value)
-xy = xyFromCell(myFct, cellNumbs)
-
-Binom.out<-as.data.frame(cbind(xy,responseBinary))
-write.table(Binom.out,file="C:\\VisTrails\\mtalbert_20110504T132851\\FieldDatBinom.csv",row.names=FALSE,col.names=TRUE,sep=",",quote=FALSE)
-
-#now for Poisson data generate a lambda surface we want a lot of zeros
-
-PoisFct<-myFct*4
-m<-as.matrix(PoisFct)
-xcoord<-sample(dim(m)[1],size=200)
-ycoord<-sample(dim(m)[2],size=200)
-cells<-cbind(xcoord,ycoord)
-cellNumbs<-cellFromRowCol(PoisFct,xcoord,ycoord)
-
-value<-extract(PoisFct,cellNumbs)
-responseCount<-rpois(length(value),value)
-xy = xyFromCell(myFct, cellNumbs)
-
-par(mfrow=c(2,2))
-plot(as.vector(as.matrix(b4)),as.vector(as.matrix(PoisFct)))
-plot(as.vector(as.matrix(b7)),as.vector(as.matrix(PoisFct)))
-plot(as.vector(as.matrix(sld)),as.vector(as.matrix(PoisFct)))
-plot(as.vector(as.matrix(b12)),as.vector(as.matrix(PoisFct)))
-
-writeRaster(PoisFct, filename="C:\\VisTrails\\mtalbert_20110504T132851\\PARC_1\\PoissonSurface.tif")
-
-Pois.out<-as.data.frame(cbind(xy,responseCount))
-write.table(Pois.out,file="C:\\VisTrails\\mtalbert_20110504T132851\\FieldDatPois.csv",row.names=FALSE,col.names=TRUE,sep=",",quote=FALSE)
-
-BRT.Out<-raster("C:\\VisTrails\\prob_map.tif")
-BRT.Bin<-raster("C:\\VisTrails\\prob_map.tif")
-resids<-BRT.Out-PoisFct
-
-par(mfrow=c(2,2))
-plot(resids)
-plot(PoisFct)
-plot(BRT.Out)
-
-par(mfrow=c(2,1))
-hist(as.matrix(PoisFct),breaks=40)
-hist(as.matrix(BRT.Out),breaks=40)
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestCountModelRuns.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestCountModelRuns.r
deleted file mode 100644
index cbd6991..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestCountModelRuns.r
+++ /dev/null
@@ -1,186 +0,0 @@
-setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
-source("FIT_BRT_pluggable.r")
-source("FIT_MARS_pluggable.r")
-source("FIT_RF_pluggable.r")
-source("FIT_GLM_pluggable.r")
-
-source("EvaluationStats.r")
-source("TestTrainRocPlot.r")
-source("read.ma.r")
-source("proc.tiff.r")
-source("PredictModel.r")
-
-# Currently testing to see if models work with
-# * new test train split
-# * separation of model fit from prediction
-# * working with count data
-# * producing correct evaluation metrics
-#Future testing will include testing that factor columns are handled correctly
-#trace(proc.tiff,browser)
-#options(error=expression(if(interactive()) recover() else dump.calls()))
-#options(error=NULL)
-#trace(proc.tiff,browser)
-#######################################################
-## Count TESTING
-#this file does not have a test training split but uses Poisson data
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110607T084252\\TestTrainingSplit_2.csv"
-rc="responseCount"
-output.dir="C:\\VisTrails"
-
-fit.brt.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "poisson", opt.methods=1,seed=1,save.model=TRUE)
-
- PredictModel(workspace=paste("C:\\VisTrails","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-
-fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r",model.family="poisson")
-
- PredictModel(workspace=paste(output.dir,"modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-fit.mars.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",model.family="poisson",script.name="mars.r")
-
- PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-############################################################################
-#Making sure some old stuff works here's a presence absence model with no
-rc="ResponseBinary"
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
-fit.brt.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", opt.methods=2,seed=1,save.model=TRUE)
-
-PredictModel(workspace=paste("C:\\VisTrails","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-## Now testing GLM model with count data
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110607T084252\\TestTrainingSplit_2.csv"
- rc="responseCount"
- output.dir="C:\\VisTrails"
-
-
-
-##this does have a test training split, trying to figure out some good output for evaluation metrics module
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110607T084252\\MergedDataset_2.csv"
- rc="responseCount"
-
-fit.brt.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "poisson", opt.methods=1,seed=1,save.model=TRUE)
-
-
-#########################################################
-## MARS TESTING
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110607T084252\\MergedDataset_1.csv"
- rc="responseCount"
-
-
-
-
-#########################################################
-## GLM TESTING
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
- rc="ResponseBinary"
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
-
-#this file does have a test training split
- input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
- rc="responseBinary"
-
-fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
-
-PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-########################################################
-## RANDOM FOREST TESTING
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
- rc="ResponseBinary"
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
-
-#this file does have a test training split
- input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
- rc="responseBinary"
-
-fit.rf.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- debug.mode=T,n.trees=1000)
-
-PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-
-#Now testing to make sure this code works with no test training split
-ma.name<-"H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\ModelOutputCheck\\NewInput.csv"
-ma.name="C:\\VisTrails\\mtalbert_20110406T093111\\sahm4h5b1t.mds"
-
-ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv"
-fit.brt.fct(ma.name=ma.name,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
-
-
-#this is the GLM_pluggable1.r under NewMDSBuilder (Works with new vistrails format)
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110510T100421\\TestTrainingSplit_1.csv"
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
-rc="responseCount"
-
- fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col=rc,make.p.tif=T,make.binary.tif=T,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
-
-
-#Mars check Works with new vistrails format
- fit.mars.fct(ma.name=ma.name,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
-
-
-fit.rf.fct(ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv",
- tif.dir=NULL,
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- debug.mode=T,n.trees=1000,ma.test=NULL,make.r.curves=T,script.name="glm.r")
-
-
-
-#this one does not subset paths set up in the old way works with old sahm as well as for
-fit.brt.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
-tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
-response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,ma.test=NULL,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
-
-
-fit.mars.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
- tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
-
-fit.glm.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
- tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",ma.test=NULL,script.name="glm.r")
-
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestFunction2.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestFunction2.r
deleted file mode 100644
index 5ad66a1..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestFunction2.r
+++ /dev/null
@@ -1,23 +0,0 @@
-TestFunction<-function(input.file,parameter.list,Debug,rc,output.dir){
-
- ifelse(Debug,
- options(error=expression(if(interactive()) recover() else dump.calls())),
- options(error=NULL))
- Brt.Out<-list()
- Mars.Out<-list()
- Glm.Out<-list()
- RF.Out<-list()
- for (i in 1:length(input.file)){
- Brt.Out[[i]]<-unit.test(i,parameter.list$brt.use.list,parameter.list$brt.list,"brt",outpur.dir,rc)
- Mars.Out[[i]]<-unit.test(i,parameter.list$mars.use.list,parameter.list$mars.list,"mars",outpur.dir,rc)
- Glm.Out[[i]]<-unit.test(i,parameter.list$mars.use.list,parameter.list$mars.list,"glm",outpur.dir,rc)
- RF.Out[[i]]<-unit.test(i,parameter.list$mars.use.list,parameter.list$mars.list,"rf",outpur.dir,rc)
- } #end file for loop
-
- options(error=NULL)
- Out.list=list(Brt.Out=Brt.Out,Mars.Out=Mars.Out,Glm.Out=Glm.Out,RF.Out)
- return(Out.list)
-}
-
-
-
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns (2).r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns (2).r
deleted file mode 100644
index bc2aef4..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns (2).r
+++ /dev/null
@@ -1,148 +0,0 @@
-setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
-source("FIT_BRT_pluggable.r")
-source("FIT_MARS_pluggable.r")
-source("FIT_RF_pluggable.r")
-source("FIT_GLM_pluggable.r")
-source("EvaluationStats.r")
-source("TestTrainRocPlot.r")
-source("read.ma.r")
-source("proc.tiff.r")
-source("PredictModel.r")
-source("PairsExplore.r")
-
-# Currently testing to see if models work with
-# * new test train split
-# * separation of model fit from prediction
-# * working with count data
-# * producing correct evaluation metrics
-#Future testing will include testing that factor columns are handled correctly
-
-
-#################################################################
-## Current test files
-input.file<-vector()
-input.file[1]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullModelTest.csv"
-input.file[2]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullSplit.csv"
-input.file[3]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetIncludeTest.csv"
-input.file[4]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetIncludeSplit.csv"
-input.file[5]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSet_1.csv"
-input.file[6]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSplitTest.csv"
-input.file[7]="C:/VisTrails/mtalbert_20110504T132851/MergedDataSetNullModelTest2.csv"
-output.file<-sub("851/","851/TestOutput/",input.file)
-output.file<-sub(".csv",".jpg",output.file)
-
-#######################################################
-Debug=FALSE
-rc="ResponseBinary"
-output.dir="C:/VisTrails/mtalbert_20110504T132851/TestOutput"
-
-#BRT TEST LIST
- brt.list<-list()
- #this is the default scenario
- brt.list[[1]]<-list(make.p.tif=TRUE,
- make.binary.tif=TRUE,
- tc=NULL,
- n.folds=3,
- alpha=1,
- learning.rate=NULL,
- bag.fraction=.5,
- model.family="\"bernoulli\"",
- prev.stratify=TRUE,
- max.trees=10000,
- opt.methods=2,
- seed=NULL,
- tolerance.method="\"auto\"",
- tolerance=.001,
- debug.mode=FALSE)
- #setting up some alternative scenarios
- brt.list[[2]]<-brt.list[[1]]
- brt.list[[2]]$learning.rate=.002
-
- brt.list[[3]]<-brt.list[[1]]
- brt.list[[3]]$bag.fraction=1
- brt.list[[3]]$opt.methods=4
-
- #which datasets to test with the given set of parameters
- brt.use.list<-list()
- brt.use.list[[1]]<-c(3,4,5)
- brt.use.list[[2]]<-c(5,6,7)
- brt.use.list[[3]]<-c(3)
-
-#MARS TEST LIST
- mars.list<-list()
- #this is the default scenario
- mars.list[[1]]<-list(make.p.tif=T,
- make.binary.tif=T,
- mars.degree=1,
- mars.penalty=2,
- model.family="\"binomial\"",
- script.name="\"mars.r\"",
- opt.methods=2,
- save.model=TRUE,
- debug.mode=FALSE)
- #setting up some alternative scenarios
- mars.list[[2]]<-mars.list[[1]]
- mars.list[[2]]$mars.degree=2
-
- mars.list[[3]]<-mars.list[[1]]
- mars.list[[3]]$mars.penalty=3
- mars.list[[3]]$opt.methods=4
-
- #which datasets to test with the given set of parameters
- mars.use.list<-list()
- mars.use.list[[1]]<-c(3)
- mars.use.list[[2]]<-c(2,5,6,7)
- mars.use.list[[3]]<-c(3,4)
-
-#GLM TEST LIST
- glm.list<-list()
- #this is the default scenario
- glm.list[[1]]<-list(make.p.tif=TRUE,
- make.binary.tif=TRUE,
- simp.method="\"AIC\"",
- model.family="\"binomial\"",
- opt.methods=2,
- save.model=FALSE,
- debug.mode=FALSE)
- #setting up some alternative scenarios
- glm.list[[2]]<-glm.list[[1]]
- glm.list[[2]]$simp.method="\"BIC\""
-
- glm.list[[3]]<-glm.list[[1]]
- glm.list[[3]]$opt.methods=4
-
- #which datasets to test with the given set of parameters
- glm.use.list<-list()
- glm.use.list[[1]]<-c(1,3)
- glm.use.list[[2]]<-c(2,5,6,7)
- glm.use.list[[3]]<-c(1,2,3,4)
-
-#RF TEST LIST
- rf.list<-list()
- #this is the default scenario
- rf.list[[1]]<-list(make.p.tif=TRUE,
- make.binary.tif=TRUE,
- simp.method="\"AIC\"",
- model.family="\"binomial\"",
- opt.methods=2,
- save.model=FALSE,
- debug.mode=FALSE)
- #setting up some alternative scenarios
- rf.list[[2]]<-rf.list[[1]]
- rf.list[[2]]$simp.method="\"BIC\""
-
- rf.list[[3]]<-rf.list[[1]]
- rf.list[[3]]$opt.methods=4
-
- #which datasets to test with the given set of parameters
- rf.use.list<-list()
- rf.use.list[[1]]<-c(1,3)
- rf.use.list[[2]]<-c(2,5,6,7)
- rf.use.list[[3]]<-c(1,2,3,4)
-
-parameter.list<-list(brt.list=brt.list,brt.use.list=brt.use.list,mars.list=mars.list,mars.use.list=mars.use.list,
- glm.list=glm.list,glm.use.list=glm.use.list,rf.list=rf.list,rf.use.list=rf.use.list)
-
-Out<-TestFunction(input.file,parameter.list,Debug,rc,output.dir)
-
-
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns.r
deleted file mode 100644
index 3cb9a15..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestModelRuns.r
+++ /dev/null
@@ -1,174 +0,0 @@
-setwd("I:\\VisTrails\\Central_VisTrailsInstall_debug\\vistrails\\packages\\sahm\\pySAHM\\Resources\\R_Modules")
-source("FIT_BRT_pluggable.r")
-source("FIT_MARS_pluggable.r")
-source("FIT_RF_pluggable.r")
-source("FIT_GLM_pluggable.r")
-
-source("EvaluationStats.r")
-source("TestTrainRocPlot.r")
-source("read.ma.r")
-source("proc.tiff.r")
-source("PredictModel.r")
-
-# Currently testing to see if models work with
-# * new test train split
-# * separation of model fit from prediction
-# * working with count data
-# * producing correct evaluation metrics
-#Future testing will include testing that factor columns are handled correctly
-#trace(proc.tiff,browser)
-#options(error=expression(if(interactive()) recover() else dump.calls()))
-#options(error=NULL)
-#trace(proc.tiff,browser)
-list.files("I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110810T153126")
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110810T153126\\CovariateCorrelationOutputMDS_anothertry.csv"
-output.dir="C:\\temp\\SAHMDebugJunk"
-rc="responseBinary"
-fit.rf.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- debug.mode=T,n.trees=1000)
-
-PredictModel(workspace=paste(output.dir,"modelWorkspace",sep="\\"),out.dir=output.dir)
-
-#######################################################
-## BRT TESTING
-
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
- rc="ResponseBinary"
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
-
-#this file does have a test training split
-input.file="N:\\Active\\FORT_RAM\\VisTrails\\workspace\\mtalbert_20110602T155823\\MergedDataset_1.csv"
- rc="responseCount"
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T095017\\MergedDataset_2.csv"
-output.dir="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110721T095017\\brtoutput_1"
-rc="responseBinary"
-
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110804T084435\\CovariateCorrelationOutputMDS_initial.csv"
-output.dir="I:\\VisTrails\\WorkingFiles\\workspace\\morisettej_20110804T084435\\brtoutput_1"
-rc="responseBinary"
-fit.brt.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,test.resp.col="response",make.p.tif=F,make.binary.tif=F,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=.3,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, max.trees = NULL,opt.methods=1,seed=1,save.model=TRUE)
-
-source("FIT_MARS_pluggable.r")
-PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-#########################################################
-## MARS TESTING
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
-
- #this input file does not have a test training split
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
- rc="ResponseBinary"
-
- #this file does have a test training split
- input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
- rc="responseBinary"
-
-fit.mars.fct(ma.name=input.file,
- tif.dir=NULL,output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- mars.degree=1,mars.penalty=2,debug.mode=F,responseCurveForm="pdf",model.family="binomial",script.name="mars.r")
-
-PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-#########################################################
-## GLM TESTING
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
- rc="ResponseBinary"
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
-
-#this file does have a test training split
- input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
- rc="responseBinary"
-
-fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
-
-PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-########################################################
-## RANDOM FOREST TESTING
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
- rc="ResponseBinary"
- input.file="C:\\VisTrails\\mtalbert_20110504T132851\\MergedDataSet_1.csv"
-
-#this file does have a test training split
- input.file<-"I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110519T121044\\TestTrainingSplit_1.csv"
- rc="responseBinary"
-
-fit.rf.fct(ma.name=input.file,
- tif.dir=NULL,
- output.dir=output.dir,
- response.col=rc,make.p.tif=F,make.binary.tif=F,
- debug.mode=T,n.trees=1000)
-
-PredictModel(workspace=paste("C:\\VisTrails\\mtalbert_20110504T132851","modelWorkspace",sep="\\"),out.dir="C:\\VisTrails")
-
-
-#Now testing to make sure this code works with no test training split
-ma.name<-"H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\ModelOutputCheck\\NewInput.csv"
-ma.name="C:\\VisTrails\\mtalbert_20110406T093111\\sahm4h5b1t.mds"
-
-ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv"
-fit.brt.fct(ma.name=ma.name,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
-
-
-#this is the GLM_pluggable1.r under NewMDSBuilder (Works with new vistrails format)
-input.file="I:\\VisTrails\\WorkingFiles\\workspace\\talbertc_20110510T100421\\TestTrainingSplit_1.csv"
-output.dir="C:\\VisTrails\\mtalbert_20110504T132851"
-rc="responseCount"
-
- fit.glm.fct(ma.name=input.file,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col=rc,make.p.tif=T,make.binary.tif=T,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",script.name="glm.r")
-
-
-#Mars check Works with new vistrails format
- fit.mars.fct(ma.name=ma.name,
- tif.dir=NULL,output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
-
-
-fit.rf.fct(ma.name="I:\\VisTrails\\WorkingFiles\\workspace\\GYA_demo\\test.csv",
- tif.dir=NULL,
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="ResponseBinary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- debug.mode=T,n.trees=1000,ma.test=NULL,make.r.curves=T,script.name="glm.r")
-
-
-
-#this one does not subset paths set up in the old way works with old sahm as well as for
-fit.brt.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
-tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
-response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="cross-validation",debug.mode=T,responseCurveForm="pdf",tc=NULL,n.folds=3,ma.test=NULL,alpha=1,script.name="brt.r",
- learning.rate =NULL, bag.fraction = 0.5,prev.stratify = TRUE, model.family = "bernoulli", max.trees = NULL)
-
-
-fit.mars.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
- tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- mars.degree=1,mars.penalty=2,debug.mode=T,responseCurveForm="pdf",ma.test=NULL,model.family="binomial",script.name="mars.r")
-
-fit.glm.fct(ma.name="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\canadathistle_gcs_grp_r_mds_train.mds",
- tif.dir="H:\\Desktop\\SAHM\\Data\\CanadaThistle\\layers",
- output.dir="H:\\Desktop\\SAHM\\Rcode\\ExposingModelParameters\\PDFCheck",
- response.col="response.binary",test.resp.col="response",make.p.tif=T,make.binary.tif=T,
- simp.method="AIC",debug.mode=T,responseCurveForm="pdf",ma.test=NULL,script.name="glm.r")
-
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestingRandomForest.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestingRandomForest.r
deleted file mode 100644
index b70a563..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/TestingRandomForest.r
+++ /dev/null
@@ -1,17 +0,0 @@
-dat<-read.csv("C:\\VisTrails\\DICK_MDS_binary.csv")
-
-rf.full <- randomForest(x=dat[,-1],y=factor(dat[,1]),importance=TRUE,
- ntree=1000, replace=FALSE)
-
-pred<-predict(rf.full, newdata=dat[,-1],type="prob")[,2]
-
-null.dev<-calc.deviance(dat[,1], rep(p.bar,times=length(dat[,1])),family="binomial")*nrow(dat)
- dev.fit<-calc.deviance(dat[,1], pred, family="binomial")*nrow(dat)
- dev.exp <- null.dev - dev.fit
- pct.dev.exp <- dev.exp/null.dev*100
-
-r<-randomForest(x=dat[,-1],y=factor(out$dat$ma$ma[,1]),xtest=xtest,ytest=ytest,importance=TRUE, ntree=n.trees,
- mtry=mtry,replace=samp.replace,sampsize=ifelse(is.null(sampsize),(ifelse(samp.replace,nrow(x),ceiling(.632*nrow(x)))),sampsize),
- nodesize=ifelse(is.null(nodesize),(if (!is.null(y) && !is.factor(y)) 5 else 1),nodesize),maxnodes=maxnodes,
- localImp=localImp, nPerm=nPerm, keep.forest=ifelse(is.null(keep.forest),!is.null(y) && is.null(xtest),keep.forest),
- corr.bias=corr.bias, keep.inbag=keep.inbag)
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/unit.test.r b/contrib/sahm/pySAHM/Resources/R_Modules/Testing/unit.test.r
deleted file mode 100644
index 83a3985..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/Testing/unit.test.r
+++ /dev/null
@@ -1,49 +0,0 @@
-unit.test<-function(i,use.list,model.list,model,outpur.dir,rc){
- list.fct<-function(x,i) sum(!is.na(match(x=i,table=x)))
- valid.params<-which(unlist(lapply(use.list,list.fct,i=i))!=0,arr.ind=TRUE)
- Model.Out<-list()
- Model.Out[[i]]<-data.frame(list("FctFailed"=rep(FALSE,times=length(valid.params)),
- "PredictFailed"=rep(FALSE,times=length(valid.params)),
- "NullDev"=rep(0,times=length(valid.params)),
- "FitDev"=rep(0,times=length(valid.params)),
- "Correlation"=rep(0,times=length(valid.params)),
- "ErrorMessage"=rep("No Error",times=length(valid.params))),row.names=valid.params)
-
- class(Model.Out[[i]]$ErrorMessage)<-"character"
- if(length(valid.params)!=0){
- for(j in 1:length(valid.params)){
-
- k<-valid.params[j]
- if(Debug==TRUE) parameter.list$brt.list[[k]]$debug.mode=TRUE
-
- a<-paste(paste(names(model.list[[k]]),model.list[[k]],sep="="),collapse=",")
- call.fct<-paste("fit.",model,".fct(ma.name=\"",input.file[i],
- "\", tif.dir=NULL,output.dir=\"",output.dir,"\", response.col=\"",rc,"\",",a,")",sep="")
- #Right here I should remove almost everything since all output is written to the global environment
- call.predict<-"PredictModel(workspace=paste(output.dir,\"modelWorkspace\",sep=\"/\"),out.dir=output.dir)"
- if(Debug==FALSE) {call.fct<-paste("try(",call.fct,",silent=TRUE)",sep="")
- call.predict<-paste("try(",call.predict,")",sep="")
- #so that we don't predict on an old copy in the next loop
- file.remove(paste(output.dir,"modelWorkspace",sep="/"))
- }
-
- fct.output<-eval(parse(text=call.fct))
- sink()
- pred.output<-eval(parse(text=call.predict))
- sink()
- if(class(fct.output)=="try-error") {
- Model.Out[[i]][j,1]=TRUE
- Model.Out[[i]][j,6]=fct.output[1]
- } else {
- Model.Out[[i]][j,1]=FALSE
- Model.Out[[i]][j,3]<-fct.output$mods$auc.output$null.dev
- Model.Out[[i]][j,4]<-fct.output$mods$auc.output$dev.fit
- Model.Out[[i]][j,5]<-fct.output$mods$auc.output$correlation
- }
- if(class(pred.output)=="try-error") Model.Out[[i]][j,2]=TRUE
-
- }
- print(Model.Out)
- } ## END BRT
-return(Model.Out)
- }
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/check.libs.r b/contrib/sahm/pySAHM/Resources/R_Modules/check.libs.r
deleted file mode 100644
index 49a16bb..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/check.libs.r
+++ /dev/null
@@ -1,16 +0,0 @@
-check.libs <- function(libs,out){
-
- lib.mssg <- unlist(suppressMessages(suppressWarnings(lapply(libs,require,quietly = T, warn.conflicts=F,character.only=T))))
- if(any(!lib.mssg)){
- install.packages(unlist(libs[!lib.mssg]), repos = "http://cran.r-project.org")
- lib.mssg <- unlist(suppressMessages(suppressWarnings(lapply(unlist(libs[!lib.mssg]),require,quietly = T, warn.conflicts=F,character.only=T))))
- }
- if(any(!lib.mssg)) {
- out$ec <- out$ec+1
- out$dat$missing.libs <- paste(unlist(libs)[!lib.mssg],collapse="; ")
- stop("the following package(s) could not be loaded:",out$dat$missing.libs)
- }
- return(out)
- }
-
-
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/make.auc.r b/contrib/sahm/pySAHM/Resources/R_Modules/make.auc.r
deleted file mode 100644
index 9e50dfa..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/make.auc.r
+++ /dev/null
@@ -1,136 +0,0 @@
-make.auc.plot.jpg<-function(ma.reduced,pred,plotname,modelname,test.split=FALSE,thresh=NULL,train=NULL,train.pred=NULL,opt.methods=2,weight,out){
-
- if(is.null(weight)) weight=rep(1,times=dim(ma.reduced)[1])
- auc.data <- data.frame(ID=1:nrow(ma.reduced),pres.abs=ma.reduced[,1],pred=pred)
- p.bar <- sum(auc.data$pres.abs * weight) / sum(weight)
- n.pres <- sum(auc.data$pres.abs>=1)
- n.abs <- nrow(auc.data)-n.pres
-
- null.dev<-calc.dev(auc.data$pres.abs, rep(p.bar,times=length(auc.data$pres.abs)), weight, family=out$input$model.family)$deviance*nrow(ma.reduced)
- dev.fit<-calc.dev(auc.data$pres.abs, pred, weight, family=out$input$model.family)$deviance*nrow(ma.reduced)
- dev.exp <- null.dev - dev.fit
- pct.dev.exp <- dev.exp/null.dev*100
- correlation<-cor(auc.data$pres.abs,pred)
- residual.smooth.fct<-NULL
- if(test.split==FALSE) residual.smooth.fct<-resid.image(calc.dev(auc.data$pres.abs, pred, weight, family=out$input$model.family)$dev.cont,pred,
- auc.data$pres.abs,out$dat$ma$train.xy[,1],out$dat$ma$train.xy[,2],out$input$model.family,out$input$output.dir,out)
-
- if(is.null(thresh) & out$input$model.family!="poisson"){
- thresh <- as.numeric(optimal.thresholds(auc.data,opt.methods=opt.methods))[2]
- }
-
- if(out$input$model.family%in%c("binomial","bernoulli")){
- auc.fit <- auc(auc.data,st.dev=T)
- if(test.split==TRUE){
- jpeg(file=plotname)
- d<-data.frame(ID=1:nrow(train),pres.abs=train[,1],pred=train.pred)
- thresh<- as.numeric(optimal.thresholds(d,opt.methods=opt.methods))[2]
- TestTrainRocPlot(DATA=d,opt.thresholds=thresh,add.legend=FALSE,lwd=2)
- TestTrainRocPlot(auc.data,model.names=modelname,opt.thresholds=thresh,add.roc=TRUE,line.type=2,color="red",add.legend=FALSE)
- legend(x=.66,y=.2,c("Training Split","Testing Split"),lty=2,col=c("black","red"),lwd=2)
- graphics.off()}
- else {
- jpeg(file=plotname)
- TestTrainRocPlot(auc.data,model.names=modelname,opt.thresholds=thresh)
- graphics.off()
- }
- cmx <- cmx(auc.data,threshold=thresh)
- PCC <- pcc(cmx,st.dev=F)*100
- SENS <- sensitivity(cmx,st.dev=F)
- SPEC <- specificity(cmx,st.dev=F)
- KAPPA <- Kappa(cmx,st.dev=F)
- TSS <- SENS+SPEC-1
- }
-
- if(out$input$model.family%in%c("poisson")){
- auc.fit <- auc(auc.data,st.dev=T)
- if(test.split==FALSE){
- jpeg(file=plotname)
- par(mfrow=c(2,2))
- #plot(out$mods$final.mod)
- plot(log(pred[pred!=0]),(auc.data$pres.abs[pred!=0]-pred[pred!=0]),xlab="Predicted Values (log scale)",ylab="Residuals",main="Residuals vs Fitted",ylim=c(-3,3))
- abline(h=0,lty=2)
- #this is the residual plot from glm but I don't think it will work for anything else
- qqnorm(residuals(out$mods$final.mod),ylab="Std. deviance residuals")
- qqline(residuals(out$mods$final.mod))
- yl <- as.expression(substitute(sqrt(abs(YL)), list(YL = as.name("Std. Deviance Resid"))))
- plot(log(pred[pred!=0]),sqrt((abs(residuals(out$mods$final.mod,type="deviance")[pred!=0]))),xlab="Predicted Values (log Scale)",ylab=yl)
- graphics.off()}
- prediction.error<-sum((auc.data$pres.abs-pred)^2)
- cmx=PCC=SENS=SPEC=KAPPA=TSS<-NA
- }
-
- calibration.stats<-calibration(auc.data$pres.abs, pred, family =out$input$model.family)
- response<-ma.reduced$response
-
- capture.output(cat("\n\n============================================================",
- "\n\nEvaluation Statistics"),file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
- if(!is.null(out$dat$ma$ma.test))
- capture.output(cat(" applied to",ifelse(!test.split,"train","test"), "split:\n",sep=" "),
- file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
- capture.output(cat( "\n",
- "\n\t Correlation Coefficient : ",cor.test(pred,response)$estimate,
- "\n\t NULL Deviance : ",null.dev,
- "\n\t Fit Deviance : ",dev.fit,
- "\n\t Explained Deviance : ",dev.exp,
- "\n\t Percent Deviance Explained : ",pct.dev.exp,
- file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE))
-
- if(out$input$model.family%in%c("binomial","bernoulli")){
- capture.output(cat(
- "\n\n Threshold Methods based on", switch(opt.methods,
- "1"=".5 threshold",
- "2"="Sens=Spec",
- "3"="maximize (sensitivity+specificity)/2",
- "4"="maximize Kappa",
- "5"="maximize percent correctly classified",
- "6"="predicted prevalence=observed prevalence",
- "7"="threshold=observed prevalence",
- "8"="mean predicted probability",
- "9"="minimize distance between ROC plot and (0,1)",
- ),
- "\n\t Threshold : ",
- thresh,
- "\n\n\t Confusion Matrix: \n\n"),
- print.table(cmx),
- cat("\n\t AUC : ",auc.fit[1,1],
- "\n\t Percent Correctly Classified : ",PCC,
- "\n\t Sensitivity : ",SENS,
- "\n\t Specificity : ",SPEC,
- "\n\t Kappa : ",KAPPA,
- "\n\t True Skill Statistic : ",TSS,"\n"),
- file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE)
- }
-
- capture.output(cat( "\n\n Calibration Statistics",
- "\n\t Intercept (general calibration) : ",calibration.stats[1],
- "\n\t Slope (direction and variation in fit) : ",calibration.stats[2],
- "\n\t Testa0b1 (overall reliability of predictors) : ",calibration.stats[3],
- "\n\t Testa0|b1(incorrect calibration given correct refinement) : ",calibration.stats[4],
- "\n\t Testb1|a (refinement given correct calibration) : ",calibration.stats[5],"\n",
- file=paste(out$dat$bname,"_output.txt",sep=""),append=TRUE))
-
- last.dir<-strsplit(out$input$output.dir,split="\\\\")
- parent<-sub(paste("\\\\",last.dir[[1]][length(last.dir[[1]])],sep=""),"",out$input$output.dir)
-
- compile.out<-paste(parent,
- paste(switch(out$input$model.family,"binomial"="Binary","bernoulli"="Binary","poisson"="Count"),ifelse(!is.null(out$dat$ma$ma.test),"TestTrain",""),
- "AppendedOutput.csv",sep="."),sep="/")
-
- if(out$input$model.family%in%c("binomial","bernoulli")){
- x=data.frame(cbind(c("Correlation Coefficient","Percent Deviance Explained","Percent Correctly Classified","Sensitivity","Specificity"),
- c(as.vector(cor.test(pred,response)$estimate),pct.dev.exp,PCC,SENS,SPEC)))
- }else x=data.frame(cbind(c("Correlation Coefficient","Percent Deviance Explained","Prediction Error"),
- c(as.vector(cor.test(pred,response)$estimate),pct.dev.exp,prediction.error)))
-
- Header<-cbind(c("","Original Field Data","Field Data Template","PARC Output Folder","PARC Template","Covariate Selection Name",""),
- c(last.dir[[1]][length(last.dir[[1]])],
- out$dat$ma$input$OrigFieldData,out$dat$ma$input$FieldDataTemp,out$dat$ma$input$ParcOutputFolder,
- out$dat$ma$input$ParcTemplate,ifelse(length(out$dat$ma$input$CovSelectName)==0,"NONE",out$dat$ma$input$CovSelectName),""))
-
-AppendOut(compile.out,Header,x,out,test.split,parent=parent)
-
- return(list(thresh=thresh,cmx=cmx,null.dev=null.dev,dev.fit=dev.fit,dev.exp=dev.exp,pct.dev.exp=pct.dev.exp,auc=auc.fit[1,1],auc.sd=auc.fit[1,2],
- plotname=plotname,pcc=PCC,sens=SENS,spec=SPEC,kappa=KAPPA,tss=TSS,correlation=correlation,residual.smooth.fct=residual.smooth.fct))
-}
-
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/modalDialog.R b/contrib/sahm/pySAHM/Resources/R_Modules/modalDialog.R
deleted file mode 100644
index 0e185ce..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/modalDialog.R
+++ /dev/null
@@ -1,46 +0,0 @@
-#This function was robbed from the dynamicGraphic library
-"modalDialog" <-
-function (title, question, entryInit, top = NULL, entryWidth = 20,
- returnValOnCancel = "ID_CANCEL", do.grab = FALSE)
-{
- dlg <- tktoplevel()
- tkwm.deiconify(dlg)
- if (do.grab)
- tkgrab.set(dlg)
- tkfocus(dlg)
- tkwm.title(dlg, title)
- textEntryVarTcl <- tclVar(paste(entryInit))
- textEntryWidget <- tkentry(dlg, width = paste(entryWidth),
- textvariable = textEntryVarTcl, background = "white")
- tkgrid(tklabel(dlg, text = " "))
- tkgrid(tklabel(dlg, text = question), textEntryWidget)
- tkgrid(tklabel(dlg, text = " "))
- ReturnVal <- returnValOnCancel
- "onOK" <- function() {
- ReturnVal <<- tclvalue(textEntryVarTcl)
- tkgrab.release(dlg)
- tkdestroy(dlg)
- if (!is.null(top))
- tkfocus(top)
- }
- "onCancel" <- function() {
- ReturnVal <<- returnValOnCancel
- tkgrab.release(dlg)
- tkdestroy(dlg)
- if (!is.null(top))
- tkfocus(top)
- }
- OK.but <- tkbutton(dlg, text = " OK ", command = onOK)
- Cancel.but <- tkbutton(dlg, text = " Cancel ", command = onCancel)
- tkgrid(OK.but, Cancel.but)
- tkgrid(tklabel(dlg, text = " "))
- tkfocus(dlg)
- tkbind(dlg, "<Destroy>", function() {
- tkgrab.release(dlg)
- tkfocus(top)
- })
- tkbind(textEntryWidget, "<Return>", onOK)
- tkwait.window(dlg)
- return(ReturnVal)
-}
-
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/proc.tiff.r b/contrib/sahm/pySAHM/Resources/R_Modules/proc.tiff.r
deleted file mode 100644
index 767e335..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/proc.tiff.r
+++ /dev/null
@@ -1,212 +0,0 @@
-proc.tiff<- function(model,vnames,tif.dir=NULL,filenames=NULL,pred.fct,factor.levels=NA,make.binary.tif=F,make.p.tif=T,
- thresh=0.5,outfile.p="brt.prob.map.tif",outfile.bin="brt.bin.map.tif",tsize=2.0,NAval=-3000,fnames=NULL,logname=NULL,out){
-
- # vnames,fpath,myfun,make.binary.tif=F,outfile=NA,outfile.bin=NA,output.dir=NA,tsize=10.0,NAval=NA,fnames=NA
- # Written by Alan Swanson, YERC, 6-11-08
- # Revised and Edited by Marian Talbert 2010-2011
- # Description:
- # This function is used to make predictions using a number of .tiff image inputs
- # in cases where memory limitations don't allow the full images to be read in.
- #
- # Arguments:
- # vname: names of variables used for prediction. must be same as filenames and variables
- # in model used for prediction. do not include a .tif extension as this is added in code.
- # fpath: path to .tif files for predictors. use forward slashes and end with a forward slash ('/').
- # myfun: prediction function. must generate a vector of predictions using only a
- # dataframe as input.
- # outfile: name of output file. placed in same directory as input .tif files. should
- # have .tif extension in name.
- # tsize: size of dataframe used for prediction in MB. this controls the size of tiles
- # extracted from the input files, and the memory usage of this function.
- # NAval: this is the NAvalue used in the input files.
- # fnames: if the filenames of input files are different from the variable names used in the
- # prediction model.
- #
- # Modification history:
- # Fixed problem with NA values causing crash 10/2010
- # Included code to produce MESS map and Mod map 8/2011
- # Removed Tiff Directory option as well as some other unused code 10/2011
- #
- # Description:
- # This function reads in a limited number of lines of each image (specified in terms of the
- # size of the temporary predictor dataframe), applies a user-specified
- # prediction function, and stores the results as matrix. Alternatively, if an
- # output file is specified, a file is written directly to that file in .tif format to
- # the same directory as the input files. Geographic information from the input images
- # is retained.
- #
-
- # Start of function #
- library(rgdal)
- library(raster)
-
- MESS=out$input$MESS
- if(is.null(thresh)) thresh<-.5
- nvars<-length(vnames)
-
-# settup up output raster to match input raster
-
- fullnames <- as.character(filenames[match(vnames,basename(sub(".tif","",filenames)))])
- goodfiles <- file.access(fullnames)==0
- if(!all(goodfiles)) stop(paste("ERROR: the following image files are missing:",paste(fullnames[!goodfiles],collapse=", ")))
-
-if(nvars<=1) MESS=FALSE
- ######################################
- # get spatial reference info from existing image file
-options(warn=-1)
- gi <- GDALinfo(fullnames[1])
-options(warn=0)
- dims <- as.vector(gi)[1:2]
- ps <- as.vector(gi)[6:7]
- ll <- as.vector(gi)[4:5]
- pref<-attr(gi,"projection")
-
-RasterInfo=raster(fullnames[1])
-RasterInfo at file@datanotation<-"FLT4S"
-NAval<- -3.399999999999999961272e+38
-
-#To remove use of the Raster package I need to see if rgdal handles area or point correctly
-if(!is.na(match("AREA_OR_POINT=Point",attr(gi,"mdata")))){
- xx<-RasterInfo #this shifts by a half pixel
-nrow(xx) <- nrow(xx) - 1
-ncol(xx) <- ncol(xx) - 1
-rs <- res(xx)
-xmin(RasterInfo) <- xmin(RasterInfo) - 0.5 * rs[1]
-xmax(RasterInfo) <- xmax(RasterInfo) - 0.5 * rs[1]
-ymin(RasterInfo) <- ymin(RasterInfo) + 0.5 * rs[2]
-ymax(RasterInfo) <- ymax(RasterInfo) + 0.5 * rs[2]
- }
- # calculate position of upper left corner and get geotransform ala http://www.gdal.org/gdal_datamodel.html
- ul <- c(ll[1],ll[2]+(dims[1])*ps[2])
- gt<-c(ul[1],ps[1],0,ul[2],0,ps[2])
-
- # setting tile size
- MB.per.row<-dims[2]*nvars*32/8/1000/1024
-
- nrows<-min(round(tsize/MB.per.row),dims[1])
- bs<-c(nrows,dims[2])
- nbs <- ceiling(dims[1]/nrows)
- inc<-round(10/nbs,1)
-
- chunksize<-bs[1]*bs[2]
- tr<-blockSize(RasterInfo,chunksize=chunksize)
-
- continuousRaster<-raster(RasterInfo)
- continuousRaster <- writeStart(continuousRaster, filename=outfile.p, overwrite=TRUE)
- if(make.binary.tif) {
- binaryRaster<-raster(RasterInfo)
- binaryRaster <- writeStart(binaryRaster, filename=outfile.bin, overwrite=TRUE)}
- if(MESS) {
- MessRaster<-raster(RasterInfo)
- ModRaster<-raster(RasterInfo)
- MessRaster <- writeStart(MessRaster, filename=sub("bin","mess",outfile.bin), overwrite=TRUE)
- ModRaster <- writeStart(ModRaster, filename=sub("bin","MoD",outfile.bin), overwrite=TRUE)
- }
-
-temp <- data.frame(matrix(ncol=nvars,nrow=tr$size*ncol(RasterInfo))) # temp data.frame.
-names(temp) <- vnames
-FactorInd<-which(!is.na(match(names(temp),names(factor.levels))),arr.ind=TRUE)
- if((nvars-length(FactorInd))==0) MESS<-FALSE #turn this off if only one factor column was selected
- if(MESS) {
- pred.rng<-temp
- CalcMESS<-function(tiff.entry,pred.vect){
- f<-sum(pred.vect<tiff.entry)/length(pred.vect)*100
- if(is.na(f)) return(NA)
- if(f==0) return((tiff.entry-min(pred.vect))/(max(pred.vect)-min(pred.vect))*100)
- if(0<f & f<=50) return(2*f)
- if(50<=f & f<100) return(2*(100-f))
- if(f==100) return((max(pred.vect)-tiff.entry)/(max(pred.vect)-min(pred.vect))*100)
- else return(NA)
- }
- }
-
- Pred.Surface(object=RasterInfo,model=out$mods$auc.output$residual.smooth.fct,filename=sub("prob_map.tif","resid_map.tif",outfile.p),NAval=NAval)
-
- min.pred<-1
- max.pred<-0
-
- for (i in 1:tr$n) {
- strt <- c((i-1)*nrows,0)
- region.dims <- c(min(dims[1]-strt[1],nrows),dims[2])
- if (i==tr$n) if(is.null(dim(temp))) { temp <- temp[1:(tr$nrows[i]*dims[2])]
- if(MESS) pred.rng<-pred.rng[1:(tr$nrows[i]*dims[2])]
- } else {temp <- temp[1:(tr$nrows[i]*dims[2]),]
- if(MESS) pred.rng<-pred.rng[1:(tr$nrows[i]*dims[2]),]
- }
- # for the last tile...
- for(k in 1:nvars) { # fill temp data frame
- if(is.null(dim(temp))){
- temp<- getValuesBlock(raster(fullnames[k]), row=tr$row[i], nrows=tr$size)
- } else {temp[,k]<- getValuesBlock(raster(fullnames[k]), row=tr$row[i], nrows=tr$size)
- }
- if(MESS & !k%in%FactorInd){
- pred.range<-out$dat$ma$ma[,c(match(sub(".tif","",basename(fullnames[k])),names(out$dat$ma$ma)))]
- if(nvars>1) pred.rng[,k]<-mapply(CalcMESS,tiff.entry=temp[,k],MoreArgs=list(pred.vect=pred.range))
- else pred.rng<-mapply(CalcMESS,tiff.entry=temp,MoreArgs=list(pred.vect=pred.range))
- }
- }
- if(MESS & length(FactorInd)>0) pred.rng<-pred.rng[,-c(FactorInd)]
- temp[temp==NAval] <- NA # replace missing values #
- temp[is.na(temp)]<-NA #this seemingly worthless line switches NaNs to NA so they aren't predicted
- if(sum(!is.na(factor.levels))){
- factor.cols <- match(names(factor.levels),names(temp))
- if(sum(!is.na(factor.cols))>0){
- for(j in 1:length(factor.cols)){
- if(!is.na(factor.cols[j])){
- temp[,factor.cols[j]] <- factor(temp[,factor.cols[j]],levels=factor.levels[[j]]$number,labels=factor.levels[[j]]$class)
- }
- }
- }}
- ifelse(sum(!is.na(temp))==0, # does not calculate predictions if all predictors in the region are na
- preds<-matrix(data=NaN,nrow=region.dims[1],ncol=region.dims[2]),
- preds <- t(matrix(pred.fct(model,temp),ncol=dims[2],byrow=T)))
- min.pred<-min(na.omit(preds),min.pred)
- max.pred<-max(na.omit(preds),max.pred)
- preds[is.na(preds)]<-NAval
- ## Writing to the rasters u
- f<-function(x){
- if(any(is.na(x))) return(NA)
- a<-which(x==min(x),arr.ind=TRUE)
- if(length(a>1)) a<-sample(a,size=1)
- return(a)
- }
- if(MESS) {
- MessRaster<-writeValues(MessRaster,apply(pred.rng,1,min), tr$row[i])
- if(!is.null(dim(pred.rng)[2])) a<-apply(as.matrix(pred.rng),1,f)
- else a<-rep(1,times=length(pred.rng))
- #if(is.list(a)) a<-unlist(a)
- ModRaster<-writeValues(ModRaster,a, tr$row[i])
- }
- if(make.binary.tif) binaryRaster<-writeValues(binaryRaster,(preds>thresh),tr$row[i])
- continuousRaster <- writeValues(continuousRaster,preds, tr$row[i])
- #NAvalue(continuousRaster) <-NAval
- rm(preds);gc() #why is gc not working on the last call
-}
-
- continuousRaster <- writeStop(continuousRaster)
- a<-readGDAL(continuousRaster at file@name)
- writeGDAL(a,continuousRaster at file@name, drivername = "GTiff",setStatistics=TRUE,mvFlag=NAval)
-
-
-
- if(make.binary.tif) {
- writeStop(binaryRaster)
- a<-readGDAL(binaryRaster at file@name)
- writeGDAL(a,binaryRaster at file@name, drivername = "GTiff",setStatistics=TRUE,mvFlag=NAval)
- }
- if(MESS) {
- writeStop(MessRaster)
- a<-readGDAL(MessRaster at file@name)
- writeGDAL(a,MessRaster at file@name, drivername = "GTiff",setStatistics=TRUE,mvFlag=NAval)
-
- writeStop(ModRaster)
- a<-readGDAL(ModRaster at file@name)
- d<-data.frame(as.integer(seq(1:ncol(pred.rng))),names(pred.rng))
- names(d)=c("Value","Class")
- ModRaster at file@datanotation<-"INT1U"
- write.dbf(d, sub(".tif",".tif.vat.dbf",ModRaster at file@name), factor2char = TRUE, max_nchar = 254)
- writeGDAL(a,ModRaster at file@name, drivername = "GTiff",setStatistics=TRUE,mvFlag=255,type="UInt16")
- }
-
- return(0)
- }
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/read.ma.r b/contrib/sahm/pySAHM/Resources/R_Modules/read.ma.r
deleted file mode 100644
index f477ebd..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/read.ma.r
+++ /dev/null
@@ -1,209 +0,0 @@
- read.ma <- function(out){
-
- ma.name <- out$input$ma.name
-
- tif.dir <- out$dat$tif.dir$dname
- out.list <- out$dat$ma
- out.list$status[1] <- file.access(ma.name,mode=0)==0
-
- try(ma<-read.csv(ma.name,skip=2))
- hl<-readLines(ma.name,1)
- hl=strsplit(hl,',')
- colnames(ma) = hl[[1]]
-
- tif.info<-readLines(ma.name,3)
- tif.info<-strsplit(tif.info,',')
- temp<-tif.info[[2]]
- temp[1:3]<-0
- include<-as.numeric(temp)
-
- paths<-as.character(tif.info[[3]])
-
- if(class(ma)=="try-error") stop("Error reading MDS")
- else out.list$status[2]<-T
-
- temp<-strsplit(tif.info[[2]][1],split="\\\\")[[1]]
- out.list$input$FieldDataTemp<-temp[length(temp)]
-
- temp<-strsplit(tif.info[[2]][2],split="\\\\")[[1]]
- out.list$input$OrigFieldData<-temp[length(temp)]
-
- temp<-strsplit(tif.info[[2]][3],split="\\\\")[[1]]
- out.list$input$CovSelectName<-temp[length(temp)]
-
- temp<-strsplit(tif.info[[3]][1],split="\\\\")[[1]]
- out.list$input$ParcTemplate<-temp[length(temp)]
-
- temp<-strsplit(tif.info[[3]][2],split="\\\\")[[1]]
- out.list$input$ParcOutputFolder<-temp[length(temp)]
-
- temp<-strsplit(tif.info[[2]][2],split="\\\\")[[1]]
- out.list$input$OrigFieldData<-temp[length(temp)]
-
- r.name <- out$input$response.col
- if(r.name=="responseCount") out$input$model.family="poisson"
-
- r.col <- grep(r.name,names(ma))
- if(length(r.col)==0) stop("Response column was not found")
- if(length(r.col)>1) stop("Multiple columns matched the response column")
- rm.list<-r.col
-
- # remove background points which aren't used here
- if(length(which(ma[,r.col]==-9999,arr.ind=TRUE))>0) ma<-ma[-c(which(ma[,r.col]==-9999,arr.ind=TRUE)),]
-
- # remove incomplete cases and warn user if this number is more than 10% of the data
-
- # find and save xy columns#
- xy.cols <- na.omit(c(match("x",tolower(names(ma))),match("y",tolower(names(ma)))))
- if(length(xy.cols)>0) rm.list<-c(rm.list,xy.cols)
-
- # remove weights column except for Random Forest
- site.weights<-match("site.weights",tolower(names(ma)))
- if(!is.na(site.weights)) rm.list<-c(rm.list,site.weights)
-
- # and index as well
- split.indx<-match("split",tolower(names(ma)))
- if(length(na.omit(split.indx))>0) rm.list<-c(rm.list,split.indx)
-
- #complete the list of columns to include
- include[is.na(include)]<-0
- rm.list<-c(rm.list,(which(include!=1,arr.ind=TRUE)))
- rm.list<-unique(rm.list[!is.na(rm.list)])
-
- ######################### REMOVING INCOMPLETE CASES ###############
- #remove incomplete cases but only for include variables
- all.cases<-nrow(ma)
- out.list$n.pres[1] <- NA
- out.list$n.abs[1] <- NA
- ma<-ma[complete.cases(ma[,-c(rm.list)]),]
- comp.cases<-nrow(ma)
- if(comp.cases/all.cases<.9) warning(paste(round((1-comp.cases/all.cases)*100,digits=2),"% of cases were removed because of missing values",sep=""))
- #########################################################################
- #split out the weights,response, and xy.columns after removing incomplete cases
- if(!is.na(site.weights)){
- out.list$train.weights<-ma[,site.weights]
- } else out.list$train.weights<-rep(1,times=dim(ma)[1])
- if(length(xy.cols)>0) out.list$train.xy<-ma[,xy.cols]
- response<-ma[,r.col]
-
- ma.names<-names(ma)
- # tagging factors and looking at their levels
- factor.cols <- grep("categorical",names(ma))
- factor.cols <- factor.cols[!is.na(factor.cols)]
- if(length(factor.cols)==0){
- out.list$factor.levels <- NA
- } else {
- names(ma) <- ma.names <- sub("_categorical","",ma.names)
- factor.names <- ma.names[factor.cols]
- factor.levels <- list()
- for (i in 1:length(factor.cols)){
- f.col <- factor.cols[i]
-
- x <- table(ma[,f.col])
- if(nrow(x)<2){
- out$dat$bad.factor.cols <- c(out$dat$bad.factor.cols,factor.names[i])
- }
- lc.levs <- as.numeric(row.names(x))[x>0] # make sure there is at least one "available" observation at each level
- lc.levs <- data.frame(number=lc.levs,class=lc.levs)
- factor.levels[[i]] <- lc.levs
-
- ma[,f.col] <- factor(ma[,f.col],levels=lc.levs$number,labels=lc.levs$class)
- }
-
- names(factor.levels)<-factor.names
- out.list$factor.levels <- factor.levels
-
- if(!is.null(out$dat$bad.factor.cols)) rm.list<-c(rm.list,match(out$dat$bad.factor.cols,names(ma)))
- }
-
- if(length(which(lapply(apply(ma,2,unique),length)==1,arr.ind=TRUE))>0){
- rm.list<-c(rm.list,which(lapply(apply(ma,2,unique),length)==1,arr.ind=TRUE))
- warning(paste("The Following Predictors will be removed because they have only 1 unique value: ",
- names(which(lapply(apply(ma,2,unique),length)==1,arr.ind=TRUE))))
- }
- #remove test training split column if present
-
- if(length(na.omit(split.indx))>0){
- split.col<-ma[,split.indx]
- out.list$ma.test<-ma[split.col=="test",]
- ma<-ma[split.col=="train",]
- out.list$test.weights<-out.list$train.weights[split.col=="test"]
- out.list$train.weights<-out.list$train.weights[split.col=="train"]
- out.list$test.xy<-out.list$train.xy[split.col=="test",]
- out.list$train.xy<-out.list$train.xy[split.col=="train",]
- out.list$n.pres[4] <- sum(out.list$ma.test[,r.col]!=0)
- out.list$n.abs[4] <- sum(out.list$ma.test[,r.col]==0)
- }
-
- # Complete cases n.pres and n.abs must be calculated after splitting data (this is train cases reported)
- out.list$n.pres[2] <- sum(ma[,r.col]!=0)
- out.list$n.abs[2] <- sum(ma[,r.col]==0)
-
- # check that response column contains only 1's and 0's, but not all 1's or all 0's if GLMFamily==binomial
- if(out$input$model.source.file=="rf.r") out$input$model.family="bernoulli"
-
- if(tolower(out$input$model.family)=="bernoulli" || tolower(out$input$model.family)=="binomial"){
- if(any(ma[,r.col]!=1 & ma[,r.col]!=0) | sum(ma[,r.col]==1)==nrow(ma) | sum(ma[,r.col]==0)==nrow(ma))
- stop("response column (#",r.col,") in ",ma.name," is not binary 0/1",sep="")
- }
-
- #check that response column contains at least two unique values for counts
-
- if(tolower(out$input$model.family)=="poisson"){
- if(length(table(unique(ma[,r.col])))==1)
- stop("response column (#",r.col,") in ",ma.name," does not have at least two unique values",sep="")
- }
-
- #ma has the first column equal to the response and removes all other remove columns
- ma <- cbind(ma[,r.col],ma[,-c(rm.list)]) #ma still needs the response column
- if(length(na.omit(split.indx))>0) out.list$ma.test <- cbind(out.list$ma.test[,r.col],out.list$ma.test[,-c(rm.list)])
- paths<-paths[-c(rm.list)]
- include<-include[-c(rm.list)]
-
- out.list$resp.name <- names(ma)[1]<-"response"
- if(length(na.omit(split.indx))>0) names(out.list$ma.test)[1]<-"response"
- ma.names<-names(ma)
-
- # if producing geotiff output, check to make sure geotiffs are available for each column of the model array #
- if(out$input$make.binary.tif==T | out$input$make.p.tif==T){
- #Check that tiffs to be used exist
- if(sum(file.access(paths),mode=0)!=0){
- temp<-as.vector(file.access(paths))==-1
- temp.paths<-paths[temp]
- stop("the following geotiff(s) are missing:",
- "\nif these are intentionally left blank, uncheck makeBinMap and makeProbabilityMap options\n",
- paste(paths[temp],collapse="\n"),sep="")
- }
-
- } else out$dat$tif.names <- ma.names[-1]
-
- out$dat$tif.ind<-paths
-
- out.list$ma <- ma
-
- out.list$dims <- dim(out.list$ma)
- out.list$ratio <- min(sum(out$input$model.fitting.subset)/out.list$dims[1],1)
- out.list$used.covs <- names(out.list$ma)[-1]
-
- if(!is.null(out$input$model.fitting.subset)){
- pres.sample <- sample(c(1:nrow(out.list$ma))[out.list$ma[,1]>=1],min(out.list$n.pres[2],out$input$model.fitting.subset[1]))
- abs.sample <- sample(c(1:nrow(out.list$ma))[out.list$ma[,1]==0],min(out.list$n.abs[2],out$input$model.fitting.subset[2]))
- out.list$ma.subset <- out.list$ma[c(pres.sample,abs.sample),]
- if(out$input$model.source.file!="rf.r") out.list$weight.subset<-out.list$train.weights[c(pres.sample,abs.sample)]
- out.list$n.pres[3] <- length(pres.sample)
- out.list$n.abs[3] <- length(abs.sample)
- } else {
- out.list$ma.subset <- NULL
- out.list$weight.subset<-NULL
- out.list$n.pres[3] <- NA
- out.list$n.abs[3] <- NA }
-
-if(tolower(out$input$model.family)=="poisson"){
-out.list$ma.subset<-out.list$ma
-out.list$weight.subset<-out.list$train.weights
-}
-
- out$dat$ma <- out.list
-
- return(out)
- }
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/read.maNew.r b/contrib/sahm/pySAHM/Resources/R_Modules/read.maNew.r
deleted file mode 100644
index c2b9004..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/read.maNew.r
+++ /dev/null
@@ -1,224 +0,0 @@
- read.ma <- function(out){
-
- ma.name <- out$input$ma.name
- browser()
- tif.dir <- out$dat$tif.dir$dname
- out.list <- out$dat$ma
- out.list$status[1] <- file.access(ma.name,mode=0)==0
-
-
- if(is.null(out$input$tif.dir)){
- try(ma<-read.csv(ma.name,skip=3))
- hl<-readLines(ma.name,1)
- hl=strsplit(hl,',')
- colnames(ma) = hl[[1]]
-
- tif.info<-readLines(ma.name,3)
- tif.info<-strsplit(tif.info,',')
- temp<-tif.info[[2]]
- temp[1:3]<-0
- include<-as.numeric(temp)
-
- paths<-as.character(tif.info[[3]])
- }
- if(class(ma)=="try-error") stop("Error reading MDS")
- else out.list$status[2]<-T
-
- temp<-strsplit(tif.info[[2]][1],split="\\\\")[[1]]
- out.list$input$FieldDataTemp<-temp[length(temp)]
-
- temp<-strsplit(tif.info[[2]][2],split="\\\\")[[1]]
- out.list$input$OrigFieldData<-temp[length(temp)]
-
- temp<-strsplit(tif.info[[2]][3],split="\\\\")[[1]]
- out.list$input$CovSelectName<-temp[length(temp)]
-
- temp<-strsplit(tif.info[[3]][1],split="\\\\")[[1]]
- out.list$input$ParcTemplate<-temp[length(temp)]
-
- temp<-strsplit(tif.info[[3]][2],split="\\\\")[[1]]
- out.list$input$ParcOutputFolder<-temp[length(temp)]
-
- temp<-strsplit(tif.info[[2]][2],split="\\\\")[[1]]
- out.list$input$OrigFieldData<-temp[length(temp)]
-
- r.name <- out$input$response.col
- if(r.name=="responseCount") out$input$model.family="poisson"
-
- r.col <- grep(r.name,names(ma))
- if(length(r.col)==0) stop("Response column was not found")
- if(length(r.col)>1) stop("Multiple columns matched the response column")
- rm.list<-r.col
-
- # remove background points which aren't used here
- if(length(which(ma[,r.col]==-9999,arr.ind=TRUE))>0) ma<-ma[-c(which(ma[,r.col]==-9999,arr.ind=TRUE)),]
- response<-ma[,r.col]
-
- # find and save xy columns#
- xy.cols <- na.omit(c(match("x",tolower(names(ma))),match("y",tolower(names(ma)))))
- if(length(xy.cols)>0) {out.list$train.xy<-ma[,xy.cols]
- rm.list<-c(rm.list,xy.cols)}
-
-
- # remove weights column except for Random Forest
- site.weights<-match("site.weights",tolower(names(ma)))
- if(!is.na(site.weights)){
- out.list$train.weights<-ma[,site.weights]
- rm.list<-c(rm.list,site.weights)
- } else out.list$train.weights<-rep(1,times=dim(ma)[1]))
-
-
- ma.names<-names(ma)
- # tagging factors and looking at their levels
- factor.cols <- grep("categorical",names(ma))
- factor.cols <- factor.cols[!is.na(factor.cols)]
- if(length(factor.cols)==0){
- out.list$factor.levels <- NA
- } else {
- names(ma) <- ma.names <- sub("_categorical","",ma.names)
- factor.names <- ma.names[factor.cols]
- factor.levels <- list()
- for (i in 1:length(factor.cols)){
- f.col <- factor.cols[i]
-
- x <- table(ma[,f.col])
- if(nrow(x)<2){
- out$dat$bad.factor.cols <- c(out$dat$bad.factor.cols,factor.names[i])
- }
- lc.levs <- as.numeric(row.names(x))[x>0] # make sure there is at least one "available" observation at each level
- lc.levs <- data.frame(number=lc.levs,class=lc.levs)
- factor.levels[[i]] <- lc.levs
-
- ma[,f.col] <- factor(ma[,f.col],levels=lc.levs$number,labels=lc.levs$class)
- }
-
- names(factor.levels)<-factor.names
- out.list$factor.levels <- factor.levels
- }
-
- #remove test training split column if present
- split.indx<-match("split",tolower(names(ma)))
- if(length(na.omit(split.indx))>0){
- split.col<-ma[,split.indx]
- out.list$ma.test<-ma[split.col=="test",]
- ma<-ma[split.col=="train",]
- out.list$test.weights<-out.list$train.weights[split.col=="test"]
- out.list$train.weights<-out.list$train.weights[split.col=="train"]
- out.list$test.xy<-out.list$train.xy[split.col=="test",]
- out.list$train.xy<-out.list$train.xy[split.col=="train",]
- rm.list<-c(rm.list,split.indx)
- }
-
-
- # check that response column contains only 1's and 0's, but not all 1's or all 0's if GLMFamily==binomial
- if(out$input$model.source.file=="rf.r") out$input$model.family="bernoulli"
-
- if(tolower(out$input$model.family)=="bernoulli" || tolower(out$input$model.family)=="binomial"){
- if(any(ma[,r.col]!=1 & ma[,r.col]!=0) | sum(ma[,r.col]==1)==nrow(ma) | sum(ma[,r.col]==0)==nrow(ma))
- stop("response column (#",r.col,") in ",ma.name," is not binary 0/1",sep="")
-
- out.list$n.pres[1] <- sum(ma[,r.col])
- out.list$n.abs[1] <- nrow(ma)-sum(ma[,r.col])
- }
-
-
-
- #check that response column contains at least two unique values for counts
-
- if(tolower(out$input$model.family)=="poisson"){
- if(length(table(unique(ma[,r.col])))==1)
- stop("response column (#",r.col,") in ",ma.name," does not have at least two unique values",sep="")
-
- out.list$n.pres[1] <- sum(ma[,r.col]!=0)
- out.list$n.abs[1] <- sum(ma[,r.col]==0)
- }
-
- out$dat$ma$resp.name <- names(ma)[r.col]<-"response"
- out.list$resp.name <- names(ma)[r.col]
-
- include[is.na(include)]<-0
- rm.list<-c(rm.list,(which(include!=1,arr.ind=TRUE)))
- rm.list<-unique(rm.list[!is.na(rm.list)])
-
- ma <- ma[,-rm.list]
- if(is.null(out$input$tif.dir)){
- paths<-paths[-c(rm.list)]
- include<-include[-c(rm.list)]
- #ma.names[-c(rm.cols)]
- }
-
- ma[ma==-9999]<-NA
- ma.names<-names(ma)
- browser()
- # if producing geotiff output, check to make sure geotiffs are available for each column of the model array #
- if(out$input$make.binary.tif==T | out$input$make.p.tif==T){
- #Now check that tiffs to be used exist
-
- ma.cols <- match(ma.names,sub(".tif","",basename(paths[-r.col])))
- if(any(is.na(ma.cols))){
- stop("the following geotiff(s) are missing in ",
- tif.dir,": ",paste(ma.names[-r.col][is.na(ma.cols)],collapse=" ,"),
- "\nif these are intentionally left blank, uncheck makeBinMap and makeProbabilityMap options",sep="")
-
- if(sum(file.access(paths[include==1]),mode=0)!=0)
- stop("the following geotiff(s) are missing : ",
- paths[(file.access(paths)!=0),][1],"\nif these are intentionally left blank, uncheck makeBinMap and makeProbabilityMap options", sep="")
-
- out$dat$tif.ind<-paths
- }
-
- if(!is.null(out$input$tif.dir)){
- tif.names <- out$dat$tif.names
- ma.cols <- match(ma.names[-r.col],sub(".tif","",basename(tif.names)))
- if(any(is.na(ma.cols)))stop("the following geotiff(s) are missing in ",
- tif.dir,": ",paste(ma.names[is.na(ma.cols)],collapse=" ,"),sep="")
-
- out$dat$tif.names <- tif.names[ma.cols]
-
- } else out$dat$tif.names <- ma.names
- #Removing NAs this might be better in a loop
- out.list$ma <- ma[complete.cases(ma),c(r.col,c(1:ncol(ma))[-r.col])]
- if(length(na.omit(split.indx))>0) out.list$test.xy<-out.list$test.xy[complete.cases(out.list$ma.test),]
- out.list$train.xy<-out.list$train.xy[complete.cases(ma),]
-
- if(!is.null(out.list$ma.test)){
- if(out$input$model.source.file!="rf.r") out.list$test.weights<- out.list$test.weights[complete.cases(out.list$ma.test)]
- out.list$ma.test<-out.list$ma.test[complete.cases(out.list$ma.test),c(r.col,c(1:ncol(out.list$ma.test))[-r.col])]
- if(out$input$model.source.file!="rf.r") out.list$test.weights<- out.list$test.weights[complete.cases(out.list$ma.test)]
- # out.list$ma.test<-out.list$ma.test[,c(r.col,c(1:ncol(out.list$ma.test))[-r.col])]
- #if(out$input$model.source.file!="rf.r") out.list$test.weights<- out.list$test.weights
- out.list$n.pres[4] <- sum(out.list$ma.test[,r.col]!=0)
- out.list$n.abs[4] <- nrow(out.list$ma.test)-sum(out.list$ma.test[,r.col]!=0)
- }
- if(out$input$model.source.file!="rf.r") out.list$train.weights <- out.list$train.weights[complete.cases(ma)]
- if(!is.null(out$dat$bad.factor.cols)) out.list$ma <- out.list$ma[,-match(out$dat$bad.factor.cols,names(out.list$ma))]
-
- out.list$dims <- dim(out.list$ma)
- out.list$ratio <- min(sum(out$input$model.fitting.subset)/out.list$dims[1],1)
- out.list$n.pres[2] <- sum(out.list$ma[,1]!=0)
- out.list$n.abs[2] <- nrow(out.list$ma)-sum(out.list$ma[,1]!=0)
- out.list$used.covs <- names(out.list$ma)[-1]
-
- if(!is.null(out$input$model.fitting.subset)){
- pres.sample <- sample(c(1:nrow(out.list$ma))[out.list$ma[,1]>=1],min(out.list$n.pres[2],out$input$model.fitting.subset[1]))
- abs.sample <- sample(c(1:nrow(out.list$ma))[out.list$ma[,1]==0],min(out.list$n.abs[2],out$input$model.fitting.subset[2]))
- out.list$ma.subset <- out.list$ma[c(pres.sample,abs.sample),]
- if(out$input$model.source.file!="rf.r") out.list$weight.subset<-out.list$train.weights[c(pres.sample,abs.sample)]
- out.list$n.pres[3] <- length(pres.sample)
- out.list$n.abs[3] <- length(abs.sample)
- } else {
- out.list$ma.subset <- NULL
- out.list$weight.subset<-NULL
- out.list$n.pres[3] <- NA
- out.list$n.abs[3] <- NA }
-
-if(tolower(out$input$model.family)=="poisson"){
-out.list$ma.subset<-out.list$ma
-out.list$weight.subset<-out.list$train.weights
-}
-
-
- out$dat$ma <- out.list
-
- return(out)
- }
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/Resources/R_Modules/tmp_ThrowsError.r b/contrib/sahm/pySAHM/Resources/R_Modules/tmp_ThrowsError.r
deleted file mode 100644
index a82bea5..0000000
--- a/contrib/sahm/pySAHM/Resources/R_Modules/tmp_ThrowsError.r
+++ /dev/null
@@ -1 +0,0 @@
-1 = 2
\ No newline at end of file
diff --git a/contrib/sahm/pySAHM/__init__.py b/contrib/sahm/pySAHM/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/contrib/sahm/pySAHM/singlePARC.py b/contrib/sahm/pySAHM/singlePARC.py
deleted file mode 100644
index c1d5dc9..0000000
--- a/contrib/sahm/pySAHM/singlePARC.py
+++ /dev/null
@@ -1,71 +0,0 @@
-#!/usr/bin/python
-"""
-This was an experiment to explore breaking the
-individual raster processes into individual
-runs that could be either run on separate
-processes on the same computer with a command line
-popopen perhaps or sent out individually to our
-Condor distributed computing cluster.
-
-"""
-
-
-import glob
-import math
-import os
-import shutil
-import struct
-import sys
-import csv
-
-from optparse import OptionParser
-from multiprocessing import Process, Queue
-
-from osgeo import gdalconst
-from osgeo import gdal
-from osgeo import osr
-
-from numpy import *
-import numpy as np
-
-import utilities
-from PARC import PARC
-
-def main(args_in):
- """
- Process commandline Arguments,
- Create an instance of PARC with the Variables,
- Kick off the parkFiles function of our PARC instance
- """
- # Process command-line args.
- usageStmt = "usage: %prog [options] <template image> <input dir or list of input files>"
- desc = "This application projects, aggregates, resamples, and clips imagery."
-
- parser = OptionParser(usage=usageStmt, description=desc)
- parser.add_option("-s", dest="source", help="print the names of all known aggregation methods")
- parser.add_option("-c", dest="categorical")
- parser.add_option("-d", dest="dest", default="./", help="directory in which to put processed images, defaults to current directory")
- parser.add_option("-v", dest="verbose", default=False, action="store_true", help="the verbose flag causes diagnostic output to print")
- parser.add_option("-t", dest="template", help="The template raster used for projection, origin, cell size and extent")
- parser.add_option("-r", dest="resampling", help="The CSV containing the list of files to process. Format is 'FilePath, Categorical, Resampling, Aggreagtion")
- parser.add_option("-a", dest="aggregation", default=True, help="'True', 'False' indicating whether to use multiple cores or not")
- (options, args) = parser.parse_args(args_in)
-
- ourPARC = PARC()
- ourPARC.verbose = options.verbose
- ourPARC.template = options.template
- outDir = os.path.split(options.dest)[0]
- ourPARC.outDir = outDir
- ourPARC.logger = utilities.logger(outDir, ourPARC.verbose)
- ourPARC.writetolog = ourPARC.logger.writetolog
- ourPARC.template_params = ourPARC.getRasterParams(options.template)
- ourPARC.parcFile([options.source, options.categorical, options.resampling, options.aggregation], options.dest)
-
-if __name__ == "__main__":
- main(sys.argv[1:])
-# try:
-## PARC().testing()
-# sys.exit(PARC().main(sys.argv[1:]))
-# except Exception as e:
-# print e
-# sys.exit(1)
diff --git a/contrib/sahm/pySAHM/singleRasterFormatConverter.py b/contrib/sahm/pySAHM/singleRasterFormatConverter.py
deleted file mode 100644
index 99ee88e..0000000
--- a/contrib/sahm/pySAHM/singleRasterFormatConverter.py
+++ /dev/null
@@ -1,73 +0,0 @@
-#!/usr/bin/python
-"""
-This script is a wrapper for the
-RasterFormatConverter which allows
-the user to run an individual raster through.
-It is used by RasterFormatConverter itself
-to allow each raster to be spawned off as
-a separate command line to take advantage of
-multiple cores on a machine.
-
-"""
-
-
-import glob
-import math
-import os
-import shutil
-import struct
-import sys
-import csv
-
-from optparse import OptionParser
-from multiprocessing import Process, Queue
-
-from osgeo import gdalconst
-from osgeo import gdal
-from osgeo import osr
-
-from numpy import *
-import numpy as np
-
-import utilities
-from RasterFormatConverter import FormatConverter
-
-def main(argv):
- usageStmt = "usage: options: -m --MDSFile -o --outputDir -f --format -v --verbose"
- desc = "Converts all of the tif files specified in an MDS to ASCII format (or optionally other formats)"
- parser = OptionParser(usage=usageStmt, description=desc)
-
- parser.add_option("-v",
- dest="verbose",
- default=False,
- action="store_true",
- help="the verbose flag causes diagnostic output to print.")
- parser.add_option("-i", "--inputfile",
- dest="input",
- help="")
- parser.add_option("-o", "--outputDir",
- dest="outputDir",
- help="Output directory to save files in.")
- parser.add_option("-f", "--format",
- dest="format",
- default='asc',
- help="The format to convert into. 'bil', 'img', 'tif', 'jpg', 'bmp', 'asc'")
-
- (options, args) = parser.parse_args(argv)
-
- ourFC = FormatConverter()
- ourFC.verbose = options.verbose
- ourFC.logger = utilities.logger(options.outputDir, ourFC.verbose)
- ourFC.writetolog = ourFC.logger.writetolog
- ourFC.outputDir = options.outputDir
- ourFC.format = options.format
- ourFC.convertEnvironmentalLayers([options.input, ], options.outputDir, options.format)
-
-if __name__ == "__main__":
- main(sys.argv[1:])
-# try:
-## PARC().testing()
-# sys.exit(PARC().main(sys.argv[1:]))
-# except Exception as e:
-# print e
-# sys.exit(1)
diff --git a/contrib/sahm/pySAHM/utilities.py b/contrib/sahm/pySAHM/utilities.py
deleted file mode 100644
index 53fe97f..0000000
--- a/contrib/sahm/pySAHM/utilities.py
+++ /dev/null
@@ -1,261 +0,0 @@
-#!/usr/bin/python
-
-''' These utility functions are shared
-between all of the Python SAHM command line
-modules
-'''
-
-import os, sys
-import time
-import csv
-import string
-
-from osgeo import gdal
-from osgeo import osr
-from osgeo import ogr
-
-_logfile = ''
-_verbose = False
-
-class logger(object):
- def __init__(self, logfile, verbose):
- self.logfile = logfile
- self.verbose = verbose
-
- #if we mistakenly get a output dir instead of a filename
- if os.path.isdir(logfile):
- self.logfile = os.path.join(logfile, 'sessionLog.txt')
- else:
- self.logfile = logfile
-
- if os.path.exists(self.logfile):
- self.writetolog("\nSession continued\n", True, True)
- else:
- logDir = os.path.split(self.logfile)[0]
- if not os.path.exists(logDir):
- raise RuntimeError('Directory of specified logfile does not exist.')
- f = open(self.logfile, "w")
- del f
- self.writetolog("\nSession started\n", True, False)
-
-
- def writetolog(self, msg, addtime=False, printtoscreen=True):
- '''Opens the log file and writes the passed msg.
- Optionally adds a time slot to the message and
- Prints the msg to the screen.
- If the logfile is not specified tries to use the global variable.
- '''
- f = open(self.logfile, "a")
- if self.verbose and printtoscreen:
- print msg
- if addtime:
- msg = ' at: '.join([msg, time.strftime("%m/%d/%Y %H:%M")])
- msg = "\n" + msg
- f.write(msg)
- del f
-
-class TrappedError(Exception):
- """Exception class indicating that an anticipated problem
- was encountered in a specific module
- """
- def __init__(self, msg=None):
- Exception.__init__(self)
- self.message = msg
-
-
-
-#def createsessionlog(roottempdir, verbose):
-# '''Creates a new log file if one doesn't already exist.
-# If one exists then writes that the session has continued.
-# '''
-# global _logfile, _verbose
-# _verbose = verbose
-#
-# logfile = os.path.join(roottempdir, "sessionLog.txt")
-# _logfile = logfile
-#
-# if os.path.exists(logfile):
-# writetolog("\nSession continued\n", True, True, logfile=logfile)
-# else:
-# f = open(os.path.join(roottempdir, "sessionLog.txt"), "w")
-# del f
-#
-# return logfile
-#
-#def writetolog(msg, addtime=False, printtoscreen=True, logfile=''):
-# '''Opens the log file and writes the passed msg.
-# Optionally adds a time slot to the message and
-# Prints the msg to the screen.
-# If the logfile is not specified tries to use the global variable.
-# '''
-# global _logfile
-# if logfile == '':
-# logfile = _logfile
-#
-# f = open(logfile, "a")
-# if _verbose and printtoscreen:
-# print msg
-# if addtime:
-# msg = ' at: '.join([msg, time.strftime("%m/%d/%Y %H:%M")])
-# msg = "\n" + msg
-# f.write(msg)
-# del f
-
-
-def isMDSFile(MDSFile):
- '''performs a check to see if a supplied file is in 'MDS' format
- This means:
- 1 - The file has three header lines
- first: x, y, responseBinary or responseCount, a series of covariate names, and an optional Split
- second: '0', '0', '0', 0 or blanks and 0 or 1 for each covariate indicate use or ignore
- third: '', '', '', the full path and filename of the tiff covariate layer.
- 2 - additionally lines contain individual occurance location, response, covariate attributes at that location, and test\train for the Split column
-
- Values of -9999 in the response column indicate a background point.
- covariate names ending in '*_categorical' indicate a categorical variable
-
- The test used in this check are by no means thorough in checking for covariate files
- existing on the file system, missing values in any columns, appropriate values in
- the response or Split columns, etc. Instead this function is intended to just give a
- best guess as to to if this is an MDS.
- '''
- MDSreader = csv.reader(open(MDSFile, 'r'))
- header1 = MDSreader.next()
- header2 = MDSreader.next()
- header3 = MDSreader.next()
-
-#These no longer apply with the new agg feature.
-# for i in [0, 1, 2]:
-# if not(header2[0] == '' or header2[0] == '0'):
-# return False
-
-# for item in header2[3:-1]:
-# if not item in ['0', '1']:
-# return False
-
- return True
- del MDSreader
-
-def process_waiter(popen, description, que):
- try:
- popen.wait()
- finally:
- que.put( (description, popen.returncode) )
-
-
-def mds_to_shape(MDSFile, outputfolder):
-
- #bit of a hack but currently saving the shape file as
- #three shape files presence, absence, and background
- #as I'm having trouble getting QGIS to display points
- #with categorical symbology
-
- h, t = os.path.split(MDSFile)
- t_no_ext = os.path.splitext(t)[0]
- outputfiles = {"pres":os.path.join(outputfolder, t_no_ext + "_pres.shp"),
- "abs":os.path.join(outputfolder, t_no_ext + "_abs.shp"),
- "backs":os.path.join(outputfolder, t_no_ext + "_backs.shp")}
-
- driver = ogr.GetDriverByName('ESRI Shapefile')
-
- MDSreader = csv.reader(open(MDSFile, 'r'))
- header1 = MDSreader.next()
- header2 = MDSreader.next()
- header3 = MDSreader.next()
-
- h, t = os.path.split(MDSFile)
- t_no_ext = os.path.splitext(t)[0]
-#
-
- for outfile in outputfiles.values():
- h, t = os.path.split(outfile)
- if os.path.exists(outfile):
- os.chdir(h)
- driver.DeleteDataSource(t)
-
- ds = driver.CreateDataSource(h)
-
- preslayer = ds.CreateLayer(t_no_ext + "_pres",
- geom_type=ogr.wkbPoint)
- abslayer = ds.CreateLayer(t_no_ext + "_abs",
- geom_type=ogr.wkbPoint)
- backslayer = ds.CreateLayer(t_no_ext + "_backs",
- geom_type=ogr.wkbPoint)
-
- #cycle through the items in the header and add
- #these to each output shapefile attribute table
- fields = {}
- for field in header1:
- field_name = Normalized_field_name(field, fields)
- fields[field_name] = field
- if field == "Split":
- #this is the test training split field that we add
- fieldDefn = ogr.FieldDefn(field_name, ogr.OFTString)
- else:
- fieldDefn = ogr.FieldDefn(field_name, ogr.OFTReal)
-
- preslayer.CreateField(fieldDefn)
- abslayer.CreateField(fieldDefn)
- backslayer.CreateField(fieldDefn)
-
- featureDefn = preslayer.GetLayerDefn()
-
- #cycle through the rows and add each geometry to the
- #appropriate shapefile
- for row in MDSreader:
- feature = ogr.Feature(featureDefn)
- point = ogr.Geometry(ogr.wkbPoint)
-
- point.SetPoint_2D(0, float(row[0]), float(row[1]))
- feature.SetGeometry(point)
-
- # for this feature add in each of the attributes from the row
- header_num = 0
- for field in header1:
- short_field = find_key(fields, field)
- if field == "Split":
- feature.SetField(short_field, row[header_num])
- else:
- feature.SetField(short_field, float(row[header_num]))
- header_num += 1
-
- response = float(row[2])
-
- if abs(response - 0) < 1e-9:
- abslayer.CreateFeature(feature)
- elif response > 0:
- preslayer.CreateFeature(feature)
- elif abs(response - -9999.0) < 1e-9:
- backslayer.CreateFeature(feature)
-
- # close the data sources
- del MDSreader
- ds.Destroy()
-
-def Normalized_field_name(field_name, previous_fields):
- short_name = field_name[:10]
-
- #remove Non alpha numeric characters
- short_name = ''.join(ch for ch in short_name if ch in (string.ascii_letters + string.digits + '_'))
-
- if previous_fields.has_key(short_name):
- i = 1
- shorter_name = short_name[:8]
- short_name = shorter_name + "_" + str(i)
- while previous_fields.has_key(short_name):
- i += 1
- short_name = shorter_name + "_" + str(i)
- return short_name
-
-def find_key(dic, val):
- """return the key of dictionary dic given the value
- from: http://www.daniweb.com/software-development/python/code/217019"""
- return [k for k, v in dic.iteritems() if v == val][0]
-
-if __name__ == "__main__":
-
- mds_to_shape(r"I:\VisTrails\WorkingFiles\workspace\talbertc_20110901T175958\CovariateCorrelationOutputMDS_anothertry2.csv", r"I:\VisTrails\WorkingFiles\workspace\talbertc_20110901T175958\CovariateCorrelationOutputMDS_anothertry2.shp")
- print "done"
-
-
-
diff --git a/contrib/sahm/utils.py b/contrib/sahm/utils.py
deleted file mode 100644
index 2933b1d..0000000
--- a/contrib/sahm/utils.py
+++ /dev/null
@@ -1,481 +0,0 @@
-'''
-These are utilites used by the VisTrails
-wrappers of the SAHM command line applications
-
- at author: talbertc
-test
-
-'''
-import os, sys, shutil
-import traceback
-import csv
-import time
-import tempfile
-import subprocess
-
-from PyQt4 import QtCore, QtGui
-
-from core.modules.basic_modules import File, Path, Directory, new_constant, Constant
-from core.modules.vistrails_module import ModuleError
-
-from osgeo import gdalconst
-from osgeo import gdal
-from osgeo import osr
-import numpy
-
-import packages.sahm.pySAHM.utilities as utilities
-import getpass
-
-_roottempdir = ""
-_logger = None
-config = None
-
-def getrasterminmax(filename):
- dataset = gdal.Open(filename, gdalconst.GA_ReadOnly)
- band = dataset.GetRasterBand(1)
-
- min = band.GetMinimum()
- max = band.GetMaximum()
-
- try:
- #our output rasters have approx nodata values
- #which don't equal the specified nodata.
- #set the specified to equal what is actually used.
- if (abs(band.GetNoDataValue() - band.GetMinimum()) < 1e-9 and
- band.GetNoDataValue() <> band.GetMinimum()):
- band.SetNoDataValue(band.GetMinimum)
-
- if min is None or max is None:
- (min,max) = band.ComputeRasterMinMax(1)
-
- except:
- pass
- return (min, max)
- dataset = None
-
-def mknextfile(prefix, suffix="", directory=""):
- global _roottempdir
- if directory == "":
- directory = _roottempdir
- files = os.listdir(directory)
- seq = 0
- for f in files:
- if f.startswith(prefix):
- old_seq = f.replace(prefix, '')
- old_seq = old_seq.replace(suffix, '')
- old_seq = old_seq.replace("_", '')
- if old_seq.isdigit():
- if int(old_seq) > seq:
- seq = int(old_seq)
- seq += 1
- filename = prefix + str(seq) + suffix
- return os.path.join(directory, filename)
-
-def mknextdir(prefix, directory=""):
- global _roottempdir
- if directory == "":
- directory = _roottempdir
- files = os.listdir(directory)
- seq = 0
- for f in files:
- if (f.startswith(prefix) and
- not os.path.isfile(f)):
- f_seq = int(f.replace(prefix, ''))
- if f_seq > seq:
- seq = f_seq
- seq += 1
- dirname = prefix + str(seq)
- os.mkdir(os.path.join(directory, dirname))
- return os.path.join(directory, dirname)
-
-def setrootdir(session_dir):
- global _roottempdir
- _roottempdir = session_dir
-
-def createrootdir(rootWorkspace):
- '''Creates a session Directory which will
- contain all of the output produced in a single
- VisTrails/Sahm session.
- '''
- global _roottempdir
- user_nospace = getpass.getuser().split(' ')[0]
- _roottempdir = os.path.join(rootWorkspace, user_nospace + '_' + time.strftime("%Y%m%dT%H%M%S"))
- if not os.path.exists(_roottempdir):
- os.makedirs(_roottempdir)
-
- return _roottempdir
-
-def map_ports(module, port_map):
- args = {}
- for port, (flag, access, required) in port_map.iteritems():
- if required or module.hasInputFromPort(port):
- #breakpoint()
- value = module.forceGetInputListFromPort(port)
- if len(value) > 1:
- raise ModuleError(module, 'Multiple items found from Port ' +
- port + '. Only single entry handled. Please remove extraneous items.')
- elif len(value) == 0:
- raise ModuleError(module, 'Multiple items found from Port ' +
- port + '. Only single entry handled. Please remove extraneous items.')
- value = module.forceGetInputFromPort(port)
- if access is not None:
- value = access(value)
- if isinstance(value, File) or \
- isinstance(value, Directory) or \
- isinstance(value, Path):
- value = path_port(module, port)
- args[flag] = value
- return args
-
-def path_port(module, portName):
- value = module.forceGetInputListFromPort(portName)
- if len(value) > 1:
- raise ModuleError(module, 'Multiple items found from Port ' +
- portName + '. Only single entry handled. Please remove extraneous items.')
- value = value[0]
- path = value.name
- path.replace("/", os.path.sep)
- if os.path.exists(path):
- return path
- else:
- raise RuntimeError, 'The indicated file or directory, ' + \
- path + ', does not exist on the file system. Cannot continue!'
-
-def PySAHM_instance_params(instance, mappedPorts):
- global _logger
- instance.__dict__['logger'] = _logger
- instance.__dict__['verbose'] = _logger.verbose
- for k, v in mappedPorts.iteritems():
- instance.__dict__[k] = v
-
-def R_boolean(value):
- if value:
- return 'TRUE'
- else:
- return 'FALSE'
-
-def dir_path_value(value):
- val = value.name
- sep = os.path.sep
- return val.replace("/", sep)
-
-def create_file_module(fname, f=None):
- if f is None:
- f = File()
- f.name = fname
- f.upToDate = True
- return f
-
-def create_dir_module(dname, d=None):
- if d is None:
- d = Directory()
- d.name = dname
- d.upToDate = True
- return d
-
-#No longer used
-#def collapse_dictionary(dict):
-# list = []
-# for k,v in dict.items():
-# list.append(k)
-# list.append(v)
-# return list
-
-#def tif_to_color_jpeg(input, output, colorBreaksCSV):
-# writetolog(" running tif_to_color_jpeg()", True, False)
-# writetolog(" input=" + input, False, False)
-# writetolog(" output=" + output, False, False)
-# writetolog(" colorBreaksCSV=" + colorBreaksCSV, False, False)
-# out_bands = 3
-# #output_tmp = mktempfile(prefix='intermediateJpegPic', suffix='.tif')
-# output_tmp = output + ".tmp.tif"
-# # Print some info
-# #print "Creating %s" % (output)
-#
-# #populate the color breaks dictionary
-# # from the colorBreaks CSV
-#
-# csvfile = open(colorBreaksCSV, "r")
-# #dialect = csv.Sniffer().sniff(csvfile.read(1024))
-# reader = csv.reader(csvfile)
-# usedPixels = {}
-# header = reader.next() #skip the header
-#
-# color_dict = {}
-# maxVal = -9999
-# for row in reader:
-# color_dict[float(row[1])] = [row[3], row[4], row[5]]
-# if row[2] > maxVal: maxVal = row[2]
-#
-# #print color_dict
-# # Open source file
-# src_ds = gdal.Open( input )
-# src_band = src_ds.GetRasterBand(1)
-#
-# # create destination file
-# dst_driver = gdal.GetDriverByName('GTiff')
-# dst_ds = dst_driver.Create(output_tmp, src_ds.RasterXSize,
-# src_ds.RasterYSize, out_bands, gdal.GDT_Byte)
-#
-# # create output bands
-# band1 = numpy.zeros([src_ds.RasterYSize, src_ds.RasterXSize])
-# band2 = numpy.zeros([src_ds.RasterYSize, src_ds.RasterXSize])
-# band3 = numpy.zeros([src_ds.RasterYSize, src_ds.RasterXSize])
-#
-# # set the projection and georeferencing info
-# dst_ds.SetProjection( src_ds.GetProjection() )
-# dst_ds.SetGeoTransform( src_ds.GetGeoTransform() )
-#
-# # read the source file
-# #gdal.TermProgress( 0.0 )
-# for iY in range(src_ds.RasterYSize):
-# src_data = src_band.ReadAsArray(0,iY,src_ds.RasterXSize,1)
-# col_values = src_data[0] # array of z_values, one per row in source data
-# for iX in range(src_ds.RasterXSize):
-# z_value = col_values[iX]
-# [R,G,B] = MakeColor(z_value, color_dict, maxVal)
-# band1[iY][iX] = R
-# band2[iY][iX] = G
-# band3[iY][iX] = B
-# #gdal.TermProgress( (iY+1.0) / src_ds.RasterYSize )
-#
-# # write each band out
-# dst_ds.GetRasterBand(1).WriteArray(band1)
-# dst_ds.GetRasterBand(2).WriteArray(band2)
-# dst_ds.GetRasterBand(3).WriteArray(band3)
-#
-# # Create jpeg or rename tmp file
-# jpg_driver = gdal.GetDriverByName("JPEG")
-# jpg_driver.CreateCopy(output, dst_ds, 0 )
-#
-# try:
-# os.remove(output_tmp)
-# except:
-# pass
-#
-# try:
-# GDALClose(output_tmp)
-# except:
-# pass
-#
-# try:
-# os.remove(output_tmp)
-# except:
-# pass
-#
-# dst_ds = None
-# writetolog(" finished running tif_to_color_jpeg()", True, False)
-# return True
-#
-#def MakeColor(z_value, color_dict, maxVal):
-#
-#
-# key_list = color_dict.keys()
-# key_list.sort()
-# while len(key_list) > 0:
-# last_val = key_list[-1]
-# #print "lastVal = ",last_val
-# #print "ZVal = ",z_value
-# if z_value >= last_val and z_value <= maxVal:
-# #"print color for ", z_value, " is ", last_val, " = ", color_dict[last_val]
-# return color_dict[last_val]
-# break
-# else:
-# key_list.remove(last_val)
-#
-# #if we get here something is wrong return black
-# #print "Value not found defaulting to black"
-# return [255, 255, 255]
-
-def MDSresponseCol(MDSFile):
- csvfile = open(MDSFile, "r")
- reader = csv.reader(csvfile)
- header = reader.next() #store the header
- responseCol = header[2]
- return responseCol
-
-def print_exc_plus( ):
- """ Print the usual traceback information, followed by a listing of
- all the local variables in each frame.
- lifted from the Python Cookbook
- """
- msg = ""
- tb = sys.exc_info( )[2]
- while tb.tb_next:
- tb = tb.tb_next
- stack = [ ]
- f = tb.tb_frame
- while f:
- if r'\sahm\\' in f.f_code.co_filename:
- stack.append(f)
- f = f.f_back
- stack.reverse( )
- traceback.print_exc( )
- msg += "\n" + "Locals by frame, innermost last"
- for frame in stack:
- msg += "\n"
- msg += "\n" + "Frame %s in %s at line %s" % (frame.f_code.co_name,
- frame.f_code.co_filename,
- frame.f_lineno)
- msg += "\n"
- for key, value in frame.f_locals.items( ):
- msg += "\t%20s = " % key
- # we must _absolutely_ avoid propagating exceptions, and str(value)
- # COULD cause any exception, so we MUST catch any...:
- try:
- msg += str(value)
- except:
- msg += "<ERROR WHILE PRINTING VALUE>"
-
- msg += "\n\n" + ' '.join([str(i) for i in sys.exc_info()[:2]])
-
- return msg
-
-def informative_untrapped_error(instance, name):
- errorMsg = "An error occurred running " + name + ", error message below: "
- errorMsg += "\n " + ' '.join([str(i) for i in sys.exc_info()[:2]])
- try:
- errorMsg += traceback.format_tb(sys.exc_info()[2], 10)[-2]
- except IndexError:
- pass
- writetolog(print_exc_plus(), False, False)
- raise ModuleError(instance, errorMsg)
-
-def breakpoint():
- ''' open up the python debugger here and poke around
- Very helpful, I should have figured this out ages ago!
- '''
- QtCore.pyqtRemoveInputHook()
- import pdb; pdb.set_trace()
-
-def writetolog(*args, **kwargs):
- '''Uses the SAHM log file writting function
- but appends our known logfile to the kwargs.
- '''
- global _logger
- _logger.writetolog(*args, **kwargs)
-
-def createLogger(outputdir, verbose):
- global _logger
- _logger = utilities.logger(outputdir, verbose)
-
-def getLogger():
- global _logger
- return _logger
-
-def getShortName(fullPathName):
- if fullPathName.endswith('hdr.adf'):
- shortname = os.path.split(fullPathName)[0]
- shortname = os.path.split(shortname)[1]
- else:
- shortname = os.path.split(fullPathName)[1]
- shortname = os.path.splitext(shortname)[0]
- return shortname
-
-def getRasterName(fullPathName):
- if fullPathName.endswith('hdr.adf'):
- rastername = os.path.split(fullPathName)[0]
- else:
- rastername = fullPathName
- return rastername
-
-def getModelsPath():
- return os.path.join(os.path.dirname(__file__), "pySAHM", "Resources", "R_Modules")
-
-def runRScript(script, args, module=None):
- global config
- r_path = config.r_path
- program = os.path.join(r_path, "i386", "Rterm.exe") #-q prevents program from running
- scriptFile = os.path.join(getModelsPath(), script)
-
- command = program + " --vanilla -f " + scriptFile + " --args " + args
-
- p = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
- writetolog("\nStarting R Processing of " + script, True)
- writetolog(" args: " + args, False, False)
- writetolog(" command: " + command, False, False)
- ret = p.communicate()
-
- if 'Error' in ret[1]:
- msg = "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
- msg +="\n An error was encountered in the R script for this module."
- msg += "\n The R error message is below: \n"
- msg += ret[1]
- writetolog(msg)
- if module:
- raise ModuleError(module, msg)
- else:
- raise RuntimeError , msg
-
- if 'Warning' in ret[1]:
- msg = "The R scipt returned the following warning(s). The R warning message is below - \n"
- msg += ret[1]
- writetolog(msg)
-
- del(ret)
- writetolog("\nFinished R Processing of " + script, True)
-
-def merge_inputs_csvs(inputCSVs_list, outputFile):
- oFile = open(outputFile, "wb")
- outputCSV = csv.writer(oFile)
- outputCSV.writerow(["PARCOutputFile", "Categorical",
- "Resampling", "Aggregation", "OriginalFile"])
- for inputCSV in inputCSVs_list:
- iFile = open(inputCSV, "rb")
- inputreader = csv.reader(iFile)
- inputreader.next()
- for row in inputreader:
- outputCSV.writerow(row)
- iFile.close()
- oFile.close()
-
-def applyMDS_selection(oldMDS, newMDS):
- """Takes a selection from a previous MDS and '
- applies it to a new MDS file.
- """
- oldvals = {}
- if os.path.exists(oldMDS):
- iFile = open(oldMDS, 'r')
- previousout = csv.reader(iFile)
- oldheader1 = previousout.next()
- oldheader2 = previousout.next()
- oldvals = dict(zip(oldheader1, oldheader2))
- iFile.close()
- del previousout
-
- tmpnewMDS = newMDS + ".tmp.csv"
- oFile = open(tmpnewMDS, "wb")
- tmpOutCSV = csv.writer(oFile)
- iFile = open(newMDS, "rb")
- outCSV = csv.reader(iFile)
-
- oldHeader1 = outCSV.next()
- oldHeader2 = outCSV.next()
- oldHeader3 = outCSV.next()
-
- selectionline = []
- for i in range(len(oldHeader1)):
- if oldvals.has_key(oldHeader1[i]) and \
- oldvals[oldHeader1[i]] == '0':
- selectionline.append('0')
- else:
- selectionline.append('1')
-
- tmpOutCSV.writerow(oldHeader1)
- tmpOutCSV.writerow(selectionline)
- tmpOutCSV.writerow(oldHeader3)
- for row in outCSV:
- tmpOutCSV.writerow(row)
-
- iFile.close()
- oFile.close()
- shutil.copyfile(tmpnewMDS, newMDS)
- os.remove(tmpnewMDS)
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/contrib/sahm/widgets.py b/contrib/sahm/widgets.py
deleted file mode 100644
index 4defe99..0000000
--- a/contrib/sahm/widgets.py
+++ /dev/null
@@ -1,369 +0,0 @@
-from PyQt4 import QtCore, QtGui
-import os
-
-from core.modules.module_configure import StandardModuleConfigurationWidget
-from core.modules.constant_configuration import ConstantWidgetMixin
-
-class PredictorListWidget(QtGui.QTreeWidget):
-
- def __init__(self, p_value, available_tree, parent=None):
-
- self.resamplingMethods = ["nearestneighbor",
- "bilinear",
- "cubic",
- "cubicspline",
- "lanczos"]
-
- self.aggregationMethods = ["Min",
- "Mean",
- "Max",
- "Majority",
- "None"]
-
- #print "p_value : ", p_value
- QtGui.QTreeWidget.__init__(self, parent)
- self.available_tree = available_tree
- self.setColumnCount(5)
- self.headerItem().setText(0, "Include")
- self.setColumnWidth(0,100)
- self.headerItem().setText(1, "Layer")
- self.setColumnWidth(1,self.width() - 350)
- self.headerItem().setText(2, "Categorical")
- self.setColumnWidth(0,90)
- self.headerItem().setText(3, "Resampling")
- self.setColumnWidth(2,125)
- self.headerItem().setText(4, "Aggregation")
- self.setColumnWidth(0,125)
-# self.setSelectionBehavior(QtGui.QTreeView.SelectRows)
-
- self.tree_items = {}
- for source, file_list in self.available_tree.iteritems():
- #print source, file_list
- source_item = QtGui.QTreeWidgetItem([source])
- self.addTopLevelItem(source_item)
- for (file, desc, categorical) in file_list:
- child_item = QtGui.QTreeWidgetItem([file, desc])#, resVal, aggVal])
- child_item.setFlags(QtCore.Qt.ItemIsUserCheckable |
- QtCore.Qt.ItemIsEnabled)
- child_item.setCheckState(0, QtCore.Qt.Unchecked)
- source_item.addChild(child_item)
-
- resamplingCB = QtGui.QComboBox(self)
- resamplingCB.addItems(self.resamplingMethods)
- aggCB = QtGui.QComboBox(self)
- aggCB.addItems(self.aggregationMethods)
- catChk = QtGui.QCheckBox(self)
-# self.connect(aggCB, QtCore.SIGNAL('currentIndexChanged(QString)'), self.testing)
- if categorical == "N":
- resamplingCB.setCurrentIndex(1)
- aggCB.setCurrentIndex(1)
- curVal = (file, "Bilinear", "Mean")
- catChk.setCheckState(QtCore.Qt.Unchecked)
- else:
- resamplingCB.setCurrentIndex(0)
- aggCB.setCurrentIndex(3)
- curVal = (file, "NearestNeighbor", "Majority")
- catChk.setCheckState(QtCore.Qt.Checked)
-
- self.setItemWidget(child_item, 2, catChk)
- self.setItemWidget(child_item, 3, resamplingCB)
- self.setItemWidget(child_item, 4, aggCB)
-
-# print "The file for dict is ", file
- self.tree_items[curVal] = child_item
- self.set_values(p_value)
-
- def set_values(self, str_value):
- #print 'set_values:', str_value
- values = []
- if str_value:
- values = eval(str_value)
- files = {}
- for k in self.tree_items.iterkeys():
- files[k[0]] = k[1:]
- for value in values:
- if value[0] in files.keys():
- try:
- oldValue = (value[0], files[value[0]][0], files[value[0]][1])
- self.tree_items[oldValue].setCheckState(0, QtCore.Qt.Checked)
- item = self.itemWidget(self.tree_items[oldValue], 2)
- if value[1] == '1':
- item.setCheckState(QtCore.Qt.Checked)
- else:
- item.setCheckState(QtCore.Qt.Unchecked)
- item = self.itemWidget(self.tree_items[oldValue], 3)
- item.setCurrentIndex(self.resamplingMethods.index(value[2]))
- item = self.itemWidget(self.tree_items[oldValue], 4)
- item.setCurrentIndex(self.aggregationMethods.index(value[3]))
- except ValueError:
- pass
-
- def get_values(self):
- #print 'get_values:'
- values = []
- for value, item in self.tree_items.iteritems():
- #print value, item
- if item.checkState(0) == QtCore.Qt.Checked:
- if self.itemWidget(item, 2).checkState() == QtCore.Qt.Checked:
- categorical = '1'
- else:
- categorical = '0'
- resampleMethod = str(self.itemWidget(item, 3).currentText())
- aggMethod = str(self.itemWidget(item, 4).currentText())
-
- values.append((value[0], categorical, resampleMethod, aggMethod))
-# print 'get_vals = ', str(values)
- return str(values)
-
- def select_all(self):
- for value, item in self.tree_items.iteritems():
- self.tree_items[value].setCheckState(0, QtCore.Qt.Checked)
-
- def switch_selection(self):
- for value, item in self.tree_items.iteritems():
- if item.checkState(0) == QtCore.Qt.Checked:
- self.tree_items[value].setCheckState(0, QtCore.Qt.Unchecked)
- else:
- self.tree_items[value].setCheckState(0, QtCore.Qt.Checked)
-
- def query_add(self, query_text):
- for value, item in self.tree_items.iteritems():
- if str(query_text) in value[0]:
- self.tree_items[value].setCheckState(0, QtCore.Qt.Checked)
-
-
-
- def query_remove(self, query_text):
- for value, item in self.tree_items.iteritems():
- if str(query_text) in value[0]:
- self.tree_items[value].setCheckState(0, QtCore.Qt.Unchecked)
-
-class PredictorListConfigurationWidget(PredictorListWidget,
- ConstantWidgetMixin):
-
- def __init__(self, param, available_tree, parent=None):
- """__init__(param: core.vistrail.module_param.ModuleParam,
- parent: QWidget)
-
- Initialize the line edit with its contents. Content type is limited
- to 'int', 'float', and 'string'
-
- """
- PredictorListWidget.__init__(self, param.strValue, available_tree,
- parent)
- ConstantWidgetMixin.__init__(self, param.strValue)
- # assert param.namespace == None
- # assert param.identifier == 'edu.utah.sci.vistrails.basic'
-# self.available_tree = available_tree
-# self.setColumnCount(2)
-# for source, file_list in self.available_tree.iteritems():
-# source_item = QtGui.QTreeWidgetItem([source])
-# self.addTopLevelItem(source_item)
-# for (file, desc) in file_list:
-# child_item = QtGui.QTreeWidgetItem([file, desc])
-# child_item.setFlags(QtCore.Qt.ItemIsUserCheckable |
-# QtCore.Qt.ItemIsEnabled)
-# child_item.setCheckState(0, QtCore.Qt.Unchecked)
-# source_item.addChild(child_item)
-
- contents = param.strValue
- contentType = param.type
-
- # need to deserialize contents and set tree widget accordingly
- # self.setText(contents)
- self._contentType = contentType
-# self.connect(self,
-# QtCore.SIGNAL('returnPressed()'),
-# self.update_parent)
-
- def contents(self):
- """contents() -> str
- Re-implement this method to make sure that it will return a string
- representation of the value that it will be passed to the module
- As this is a QLineEdit, we just call text()
-
- """
- return self.get_values()
-
- def setContents(self, strValue, silent=True):
- """setContents(strValue: str) -> None
- Re-implement this method so the widget can change its value after
- constructed. If silent is False, it will propagate the event back
- to the parent.
- As this is a QLineEdit, we just call setText(strValue)
- """
-# self.setText(strValue)
-# self.update_text()
-# if not silent:
-# self.update_parent()
- self.set_values(strValue)
-# self.update_text()
- if not silent:
- self.update_parent()
-
-# def update_text(self):
-# """ update_text() -> None
-# Update the text to the result of the evaluation
-
-# """
-# # FIXME: eval should pretty much never be used
-# base = expression.evaluate_expressions(self.text())
-# if self._contentType == 'String':
-# self.setText(base)
-# else:
-# try:
-# self.setText(str(eval(str(base), None, None)))
-# except:
-# self.setText(base)
-
- def sizeHint(self):
- return QtCore.QSize(912, 912)
-
-# def sizeHint(self):
-# metrics = QtGui.QFontMetrics(self.font())
-# width = min(metrics.width(self.text())+10,70)
-# return QtCore.QSize(width,
-# metrics.height()+6)
-
- def minimumSizeHint(self):
- return self.sizeHint()
-
- ###########################################################################
- # event handlers
-
- def focusInEvent(self, event):
- """ focusInEvent(event: QEvent) -> None
- Pass the event to the parent
-
- """
- self._contents = self.get_values()
- if self.parent():
- QtCore.QCoreApplication.sendEvent(self.parent(), event)
- QtGui.QTreeWidget.focusInEvent(self, event)
-
- def focusOutEvent(self, event):
- self.update_parent()
- QtGui.QTreeWidget.focusOutEvent(self, event)
- if self.parent():
- QtCore.QCoreApplication.sendEvent(self.parent(), event)
-
-class PredictorListConfiguration(StandardModuleConfigurationWidget):
- # FIXME add available_dict as parameter to allow config
- def __init__(self, module, controller, available_tree, parent=None):
- StandardModuleConfigurationWidget.__init__(self, module, controller,
- parent)
-
- # set title
- if module.has_annotation_with_key('__desc__'):
- label = module.get_annotation_by_key('__desc__').value.strip()
- title = '%s (%s) Module Configuration' % (label, module.name)
- else:
- title = '%s Module Configuration' % module.name
- self.setWindowTitle(title)
- self.build_gui(available_tree)
-
- def build_gui(self, available_tree):
- layout = QtGui.QVBoxLayout()
- # precompute tree so we only load once
-
- # factor PredictorListConfigurationWidget so that it can be reused in
- # both cases
- self.p_value = ''
- for function in self.module.functions:
- if function.name == 'value':
- self.p_value = function.parameters[0].strValue
- # should just be able to pass this across to the PredictorList config
- self.list_config = PredictorListWidget(self.p_value, available_tree)
- layout.addWidget(self.list_config)
-
- self.buttonLayout = QtGui.QHBoxLayout()
- self.buttonLayout.setMargin(5)
- self.okButton = QtGui.QPushButton('&OK', self)
- self.okButton.setFixedWidth(110)
- self.buttonLayout.addWidget(self.okButton)
- self.cancelButton = QtGui.QPushButton('&Cancel', self)
- self.cancelButton.setShortcut('Esc')
- self.cancelButton.setFixedWidth(110)
- self.buttonLayout.addWidget(self.cancelButton)
-
- self.selectAllButton = QtGui.QPushButton('&Select All', self)
- self.selectAllButton.setFixedWidth(110)
- self.buttonLayout.addWidget(self.selectAllButton)
-
- self.switchSelectionButton = QtGui.QPushButton('&Switch Selection', self)
- self.switchSelectionButton.setFixedWidth(110)
- self.buttonLayout.addWidget(self.switchSelectionButton)
-
- spacerItem = QtGui.QSpacerItem(10, 0, QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Minimum)
- self.buttonLayout.addItem(spacerItem)
-
- self.queryLabel = QtGui.QLabel("Query")
- self.buttonLayout.addWidget(self.queryLabel)
-
- self.queryText = QtGui.QLineEdit(self)
- self.queryText.setFixedWidth(110)
- self.buttonLayout.addWidget(self.queryText)
-
- self.addQuery = QtGui.QPushButton('&Add', self)
- self.addQuery.setFixedWidth(60)
- self.buttonLayout.addWidget(self.addQuery)
-
- self.removeQuery = QtGui.QPushButton('&Remove', self)
- self.removeQuery.setFixedWidth(60)
- self.buttonLayout.addWidget(self.removeQuery)
-
- layout.addLayout(self.buttonLayout)
- self.connect(self.okButton, QtCore.SIGNAL('clicked(bool)'),
- self.okTriggered)
- self.connect(self.cancelButton, QtCore.SIGNAL('clicked(bool)'),
- self.close)
- self.connect(self.selectAllButton, QtCore.SIGNAL('clicked(bool)'),
- self.selectAllTriggered)
- self.connect(self.switchSelectionButton, QtCore.SIGNAL('clicked(bool)'),
- self.switchSelectionTriggered)
- self.connect(self.addQuery, QtCore.SIGNAL('clicked(bool)'),
- self.queryAdd)
- self.connect(self.removeQuery, QtCore.SIGNAL('clicked(bool)'),
- self.queryRemove)
- self.setLayout(layout)
-
- def okTriggered(self):
- str_value = self.list_config.get_values()
- #print str_value, "=?=", self.p_value
- if str_value != self.p_value:
-# print 'okTriggered:', str_value
- functions = [('value', [str_value])]
- self.controller.update_functions(self.module, functions)
- self.close()
-
- def selectAllTriggered(self):
- self.list_config.select_all()
-
- def switchSelectionTriggered(self):
- self.list_config.switch_selection()
-
- def sizeHint(self):
- return QtCore.QSize(912, 912)
-
- def queryAdd(self):
- self.list_config.query_add(self.queryText.text())
-
- def queryRemove(self):
- self.list_config.query_remove(self.queryText.text())
-
-def get_predictor_widget(class_name, tree):
- def __init__(self, param, parent=None):
- PredictorListConfigurationWidget.__init__(self, param, tree, parent)
- class_name += "PredictorListWidget"
- widget_class = type(class_name, (PredictorListConfigurationWidget,),
- {'__init__': __init__})
- return widget_class
-
-def get_predictor_config(class_name, tree):
- def __init__(self, module, controller, parent=None):
- PredictorListConfiguration.__init__(self, module, controller, tree,
- parent)
- class_name += "PredictorListConfig"
- widget_class = type(class_name, (PredictorListConfiguration,),
- {'__init__': __init__})
- return widget_class
diff --git a/contrib/stem/__init__.py b/contrib/stem/__init__.py
deleted file mode 100644
index b8326dd..0000000
--- a/contrib/stem/__init__.py
+++ /dev/null
@@ -1,6 +0,0 @@
-name = 'STEM'
-identifier = 'edu.cornell.birds.stem'
-version = '0.0.2'
-
-def package_dependencies():
- return ['edu.utah.sci.vistrails.rpy']
diff --git a/contrib/stem/code/STEM_Globals.R b/contrib/stem/code/STEM_Globals.R
deleted file mode 100644
index e0907b9..0000000
--- a/contrib/stem/code/STEM_Globals.R
+++ /dev/null
@@ -1,236 +0,0 @@
-
-debugOutput <- FALSE
-# Slash direction for directory creation
-platform = "linux"
-# Possibly Spp names info
-
-# Required Packages
-require(rpart)
-require(mgcv)
-require(gbm)
-require(fields)
-require(splancs)
-require(maps)
-require(maptools)
-
-# Source STEM Libraries
-source(paste(code.directory,"stem.library.A.R",sep=""))
-source(paste(code.directory,"stem.library.B.R",sep=""))
-source(paste(code.directory,"stem.library.ST.R",sep=""))
-
-# Source MORE STEM Functions
-#source(paste(code.directory,"STEM_erd.data.creation.R",sep=""))
-source(paste(code.directory,"STEM_erd.srd.data.subsetting.R",sep=""))
-source(paste(code.directory,"STEM_ModelFitting.R",sep="") )
-source(paste(code.directory,"predict.eBird.ST.matrix.R",sep=""))
-source(paste(code.directory,"STEM_st.matrix.cv.average.R",sep=""))
-
-
-## Name of space time matrix sub-directory
-st.matrix.name <- "stm"
-
-## Name of space time matrix ave map sub-directory
-st.matrix.ave.maps <- "stm.ave.maps"
-
-
-
-# ------------------------
-# Select One Species
-# speciesList - a list of vectors. vector[1] = scientificName & vector[2] = commonName
-# ------------------------
-speciesList <- list(
-c("Hylocichla_mustelina", "Wood_Thrush"))
-#c("Cyanocitta_cristata", "Blue_Jay"))
-#c("Euphagus_carolinus", "Rusty_Blackbird"))
-#c("Turdus_migratorius", "American_Robin"))
-#c("Seiurus_aurocapilla", "Ovenbird"),
-#c("Vireo_olivaceus", "Red-eyed_Vireo"))
-#c("Cardinalis_cardinalis", "Northern_Cardinal"))
-#c("Junco_hyemalis", "Dark-eyed_Junco"),
-#c("Piranga_olivacea", "Scarlet_Tanager"))
-#c("Carduelis_pinus", "Pine_Siskin"))
-#c("Hylocichla_mustelina", "Wood_Thrush"))
-#c("Colinus_virginianus", "Northern_Bobwhite"))
-
-# -----------------------------------------------------
-# SRD maximum sample size - this further restricts SRD
-# in addition to ERD spatial restrictions above)
-# -----------------------------------------------------
-srd.max.sample.size <- 5000
-
-## response.family = "bernoulli" or "gaussian"
-response.family <- "bernoulli"
-
-# ----------------------------------------------------------------------
-# Spatial Extent by Point in Rectangle, Polygon, or ShapeFile
-# ----------------------------------------------------------------------
-#spatial.extent.list <- NULL # Full US
-# -----------
-#spatial.extent.list <- list(type = "rectangle",
-# lat.min = 25.0,
-# lat.max = 50.0,
-# lon.min = -130.0,
-# lon.max = -65.0)
-# -----------
-spatial.extent.list <- list(type = "polygon",
- # data.frame with named vertices x and y
- polygon.vertices =
- data.frame(x = c(-85,-85,-70,-70),
- y = c(35, 50, 50, 35)) )
-# -----------
-#spatial.extent.list <- list(type="shapefile",
-# shape.dir = data.dir.shapefiles,
-# att.selection.column.name = "BCR",
-# # watch capitalization!
-# shape.filename = "bcr.shp",
-# selected.shape.names = c(13))
-# -----------
-#spatial.extent.list <- list(type="shapefile",
-# shape.dir = data.dir.shapefiles,
-# att.selection.column.name = "STATE_NAME",
-# shape.filename = "STATES.shp",
-# selected.shape.names = c("New York"))
-
-
-# -------------------------------------------------------------------
-# Temporal Extent
-# -------------------------------------------------------------------
-temporal.extent.list <- list(begin.jdate = 1,
- begin.year = 2006,
- end.jdate = 366,
- end.year = 2008)
-iii.year <- 2008
-n.intervals.per.year <-52
-n.intervals <- n.intervals.per.year + 1
-jdate.seq <- seq(from = temporal.extent.list[['begin.jdate']], to = temporal.extent.list[['end.jdate']], length = (n.intervals))
-if (n.intervals > 1) {
- jdate.seq <- round((jdate.seq[2:n.intervals] + jdate.seq[1:(n.intervals-1)])/2)
-}
-year.seq <- rep(iii.year, length(jdate.seq))
-begin.seq <- 1
-end.seq <- length(jdate.seq)
-
-
-
-# ------------------------
-# Select predictors - must be a subset of what is in erd…..
-# ------------------------
-predictor.names <- c("YEAR", "TIME", "DAY",
- "EFFORT_HRS", "EFFORT_DISTANCE_KM",
- "NUMBER_OBSERVERS", "HOUSING_DENSITY",
- "ELEV_NED",
- "CAUS_TEMP_AVG",
- "CAUS_TEMP_MIN", "CAUS_TEMP_MAX",
- "CAUS_PREC", "CAUS_SNOW",
- "NLCD2001_FS_C11_750_PLAND", "NLCD2001_FS_C12_750_PLAND",
- "NLCD2001_FS_C21_750_PLAND", "NLCD2001_FS_C22_750_PLAND",
- "NLCD2001_FS_C23_750_PLAND", "NLCD2001_FS_C24_750_PLAND",
- "NLCD2001_FS_C31_750_PLAND", "NLCD2001_FS_C41_750_PLAND",
- "NLCD2001_FS_C42_750_PLAND", "NLCD2001_FS_C43_750_PLAND",
- "NLCD2001_FS_C52_750_PLAND", "NLCD2001_FS_C71_750_PLAND",
- "NLCD2001_FS_C81_750_PLAND", "NLCD2001_FS_C82_750_PLAND",
- "NLCD2001_FS_C90_750_PLAND", "NLCD2001_FS_C95_750_PLAND")
-
-# -------------------------------------------------------------------
-# Data Splitting Parameters
-# -------------------------------------------------------------------
-split.par.list <- list(grid.cell.min.lat = 0.75,
- grid.cell.min.lon = 0.75,
- min.val.cell.locs = 2,
- fraction.training.data=0.8,
- mfrac=1.0,
- plot.it=FALSE)
-
-# -------------------------------------------------------------------
-# CV Fold Splitting Parameters
-# -------------------------------------------------------------------
-cv.folds <- 1
-cv.list <- c(1:cv.folds)
-cv.folds.par.list <- list(grid.cell.min.lat = 0.75,
- grid.cell.min.lon = 0.75,
- min.val.cell.locs = 2,
- fraction.training.data = 0.8,
- mfrac = 1.0,
- plot.it = FALSE)
-
-# ---------------------------------------------------------------------
-# STEM Ensemble Design
-# ---------------------------------------------------------------------
-iii.scale <- 2 # largest scale in STEM MS ==> current magic value
-stem.init.par.list <- list(
- # --------------------------------------------------
- # Spatial Design
- # --------------------------------------------------
- spatial.extent.list = NULL,
- spatial.region.par.list = list(
- # Number of MC regionalizations for each time interval
- n.mc.regions=1,
- # define minimum area & sample size of rectangles
- regional.cell.min.lat = 3.00*iii.scale,
- regional.cell.min.lon = 4.00*iii.scale,
- # Underlying Coverage Grid
- # Older declarations
- # grid.cell.min.lat = 1*(iii.scale^0.5), #5 degrees
- # grid.cell.min.lon = 1.75*(iii.scale^0.5), # 10 degrees
- # Simplified
- grid.cell.min.lat = 3.00*iii.scale/3, #5 degrees
- grid.cell.min.lon = 4.00*iii.scale/3, # 10 degrees
- n.centers.per.region = 1, # Density Dependent!!!
- min.data.size = 10),
- # --------------------------------------------------
- # Temporal Design:
- # Slice year into n.intervals prediction points
- # --------------------------------------------------
- n.intervals=60, #add 1! # 81 for migration
- begin.jdate=1 ,
- end.jdate = 366,
- season.window.width=40, #40 # Fitting window
- prediction.window.width=36, #36
- # --------------------------------------------------
- # Sampling
- # --------------------------------------------------
- sampling.par.list = list(
- split.by.location = FALSE,
- # if TRUE uses locs == ensemble.data.locs
- ST.basis.rotation = FALSE,
- # if TRUE assumes {lat,lon} ={$y, $ x}
- # and julian date == $JDATES
- p.train=0.75))
-
-base.model.par.list <- rpart.control(cp = 0.01, xval = 0, minbucket = 10)
-
-# ---------------------------------------------------------------------
-# conditioning variables
-# ---------------------------------------------------------------------
-
-conditioning.vars <- list(EFFORT_HRS = 1.0,
- EFFORT_DISTANCE_KM = 1.0,
- TIME = 7.0,
- NUMBER_OBSERVERS = 1.0,
- I.STATIONARY = 0)
-
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-# ST Matrix Maps
-# (AKA Halloween Maps)
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-
-ns.rows <- 40
-map.plot.pixel.width <- 1000
-z.max <- 0.50
-z.min <- 0.0
-map.filename.tag <- "demo."
-state.map <- TRUE
-state.map.lwd <- 1.0
-county.map <- TRUE
-county.map.lwd <- 0.5
-pred.grid.size <- ns.rows
-## map.plot.width <- map.plot.pixel.width
-map.plot.width <- 1000
-## This is duplicated in stem.init.par.list
-spatial.extent.list <- NULL
-map.tag <- map.filename.tag
-date.bar <- TRUE
-print.date <- TRUE
-## KFW resp.transformation.code <- NULL
diff --git a/contrib/stem/code/STEM_Globals.R.bkup b/contrib/stem/code/STEM_Globals.R.bkup
deleted file mode 100644
index e0907b9..0000000
--- a/contrib/stem/code/STEM_Globals.R.bkup
+++ /dev/null
@@ -1,236 +0,0 @@
-
-debugOutput <- FALSE
-# Slash direction for directory creation
-platform = "linux"
-# Possibly Spp names info
-
-# Required Packages
-require(rpart)
-require(mgcv)
-require(gbm)
-require(fields)
-require(splancs)
-require(maps)
-require(maptools)
-
-# Source STEM Libraries
-source(paste(code.directory,"stem.library.A.R",sep=""))
-source(paste(code.directory,"stem.library.B.R",sep=""))
-source(paste(code.directory,"stem.library.ST.R",sep=""))
-
-# Source MORE STEM Functions
-#source(paste(code.directory,"STEM_erd.data.creation.R",sep=""))
-source(paste(code.directory,"STEM_erd.srd.data.subsetting.R",sep=""))
-source(paste(code.directory,"STEM_ModelFitting.R",sep="") )
-source(paste(code.directory,"predict.eBird.ST.matrix.R",sep=""))
-source(paste(code.directory,"STEM_st.matrix.cv.average.R",sep=""))
-
-
-## Name of space time matrix sub-directory
-st.matrix.name <- "stm"
-
-## Name of space time matrix ave map sub-directory
-st.matrix.ave.maps <- "stm.ave.maps"
-
-
-
-# ------------------------
-# Select One Species
-# speciesList - a list of vectors. vector[1] = scientificName & vector[2] = commonName
-# ------------------------
-speciesList <- list(
-c("Hylocichla_mustelina", "Wood_Thrush"))
-#c("Cyanocitta_cristata", "Blue_Jay"))
-#c("Euphagus_carolinus", "Rusty_Blackbird"))
-#c("Turdus_migratorius", "American_Robin"))
-#c("Seiurus_aurocapilla", "Ovenbird"),
-#c("Vireo_olivaceus", "Red-eyed_Vireo"))
-#c("Cardinalis_cardinalis", "Northern_Cardinal"))
-#c("Junco_hyemalis", "Dark-eyed_Junco"),
-#c("Piranga_olivacea", "Scarlet_Tanager"))
-#c("Carduelis_pinus", "Pine_Siskin"))
-#c("Hylocichla_mustelina", "Wood_Thrush"))
-#c("Colinus_virginianus", "Northern_Bobwhite"))
-
-# -----------------------------------------------------
-# SRD maximum sample size - this further restricts SRD
-# in addition to ERD spatial restrictions above)
-# -----------------------------------------------------
-srd.max.sample.size <- 5000
-
-## response.family = "bernoulli" or "gaussian"
-response.family <- "bernoulli"
-
-# ----------------------------------------------------------------------
-# Spatial Extent by Point in Rectangle, Polygon, or ShapeFile
-# ----------------------------------------------------------------------
-#spatial.extent.list <- NULL # Full US
-# -----------
-#spatial.extent.list <- list(type = "rectangle",
-# lat.min = 25.0,
-# lat.max = 50.0,
-# lon.min = -130.0,
-# lon.max = -65.0)
-# -----------
-spatial.extent.list <- list(type = "polygon",
- # data.frame with named vertices x and y
- polygon.vertices =
- data.frame(x = c(-85,-85,-70,-70),
- y = c(35, 50, 50, 35)) )
-# -----------
-#spatial.extent.list <- list(type="shapefile",
-# shape.dir = data.dir.shapefiles,
-# att.selection.column.name = "BCR",
-# # watch capitalization!
-# shape.filename = "bcr.shp",
-# selected.shape.names = c(13))
-# -----------
-#spatial.extent.list <- list(type="shapefile",
-# shape.dir = data.dir.shapefiles,
-# att.selection.column.name = "STATE_NAME",
-# shape.filename = "STATES.shp",
-# selected.shape.names = c("New York"))
-
-
-# -------------------------------------------------------------------
-# Temporal Extent
-# -------------------------------------------------------------------
-temporal.extent.list <- list(begin.jdate = 1,
- begin.year = 2006,
- end.jdate = 366,
- end.year = 2008)
-iii.year <- 2008
-n.intervals.per.year <-52
-n.intervals <- n.intervals.per.year + 1
-jdate.seq <- seq(from = temporal.extent.list[['begin.jdate']], to = temporal.extent.list[['end.jdate']], length = (n.intervals))
-if (n.intervals > 1) {
- jdate.seq <- round((jdate.seq[2:n.intervals] + jdate.seq[1:(n.intervals-1)])/2)
-}
-year.seq <- rep(iii.year, length(jdate.seq))
-begin.seq <- 1
-end.seq <- length(jdate.seq)
-
-
-
-# ------------------------
-# Select predictors - must be a subset of what is in erd…..
-# ------------------------
-predictor.names <- c("YEAR", "TIME", "DAY",
- "EFFORT_HRS", "EFFORT_DISTANCE_KM",
- "NUMBER_OBSERVERS", "HOUSING_DENSITY",
- "ELEV_NED",
- "CAUS_TEMP_AVG",
- "CAUS_TEMP_MIN", "CAUS_TEMP_MAX",
- "CAUS_PREC", "CAUS_SNOW",
- "NLCD2001_FS_C11_750_PLAND", "NLCD2001_FS_C12_750_PLAND",
- "NLCD2001_FS_C21_750_PLAND", "NLCD2001_FS_C22_750_PLAND",
- "NLCD2001_FS_C23_750_PLAND", "NLCD2001_FS_C24_750_PLAND",
- "NLCD2001_FS_C31_750_PLAND", "NLCD2001_FS_C41_750_PLAND",
- "NLCD2001_FS_C42_750_PLAND", "NLCD2001_FS_C43_750_PLAND",
- "NLCD2001_FS_C52_750_PLAND", "NLCD2001_FS_C71_750_PLAND",
- "NLCD2001_FS_C81_750_PLAND", "NLCD2001_FS_C82_750_PLAND",
- "NLCD2001_FS_C90_750_PLAND", "NLCD2001_FS_C95_750_PLAND")
-
-# -------------------------------------------------------------------
-# Data Splitting Parameters
-# -------------------------------------------------------------------
-split.par.list <- list(grid.cell.min.lat = 0.75,
- grid.cell.min.lon = 0.75,
- min.val.cell.locs = 2,
- fraction.training.data=0.8,
- mfrac=1.0,
- plot.it=FALSE)
-
-# -------------------------------------------------------------------
-# CV Fold Splitting Parameters
-# -------------------------------------------------------------------
-cv.folds <- 1
-cv.list <- c(1:cv.folds)
-cv.folds.par.list <- list(grid.cell.min.lat = 0.75,
- grid.cell.min.lon = 0.75,
- min.val.cell.locs = 2,
- fraction.training.data = 0.8,
- mfrac = 1.0,
- plot.it = FALSE)
-
-# ---------------------------------------------------------------------
-# STEM Ensemble Design
-# ---------------------------------------------------------------------
-iii.scale <- 2 # largest scale in STEM MS ==> current magic value
-stem.init.par.list <- list(
- # --------------------------------------------------
- # Spatial Design
- # --------------------------------------------------
- spatial.extent.list = NULL,
- spatial.region.par.list = list(
- # Number of MC regionalizations for each time interval
- n.mc.regions=1,
- # define minimum area & sample size of rectangles
- regional.cell.min.lat = 3.00*iii.scale,
- regional.cell.min.lon = 4.00*iii.scale,
- # Underlying Coverage Grid
- # Older declarations
- # grid.cell.min.lat = 1*(iii.scale^0.5), #5 degrees
- # grid.cell.min.lon = 1.75*(iii.scale^0.5), # 10 degrees
- # Simplified
- grid.cell.min.lat = 3.00*iii.scale/3, #5 degrees
- grid.cell.min.lon = 4.00*iii.scale/3, # 10 degrees
- n.centers.per.region = 1, # Density Dependent!!!
- min.data.size = 10),
- # --------------------------------------------------
- # Temporal Design:
- # Slice year into n.intervals prediction points
- # --------------------------------------------------
- n.intervals=60, #add 1! # 81 for migration
- begin.jdate=1 ,
- end.jdate = 366,
- season.window.width=40, #40 # Fitting window
- prediction.window.width=36, #36
- # --------------------------------------------------
- # Sampling
- # --------------------------------------------------
- sampling.par.list = list(
- split.by.location = FALSE,
- # if TRUE uses locs == ensemble.data.locs
- ST.basis.rotation = FALSE,
- # if TRUE assumes {lat,lon} ={$y, $ x}
- # and julian date == $JDATES
- p.train=0.75))
-
-base.model.par.list <- rpart.control(cp = 0.01, xval = 0, minbucket = 10)
-
-# ---------------------------------------------------------------------
-# conditioning variables
-# ---------------------------------------------------------------------
-
-conditioning.vars <- list(EFFORT_HRS = 1.0,
- EFFORT_DISTANCE_KM = 1.0,
- TIME = 7.0,
- NUMBER_OBSERVERS = 1.0,
- I.STATIONARY = 0)
-
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-# ST Matrix Maps
-# (AKA Halloween Maps)
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-
-ns.rows <- 40
-map.plot.pixel.width <- 1000
-z.max <- 0.50
-z.min <- 0.0
-map.filename.tag <- "demo."
-state.map <- TRUE
-state.map.lwd <- 1.0
-county.map <- TRUE
-county.map.lwd <- 0.5
-pred.grid.size <- ns.rows
-## map.plot.width <- map.plot.pixel.width
-map.plot.width <- 1000
-## This is duplicated in stem.init.par.list
-spatial.extent.list <- NULL
-map.tag <- map.filename.tag
-date.bar <- TRUE
-print.date <- TRUE
-## KFW resp.transformation.code <- NULL
diff --git a/contrib/stem/code/STEM_ModelFitting.R b/contrib/stem/code/STEM_ModelFitting.R
deleted file mode 100644
index cde239e..0000000
--- a/contrib/stem/code/STEM_ModelFitting.R
+++ /dev/null
@@ -1,201 +0,0 @@
-
-
-# --------------------------------------------------------------------
-# --------------------------------------------------------------------
-#
-# cv.folds = 0 : fit complete training data, no splitting
-# cv.folds >= 1: fit nfold data
-#
-# ---------------------------------------------------------------------
-# Fit & Save The bagged rpart Ensemble
-# ------------------------------------------------
-# Note: Ensemble Model information is autmatically stored
-# with the tag ".ensemble.index.RData" in the model directory.
-# This is essential information along with the
-# ensemble parameter list. So we save that too.
-# ----------------------
-# Brieman rpart parameters
-#control=rpart.control(cp=0,xval=0,minsplit=2))
-# Limit infludence of any one point.
-# And for node-level predictions, it means that a
-# single positive value may have a maximum of
-# 1/minbucket. Which was one
-#parms=list(split="information")) # bernoulli deviance
-# Its huge and all the information is in the index file
-# ---------------------------------------------------------------------
-#
-#
-# TO DO:
-# ** Add functionality for
-# keep.data = TRUE,# verbose = TRUE,
-# and check functionality for RNG.seed in the fit.ensemble()
-# routine.
-# --------------------------------------------------------------------
-# --------------------------------------------------------------------
-# DMF 3.19.10 VT Changes
-# * remove creation of stem.results.directories
-stem <- function(train.data,
- stem.directory,
- weights = NULL,
- offset = NULL,
- response.family = "bernoulli",
- cv.folds=0,
- cv.folds.par.list=NULL,
- stem.init.par.list,
- base.model.par.list = NULL,
- keep.data = TRUE,
- verbose = TRUE,
- RNG.seed= 12345,
- block.save.size=100) # (training sample size x block.save.size )
-{# begin function
-# --------------------------------------------------------------------
-# use constant tag value to simplify inputs
-stem.model.tag <- "stem."
-for (iii.cv in 1:cv.folds){
- print(paste("iii.cv", iii.cv))
- # -------------------------------------------------------------
- # Create Directories
- # -------------------------------------------------------------
- if (iii.cv == 1) {
- system(paste("mkdir ",stem.directory,sep=""), intern=TRUE)
-
- if( "/" != substring(stem.directory, nchar(stem.directory), nchar(stem.directory))) {
- stem.model.directory <- paste(stem.directory,"/model/",sep="")
- }
- else {
- stem.model.directory <- paste(stem.directory,"model/",sep="")
- }
-
- system(paste("mkdir ",stem.model.directory,sep=""), intern=TRUE)
- }
- model.dir <- paste(stem.model.directory,
- "stem.models.", as.character(iii.cv), "/",sep="")
- ttt.statement <- paste("mkdir ",model.dir,sep="")
- #print(ttt.statement)
- system(ttt.statement, intern=TRUE)
- #results.dir <- paste(stem.directory,
- # "stem.results.", as.character(iii.cv), "/",sep="")
- #ttt.statement <- paste("mkdir ",results.dir,sep="")
- #print(ttt.statement)
- #system(ttt.statement, intern=TRUE)
- # -------------------------------------------------------------
- # Split-Fold Training Data
- # -------------------------------------------------------------
- print(paste("cv.folds", cv.folds))
- if (cv.folds<=0) {
- cv.train.data <- list(
- X = train.data$X,
- y = train.data$y,
- locs = train.data$loc,
- jdates = train.data$jdates)
- }
- if (cv.folds>0) {
- D.split <- maximum.coverage.selection(
- locs=data.frame(
- x=train.data$locs$x ,
- y=train.data$locs$y),
- jdates=train.data$jdates,
- grid.cell.min.lat = cv.folds.par.list$grid.cell.min.lat, grid.cell.min.lon = cv.folds.par.list$grid.cell.min.lon, min.val.cell.locs = cv.folds.par.list$min.val.cell.locs, fraction.training.data = cv.folds.par.list$fraction.training.data, mfrac = cv.folds.par.list$mfrac, plot.it=cv.folds.par.list$plot.it)
- cv.train.data <- list(
- X = train.data$X[ D.split$train.index, ],
- y = train.data$y[ D.split$train.index ],
- locs =
- list(x=train.data$loc$x[ D.split$train.index ],
- y=train.data$loc$y[ D.split$train.index ]),
- jdates = train.data$jdates[ D.split$train.index ])
-
- }
- # -------------------------------------------------------------
- # Create Ensemble based on Training Data
- # -------------------------------------------------------------
-
- print("creating ensemble")
- stem.par.list <- create.simple.STEM.ensemble(
- ensemble.data.locs = cv.train.data$locs,
- ensemble.data.jdates = cv.train.data$jdates,
- #ensemble.model.filename = stem.model.tag,
- # --------------------------------------------------
- # Spatial Design
- # --------------------------------------------------
- spatial.extent.list = stem.init.par.list$spatial.extent.list , #default to train data convex hull
- spatial.region.par.list = stem.init.par.list$spatial.region.par.list,
- #~ # Number of MC regionalizations for each time interval
- #~ n.mc.regions=1,
- #~ # Underlying Coverage Grid
- #~ grid.cell.min.lat = 1.5*(iii.scale^0.5), #5 degrees
- #~ grid.cell.min.lon = 2*(iii.scale^0.5), # 10 degrees
- #~ n.centers.per.region = 1, # Density Dependent!!!
- #~ # Maximum Rectangular Region Growth Factor
- #~ #max.random.scale.factor = 0.25,
- #~ # define minimum area & sample size of rectangles
- #~ regional.cell.min.lat = 3.00*iii.scale,
- #~ regional.cell.min.lon = 4.00*iii.scale,
- #~ min.data.size = 25),
- # --------------------------------------------------
- # Temporal Design:
- # Slice year into n.intervals prediction points
- # --------------------------------------------------
- n.intervals = stem.init.par.list$n.intervals, #add 1! # 81 for migration
- begin.jdate= stem.init.par.list$begin.jdate,
- end.jdate = stem.init.par.list$end.jdate,
- season.window.width= stem.init.par.list$season.window.width, #40 # Fitting window
- prediction.window.width=stem.init.par.list$prediction.window.width, #36
- # --------------------------------------------------
- # Sampling
- # --------------------------------------------------
- sample.ensemble.function = sample.ST.ensemble,
- sampling.par.list = stem.init.par.list$sampling.par.list,
- #~ split.by.location = FALSE,
- #~ # if TRUE uses locs == ensemble.data.locs
- #~ ST.basis.rotation = FALSE,
- #~ # if TRUE assumes {lat,lon} ={$y, $ x}
- #~ # and julian date == $JDATES
- #~ p.train=0.63),
- # --------------------------------------------------
- # Prediction
- # --------------------------------------------------
- predict.ensemble.function = predict.ST.ensemble)
-# ---------------------------------------------------------------------
-
- # -------------------------------------------------------------
- # STEM Fit
- # -------------------------------------------------------------
- print("running fit")
- D.ttt <- fit.ensemble(
- train.data = cv.train.data,
- resp.family= response.family,
- filename = paste(model.dir,stem.model.tag,sep=""),
- RNG.seed = RNG.seed,
- ensemble.par.list = stem.par.list,
- ensemble.weights = weights,
- block.save.size=block.save.size,
- control=base.model.par.list)
- # ------------------------------------------------------------- # Pack additional info into stem.par.list # -------------------------------------------------------------
- stem.par.list$cv.fold.train.index <- D.split$train.index
- stem.par.list$realized.sample.par <- D.ttt$realized.sample.par
- stem.par.list$RNG.seed <- D.ttt$RNG.seed
- stem.par.list$function.call <- D.ttt$function.call
- D.stem <- stem.par.list
- save(D.stem,
- file = paste(model.dir, "stem.model.par.list.",
- iii.cv,".RData" , sep = ""))
- rm(D.stem, D.split, stem.par.list, D.ttt)
- ## KFW gc()
- # ------------------------------------------------------------- # Debug output # -------------------------------------------------------------
- if (debugOutput == TRUE) {
- print("----- Memory usage before system() call gc() -----")
- memoryMsg <- paste("Memory info =", gc(verbose=TRUE), sep=" ")
- print(memoryMsg)
- print("----- Memory usage before system() call object.size()-----")
- mem <- sapply(ls(), function(x) object.size(get(x)))
- print(mem)
- print("----- Sum of object.size()-----")
- print(sum(mem))
- }
-} ## End for (iii.cv in 1:nnn.cv)
-# -----------------------------------------------------------------------------
-# No Return Value Object
-} # end function
-# --------------------------------------------------------------------
-
-
diff --git a/contrib/stem/code/STEM_erd.srd.data.subsetting.R b/contrib/stem/code/STEM_erd.srd.data.subsetting.R
deleted file mode 100644
index 36f6004..0000000
--- a/contrib/stem/code/STEM_erd.srd.data.subsetting.R
+++ /dev/null
@@ -1,273 +0,0 @@
-#------------------------------------------------------------------------------
-# I envision ERD data creation this way
-# * STEM_erd.data.creation - processes data from CSV files
-# * STEM_erd.data.subsetting - load and further subset data
-#
-# * Consider SRD & ERD data together as a single functional step
-# because they rely on the same parameters
-# ==> subsetting should also be done together
-#
-# Kevin, we will need to talk about how to incorporate
-# your work on ERD & NDVI data creation.
-# In general we want this to extend to other SRD with
-# temporally varying covariates.
-#
-# Kevin, I dont know where this fits
-#------------------------------------------------------------------------------
-# Load NDVI Data
-#-----------------------------------------------------------------------------
-## KFW
-## vegetationIndexData <- read.csv(file="ebird_reference_data/processed_VI_Data_SRD.csv", na.strings = c("NA", "?"))
-#vegetationIndexData <- matrix(scan("ebird_reference_data/custom_vi.txt"), 18880842, 6, byrow=TRUE)
-#print(class(vegetationIndexData))
-#print(nrow(vegetationIndexData))
-#print(ncol(vegetationIndexData))
-
-testRpyCall <- function(object) {
- print(class(object))
- print(object)
-}
-
-
-
-#------------------------------------------------------------------------------
-erd.srd.data.subsetting <- function(
- erd.data.filename, #erd.data.tag,
- srd.pred.design.filename,
- spatial.extent.list,
- temporal.extent.list,
- ## KFW speciesList,
- species.name,
- predictor.names,
- response.family,
- srd.max.sample.size,
- split.par.list,
- response.truncation.cutoff=20){
- #---------------------------------------------------------------------------
- # Load SRD Data #------------------------------------------------------------------------------------------------------------
- print(srd.pred.design.filename)
- load(file=srd.pred.design.filename) # pred.data
- #dim(pred.data$D.pred)
- #dim(pred.data$locs)
- # ----------------------------------------------------------------------
- # Limit Spatial Extent by Point in Rectangle, Polygon, or ShapeFile
- # ----------------------------------------------------------------------
- xxx <- pred.data$locs$x
- yyy <- pred.data$locs$y
- region.index <- rep(TRUE, nrow(pred.data$D.pred) )
- if (!is.null(spatial.extent.list)){
- ## KFW if (spatial.extent.list$type == "rectangle"){
- if (spatial.extent.list[['type']] == "rectangle"){
- ttt.index <- (
- yyy > spatial.extent.list$lat.min &
- yyy < spatial.extent.list$lat.max &
- xxx > spatial.extent.list$lon.min &
- xxx < spatial.extent.list$lon.max )
- region.index <- (ttt.index & region.index)
- }
- ## KFW if (spatial.extent.list$type == "polygon"){
- if (spatial.extent.list[['type']] == "polygon"){
- ttt.index <- point.in.polygon(
- xxx = xxx,
- yyy = yyy,
- polygon.vertices =
- spatial.extent.list$polygon.vertices)
- region.index <- (ttt.index & region.index)
- }
- ## KFW if (spatial.extent.list$type == "shapefile"){
- if (spatial.extent.list[['type']] == "shapefile"){
-
- ttt.index <- point.in.shapefile(
- sites = data.frame(lon=xxx, lat=yyy),
- shape.dir=spatial.extent.list$shape.dir,
- shape.filename=spatial.extent.list$shape.filename,
- att.selection.column.name=
- spatial.extent.list$att.selection.column.name,
- selected.shape.names=
- spatial.extent.list$selected.shape.names)
- region.index <- (ttt.index & region.index)
- }
- } # if (!is.null(spatial.extent.list)){
- # ------------------
- # Subset SRD
- # ------------------
- srd.data <-NULL
- srd.data$D.pred <- pred.data$D.pred[region.index, ]
- srd.data$locs <- pred.data$locs[region.index, ]
- #dim(pred.data$D.pred)
- #dim(pred.data$locs)
- rm(pred.data)
- ## KFW gc()
- # ------------------
- # Subset SRD
- # DMF 3.17.10
- # ------------------
- if (!is.null(srd.max.sample.size)) {
- if (nrow(srd.data$D.pred) > srd.max.sample.size){
- ttt.index <- sample(x=c(1:nrow(srd.data$D.pred)),
- size=srd.max.sample.size)
- srd.data$D.pred <- srd.data$D.pred[ttt.index, ]
- srd.data$locs <- srd.data$locs[ttt.index, ]
- }
- }
- # --------------------------
-
-
- #-----------------------------------------------------------------------------
- # Load ERD parameter data & Data
- #
- # Wish List for erd.data.creation
- # ** combine data & parameters into a single list object
- # ** save only index to identify train & test sets. There is no need to
- # save entire thing twice.
- #------------------------------------------------------------------------------
- #erdParameterListFile <- paste(data.dir, erd.data.tag, "erd.data.par.list.RData", sep="")
- #load(file=erdParameterListFile) #return.list
- #D.erd.data.par.list <- return.list
-
- #erdDataFile <- paste(data.dir, D.erd.data.par.list$erd.data.tag, "erd.data.RData", sep="")
- load(file=erd.data.filename) # erdDataFile) #D
- # ----------------------------------------------------------------------
- # Limit Spatial Extent by Point in Rectangle, Polygon, or ShapeFile
- # ----------------------------------------------------------------------
- xxx <- D$LONGITUDE
- yyy <- D$LATITUDE
- region.index <- rep(TRUE, nrow(D) )
- if (!is.null(spatial.extent.list)){
- ## KFW if (spatial.extent.list$type == "rectangle"){
- if (spatial.extent.list[['type']] == "rectangle"){
- ttt.index <- (
- yyy > spatial.extent.list$lat.min &
- yyy < spatial.extent.list$lat.max &
- xxx > spatial.extent.list$lon.min &
- xxx < spatial.extent.list$lon.max )
- region.index <- (ttt.index & region.index)
- }
- ## KFW if (spatial.extent.list$type == "polygon"){
- if (spatial.extent.list[['type']] == "polygon"){
- ttt.index <- point.in.polygon(
- xxx = xxx,
- yyy = yyy,
- polygon.vertices =
- spatial.extent.list$polygon.vertices)
- region.index <- (ttt.index & region.index)
- }
- ## KFW if (spatial.extent.list$type == "shapefile"){
- if (spatial.extent.list[['type']] == "shapefile"){
- ttt.index <- point.in.shapefile(
- sites = data.frame(lon=xxx, lat=yyy),
- shape.dir=spatial.extent.list$shape.dir,
- shape.filename=spatial.extent.list$shape.filename,
- att.selection.column.name=
- spatial.extent.list$att.selection.column.name,
- selected.shape.names=
- spatial.extent.list$selected.shape.names)
- region.index <- (ttt.index & region.index)
- }
- } # if (!is.null(spatial.extent.list)){
- # -------------------------------------------------------------------
- # -------------------------------------------------------------------
- # Limit Temporal Extent
- # -------------------------------------------------------------------
- season.index <- rep(TRUE, nrow(D) )
- if (!is.null(temporal.extent.list)){
- # Convert JDATE + YEAR to single temporal index
- begin.tindex <- temporal.extent.list$begin.year +
- temporal.extent.list$begin.jdate/366
- end.tindex <- temporal.extent.list$end.year +
- temporal.extent.list$end.jdate/366
- D.tindex <- D$YEAR + D$DAY/366
- season.index <- D.tindex >= begin.tindex &
- D.tindex <= end.tindex
- }
- # -------------------------------------------------------------------
- # ST extent
- # -------------------------------------------------------------------
- regional.seasonal.index <- region.index & season.index
- sum(regional.seasonal.index)
- ebirdReferenceDataFrame <- D[regional.seasonal.index, ]
- rm(D)
- ## KFW gc(D)
- #------------------------------------------------------------------------------------------------------------
- # Train:Test Set Split : maximum coverage, eq wt train-test split
- #------------------------------------------------------------------------------------------------------------
- D.split <- maximum.coverage.selection(locs=data.frame(x=ebirdReferenceDataFrame$LONGITUDE ,
- y=ebirdReferenceDataFrame$LATITUDE),
- jdates=ebirdReferenceDataFrame$DAY,
- # vector length n
- grid.cell.min.lat = split.par.list$grid.cell.min.lat,
- grid.cell.min.lon = split.par.list$grid.cell.min.lon,
- min.val.cell.locs = split.par.list$min.val.cell.locs,
- fraction.training.data = split.par.list$fraction.training.data,
- mfrac = split.par.list$mfrac,
- plot.it=split.par.list$plot.it)
- # -----------------------------------------------
- train.index <- D.split$train.index
- test.index <- D.split$test.index
- rm(D.split)
- ## KFW response.index <- names(ebirdReferenceDataFrame) %in% speciesList[[1]][1]
- response.index <- names(ebirdReferenceDataFrame) %in% species.name
- predictors.index <- names(ebirdReferenceDataFrame) %in% predictor.names
- train.data <- NULL
- test.data <- NULL
- # ---------------------
- train.data$X <- ebirdReferenceDataFrame[train.index, predictors.index]
- ttt.y <- ebirdReferenceDataFrame[, response.index]
- train.data$y <- ttt.y[train.index]
- rm(ttt.y)
- train.data$locs$x <- ebirdReferenceDataFrame$LONGITUDE[train.index]
- train.data$locs$y <- ebirdReferenceDataFrame$LATITUDE[train.index]
- train.data$jdates <- ebirdReferenceDataFrame$DAY[train.index]
- # ------------------------------------
- test.data$X <- ebirdReferenceDataFrame[test.index,predictors.index]
- ttt.y <- ebirdReferenceDataFrame[, response.index]
- test.data$y <- ttt.y[test.index]
- rm(ttt.y)
- test.data$locs$x <- ebirdReferenceDataFrame$LONGITUDE[test.index]
- test.data$locs$y <- ebirdReferenceDataFrame$LATITUDE[test.index]
- test.data$jdates <- ebirdReferenceDataFrame$DAY[test.index]
- # --------------------------------------------
- rm(ebirdReferenceDataFrame)
- # ----------------------------------------------------------------------
- # ERD parameters
- # ----------------------------------------------------------------------
- #protocol.tag <- D.erd.data.par.list$protocol.tag
- #c("traveling","stationary") #,"casual.obs")
- #if (D.erd.data.par.list$response.type == "occurrence") {
- # resp.family <- "bernoulli" # "gaussian" or "bernoulli"
- # }
- #if (D.erd.data.par.list$response.type == "abundance"){
- # resp.family <- "gaussian" # "gaussian" or "bernoulli"
- # }
- # --------------------------------
- if ( response.family =="bernoulli") {
- # ------------------------------------
- # Logical - where the predicted response is the
- # probability of a positive/True class
- # -------------------------------------
- train.data$y <- as.factor( train.data$y > 0) # TRUE if positive
- test.data$y <- as.factor( test.data$y > 0) # TRUE if positive
- }
- # Create Truncated Gaussian Response
- if ( response.family == "gaussian"){
- #
- # truncate responses @ 10
- #sum(train.data$y > response.truncation.cutoff)
- train.data$y[train.data$y > response.truncation.cutoff] <- response.truncation.cutoff
- test.data$y[test.data$y >response.truncation.cutoff] <- response.truncation.cutoff
- }
-# --------------------------------------------------------------------------
- return.list <- list(
- train.index = train.index,
- test.index = test.index,
- #protocol.tag=protocol.tag,
- response.family=response.family,
- train.data = train.data,
- test.data = test.data,
- srd.data = srd.data)
-# --------------------------------------------------------------------------
- return(return.list)
- }
-# --------------------------------------------------------------------------
-
-
diff --git a/contrib/stem/code/STEM_st.matrix.cv.average.R b/contrib/stem/code/STEM_st.matrix.cv.average.R
deleted file mode 100644
index 7d62b24..0000000
--- a/contrib/stem/code/STEM_st.matrix.cv.average.R
+++ /dev/null
@@ -1,95 +0,0 @@
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-# Compute ST Matrix fold-average
-# # DMF 3.19.10
-#
-# The fold-average st.mat predictions produces
-# a single ST matrix object and stores it in the output dir.
-#
-# The idea here is the ST matrix handle is the directory name
-# So, different ST matrices need to live in different directories
-# because each directory will have the same file names.
-#
-# Remember, we are assuming that the loc list is identical for
-# all cv.folds.
-#
-#
-#
-# Inputs
-# stem.dir
-# st.matrix.input.name
-# jdate.seq
-# year.seq
-# Outputs:
-# ST.matrix
-#
-#
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-st.matrix.cv.average <- function(
- stem.directory, #=stem.directory
- st.matrix.input.directory, # st.matrix project name #st.matrix.file.tag, # = "demo."
- cv.list, # = c(1:cv.folds)
- jdate.seq = jdate.seq,
- year.seq = year.seq,
- st.matrix.output.directory){
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-
- if ("/" == substring(st.matrix.input.directory, nchar(st.matrix.input.directory), nchar(st.matrix.input.directory))) {
- st.matrix.directory <- st.matrix.input.directory
- }
- else {
- st.matrix.directory <- paste(st.matrix.input.directory, "/", sep="")
- }
-
- if ("/" == substring(st.matrix.output.directory, nchar(st.matrix.output.directory), nchar(st.matrix.output.directory))) {
- st.matrix.output.directory <- st.matrix.output.directory
- }
- else {
- st.matrix.output.directory <- paste(st.matrix.output.directory, "/", sep="")
- }
-
- system(paste("mkdir ", st.matrix.output.directory,sep=""), intern=TRUE)
-# -----------------
-for (iii in 1:length(jdate.seq)){
- cv.pred <- NULL
- for (iii.cv in cv.list){
- # --------------------------------------------------------------------
- # Load data into (location, time) matrix
- # --------------------------------------------------------------------
- #results.dir <- paste(stem.directory,"stem.results.",iii.cv, "/",sep="")
- #stem.ST.matrix.file.tag <-
- # paste(results.dir,st.matrix.file.tag,"st.matrix.",sep="")
- results.dir <- paste(st.matrix.directory, "st.matrix.",
- as.character(iii.cv), "/",sep="")
- stem.ST.matrix.file.tag <-
- paste(results.dir,"st.matrix.",sep="")
- stp.name <- paste(stem.ST.matrix.file.tag,".",iii,".RData",sep="")
- load(stp.name) # st.pred
- #names(st.pred) #xxx yyy pred sd
- if (iii.cv == cv.list[1]) cv.pred <- st.pred$pred
- if (iii.cv != cv.list[1]) cv.pred <- cv.pred + st.pred$pred
- } # iii.cv
- st.pred$pred <- cv.pred/length(cv.list)
- # -----------------------
- # Save st.pred
- # -----------------------
- # map.dir
- cv.ave.st.pred.filename <- paste(st.matrix.output.directory,
- "st.matrix..",iii,".RData",sep="")
-
- save(st.pred, file = cv.ave.st.pred.filename) # st.pred
-} # end iii - intervals
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-} # end function
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-
-
-
-
-
-
-
diff --git a/contrib/stem/code/predict.eBird.ST.matrix.R b/contrib/stem/code/predict.eBird.ST.matrix.R
deleted file mode 100644
index e46cd31..0000000
--- a/contrib/stem/code/predict.eBird.ST.matrix.R
+++ /dev/null
@@ -1,200 +0,0 @@
-
-
-# --------------------------------------------------------------------
#
-# ==> This function is just a CV wrapper to
-# predict.st.matrix.ebird.ref.data!!!
-# ==> Also new is the creation of an "index" file
-# to hold all of the parameters needed to describe
-# the st.matrix (file sequence)
-#
-#
-# The ST Matrix:
-# ------------------
-# Basis for predictive experiments or ST analysis
-# is predictions across a region in space and across.
-# Often we want to know how spatial distrivution changed shrought time.
-#
-# Conceptually the ST Matrix as a data object is a set of
-# prediction across a lattice in space and time.
-# The st.matrix data object is a sequence of files
-# Each one contains the predictions across a set of locations
-# during a single time step.
-# Each file in the sequence contains the predictions across
-# the same set of locations evaluated at each of times
-# in the temporal sequence.
-#
-# One set of ST.matrix files is written for each CV-fold
-# model in cv.list
-#
-# The ST matrix can be thougth of as a source of psuedo-data
-# with 3 added benefits:
-# 1) Cleaned
-# 2) Filled In
-# 3) Uncertainty Estimates
-#
-#
-# File Namining Conventions
-# ---------------------------
-#
-#
-# Naming Standards are being hardcoded for convenience/simplicity
-# For example, one stem analysis per directory means that the
-# STEM objects are uniquely identified by the directory name.
-# So, I fixed the model names by hardcoding
-# stem.model.tag <- "stem."
-#
-# st.matrix Names = paste(results.dir,st.matrix.file.tag,"st.matrix.",
-# [sequence number], ".RData",sep="")
-# These are kept in the CV result directories
-# because they are CV specific.
-#
-# --------------------------------------------------------------------
# --------------------------------------------------------------------
-# DMF 3.19.10 VT modifications
-# * change formal parameter st.matrix.name, # st.matrix project name
-predict.erd.st.matrix <- function(
- stem.directory, # equivalent to stem.object
- pred.data, #= srd.data,
- cv.list, # subset of cv's
- stem.predictor.names,
- # --------------
- st.matrix.name, # st.matrix project name
- #st.matrix.directory,
- jdate.seq,
- year.seq,
- conditioning.vars){ #= conditioning.vars)
-# --------------------------------------------------------------------
- stem.model.tag <- "stem." #hardcoded for convenience
-
- print("**********")
- print(stem.directory)
-
-
- if ("/" == substring(stem.directory, nchar(stem.directory), nchar(stem.directory))) {
- st.matrix.directory <- paste(stem.directory, st.matrix.name, "/", sep="")
- stem.model.directory <- paste(stem.directory, "model", "/", sep = "")
- }
- else {
- st.matrix.directory <- paste(stem.directory, "/", st.matrix.name, "/", sep="")
- stem.model.directory <- paste(stem.directory, "/", "model", "/", sep="")
- }
-
- system(paste("mkdir ",st.matrix.directory, sep=""), intern=TRUE)
-
-# ---------------------------
-for (iii.cv in cv.list){
- results.dir <- paste(st.matrix.directory, "st.matrix.",
- as.character(iii.cv), sep = "")
- system(paste("mkdir ",results.dir,sep=""), intern=TRUE)
- # ------
- model.dir <- paste(stem.model.directory, "stem.models.",
- as.character(iii.cv), "/", sep="")
- stem.ST.matrix.file.tag <-
- paste(results.dir,"/", "st.matrix.",sep="")
- ## Load nfold specific parameter list
- load(file = paste(model.dir,
- "stem.model.par.list.", iii.cv, ".RData" , sep = "")) # D.stem
- # ----------------------------
- # Write ST.Matrix object to stem.results directories
- # ----------------------------
-
- print(names(pred.data$D.pred))
- print(nrow(pred.data$D.pred))
-
-
- predict.st.matrix.ebird.ref.data(
- prediction.design = pred.data$D.pred,
- prediction.design.locs = pred.data$locs,
- # prediction.design.jdates, #not needed here
- #--------------
- model.predictor.names = stem.predictor.names,
- model.filename = #stem.model$ensemble.model.filename,
- paste(model.dir, stem.model.tag,sep=""),
- ensemble.par.list = D.stem, #stem.model, #ensemble.par.list,
- # --------------
- save.name = stem.ST.matrix.file.tag,
- # Temporal Sequence
- jdate.seq =jdate.seq,
- year.seq =year.seq,
- # Conditioning Vars - Observation Process Design
- conditioning.vars = conditioning.vars)
- # ----------------------
- # Save Index File
- # ----------------------
- st.matrix.list <- list(
- stem.directory = stem.directory,
- pred.data.locs = pred.data$locs,
- cv.number=iii.cv, # subset of cv's
- stem.predictor.names=stem.predictor.names,
- # --------------
- st.matrix.name = st.matrix.name,
- jdate.seq = jdate.seq,
- year.seq = year.seq,
- conditioning.vars=conditioning.vars)
- filename.tag <-
- paste(results.dir,"st.matrix.list.",iii.cv,".RData",sep="")
- save(st.matrix.list, file=filename.tag)
- # ------------------
- ## KFW DF
- ## Local memory recovery block
- rm(D.stem,st.matrix.list)
- ## KFW gc()
-} # end iii.cv - data folds
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-## Clear the deck
-rm(list = c("bs.rpart.maps", "conditioning.vars", "create.pd.grid",
- "create.simple.STEM.ensemble", "D", "data.filename",
- "D.erd.data.par.list", "D.erd.test.data.par.list",
- "D.erd.train.data.par.list", "deviance.explained",
- "ebirdReferenceDataFrame", "ensemble.partial.dependence",
- "equal.wt.max.coverage.selection", "erdDataFile", "erdParameterListFile",
- "exp.name", "fit.ensemble", "fit.stem", "halloween.maps", "iii.cv",
- "iii.year", "initizalize.map.grid", "jdate.seq", "make.erd.data",
- "make.functional.data.design.matrix", "make.SPAT.COVAR.pred.data",
- "make.spatial.erd.prediction.design", "map.tag",
- "maximum.coverage.selection", "model.dir", "monthly.maps", "n.intervals",
- "n.intervals.per.year", "n.red", "plot.diagnostics",
- "plot.STEM.temporal.design", "plot.ST.ensemble", "plot.vi.bdt",
- "point.in.polygon", "point.in.polygon.contours", "point.in.shapefile",
- "poisson.accuracy", "poisson.deviance", "poisson.pearson", "pop.rpart",
- "pred.data", "predictive.performance", "predictors.index",
- "predict.stem.ST.matrix", "predict.ST.ensemble", "predict.st.matrix",
- "predict.st.matrix.ebird.ref.data", "protocol.tag", "resp.family",
- "response.index", "response.truncation.cutoff", "results.dir", "return.list",
- "rotate.ST.basis.pred", "rotate.ST.basis.sample",
- "rpart.ensemble.diagnostics", "sample.ST.ensemble", "seasonal.window",
- "smooth.st.predictions", "spatial.density.contours",
- "spatial.performance.plot", "spp.common.name", "spp.dir", "spp.list",
- "stateMapEnv", "stem.map.inference.split", "STEM.partial.dependence",
- "stem.ST.matrix.file.tag", "st.ttt.pred", "summarize.ensemble",
- "summary.1D.PD.ensemble", "surface.maps", "test.set.prediction.filename",
- "ttsplit", "ttt.statement", "unique.locs.splitting",
- "year.seq", "zzz.max"))
-if (debugOutput == TRUE) {
- rm(list = c("mem", "memoryMsg"))
-}
-## KFW gc()
-# --------------------------------------------------------------------------
-} #end function
-# --------------------------------------------------------------------------
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/contrib/stem/code/stem.library.A.R b/contrib/stem/code/stem.library.A.R
deleted file mode 100644
index 60b9074..0000000
--- a/contrib/stem/code/stem.library.A.R
+++ /dev/null
@@ -1,2088 +0,0 @@
-
-#--------------------------------------------------------------------------------
-# Predictive.Ensemble.Modeling.Library
-# 1.22.09
-# DMF
-#
-#
-#--------------------------------------------------------------------------------
-#
-# One Stop Shopping for BDT's
-# Bigger vision - this is a flexible bootstrap CV wrapper
-# for predictive modeling.
-#
-#
-# 3.11.09 - Added New STEM Spatial Design
-# Tested standalone
-#
-# Tested with Demo - performed favorably on NE Norcar data
-# compared with BDT!!! Bernoulli -
-# spatial design - no temporal segmentation.
-#
-#New Strategy for saving smaller rpart objects.
-# ----------------------------------------------------
-#Sucess = saving minimal structure for making predicitons
-# & CALCULATING diagnostics (VI's)
-#Test:
-#Pass data frame to predict function.
-#How big are the terms?
-#Can they be left out and still make preds & VI's?
-#--------------------------------------
-# ans <- list(frame = frame, where = where, call = call,
-# terms = Terms, cptable = t(rp$cptable), splits = splits,
-# method = method, parms = init$parms, control = controls,
-# functions = functions)
-# class(ans) <- "rpart"
-#
-#
-# 4/15
-# -------
-# ** sample.ST.ensemble - fixed temporal index problem
-# ** predict.ST.ensemble - fixed temporal index problem
-# ** fixed response factor input
-# ==> This means that the ST ensemble is finally doing
-# what I THOUGHT it was doing all the time.
-# ** reduced memory footprint & speed up run times
-# ==> Run very many more small models - improving
-# ensemble depth.
-#
-# 4.15 TO DO LIST:
-# -------------------------
-# ** Batch processing for Partial Calculations
-# ** I need to figure out some logic to deal with possibilites
-# of region-seasons that do not contain any data, or
-# perhaps do not contain any sampled training data.
-# this will affect sample.ST.ensemble
-# create.ST.ensemble - one option may be to simply exclude them
-# and fit.ST.ensemble & predict.ST.ensemble
-# ** Need to make location information names and parameters
-# consistent across all ST.ensmble functions
-# This means do not assume that train.data$X$x & $X$y are there!!
-# ** sample.ST.ensemble
-# ** missing logic for sampling options
-# ** currently writing $X.loc to the GLOBAL instance
-# of ensemble.par.list. This is BAD - and unnecessary
-# need to clean logic.
-#
-#
-#
-# predict.ST.ensemble - Assumes existance of
-# prediction.design$x, $y, & $JDATE
-#
-#
-#--------------------------------------------------------------------------------
-
-
-
-# ---------------------------------------------------------------------
-# ---------------------------------------------------------------------
-# FUNCTION: Fit and Save BDT Ensemble
-# ---------------------------------------------------------------------
-# ---------------------------------------------------------------------
-# D.Fink
-# Cornell Lab of Ornithology
-# Department of Statistical Science
-# 7.14.08
-#
-# Description
-# -------------
-#
-# Usage:
-# --------
-#
-# Arguments:
-# -----------
-# y response vector
-# X matrix/data.frame of predictors only!!!
-# one predictor per column. Describe how predictors enter model
-# as main effects and interactions of smooth & nonsmooth funcitional
-# forms. Invariant to Monotone transformations.etc.
-# ensemble.weights = from ben's experience rpart likes variances (as
-# opposed to sd or reciprocals of ...)
-# it looks like gam likes st.dev.
-#
-# Value
-# --------
-# ib.sample.index = logical matrix dimension (n x bs.trials)
-# indicates training samples for each ensemble
-#
-# Details
-# --------
-#
-# TO DO List
-# -------------
-#
-# 3.25.09 Added code to pass weights to rpart
-#
-# 4.14.09
-# -------------
-# Modified code to save oob. & ib.sample.index's
-# ** in batches
-# ** to separate file sets
-# This in order to reduce the memory overhead.
-# Both of these matrices were being stored as
-# size = N x (# of ensemble model).
-# Moreover, I almost never use this information for predictions.
-# So, I am going to write it to disk , just in case.
-# Meanwhile - The index file has been modified to hold:
-# # * Number of models in ensemble
-# # * ensemble resp.family
-# # * realized.sample.par
-# and I might add the ensemble.par.list for good measure.
-#
-#
-# **** I NEED LOGIC TO CHECK FOR "NULL" SAMPLES!!!
-#
-#
-# ---------------------------------------------------------------------
-# ---------------------------------------------------------
-# Design Notes:
-#
-# * Individual-Model Paramters will pass through, since cant anticipate
-# how to handle parameters from other models!!!
-# * Ensemble Parameters will be passed with a dedicated list name
-# since this is something that I CAN control
-# ---------------------------------------------------------
-fit.ensemble <- function(
- train.data,
- resp.family,
- RNG.seed = NULL,
- #sample.ensemble.function,
- ensemble.par.list=NULL,
- filename,
- ensemble.weights=NULL,
- block.save.size=100, # (training sample size x block.save.size )
- # Model Parameter Pass Through
- ...){
- # ---------------------------------------------------------
- # Inits
- # ---------------------------------------------------------
- function.call <- match.call()
- ib.sample.index <- NULL
- oob.sample.index <- NULL
- realized.sample.par <- NULL
- n <- length(train.data$y)
- ensemble.trials <- ensemble.par.list$n.ensemble.models
- # -----------------------------------------------
- if (resp.family=="gaussian") bs.method <- "anova"
- if (resp.family=="bernoulli") bs.method <- "class"
- if (resp.family=="multiclass") bs.method <- "class"
- if (resp.family=="poisson") bs.method <- "poisson"
- # ---------------------------------------------------------
- # Bootstrap Samples
- # ---------------------------------------------------------
- block.number <- 1
- for (iii in 1:ensemble.trials) {
- # -------------------------------------
- # RNG.seed parameter
- # ------------------------------------------------
- if (iii==1 & !is.null(RNG.seed)) set.seed(RNG.seed)
- # --------------------------
-
- sample.data <- ensemble.par.list$sample.ensemble.function(
- ensemble.model.number = iii,
- ensemble.data = train.data,
- ensemble.par.list = ensemble.par.list,
- diagnostic.plot = FALSE)
-
- #cat("fe: iii,",iii, " length(yyy)=", length(sample.data$y),
- # sum(is.na(sample.data$y)) "\n")
- #cat("fit.ensemble: iii,",iii, " sum(is.na(yyy))=", sum(is.na(sample.data$y)), "\n")
- #if (length(sample.data$y) == sum(is.na(sample.data$y)) ){
- # print(sample.data$y)
- #}
- # ---------------------------------------------
- # Fit Ensemble Member with sampled data
- # ---------------------------------------
- # First check for weights
- if (is.null(ensemble.weights)) {
- f.rpart <- try(rpart( yyy ~ .,
- data= data.frame(yyy=sample.data$y,sample.data$X),
- method=bs.method,
- ...))
- # If there is an error, try it again
- if (class(f.rpart) == "try-error") {
- cat("fit.ensemble: rpart error \n")
- f.rpart <- try(rpart( yyy ~ .,
- data= data.frame(yyy=sample.data$y,sample.data$X),
- method=bs.method,
- ...))
- }
- }
- else {
- f.rpart <- try(rpart( yyy ~ .,
- data= data.frame(yyy=sample.data$y,sample.data$X),
- weights= ensemble.weights[sample.data$ib.num.ind],
- method=bs.method,
- ...))
- # If there is an error, try it again
- if (class(f.rpart) == "try-error") {
- cat("fit.ensemble: rpart error \n")
- f.rpart <- try(rpart( yyy ~ .,
- data= data.frame(yyy=sample.data$y,sample.data$X),
- weights= ensemble.weights[sample.data$ib.num.ind],
- method=bs.method,
- ...))
- }
- }
- # ----------------------
- # Save Ensemble Model
- #-----------------------
- num.txt <- formatC(iii, format="fg", width=6)
- num.txt <- chartr(" ","0",num.txt)
- temp.filename <- paste(filename,".",num.txt,".RData",sep="")
- if (iii == 1) save(f.rpart, file=temp.filename)
- if (iii > 1) {
- rpart.parts <-
- list( frame = f.rpart$frame,
- where = f.rpart$where, # - vector
- splits= f.rpart$splits, #- numeric matrix
- cptable = f.rpart$cptable)
- if (sum(names(f.rpart) == "csplit") > 0)
- rpart.parts$csplit <- f.rpart$csplit
- save(rpart.parts, file=temp.filename)
- }
- # --------------------------------
- # Save sampled data information
- # --------------------------------
- ttt.logical <- rep(FALSE, n)
- ttt.logical[sample.data$oob.num.ind] <- TRUE
- oob.sample.index <- cbind(oob.sample.index, ttt.logical)
- ttt.logical <- rep(FALSE, n)
- ttt.logical[sample.data$ib.num.ind] <- TRUE
- ib.sample.index <- cbind(ib.sample.index, ttt.logical)
- # ----------------
- realized.sample.par <- cbind(realized.sample.par, sample.data$realized.par)
-
- # ----------------------------------------------------
- # Block Save of Sampling Index Information
- # ----------------------------------------------------
- if ( round(iii/block.save.size) == (iii/block.save.size)) {
- return.list <- list(oob.sample.index = oob.sample.index,
- ib.sample.index = ib.sample.index,
- realized.sample.par = realized.sample.par,
- function.call = function.call)
- temp.filename <- paste(filename,".bs.sampling.index.", block.number,".RData",sep="")
- save(return.list, file=temp.filename)
- # -------------------------------
- # Reinitialize Results
- # -------------------------------
- ib.sample.index <- NULL
- oob.sample.index <- NULL
- # Next block number
- block.number <- block.number + 1
- }
- }# End for(iii) :Bootstrap
-
- # ---------------------------------------------------------
- # ----------------------------------------------------
- # Final Block Save of Sampling Index Information
- # ----------------------------------------------------
- if (!is.null(oob.sample.index)){
- return.list <- list(oob.sample.index = oob.sample.index,
- ib.sample.index = ib.sample.index,
- realized.sample.par = realized.sample.par,
- function.call = function.call)
- temp.filename <- paste(filename,".bs.sampling.index.",
- block.number,".RData",sep="")
- save(return.list, file=temp.filename)
- rm(ib.sample.index)
- rm(oob.sample.index)
- ## KFW gc()
- }
- # ---------------------------------------------------------
- # Return Value
- # ** I need to return enough information to act as a
- # handle to the ensemble for prediction, diagnostics, etc.
- # ** Save all this information as a header/providence
- # index file with the ensemble itself
- # ---------------------------------------------------------
- rm(rpart.parts)
- rm(num.txt)
- return.list <- list(realized.sample.par = realized.sample.par,
- resp.family=resp.family,
- RNG.seed = RNG.seed,
- block.save.size=block.save.size,
- function.call = function.call)
- temp.filename <- paste(filename,".ensemble.index.RData",sep="")
- save(return.list, file=temp.filename)
-
- return(return.list)
-}# End FUNCTION
-# ---------------------------------------------------------
-
-
-
-
-
-# ---------------------------------------------------------------------
-# This is a simple function to compute
-# OOB Predictions,
-# SD,
-# OOB Matrix,
-# * Handle NA's for samples that have not been predited
-# OOB. This is more of a concern when the number of
-# bootstraps is small.
-#
-#
-# OUTPUT:
-# count = (n x 1) vector count of BS reps for each obs
-# mean = (n x 1) vector count of BS reps for each obs
-# sd = OOB.sd,
-# matrix = OOB.pred.index)
-#
-# predict.oob.bdt
-# ---------------------------------------------------------------------
-#predict.oob.bdt <- function(filename, X.train){
-## ---------------------------------------------------------------------
-# # ---------------------------------------------------------
-# # Inits
-# # ---------------------------------------------------------
-# temp.filename <- paste(filename,".ensemble.index.RData",sep="")
-# load(file=temp.filename) #return.list
-# # ---------------------------------------------------------
-# # OOB Predictions - Means & SD's
-# # ---------------------------------------------------------
-# #KISS-Predict entire training set, then extract OOB preds
-# training.pred <- predict.bdt(
-# filename = filename, #model specific stuff stored here
-# prediction.design=X.train)
-# OOB.pred.index <- training.pred$matrix
-# OOB.pred.index[return.list$ib.sample.index==TRUE] <- NA
-# # -------------------
-# OOB.count <- apply(!return.list$ib.sample.index, 1, sum)
-# OOB.pred <- apply(OOB.pred.index, 1, mean, na.rm = TRUE)
-# OOB.sd <- apply(OOB.pred.index, 1, sd, na.rm = TRUE)
-# # ---------------------------------------------------------
-# # Return Value
-# # ---------------------------------------------------------
-# return.list <- list(
-# count = OOB.count,
-# mean = OOB.pred,
-# sd = OOB.sd,
-# matrix = OOB.pred.index)
-# return(return.list)
-## ---------------------------------------------------------
-#}# END OOB FUNCTION
-## ---------------------------------------------------------------------
-## ---------------------------------------------------------------------
-#
-
-# -------------------------------------------------------------------
-# -------------------------------------------------------------------
-# Variable Importances & Summaries
-# DT-rpart Specific Diagnostics
-# -------------------------------------------------------------------
-# -------------------------------------------------------------------
-# var.imp[ ,1]
-# a vector of all the variable importances measured as the empirical
-# improvement in the splitting criterion. Importances are in the
-# same order as the columns in X (design matrix).
-# See above notes for more info.
-# var.imp[ ,2]
-# variable importance weighted by height in tree
-# var.imp[ ,3]
-# variable importance weighted by support - number of data pts affected by
-# split. I need to look at code
-#
-# leaf.count = # of terminal leafs
-# ave.leaf.obs = average number of observations per leaf
-# min.leaf.obs = minimum number of observation in leaf
-# (this value is controled by min.bucket too!)
-#
-# -------------------------------------------------------------------
-rpart.ensemble.diagnostics <- function(
- filename,
- ensemble.par.list,
- X,
- ensemble.index=NULL){
-# -------------------------------------------------------------------
-
- # ---------------------------------------------------------
- # Inits
- # ---------------------------------------------------------
-
- bs.trials <- ensemble.par.list$n.ensemble.models
- # -------------------------------------------------------------------
- # ** I can pull out the number of predictors
- # used in the rpart ensemble from the files that
- # are saved. Then I can remove X.train from the parameter list
- # -------------------------------------------------------------------
- # Results
- # ----------
- var.imp1 <- matrix(0,NCOL(X), bs.trials)
- var.imp2 <- matrix(0,NCOL(X), bs.trials)
- var.imp3 <- matrix(0,NCOL(X), bs.trials)
- leaf.count <- rep(0,bs.trials)
- ave.leaf.obs <- rep(0,bs.trials)
- min.leaf.obs <- rep(0,bs.trials)
- # ----------------------------------------------------------
- # Load First Ensemble Model
- # -----------------------------------------------------------
- iii <- 1
- num.txt <- formatC(iii,format="fg", width=6)
- num.txt <- chartr(" ","0",num.txt)
- temp.filename <- paste(filename,".",num.txt,".RData",sep="")
- load( file=temp.filename)
- # Save ensemble rpart.object stub
- ttt.rpart <- f.rpart
- if (is.null(ensemble.index)) ensemble.index <- 1:bs.trials
- # ----------------------------------------------------------
- # Loop over Ensemble.Index
- # KISS - but not the most efficient programming
- # -----------------------------------------------------------
- for (iii in 1:length(ensemble.index)){
- # ----------------------------------------------------------
- # Load/Construct rpart.object
- # -----------------------------------------------------------
- f.rpart <- ttt.rpart
- if (ensemble.index[iii]!=1){
- num.txt <- formatC(ensemble.index[iii],format="fg", width=6)
- num.txt <- chartr(" ","0",num.txt)
- temp.filename <- paste(filename,".",num.txt,".RData",sep="")
- load( file=temp.filename) #rpart.parts
- # Reassemble f.rpart from ttt.rpart stub
- # ----------------------------
- f.rpart$frame <- rpart.parts$frame
- f.rpart$where <- rpart.parts$where
- f.rpart$splits <- rpart.parts$splits
- f.rpart$cptable <- rpart.parts$cptable
- if (sum(names(rpart.parts) == "csplit") > 0)
- f.rpart$csplit <- rpart.parts$csplit
- }
- # -------------------------------------------------------------------
- # DT-rpart Specific Variable Importance Measures
- # -------------------------------------------------------------------
- # Split Variables = row.names(d.rpart$split)
- # Empirical Improvement = Change in Deviance= d.rpart$split[,3]
- # var.imp is a vector of all the variable importances in the
- # same order as the columns in X (design matrix)
- # -------------------------------------------------------------------
- # sort out info about leaf nodes (I just want splits!)
- dnodes <- f.rpart$frame[ f.rpart$frame[ ,1] != "<leaf>", ]
- ncompete <- dnodes[,7]
- nsurrogate <- dnodes[,8]
- nsupport <- dnodes[, 2] # no. of pts affected by split
- nheight <- as.numeric(row.names(dnodes)) # height in pascal's triange
- nheight <- floor(log2(nheight)) + 1
- split.index <- 1 # initialize split index
- # variable look-up table
- var.table <- data.frame(pos=seq(1:NCOL(X)), varname=names(X))
- # add "<leaf>" level to var.table$varname so that var.index works
- levels(var.table$varname) <- c(levels(var.table$varname),"<leaf>")
- if (!is.null(f.rpart$split)){
- # Loop through all splits (rows)
- for (ii in 1:NROW(dnodes)){
- # ID split predictor
- # --------------------------------------------------
- # Summer & Fall 2007
- # Generating error number of levels in the factor is different
- # But I not understand exactly when this error is generated
- # so I dont know why it occurrs!
- # ---------------------------------------------------
-
- var.index <- var.table[as.character(dnodes[ii,1]) == as.character(var.table$varname) , 1]
- # extract & store improvement in empirical purity from split frame
- # Use twice emprical improvement to get actual deviance for entropy splitting rule
- var.imp1[var.index,iii] <- var.imp1[var.index,1] + 2*f.rpart$split[split.index,3]
- # update current row index in d.rpart$split
- split.index <- split.index + ncompete[ii] + nsurrogate[ii]+1
- # variable importance weighted by height in tree
- var.imp2[var.index,iii] <- var.imp2[var.index,2] + nheight[ii]
- # variable importance weighted by support
- var.imp3[var.index,iii] <- var.imp3[var.index,3] + nsupport[ii]
- } #endfor ii
- } #end if is.null
-
-
- # ----------------------------------------------------------
- # 10.2.07
- # I need information on ensemble trees to understand laplacian
- # smoothing.
- # leaf.count = # of terminal leafs
- # ave.leaf.obs = average number of observations per leaf
- # min.leaf.obs = minimum number of observation in leaf
- # (this value is controled by min.bucket too!)
- # ----------------------------------------------------------
- is.leaf.ind <- (f.rpart$frame$var == "<leaf>")
- leaf.count[iii] <- sum(is.leaf.ind)
- ave.leaf.obs[iii] <- mean(f.rpart$frame$n[is.leaf.ind])
- min.leaf.obs[iii] <- min(f.rpart$frame$n[is.leaf.ind])
- # -------------------------------------------------------------------
- } #end ensemble.index
-
- # ----------------------------------------------------------
- # Return Prediction Matrix
- # -----------------------------------------------------------
- return.list <- list(var.imp1 = var.imp1,
- var.imp2 = var.imp2,
- var.imp3 = var.imp3,
- leaf.count = leaf.count,
- ave.leaf.obs = ave.leaf.obs,
- min.leaf.obs=min.leaf.obs)
- return(return.list)
-# ---------------------------------------------------------
-}# End FUNCTION
-# ---------------------------------------------------------
-
-
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-# Variable Importance Barplot
-# -----------------------------------------------------------------------------
-# Daniel Fink
-#
-#
-# Description
-# -----------------
-# This function ....
-# I need to describe what the measure of relative variable importance
-# is and how it is aggregated over the ensemble.
-# * key assumptions
-# * uses, strengths & weaknesses
-#
-#
-# Input
-# ----------
-# vi = (n x 1) numeric vector of VI point estimates
-# where n is the number of Variables
-# barplot
-# vi.mat = ( n x bs.trials) numeric matrix of VI estimates
-# one set of estimates per column.
-# Variabliltiy in estimates plotted with boxplot
-# plot.it=FALSE
-#
-# Output
-# ----------
-# A plot may be produced or the predictive performances for train & test
-# returned.
-#
-# Notes:
-# ---------
-#
-# Further Development:
-# ----------------------------
-# ** common parameter names and calling proceedures for
-# all functions
-# ** return variable importances and names as data.frame
-# -----------------------------------------------------------------------------
-plot.vi.bdt <- function(
- vi=NULL,
- vi.mat=NULL,
- predictor.names,
- max.vars = 25,
- file.name = NULL,
- plot.width = 600,
- plot.height = 800 ){
- # --------------------------------------------------------------
- # VI Point Estimate Plot
- # --------------------------------------------------------------
- if (!is.null(vi)) {
- # --------------------------------------------------------------
- # Assemble Scaled VI & Names
- # ---------------------------------------------------------------
- ttt <- data.frame(Predictor = predictor.names, Deviance = vi/sum(vi)*100)
- # Re-order ttt in terms of descending Deviance
- ttt.ind <- order(ttt[,2],decreasing=TRUE)
- ttt <- ttt[ttt.ind, ]
- ttt$Predictor <- as.character(ttt$Predictor)
- # ---------------------------------------------------
- # Save image to disk
- # ---------------------------------------------------
- if (!is.null(file.name)) {
- png(file=file.name,
- bg="white",
- width=plot.width,
- height=plot.height)
- }
-
- # ---------------------------------------------------
- # Barplot
- # ---------------------------------------------------
- xmax <- max(ttt$Deviance) # scale max bar length
- x.stretch <- 1.4 # scale max bar length
- nbars <- max.vars # number of bars to plot
- bar.length <- ttt$Deviance
- bar.names <- ttt$Predictor
- tcol <- rainbow(nbars, start = 3/6, end = 4/6)
- tcol <- tcol[nbars:1] # reorder from dark to light colors
- barplot(bar.length[1:nbars],
- horiz=TRUE,
- xlim=c(0,(xmax*x.stretch)),
- xlab="Relative Importance",
- col = tcol,
- axes=F)
- axis(1)
- for (ii in 1:nbars) {
- text( bar.length[ii] + 1,
- 1.2*(ii-1) + .75,
- as.character(bar.names[ii]),
- cex=0.75,
- pos=4)
- }
- title(main="Ensemble Averages")
- # ---------------------------------------------------
- # Save image to disk
- # ---------------------------------------------------
- if (!is.null(file.name)) dev.off()
- }
-
- # --------------------------------------------------------------
- # VI Estimates BoxPlot
- # --------------------------------------------------------------
- if (!is.null(vi.mat)) {
- mean.vi <- apply(vi.mat, 1, mean)
- mean.index <- order(mean.vi, decreasing=TRUE)
- mean.vi <- mean.vi[mean.index]
- vi.mat <- vi.mat[mean.index,]/sum(mean.vi)*100
- mean.vi <- mean.vi/sum(mean.vi)*100
- predictor.names <- predictor.names[mean.index]
- # --------------------
- nbars <- max.vars
- mean.vi <- mean.vi[c(1:nbars)]
- predictor.names <- predictor.names[c(1:nbars)]
- vi.mat <- vi.mat[c(1:nbars), ]
- ttt.stack <- stack(data.frame(vi.mat))
- ttt.stack <- data.frame(ttt.stack, var=c(1:nbars))
- # --------------------
- xmax <- max(ttt.stack[,1]) # scale max bar length
- x.stretch <- 1.3 # scale max bar length
- bar.length <- mean.vi
- bar.names <- predictor.names
- tcol <- rainbow(nbars, start = 3/6, end = 4/6)
- tcol <- tcol[nbars:1] # reorder from dark to light colors
- # ---------------------------------------------------
- # Save image to disk
- # ---------------------------------------------------
- if (!is.null(file.name)) {
- png(file=file.name, bg="white",
- width=plot.width,
- height=plot.height)
- }
-
- # --------------
-
- boxplot(-values ~ as.factor(var),
- data = ttt.stack,
- horizontal=TRUE,
- outline=FALSE,
- #xlim=c(0,(nbars)),
- ylim=c(-(xmax*x.stretch),(.5*xmax)),
- xlab="Relative Importance",
- col = tcol,
- axes=F)
- axis(1)
- for (ii in 1:nbars) { #bar.length[ii]
- #text( ttt.stack$values[ii] + 1, 1.2*(ii-1) + .75,
- text( 0.5 , 1.*(ii-1) + 1,
- as.character(bar.names[ii]), cex=1.0, pos=4)
- }
- title(main="Ensemble BoxPlot")
- # ------------
- # ---------------------------------------------------
- # Save image to disk
- # ---------------------------------------------------
- if (!is.null(file.name)) dev.off()
- } # end vi.mat
-} # end function
-
-
-# -------------------------------------------------------------------
-# create.pd.grid - Function to Create List of Prediction Grid(s)
-# -------------------------------------------------------------------
-# based on plot.gbm!
-# Input
-# XX - DTM Design matrix
-# arguments that are lists
-# # --------------------------
-# i.var.list = list of i.var vectors
-# for now- these two arguments must be scalars
-# continuous.resolution = list/vector of cont.resolutions
-#
-# Output
-# for each of member of the list, the following objects will be
-# produced:
-# pd.grids
-#
-# Notes:
-# -------
-# There may be times when we actually want to see what the
-# predictions are for NA's - I have left this out, as an extra item.
-# I need to document how I am handling NA's.
-# -------------------------------------------------------------------
-# ---------------------------------------------------------------------
-create.pd.grid <- function(XX,
- i.var.list,
- continuous.resolution,
- na.flag=NULL) {
- # Cycle through elements of list
- # --------------------------------
- pd.grids <- vector(mode="list", length=length(i.var.list))
- for (iii in 1:length(i.var.list)){
- i.var <- i.var.list[[iii]]
-
- # --------------------------------------------
- # Check User Input
- # --------------------------------------------
- if (all(is.character(i.var))) {
- i <- match(i.var, names(XX))
- if (any(is.na(i))) {
- stop("i.var.list contains variables that are not used in model",
- i.var[is.na(i)])
- }
- else {
- i.var <- i
- }
- }
-
- if ((min(i.var) < 1) || (max(i.var) > length(names(XX)))) {
- warning("i.var must be between 1 and ", length(names(XX)))
- }
-
-
- # --------------------------------------------
- # Create Prediction Grid
- # --------------------------------------------
- # vector produces a vector of the given length and mode.
- grid.levels <- vector(mode="list", length=length(i.var))
- for (i in 1:length(i.var)) {
- X.vars <- XX[ ,i.var[i]]
- # Check for missing values flag other than "NA"
- # (for ex. I do not want RF 9e30 flag to affect the
- # quantile calculations below
- # ----------------------------------------------
- if (!is.null(na.flag)){
- na.ind <- (X.vars == na.flag)
- # replace with NA's
- X.vars[na.ind] <- NA
- }
-
- # ----------------------
- # Integer Predictors
- # ----------------------
- # continuous resolution - use minimum of either
- # the range of integers or continuous.resolution
- if (is.integer(X.vars)) {
- cont.res <- min((max(X.vars,na.rm=TRUE) - min(X.vars,na.rm=TRUE) + 1), continuous.resolution)
- grid.levels[[i]] <- seq(min(X.vars,na.rm=TRUE), max(X.vars,na.rm=TRUE), length = cont.res)
- grid.levels[[i]] <- sort(unique(grid.levels[[i]]))
- }
- # ----------------------
- # Double Predictors
- # ----------------------
- if (is.double(X.vars)) {
- # Sequential Grid
- # grid.levels[[i]] <- seq(min(XX[ ,i.var[i]],na.rm=TRUE),
- # max(XX[ ,i.var[i]],na.rm=TRUE),
- # length = continuous.resolution)
- # Grid at Equi-spaced Quantiles
- prob.seq <- seq(from=0, to=1, length= (continuous.resolution+2))
- # Remove the endpoints of this sequence
- prob.seq <- prob.seq[2:(continuous.resolution+1)]
- grid.levels[[i]] <- quantile(X.vars, probs = prob.seq, na.rm = TRUE)
- grid.levels[[i]] <- sort(unique(grid.levels[[i]]))
- } #end double
- # ----------------------
- # Factors: code levels numerically
- # ----------------------
- if (is.factor(X.vars)) {
- # What happens with missing values here?
- grid.levels[[i]] <- sort(unique(as.numeric(X.vars) ))
- } # end factor
- } #end for i: Making grid.levels
- # ----------------------
- pd.grid <- expand.grid(grid.levels)
- names(pd.grid) <- names(XX)[i.var]
- # ----------------------------------------
- pd.grids[[iii]] <- pd.grid
- } # end for i.var.lists
-
- return(pd.grids)
-} # end function
-
-
-
-# -------------------------------------------------------------------
-# Predict.pd.grid - Function to make Predictions over PD.grids
-# -------------------------------------------------------------------
-# Input
-# XX = DTM Design matrix
-# pd.quant.grids = create.pd.grid obejct
-# nn.sample = # of randomly selected samples from XX
-# Output
-# list of predictions for each member of the create.pd.grid.object
-#
-#
-#
-# TO DO:
-# --------------------------------
-# 1) Add key parameters to output object!!!
-# partial.dependence.list,
-# continuous.resolution = 15,
-# nn.sample = 500
-#
-# 2) Need to Recode Categorical predictors
-# eg. if BCR was a predictor we would need to recode it
-# to its proper level labels !!!!!
-# Currently, BCR is coded as the number of the LEVEL
-# xxx.grid[,2] <- levels(train.data$X$BCR)[xxx.grid[,2]]
-#
-#
-# HPM Use:
-# HPM will need to store and accululate these predictions or
-# lists of predictions for plotting.
-# ------------------------------------------------------------------------------------------------------
-# ------------------------------------------------------------------------------------------------------
-ensemble.partial.dependence <- function(filename,
- ensemble.par.list,
- XX,
- partial.dependence.list,
- continuous.resolution = 15,
- nn.sample = 500) {
- # ------------------------------------------------------------------------------------------------------
- # Inits Formal Parameters
- # ------------------------------------------------------------------------------------------------------
- # Results
- pd.means <- vector(mode="list", length=length(partial.dependence.list))
- pd.matrices <- vector(mode="list", length=length(partial.dependence.list))
- # ------------------------------------------------------------------------------------------------------
- # Compute Partial Dependence Quantile Grids
- # ------------------------------------------------------------------------------------------------------
- pd.quant.grids <- create.pd.grid(XX=XX,
- i.var.list=partial.dependence.list,
- continuous.resolution = continuous.resolution)
- # ------------------------------------------------------------------------------------------------------
- # Check Function input
- # ------------------------------------------------------------------------------------------------------
- if (nn.sample > NROW(XX)) {
- nn.sample <- NROW(XX)
- }
- # ------------------------------------------------------------------------------------------------------
- # Random Sample of Data Rows (same sample for all PD elements)
- # ------------------------------------------------------------------------------------------------------
- # Sample without replacement from data rows
- if (nn.sample == NROW(XX)) sample.index <- c(1:NROW(XX))
- if (nn.sample < NROW(XX)) sample.index <- sample(1:NROW(XX), nn.sample, replace = FALSE)
-
- # ------------------------------------------------------------------------------------------------------
- # Find factors in XX
- # Note : I can not use apply b/c XX is class data.frame
- # ------------------------------------------------------------------------------------------------------
- XX.factor.ind <- rep(FALSE, NCOL(XX))
- ttt <- XX[1,] # it is much faster to search a 1D data.frame!
- for (ii in 1:NCOL(XX)) XX.factor.ind[ii] <- is.factor(ttt[,ii])
-
- # Extract an index of column positions for factors (wo zeros!)
- factor.index <- as.numeric(XX.factor.ind)*seq(1,NCOL(XX))
- factor.index <- factor.index[factor.index > 0 ]
- # ------------------------------------------------------------------------------------------------------
- # Loop Over PD list elements
- # ------------------------------------------------------------------------------------------------------
- for (iii in 1:length(pd.quant.grids)){
- # ------------------------------------
- # 1. Expand Quantile Grid into PD Prediction Design
- # 2. BDT Predictions
- # 3. Assemble Results
- # ------------------------------------
- i.var <- match( names(pd.quant.grids[[iii]]), names(XX))
- XX.sample <- XX[sample.index, setdiff(names(XX), names(XX)[i.var]) ]
- pd.grid <- pd.quant.grids[[iii]]
- # ----------------------------
- # NOTE** The size of the PD design = nn.sample * length(pd.grid)
- # If this too large, there should be a loop here that can
- # break this computation into pieces by breaking up
- # nn.sample
- # ----------------------------
- # ------------------------------------------------------------------------------------------------------
- # Construct Partial Dependence Prediction Data Frame
- # NOTE: the use of data.matrix converts factors to numerics
- # ------------------------------------------------------------------------------------------------------
- # Stack Randomly Sampled Data Rows
- XX.stack <- kronecker( matrix(1, NROW(pd.grid), 1), data.matrix(XX.sample))
- XX.stack <- as.data.frame(XX.stack)
- names(XX.stack) <- names(XX.sample)
- # Stack Partial Dependence Grids
- pd.stack <- kronecker( data.matrix(pd.grid), matrix(1, nn.sample, 1))
- pd.stack <- as.data.frame(pd.stack)
- names(pd.stack) <- names(pd.grid)
- PD.prediction.frame <- cbind(pd.stack,XX.stack)
- # ------------------------------------------------------------------------------------------------------
- # Reconstruct Factor structure for data.frame
- # ------------------------------------------------------------------------------------------------------
- # XX = original data frame that may include factors
- # PD.prediction.frame = the data.frame currently with numeric
- # values for all predictors. The prediction data.frame needs
- # to have the same column/predictor structure as XX
- # ------------------------------------------------
- # 1) Reorder PD.prediction.frame to match XX
- col.order <- match( names(XX), names(PD.prediction.frame))
- PD.prediction.frame <- PD.prediction.frame[,col.order]
- # 2) Convert PD.prediction.frame cols to factors
- for (i in factor.index) {
- PD.prediction.frame[,i] <- factor(levels(XX[,i])[PD.prediction.frame[,i]], levels=levels(XX[,i]))
- }
- # ------------------------------------------------------------------------------------------------------
- # Ensemble PD Predictions
- # ------------------------------------------------------------------------------------------------------
-
- ttt.pred <- ensemble.par.list$predict.ensemble.function(
- filename = filename,
- ensemble.par.list = ensemble.par.list,
- prediction.design= PD.prediction.frame)
- # BDT ensemble mean predictions
- pred.X <- ttt.pred$mean
- pred.X.matrix <- ttt.pred$matrix
- rm(ttt.pred)
- # -----------------------------
- # PD Design Loop would (somewhere?) end here, I think, hmmm
- # -----------------------------
- # --------------------------------------------
- # Ensemble Matrix PD estimates
- # --------------------------------------------
- pdf.grid.matrix <- NULL
- pred.index <- (rep(c(1:NROW(pd.grid)),each=nn.sample))
- for (jjj in 1:NCOL(pred.X.matrix)){
- pdf.grid.matrix <- cbind(pdf.grid.matrix, tapply(pred.X.matrix[,jjj], pred.index, mean,na.rm=T))
- }
- rm(pred.X.matrix)
- # --------------------------------------------
- # Average to get Ensemble average PD estimates
- # --------------------------------------------
- pred.index <- (rep(c(1:NROW(pd.grid)), each=nn.sample))
- ppp <- tapply(pred.X, pred.index, mean,na.rm=T)
- # recode pd.grid factors
- f.factor <- rep(FALSE, NCOL(pd.grid))
- for (i in 1:NCOL(pd.grid)) {
- col.index <- match( names(pd.grid)[i], names(XX))
- if (!is.numeric( XX[,col.index] )) {
- f.factor[i] <- TRUE
- pd.grid[,i] <- factor(levels(XX[,col.index])[pd.grid[,i]], levels=levels(XX[,col.index]))
- }
- } #end for i
- # Reassociate pd.grid with predictions
- pdf.grid <- data.frame(pd.grid, pred=ppp)
-
- # -----------------------------------
- # Store results in PD.list
- # -----------------------------------
- # pd.means = the Partial Dependence Estimate averaged over bags
- # pd.matrices = the PD estimates, one col per bag/model
- pd.means[[iii]] <- pdf.grid
- pd.matrices[[iii]] <- pdf.grid.matrix
- #names(pdf.grid)
- #dim(pdf.grid)
- } # end iii
-
- return(list(pd.quant.grids=pd.quant.grids, pd.means=pd.means, pd.matrices=pd.matrices))
-} # end function
-
-# ---------------------------------------------------------
-# Summary (TEXT) Function
-# ---------------------------------------------------------
-summarize.ensemble <- function(model.filename,
- ensemble.par.list,
- train.data,
- test.data=NULL,
- diag.bdt = NULL,
- oob.pred = NULL,
- train.pred = NULL,
- test.pred = NULL){
- # ---------------------------------------------------------
- # Inits
- # ---------------------------------------------------------
- temp.filename <- paste(model.filename,".ensemble.index.RData",sep="")
- load(file=temp.filename) #return.list
- bs.trials <- ensemble.par.list$n.ensemble.models
- resp.family <- return.list$resp.family
- # ---------------------------------------------------------
- cat(" -------------------------------------\n")
- cat(" Bagged Decision Trees \n")
- cat(" -------------------------------------\n")
- cat(" Model Name: ", model.filename , "\n")
- cat(" Response type = ", resp.family , "\n")
- cat(" Number of Predictors = ", NCOL(train.data$X) , "\n")
- cat(" Training sample size = ", NROW(train.data$X) , "\n")
- cat(" -------------------------------------\n")
- cat(" Ensemble \n")
- cat(" -------------------------------------\n")
- cat(" ensemble size = ", bs.trials,"\n")
- cat(" Ensemble parameters: \n")
- for (iii in 2:length(ensemble.par.list)){
- cat( " ",names(ensemble.par.list)[iii],"\n")
- }
- # ----------------------------------------------------
- # Ensemble size stats
- # ----------------------------------------------------
- if (!is.null(diag.bdt)) {
- cat(" Average # leaves per tree =",
- mean(diag.bdt$leaf.count) ,"\n")
- cat(" Average # obs per leaf =",
- mean(diag.bdt$ave.leaf.obs) ,"\n")
- cat(" Minimum # obs per leaf =",
- mean(diag.bdt$min.leaf.obs) ,"\n")
- }
- # -----------------------------------------
- pp <- NULL
- pp.names <- NULL
- # -----------------------------------------
- if (resp.family == "gaussian" | resp.family == "poisson"){
- if (!is.null(train.pred)) {
- # -------------------
- ttt.ind <- (!is.na(train.pred$mean))
- ttt <- predictive.performance(
- obs=train.data$y[ttt.ind],
- ppp=train.pred$mean[ttt.ind],
- resp.family=resp.family )
- pp <- cbind(pp, ttt)
- pp.names <- rbind(pp.names, "Training")
- }
- # -----------------
- if (!is.null(oob.pred)) {
- ttt.ind <- (oob.pred$count > 0 & !is.na(oob.pred$mean))
- ttt <- predictive.performance(
- obs=train.data$y[ttt.ind],
- ppp=oob.pred$mean[ttt.ind],
- resp.family=resp.family)
- pp <- cbind(pp, ttt)
- pp.names <- rbind(pp.names, "OOB")
- }
- # ----------------
- if (!is.null(test.pred)){
- ttt.ind <- (!is.na(test.pred$mean))
- ttt <- predictive.performance(
- obs=test.data$y[ttt.ind],
- ppp=test.pred$mean[ttt.ind],
- resp.family=resp.family)
- pp <- cbind(pp, ttt)
- pp.names <- rbind(pp.names, "Test")
- }
- if (!is.null(pp)) pp <- data.frame(pp)
- # -----------------
- } # end if gaussian or poisson
- # ----------------------------------------
- if (resp.family == "bernoulli"){
- if (!is.null(train.pred)) {
- # -------------------
- ttt.ind <- (!is.na(train.pred$mean))
- ttt <- predictive.performance(
- obs=train.data$y[ttt.ind],
- ppp=train.pred$mean[ttt.ind],
- resp.family=resp.family )
- pp <- cbind(pp, c(ttt$acc, ttt$rmse, ttt$auc))
- pp.names <- rbind(pp.names, "Training")
- }
- # -----------------
- if (!is.null(oob.pred)) {
- ttt.ind <- (oob.pred$count > 0 & !is.na(oob.pred$mean))
- ttt <- predictive.performance(
- obs=train.data$y[ttt.ind],
- ppp=oob.pred$mean[ttt.ind],
- resp.family=resp.family)
- pp <- cbind(pp, c(ttt$acc, ttt$rmse, ttt$auc))
- pp.names <- rbind(pp.names, "OOB")
- }
- # ----------------
- if (!is.null(test.pred)){
- ttt.ind <- (!is.na(test.pred$mean))
- ttt <- predictive.performance(
- obs=test.data$y[ttt.ind],
- ppp=test.pred$mean[ttt.ind],
- resp.family=resp.family)
- pp <- cbind(pp, c(ttt$acc, ttt$rmse, ttt$auc))
- pp.names <- rbind(pp.names, "Test")
- }
- if (!is.null(pp)) pp <- data.frame(pp)
- # -----------------
- rownames(pp) <- c("Accuracy", "RMSE", "AUC")
- } # end if bernoulli
-
- cat(" -------------------------------------\n")
- cat(" Predictive Performance \n")
- cat(" -------------------------------------\n")
- n.row <- NROW(pp)
- n.col <- NCOL(pp)
- for (ii in 1:n.col){
- cat( " ",pp.names[ii]," ")
- }
- cat("\n")
-
- for (ii in 1:n.row){
- cat(" ", rownames(pp)[ii], " ")
- for (jj in 1:n.col) {
- cat( as.character(format(pp[ii,jj], digits=5))," ")
- }
- cat("\n")
- }
- # ----------------------------------------------------
- # Relative Variable Importance -
- # ----------------------------------------------------
- if (!is.null(diag.bdt)) {
- cat(" ---------------------------------------------------------------------\n")
- cat(" Relative Variable Importance - Top 10 \n")
- cat(" ---------------------------------------------------------------------\n")
- # Re-order ttt in terms of descending Deviance
- ttt <- data.frame(Predictor = c(names(train.data$X)), Deviance = diag.bdt$var.imp1/sum(diag.bdt$var.imp1)*100 )
- ttt.ind <- order(ttt[,2],decreasing=TRUE)
- ttt <- ttt[ttt.ind, ]
- ttt$Predictor <- as.character(ttt$Predictor)
- for (iii in 1:10) cat(" ", iii, " ",ttt[iii, 2]," ", ttt[iii, 1], "\n")
- cat(" ---------------------------------------------------------------------\n")
- cat("\n")
- cat("\n")
- }
-}# end summary function
-
-
-# -----------------------------------------------------------------------------------------------------------
-# -----------------------------------------------------------------------------------------------------------
-# Predictive Performance Functions
-# 10.23.08
-#
-# Compute predictive Performance measures. The basic idea is to
-# measure the average distance between observation & prediction.
-# ave (distance(obs - pred))
-# Methods vary according to the family of the response, how the
-# averaging is performed and how distance is measured.
-#
-# ** Assumed that there are no NA's in either obs or predicted.
-#
-# Input:
-# ---------
-# obs = observed response
-# ppp = corresponding predicted response (on response scale!)
-# family = family or name of response type
-#
-# Output:
-# ---------
-# Family = "bernoulli" == binary (numerical? logical?)
-# ------------------------------------------------
-# Family = "gaussian" == numerical
-# ------------------------------------------------
-# Family = "poisson" == counts
-# ------------------------------------------------
-# ** I am no longer computing Pearson's Chi-Squared measure
-# because the predictions in the denominator make is very
-# unstable when there are lots of small predictions.
-# (for the relative abundance analyses)
-# p <- sum( ((yyy - ppp)^2)/(ppp) )
-# ** Deviance Calculations
-#
-# Demo Code:
-# -----------
-# yyy <- p.data$yp
-# ppp <- (d.dtm$pred.Xp)^2 #Untransformed
-# res <- residuals.dtm(obs = yyy,
-# ppp = ppp,
-# family="poisson")
-#
-# Needed:
-# --------------------
-# * More documentation
-# * Example showing ROC curve using pred.obj (ROCR library help(performance))
-# * Add gaussian & binary deviance functions & measures
-# * erorr checking for different types of binary obs & pred
-#
-# -----------------------------------------------------------------------------------------------------------
-# -----------------------------------------------------------------------------------------------------------
-predictive.performance <- function(obs, ppp, resp.family) {
- if (resp.family=="poisson"){
- # ----------------------------------
- MSE <- mean((ppp - obs)^2)
- R2 <- 1 - mean((ppp - obs)^2)/mean((mean(obs) - obs)^2)
- MSE.sqrt <- mean((sqrt(ppp) - sqrt(obs))^2)
- R2.sqrt <- 1 - mean((sqrt(ppp) - sqrt(obs))^2)/
- mean((mean(sqrt(obs)) - sqrt(obs))^2)
- MAD <- mean(abs(ppp - obs))
- rho <- cor(obs,ppp)
- rho.sqrt <- cor(sqrt(obs),sqrt(ppp))
- # ----------------------------
- # Poisson Deviance can not have zero predictions
- # Substitute predicted zero's with small values
- # ------------------------------------
- epsilon <- 1e-8
- ppp[ppp == 0] <- epsilon
- # ---------------------------------------------------------
- null.deviance <- poisson.deviance(
- yyy=obs,
- ppp=rep(mean(obs),length(obs) ))
- obs.deviance <- poisson.deviance(
- yyy=obs,
- ppp=ppp)
- deviance.explained <- (null.deviance - obs.deviance)/null.deviance
- # ----------------------------------
- return(list(
- MSE = MSE,
- R2=R2,
- MSE.sqrt = MSE.sqrt,
- R2.sqrt=R2.sqrt,
- MAD=MAD,
- rho=rho,
- rho.sqrt=rho.sqrt,
- deviance.explained=deviance.explained,
- obs.deviance=obs.deviance,
- null.deviance=null.deviance))
- }
-
- if (resp.family=="bernoulli"){
- acc <- 1 - sum(abs(obs-ppp))/length(ppp)
- require(ROCR)
- pred.obj <- prediction(prediction=ppp, labels=as.numeric(obs))
- perf <- performance(pred.obj, "auc")
- auc <- perf at y.values[[1]][1]
- perf <- performance(pred.obj, "rmse")
- rmse <- perf at y.values[[1]][1]
- return(list(
- acc=acc,
- rmse = rmse,
- auc = auc,
- pred.obj = pred.obj))
- }
- if (resp.family=="gaussian"){
- # ----------------------------------
- MSE <- mean((ppp - obs)^2)
- R2 <- 1 - mean((ppp - obs)^2)/mean((mean(obs) - obs)^2)
- MAD <- mean(abs(ppp - obs))
- rho <- cor(obs,ppp)
- # ----------------------------
- return(list(
- MSE = MSE,
- R2=R2,
- MAD=MAD,
- rho=rho))
- }
-}
-# -----------------------------------------------------------------------------------------------------------
-# -----------------------------------------------------------------------------------------------------------
-
-
-# -----------------------------------------------------------------------------------------------------------
-# Poisson Predictive Performance Measures
-# -----------------------------------------------------------------------------------------------------------
-# yyy = observations
-# ppp = predicted value - response scale
-#
-# Verified - replicated GAM deviance calcuatlions for poisson
-# -----------------------------------------------------------------------------------------------------------
-poisson.deviance <- function(yyy,ppp){
- # if predictions (ppp) equal zero we will get underflow
- # problems from log function.
- # -------------
- # break deviance into two pieces - where obs == 0
- ttt.zero <- (yyy == 0)
- ttt.pos <- (yyy > 0)
- dev1 <- sum( (yyy[ttt.zero] - ppp[ttt.zero]) )
- dev2 <- sum( yyy[ttt.pos]*log(yyy[ttt.pos]/ppp[ttt.pos]) -
- (yyy[ttt.pos] - ppp[ttt.pos]))
- dev <- 2*(dev2 - dev1)
- return(dev)
-}
-# -----------------------------------------------------------------------------------------------------------
-# -----------------------------------------------------------------------------------------------------------
-
-
-# ------------------------------------------------------------------------
-# ------------------------------------------------------------------------
-# Random Train/Test Split
-# ------------------------
-# n = length of index
-# p.train = percentage for training
-#
-# This function simply returns two indices that partition
-# a set of n iterms into two mutually exclusive sets.
-#
-# Demo
-#ttt <- ttsplit(n=100, p.train=0.5)
-#length(ttt$train.index)
-#length(ttt$test.index)
-# ---------------------------------------------------
-ttsplit <- function(n, p.train){
- train.index <- NULL
- val.index <- NULL
- ttt.index <- 1:n
- nnn.train <- round(n * p.train)
- nnn.val <- n - nnn.train
- if (nnn.train <= n)
- train.index <- sample((1:n), nnn.train)
- if (nnn.val > 0 ) {
- full.index <- c(1:n)
- val.index <- setdiff(full.index, train.index)
- val.index <- sample( val.index, min(nnn.val, length(val.index)))
- }
- return(list(train.index=train.index, test.index=val.index))
-} # end function
-
-# ------------------------------------------------------------------------
-# ------------------------------------------------------------------------
-
-# ------------------------------------------------------------------------
-# ------------------------------------------------------------------------
-# Simple Unique Location Train/Test Splitting
-# 11.3.07
-#
-# Randomly select a unique set of locations for the train and
-# test sets. This function will collect all records for a given
-# location and assign them according to the train/test split.
-# This sampling design does NOT preserve the relative sampling
-# density across locations because there are no repeat locations
-# sampled.
-#
-# Input:
-# ---------
-# locs - location data frame/matrix
-# p.train - proportion of locations for training
-# m.frac - fraction of multiple observations to include for
-# each location
-#
-# Output:
-# ---------
-# unique.index= unique loc index ( I believe that the
-# first instance for each repeated loc is indicated here)
-# train.index.single & test.locs.single
-# index to one observation from a unique set of locations.
-# Train & test sets form a random partition of the locations
-# in the unique.index.
-# train.locs.index & test.locs.index
-# Collect a fraction of available observations at each of
-# the randomly selected training locations. If there are repeat observations at
-# a unique location, then all of these observations will
-# be included in this set. Same for the test set.
-#
-# Demo Code:
-# -----------
-# # Create Data with Repeat Obs at specific locations
-# #nnn <- 10000
-# #locs <- data.frame(x=rnorm(nnn), y=rnorm(nnn))
-# locs <- cc.data$loc
-# ddd <- unique.locs.splitting(locs, p.train=0.75, m.frac=0.5)
-# length(ddd$train.locs.single)
-# length(ddd$train.locs.multiple)
-# length(ddd$test.locs.single)
-# length(ddd$test.locs.multiple)
-# # ----------------------------
-# # Plot Map of Train/Test Sets
-# # ----------------------------
-# plot(locs$x[ddd$train.locs.single],
-# locs$y[ddd$train.locs.single],
-# xlab ="lon", ylab="lon",
-# pch=24,
-# col="red",
-# cex=.5)
-# points(locs$x[ddd$test.locs.single],
-# locs$y[ddd$test.locs.single],
-# col="blue",
-# pch=25,
-# cex=0.5)
-# title(main="eBird Northern Cardinal Summer 2006", font.main = 4 )
-# box(lwd=3.0)
-# require(maps)
-# require(mapdata)
-# map('state',add=TRUE)
-# ------------------------------------------------------------------------
-# ------------------------------------------------------------------------
-unique.locs.splitting <- function(locs, p.train, m.frac=1.0){
- # Extract unique locs as ttt
- ttt <- unique(locs)
- # 1) Randomly select proportion of unique locations
- split.ind <- ttsplit(n=NROW(ttt), p.train=p.train)
- train.index <- split.ind$train.index
- test.index <- split.ind$test.index
- # ----------------------
- # 2) Process Test Set
- test.locs.single <- NULL
- test.locs.multiple <- NULL
- for (iii in 1:length(test.index)){
- temp.ind <- (locs$x == ttt$x[test.index[iii]] &
- locs$y == ttt$y[test.index[iii]])
- #Convert to index into locs for matches
- temp.ind <- as.numeric(temp.ind) * c(1:NROW(locs))
- temp.ind <- temp.ind[temp.ind > 0]
- # Random Selection Single
- temp.ind.single <-temp.ind[
- sample(1:length(temp.ind), size=1, replace=FALSE) ]
- test.locs.single<- c(test.locs.single, temp.ind.single)
- # Random Selection Multiple
- m.size <- max(1,round(m.frac*length(temp.ind)))
- temp.ind.multiple <- temp.ind[
- sample(1:length(temp.ind), size=m.size, replace=FALSE)]
- test.locs.multiple <- c(test.locs.multiple, temp.ind.multiple)
- }
- # -------------------------
- # 3) Process Train Set
- train.locs.single <- NULL
- train.locs.multiple <- NULL
- for (iii in 1:length(train.index)){
- temp.ind <- (locs$x == ttt$x[train.index[iii]] &
- locs$y == ttt$y[train.index[iii]])
- #Convert to index into locs for matches
- temp.ind <- as.numeric(temp.ind) * c(1:NROW(locs))
- temp.ind <- temp.ind[temp.ind > 0]
- # Random Selection Single
- temp.ind.single <-temp.ind[
- sample(1:length(temp.ind), size=1, replace=FALSE) ]
- train.locs.single<- c(train.locs.single, temp.ind.single)
- # Random Selection Multiple
- m.size <- max(1,round(m.frac*length(temp.ind)))
- temp.ind.multiple <- temp.ind[
- sample(1:length(temp.ind), size=m.size, replace=FALSE)]
- train.locs.multiple <- c(train.locs.multiple, temp.ind.multiple)
- }
- # -------------------------
- return(list(train.locs.single = train.locs.single,
- train.locs.multiple = train.locs.multiple,
- test.locs.single = test.locs.single,
- test.locs.multiple = test.locs.multiple,
- unique.index=as.numeric(rownames(ttt))
- ))
-} # end function
-# ------------------------------------------------------------------------
-# ------------------------------------------------------------------------
-
-
-
-# ----------------------------------------------------------------------
-# ----------------------------------------------------------------------
-# Loop Over 1 Grid Realization - Compute & Store Distribution
-# ----------------------------------------------------------------------
-# ----------------------------------------------------------------------
-# ----------------------------------------------------------------------
-# Create Train:Test sets with Unique Locations
-# ----------------------------------------------------------------------
-# dsplit <- unique.locs.splitting(locs=cc.data$loc,
-# p.train=fraction.training.data,
-# m.frac=1.0)
-# train.index <- dsplit$train.locs.multiple
-# test.index <- dsplit$test.locs.multiple
-# ---------------------------
-# Maximum Coverage Selection
-# for Train:Test Set
-# ---------------------------
-maximum.coverage.selection <- function(
- locs, # data.frame(x , y) length n
- jdates, # vector length n
- #grid.parameters,
- grid.cell.min.lat,
- grid.cell.min.lon,
- min.val.cell.locs,
- fraction.training.data,
- mfrac=1.0,
- plot.it =FALSE ){
-# ----------------------------------------------------------------
-# RETURN:
-# train.index <-
-# test.index <-
-# -------------------------------------------------------------------
-# Formal test values
-# locs=cc.data$locs data.frame(x , y) length n
-# jdates=cc.data$X$JDATE vector length n
-# grid.parameters,
-# grid.cell.min.lat=1.0
-# grid.cell.min.lon=1.5
-# min.val.cell.locs=5
-# fraction.training.data=0.8
-# mfrac=1.0
-# ----------------------
- lon.min <- min(locs$x)
- lon.max <- max(locs$x)
- lat.min <- min(locs$y)
- lat.max <- max(locs$y)
-
- #for (iii.loop in 1:nnn.grids) {
- iii.loop <- 1
- # 1) Randomize Coordinate for first grid cell boundary
- r.lat <- runif(1,min=0, max=grid.cell.min.lat)
- r.lon <- runif(1,min=0, max=grid.cell.min.lon)
- # 2) lay down equally spaced grid until x.max reached
- grid.ttt <- seq(from=(lon.min+r.lon),
- to=lon.max,
- by=grid.cell.min.lon)
- grid.xxx <- c(lon.min, grid.ttt, lon.max)
- grid.ttt <- seq(from=(lat.min+r.lat),
- to=lat.max,
- by=grid.cell.min.lat)
- grid.yyy <- c(lat.min, grid.ttt, lat.max)
- # incase of any duplicates!
- grid.xxx <- sort(unique(grid.xxx))
- grid.yyy <- sort(unique(grid.yyy))
- # ---------------------------
- # Sample Maximal Coverage Validation Data
- # Then use the rest for Training
- # ** Take up to the first min.val.cell.locs
- # ** Then randomly select the rest, by unique loc
- # ---------------------------
- kkk <- 0 # counter for grid cell regions
- nnn.grid.cells <- (length(grid.xxx)-1)*(length(grid.yyy)-1)
- u.test.locs <- NULL
- # -----------------------------------------------------------------
- # Cycle over Columns(xxx_iii) within Given Row (yyy_jjj)
- # -----------------------------------------------------------------
- for (jjj in 1:(length(grid.yyy)-1)){
- for (iii in 1:(length(grid.xxx)-1)){
- #iii <- 10
- #jjj <- 20
-
- kkk <- kkk + 1
- # --------------------------------
- xxx <- locs$x
- yyy <- locs$y
- cell.index <- xxx >= grid.xxx[iii] & xxx < grid.xxx[iii+1] &
- yyy >= grid.yyy[jjj] & yyy < grid.yyy[jjj+1]
- # Check for minimum Prediction Cell Locations
- # ---------------------------------------------
- u.locs <- unique(data.frame(x=locs$x[cell.index],
- y=locs$y[cell.index]))
- sum(cell.index)
- dim(u.locs)
-
- if (NROW(u.locs) <= min.val.cell.locs) {
- # Randomly Select first min.val.cell.locs
- u.test.locs <- rbind(u.test.locs,u.locs)
- }
- if (NROW(u.locs) > min.val.cell.locs) {
- # Randomly Select first min.val.cell.locs
- # Then Randomly split the rest
- # ---------------------------------
- ttt.ind <- sample(1:NROW(u.locs), size=min.val.cell.locs)
- u.test.locs <- rbind(u.test.locs,u.locs[ttt.ind,])
- u.locs <- u.locs[ (setdiff(1:NROW(u.locs),ttt.ind)) , ]
- dsplit <- unique.locs.splitting(locs=u.locs,
- p.train=fraction.training.data,
- m.frac=1.0)
- u.test.locs <- rbind(u.test.locs,
- u.locs[dsplit$test.locs.multiple,])
- }
- }}# end grid loop
- # -----------------------------------------
- #
- # -----------------------------------------
- # Should be locs DF with all unique locs for valiation set
- # Now, I need to divide data accordingly
- # ------------------------------
- test.index <- (locs$x %in% u.test.locs$x) & (locs$y %in% u.test.locs$y)
- train.index <- !test.index
- # -------------------------
- # Test Plot of Grid
- # -------------------------
- if ( plot.it == TRUE){
- plot(1,1,
- xlim=c(lon.min,lon.max),
- ylim=c(lat.min, lat.max),
- type="n",
- cex=0.25,
- main =paste("Train=Blue(",sum(train.index),
- ") Test=Red(",sum(test.index),")"))
- require(maps)
- map("state", add=TRUE, col="black", lwd=2)
- for (jjj in 1:length(grid.yyy)){
- lines(c(lon.min,lon.max),rep(grid.yyy[jjj],2),col="grey")
- }
- for (jjj in 1:length(grid.xxx)){
- lines(rep(grid.xxx[jjj],2),c(lat.min,lat.max),col="grey")
- }
- #dim(u.test.locs)
- points(locs[train.index,], col="blue", cex=0.5, pch=19)
- points(u.test.locs, cex=0.5, col=2,pch=19)
- }
-# ------------------
-return(list( test.index = test.index,
- train.index = train.index))
-# ---------------------------------------------------------------------------------
-} #end FUNCTION
-# ---------------------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# ----------------------------------------------------------------------
-# equal.wt.max.coverage.selection
-# max.uniform.coverage.split
-# DFink
-# 3.22.10
-#
-# This function splits a set of locations into "test" and "training"
-# set with with the goal that the test set meet two objectives:
-# 1) The test set covers the broadest extent possible, and
-# 2) The test set is approximately uniform over the extent.
-#
-# The first goal is met by constructing a randomly located rectangular
-# grid over the extent of the data and then preferentially select
-# test locations that populate as many cells as possible. Within
-# grid cell density is controlled, i.e. made more uniform, by
-# setting the maximum number of unique locations included in cell.
-# Small value of the maximum cell sample size parameter help
-# to produce more uniformly distributed test set samples.
-#
-# Note, if locations are repeated, all the repeats for each location
-# are all assigned to either the test or training sets.
-#
-# Inputs:
-# ---------
-# locs - data frame or list with elements x & y.
-# grid.cell.min.lat - height of grid cells
-# grid.cell.min.lon - width of grid cells
-# max.cell.locs - integer giving maximum number of unique locations
-# per cell
-# plot.it =FALSE - flag for diagnostic plot
-#
-# Outputs:
-# ---------
-# test.index = boolean index of length = nrows(locs)
-# train.index = same.
-#
-# ----------------------------------------------------------------------
-# ----------------------------------------------------------------------
-# Equal Weight with Maximum Coverage Splitting
-# for Train:Test Set
-# ---------------------------
-equal.wt.max.coverage.selection <- function(
- locs,
- grid.cell.min.lat,
- grid.cell.min.lon,
- max.cell.locs=1,
- plot.it =FALSE ){
-# ----------------------------------------------------------------
-# Formal test values
-# locs=cc.data$locs data.frame(x , y) length n
-# grid.cell.min.lat=1.0
-# grid.cell.min.lon=1.5
-# max.cell.locs=5
-# ----------------------
- lon.min <- min(locs$x)
- lon.max <- max(locs$x)
- lat.min <- min(locs$y)
- lat.max <- max(locs$y)
- iii.loop <- 1
- # 1) Randomize Coordinate for first grid cell boundary
- r.lat <- runif(1,min=0, max=grid.cell.min.lat)
- r.lon <- runif(1,min=0, max=grid.cell.min.lon)
- # 2) lay down equally spaced grids from min to max
- grid.ttt <- seq(from=(lon.min+r.lon),
- to=lon.max,
- by=grid.cell.min.lon)
- grid.xxx <- c(lon.min, grid.ttt, lon.max)
- grid.ttt <- seq(from=(lat.min+r.lat),
- to=lat.max,
- by=grid.cell.min.lat)
- grid.yyy <- c(lat.min, grid.ttt, lat.max)
- # incase of any duplicates!
- grid.xxx <- sort(unique(grid.xxx))
- grid.yyy <- sort(unique(grid.yyy))
- # ---------------------------------------------------
- # Sample Maximal Coverage Test Set
- # Then use the rest for Training
- # ** Take up to the first max.cell.locs
- # ** Then randomly select the rest, by unique loc
- # ---------------------------------------------------
- kkk <- 0 # counter for grid cell regions
- nnn.grid.cells <- (length(grid.xxx)-1)*(length(grid.yyy)-1)
- u.test.locs <- NULL
- # -----------------------------------------------------------------
- # Cycle over Columns(xxx_iii) within Given Row (yyy_jjj)
- # -----------------------------------------------------------------
- for (jjj in 1:(length(grid.yyy)-1)){
- for (iii in 1:(length(grid.xxx)-1)){
- kkk <- kkk + 1
- xxx <- locs$x
- yyy <- locs$y
- cell.index <- xxx >= grid.xxx[iii] & xxx < grid.xxx[iii+1] &
- yyy >= grid.yyy[jjj] & yyy < grid.yyy[jjj+1]
- # Check for minimum Prediction Cell Locations
- # ---------------------------------------------
- u.locs <- unique(data.frame(x=locs$x[cell.index],
- y=locs$y[cell.index]))
- #sum(cell.index)
- #dim(u.locs)
- #cat(NROW(u.locs),"\n")
- #cat( max.cell.locs, "\n")
- if (NROW(u.locs) <= max.cell.locs) {
- # Randomly Select first max.cell.locs
- u.test.locs <- rbind(u.test.locs,u.locs)
- }
- if (NROW(u.locs) > max.cell.locs) {
- # Randomly Select first max.cell.locs
- # Then Randomly split the rest
- # ---------------------------------
- ttt.ind <- sample(1:NROW(u.locs), size=max.cell.locs)
- u.test.locs <- rbind(u.test.locs,u.locs[ttt.ind,])
- }
- }}# end grid loops
- # -----------------------------------------
- # Build index into all locations.
- # ------------------------------
- test.index <- (locs$x %in% u.test.locs$x) & (locs$y %in% u.test.locs$y)
- train.index <- !test.index
- # -------------------------
- # Test Plot of Grid
- # -------------------------
- if ( plot.it == TRUE){
- plot(1,1,
- xlim=c(lon.min,lon.max),
- ylim=c(lat.min, lat.max),
- type="n",
- cex=0.25,
- main =paste("Train=Blue(",sum(train.index),
- ") Test=Red(",sum(test.index),")"))
- require(maps)
- map("state", add=TRUE, col="black", lwd=2)
- for (jjj in 1:length(grid.yyy)){
- lines(c(lon.min,lon.max),rep(grid.yyy[jjj],2),col="grey")
- }
- for (jjj in 1:length(grid.xxx)){
- lines(rep(grid.xxx[jjj],2),c(lat.min,lat.max),col="grey")
- }
- #dim(u.test.locs)
- points(locs$x, locs$y, col="blue", cex=0.25, pch=1)
- points(u.test.locs, cex=0.25, col=2,pch=1)
- } # plot.it
-# ------------------
-return(list(test.index = test.index,
- train.index = train.index))
-# ---------------------------------------------------------------------------------
-} #end FUNCTION
-# ---------------------------------------------------------------------------------
-
-
-
-
-
-# ---------------------------------------------------------------------
-# ---------------------------------------------------------------------
-# OOB Diagnositic Plots
-# ---------------------------------------------------------------------
-plot.diagnostics <- function(pred, ensemble.data, resp.family) {
- # ---------------------------------------------------------------------
- # ---------------------------------------------------------------------
- #
- # pred = test.pred
- # oob <- FALSE
- # ensemble.data = test.data
- # ---------------------------------------------------------------------
- require(mgcv)
- par(mfrow=c(3,2))
- # Plot Residuals
- # --------------
- ttt.ind <- !is.na(pred$mean)
- res <- (ensemble.data$y[ttt.ind] - pred$mean[ttt.ind])
- hist(res,
- xlab = "Observation - Prediction",
- main = "Residuals")
- lines(c(0,0), c(-9e9,9e9), col="blue")
- # ------------------------------------
- # How many models support In-Bag Predicitons
- # and Out Of Bag/Sample Predictions
- # --------------------------------------------
- hist(apply(!is.na(pred$matrix), 1, sum, na.rm=T),
- main="Ensemble Support",
- xlab="Number of Models per Prediction")
- # Note: Zero column is the number of training points
- # that were never predicted OOB
- # Plot predictions vs Obs.
- # ---------------------------
- ttt.ind <- !is.na(pred$mean)
- xxx <- pred$mean[ttt.ind]
- yyy <- ensemble.data$y[ttt.ind]
- plot(xxx,
- yyy,
- xlab="Prediction",
- ylab="Observation")
- abline(0,1, col="blue")
- require(mgcv)
- d.gam <- gam(yyy ~ s(xxx), data=data.frame(yyy,xxx), gamma=1.2)
- ttt <- seq(from=min(xxx), to=max(xxx), length=15)
- p.ttt <- predict(d.gam, newdata=data.frame(xxx=ttt))
- lines(ttt,p.ttt, col=2)
- # Mean - Var Scaling
- # -------------------
- ttt.ind <- ( !is.na(pred$sd) & !is.na(pred$mean) )
- xxx <- pred$mean[ttt.ind]
- yyy <- pred$sd[ttt.ind]
- plot(xxx,
- yyy,
- xlab="Ensemble Pointwise Mean",
- ylab="Ensemble Pointwise SD")
- abline(0,1, col="blue")
- d.gam <- gam(yyy ~ s(xxx), data=data.frame(yyy,xxx), gamma=1.2)
- ttt <- seq(from=min(xxx), to=max(xxx), length=15)
- p.ttt <- predict(d.gam, newdata=data.frame(xxx=ttt))
- lines(ttt,p.ttt, col=2)
- # ------------------------------
- # -------------------------------------------------------------
- # Add Bootstrap Trajectory for MSE(oob.pred, training.obs)
- # -------------------------------------------------------------
- if (resp.family=="gaussian" | resp.family=="poisson") {
- ppp <- pred$matrix # continous.res x btrials
- j.length <- 25
- j.ind <- seq(from=1, to=NCOL(ppp), length=j.length)
- MSE <- rep(0, j.length)
- for (jjj in 1:j.length){
- if (jjj == 1) ttt.pred <- ppp[,1]
- if (jjj > 1) ttt.pred <- apply(ppp[,c(1:j.ind[jjj])],1,
- mean,
- na.rm=TRUE)
- MSE[jjj] <- predictive.performance(obs=ensemble.data$y[!is.na(ttt.pred)],
- ppp=ttt.pred[!is.na(ttt.pred)],
- resp.family=resp.family)$MSE
- }
- plot(j.ind,
- MSE,
- xlab="Ensemble Size",
- main=" MSE vs Ensemble Size ",
- type="l", lwd=2)
- } #
- # -------------------------------------------------
- # -------------------------------------------------------------
- # Add Bootstrap Trajectory for MSE(oob.pred, training.obs)
- # -------------------------------------------------------------
- if (resp.family=="bernoulli") {
- ppp <- pred$matrix # continous.res x btrials
- j.length <- 25
- j.ind <- seq(from=1, to=NCOL(ppp), length=j.length)
- MSE <- rep(0, j.length)
- for (jjj in 1:j.length){
- if (jjj == 1) ttt.pred <- ppp[,1]
- if (jjj > 1) ttt.pred <- apply(ppp[,c(1:j.ind[jjj])],1,
- mean,
- na.rm=TRUE)
- # ---------------------------------------------------------------
- # This is a hack to accomodate
- # an error from the ROCR prediction() function
- # encountered when all the observations are of a
- # single class!
- # "Error in prediction(prediction = ppp, labels = as.numeric(obs)) :
- # "Number of classes is not equal to 2.
- # ---------------------------------------------------------------
- if (length((unique(ensemble.data$y[!is.na(ttt.pred)]))) ==2)
- MSE[jjj] <- predictive.performance(
- obs=ensemble.data$y[!is.na(ttt.pred)],
- ppp=ttt.pred[!is.na(ttt.pred)],
- resp.family=resp.family)$auc
- }
- plot(j.ind,
- MSE,
- ylim=c(0.5, 1.0),
- xlab="Ensemble Size",
- ylab="AUC",
- main=" AUC vs Ensemble Size ",
- type="l", lwd=2)
- } #
- # -------------------------------------------------
-# -------------------------------------------------------------
-} # end function
-# ---------------------------------------------------------------------
-# ---------------------------------------------------------------------
-
-# ---------------------------------------------------------
-# Simple Plot for 1D PD plots
-#
-# This needs to really be cleaned up
-# ---------------------------------------------------------
-summary.1D.PD.ensemble<- function(filename=NULL,
- ensemble.par.list,
- pd.data,
- pd.bdt.object.name = NULL,
- continuous.resolution = 15,
- nn.sample = 100,
- # ----------------------
- partial.datafile = NULL,
- diag.bdt=NULL,
- n.pd = 4,
- pd.filename,
- # ----------------------
- plot.it = TRUE,
- plot.range = "common",
- n.row = 2,
- n.col =2) {
- # ---------pd.data------------------------------------------------
- X.names <- names(pd.data$X)
- X.factor.ind <- rep(FALSE, NCOL(pd.data$X))
- ttt <- pd.data$X[1,] # it is much faster to search a 1D data.frame!
- for (ii in 1:NCOL(pd.data$X))
- X.factor.ind[ii] <- is.factor(ttt[,ii])
- # ------------------------------
- ttt.ind <- order(apply(diag.bdt$var.imp1,1,median), decreasing=TRUE)
- pd.names <- X.names[ttt.ind]
- pd.names <- pd.names[1:n.pd]
- pd.factor.ind <- X.factor.ind[ttt.ind]
- pd.factor.ind <- pd.factor.ind[1:n.pd]
- pd.list <- as.list(pd.names)
-
- if (is.null(pd.bdt.object.name) ){
- # ------------------------------------------------
- pd.bdt <- ensemble.partial.dependence(
- filename = filename,
- ensemble.par.list = ensemble.par.list,
- XX = pd.data$X,
- partial.dependence.list = pd.list,
- continuous.resolution = continuous.resolution,
- nn.sample = nn.sample)
- save(pd.bdt, file=paste(pd.filename,sep=""))
- }
-
- if (!is.null(pd.bdt.object.name) ){
- # ------------------------------------------------
- load(pd.bdt.object.name) # Assumed name is pd.bdt
- }
-
- # ---------------------------
- if (plot.it == TRUE) {
- # Calc Centered PD means &
- # Find y-limits for these plots
- # --------------------------------
- y.min <- 0.0
- y.max <- 0.0
- for (iii in 1:n.pd) {
- # Calculate Centered Mean
- ppp <- pd.bdt$pd.matrices[[iii]]
- ppp.mean <- apply(ppp, 1, mean, na.rm=T)
- ppp.mean <- ppp.mean - mean(ppp.mean)
- y.min <- min(c(y.min,min(ppp.mean)))
- y.max <- max(c(y.max,max(ppp.mean)))
- }
- y.range <- NULL
- if (plot.range=="common") y.range <- c(y.min, y.max)
-
- # -------------------------------------------------------------------------------------------------------
- par(mfrow=c(n.row,n.col), mar=c(2,2,4,2))
- # mar = c(bottom, left, top, right)
- for (iii in 1:n.pd) {
- # --------------------------
- # Continuous Plot
- # ----------------------------------
- if (pd.factor.ind[iii] == FALSE) {
- xxx <- pd.bdt$pd.quant.grids[[iii]] #
- ppp <- pd.bdt$pd.matrices[[iii]] # matrix: continous.res x btrials
- # Change ppp to data.frame
- ppp <- data.frame(ppp)
- # Calculate Centered Mean
- ppp.mean <- apply(ppp, 1, mean, na.rm=T)
- ppp.center <- mean(ppp.mean)
- ppp.mean <- ppp.mean - ppp.center
- #names(ppp) <- as.character(c(1:NCOL(ppp)))
- #yyy.stacked <- stack(ppp)
- #yyy.stacked <- as.numeric(yyy.stacked[,1])- ppp.center
- #xxx.stacked <- rep(as.numeric(xxx[,1]), times=NCOL(ppp))
- #----
- plot(xxx[,1],
- ppp.mean,
- ylim=y.range ,
- type = "p",
- col="black",
- pch = 19,
- cex=.75,
- xlab = " ",
- main = names(xxx),
- ylab = " ")
- abline(0,0)
-
- # -----------------------------------------------
- # Plot when there enough unique levels to smooth
- # ----------------------------------------------
- if (length(sort(unique(xxx[,1]))) >= 10) {
- # ----------------------------------------------------
- yyy.stacked <- ppp.mean
- xxx.stacked <- xxx[,1]
- # ---------------
- require(mgcv)
- d.gam <- gam( yyy.stacked ~ s(xxx.stacked),
- gamma=1.2)
- xxx.pred <- seq(from=min(xxx.stacked),
- to=max(xxx.stacked),
- length=25)
- pred.gam <- predict(d.gam,
- newdata=data.frame(xxx.stacked=xxx.pred),
- se.fit=TRUE, type="response")
- lines(xxx.pred,pred.gam$fit,col="blue", lwd=2.0)
- }}
- # ----------------------------------
- # Factor Plot
- # ----------------------------------
- if (pd.factor.ind[iii] == TRUE){
- xxx <- pd.bdt$pd.quant.grids[[iii]] #
- ppp <- pd.bdt$pd.matrices[[iii]] # continous.res x btrials
- # Calculate Centered Mean
- ppp.mean <- apply(ppp, 1, mean, na.rm=T)
- ppp.center <- mean(ppp.mean)
- ppp.mean <- ppp.mean - ppp.center
- # -----------------------------------------------
- # Change xxx to class factor for plot
- # -----------------------------------------------
- factor.levels <-
- levels(pd.data$X[, names(pd.data$X) == names(xxx)])
- xxx.recoded <- factor.levels[ xxx[,1]]
- plot(as.factor(xxx.recoded),
- ppp.mean,
- ylim= y.range,
- xlab = " ",
- main = names(xxx),
- ylab = " ")
- abline(0,0)
- }
- }# end plotting
- } # end plot.it
-} # end function
-# -------------------------------------------------------------------
-# ---------------------------------------------------------------------
-
-
-
-#------------------------------------------------------------------------------------------------------------
-#------------------------------------------------------------------------------------------------------------
-# Extract Seasonal p.data
-# function st.gam relies on this function.
-#
-# 1.13.08
-# Modified to only do a single "training/test" data set
-# and to return only the index (logical index).
-#
-#
-#Demo:
-# -----------
-# ttt.data <- seasonal.window(
-# begin.window=30,
-# end.window=80,
-# p.data=p.data)
-# names(ttt.data$X)
-# dim(ttt.data$X)
-# dim(ttt.data$Xp)
-# sort(unique(ttt.data$X$JDATE))
-#
-#
-# Tree Swallow Notes:
-# ---------------------------------
- # -----------------------------------------
- # Define Seasons
- # -----------------------------------------
- #ttt<- c( 320, 45, #winter
- # 45, 110, #spring
- # 110, 200, #Breeding
- # 200, 320) # Fall
- #season.boundaries <- matrix(ttt,4,2, byrow=TRUE)
-#------------------------------------------------------------------------------------------------------------
-#------------------------------------------------------------------------------------------------------------
-seasonal.window <- function(
- begin.window,
- end.window,
- p.data){
- season.boundaries <- matrix(c(begin.window, end.window),
- 1,2, byrow=TRUE)
- jjj <- 1
- winter <- (begin.window > end.window)
- # -----------------------------------------
- # Training p.data
- # -----------------------------------------
- season.index <- p.data$jdates >= season.boundaries[jjj,1] &
- p.data$jdates <= season.boundaries[jjj,2]
- if (winter) { # Winter
- season.index <- p.data$jdates >= season.boundaries[jjj,1] |
- p.data$jdates <= season.boundaries[jjj,2]
- }
- return(
- list(
- #p.data=p.data,
- season.index = season.index))
- #season.p.index = season.p.index))
- } #end function
-# -------------------------------------------------------------------------------------------
-# -------------------------------------------------------------------------------------------
-
-
-## Clear the deck of all local variables
-## rm(list = c("arrival.dates", "begin.date", "bs.rpart.maps", "by.tic", "color.palette", "create.pd.grid", "create.simple.STEM.ensemble", "D.erd.data.par.list", "deviance.explained", "end.date", "ensemble.partial.dependence", "equal.wt.max.coverage.selection", "fit.ensemble", "halloween.colors", "halloween.maps", "iii", "initizalize.map.grid", "jdate.index", "jdate.seq", "jdate.tic.names", "jdate.tics", "j.index", "make.functional.data.design.matrix", "make.SPAT.COVAR.pred.data", "map.i [...]
-## KFW gc()
\ No newline at end of file
diff --git a/contrib/stem/code/stem.library.B.R b/contrib/stem/code/stem.library.B.R
deleted file mode 100644
index 3d54a90..0000000
--- a/contrib/stem/code/stem.library.B.R
+++ /dev/null
@@ -1,2124 +0,0 @@
-
-# STEM LIBRARY INDEX
-# ---------------------------------------------------------
-# FUNCTION: Create Simple ST Ensemble, 5.1.09
-# * cleaned
-#
-# sample.ST.ensemble <- function( 5.1.09
-# * cleaned, consistent use of locs
-# * STEM ensemble requires ensemble.locs & ensemble.jdates
-# WTIHOUT requiring predictors ($x, $y, & $JDATE)
-# * These predictors are required if basis rotation used!
-#
-# rotate.ST.basis.sample - added ensemble.locs
-# this means that you can split by location within DT
-# without having layt & lon predictors!
-#
-# FUNCTION: Plot STEM Spatial Design
-#
-# FUNCTION: predict.ST.ensemble -
-# explicit locs & jdate incices
-# better handling of null predictions
-# verified
-#
-# FUNCTION: predict.ST.matrix
-# FUNCTION: STEM.partial.dependence
-# ** NOT yet working for lat,lon effects!!!
-#
-#
-# plot ST design Function
-# ---------------------------------------------------------
-# STEM Specific functionality that is Needed:
-# --------------
-# Histogram of ensemble sample sizes
-# Support Map at a point
-# Support Depth Map
-# -------------------------------------------
-
-
-
-
-
-
-
-
-# ---------------------------------------------------------
-# FUNCTION: Create Simple ST Ensemble
-# D Fink
-# 5.1.09
-# ---------------------------------------------------------
-#
-# Becuase the spatial regions are generated randomly, I want
-# to incorporate as much of this variation as possible in
-# the sample. We use a different spatial
-# regionalization for each time interval.
-#
-# Note with spatial design.
-# if locations are only unique locations, then min.data.size
-# if applied to unique locations. Otherwise min.data.size
-# is applied to total number of data pts w/in STEM cell.
-#
-#
-# -----------------------------------------------------------
-# Temporal Design - Seasonal Tiles
-# -----------------------------------------------------------
-# 1) jdate.seq are centers of symmetric temporal window
-# Evenly spaced slices throughout year
-# ** begin.window = vector of jdates for beginning of window
-# centered at jdate.seq
-# ** end.window = same
-# ** begin.pred.window = is the beginning of the prediction
-# window. This controls how the
-# averaging of the ensemble is done.
-# Eg. If prediction.window.width <
-# season.window.width. This can be used to remove bias
-# often encountered when predicting at end of time series.
-# If prediction.window.width > season.window.width
-# then this allows forecasting, predictions beyond the
-# time horizon of the data. This should give a more
-# realistic errors if goal is forecasting.
-# ------------------------------------------------------------
-#
-# INPUT:
-# -----------
-# y = (n x 1) full response vector
-# (Should I remove this or make it optional??)
-# X = (n x p) full design matrix
-#
-# sampling.par.list=NULL
-# split.by.location==TRUE
-# X.loc = data.frame used to split data.
-# note - the NROWS(X.loc) must equal NROWS(X) the
-# training design!!!
-# p.train = proportion data sampled for training
-# # Default ==> Use all available data for
-# # test & training sets by including all replicate locations.
-# m.frac <- 1.0
-# OUTPUT:
-# -------------
-# Regional.polygons = data.frame with components
-# x = vertices of polygons
-# y = vertices of polygons
-# region.code = sequential number code,
-#
-# Cluster.codes = (rows = NROW(ensemble.data$X)
-# cols = n.mc.regions)
-# contains the clusterings for each mc realization
-# regional.polygons = data.frame that defines the regional polygons
-# the partition the global region.
-# Here, regions are defined by clustering algorithm
-# number of polygons = n.region
-# (longitude, latitude, region.number)
-# design.summary <- Center of region mass
-# (good for Knot locations & text titles)
-# ----------------------------------------------------------------------
-# Future Development -
-# ** add logic to cycle through limited
-# number of n.mc.regions for all btrial x n.interval combinations.
-# ------------------------------------------------------------
-create.simple.STEM.ensemble <- function(
- # Data
- # ------------------------
- ensemble.data.locs, # <- data.frame(x=ensemble.data$X$x, y=ensemble.data$X$y)
- ensemble.data.jdates, # "JDATE" = Julian date from 0 to 365
- # ------------------------
- # Spatial Design
- # ------------------------
- spatial.region.par.list, # All Random Rectangle Inits
- # Temporal Design
- # ------------------------
- n.intervals, # Slice year into n.intervals prediction points
- begin.jdate = 0, #
- end.jdate = 365,
- season.window.width, # Fitting/Training window width in days
- prediction.window.width, # Prediction window width in days
- # Sampling parameters (pass through only)
- # ------------------------------------
- sample.ensemble.function,
- sampling.par.list,
- predict.ensemble.function,
- spatial.extent.list=NULL)
-{# ---------------------------------------------------------
-# # ----------------------------------------------------------------------
-# # Formal parameter Test Values
-# # ----------------------------------------------------------------------
-
-# ----------------------------------------------------------------------
-# Temporal Design - Seasonal Tiles
-# ----------------------------------------------------------------------
- jdate.seq <- seq(from=begin.jdate, to=end.jdate, length=(n.intervals+1))
- jdate.seq <- round((jdate.seq[2:(n.intervals+1)] + jdate.seq[1:(n.intervals)])/2)
- begin.window <- jdate.seq - round(season.window.width/2)
- begin.window[ begin.window < 0 ] <- begin.window[ begin.window < 0 ] + 365
- end.window <- jdate.seq + round(season.window.width/2)
- end.window[ end.window > 365 ] <- end.window[ end.window > 365 ] - 365
- # ----------------------
- begin.pred.window <- jdate.seq - round(prediction.window.width/2)
- begin.pred.window[ begin.pred.window < 0 ] <-
- begin.pred.window[ begin.pred.window < 0 ] +365
- end.pred.window <- jdate.seq + round(prediction.window.width/2)
- end.pred.window[ end.pred.window > 365 ] <-
- end.pred.window[ end.pred.window > 365 ] -365
-
-# ----------------------------------------------------------------------
-# Spatial Design - Random Rectangular Regional Tiles
-# ----------------------------------------------------------------------
- # --------------------------------------------------------------------------------------------
- # Inits
- # --------------------------------------------------------------------------------------------
- n.mc.regions <- spatial.region.par.list$n.mc.regions
- # Underlying Coverage Grid
- grid.cell.min.lat <- spatial.region.par.list$grid.cell.min.lat
- grid.cell.min.lon <- spatial.region.par.list$grid.cell.min.lon
- # Randomized Rectangular Regions
- n.centers.per.region <- spatial.region.par.list$n.centers.per.region
- regional.cell.min.lat <- spatial.region.par.list$regional.cell.min.lat
- regional.cell.min.lon <- spatial.region.par.list$regional.cell.min.lon
- min.data.size <- spatial.region.par.list$min.data.size
- # Unpack location info
- # ----------------------
- xxx <- ensemble.data.locs$x # Longitude
- yyy <- ensemble.data.locs$y # Longitude
- lat.min <- min(yyy)
- lat.max <- max(yyy)
- lon.min <- min(xxx)
- lon.max <- max(xxx)
- iii.count <- 0
-# --------------------------------------------------------------------------------------------
-# Loop MC Regions - one SET of regions for each MC x Time Interval Combination
-# --------------------------------------------------------------------------------------------
-regional.polygons <- NULL
-design.summary <- NULL
-for (iii.interval in 1:n.intervals){
-for (iii.mc.region in 1:(n.mc.regions)){ # 1){ #
- # ----------------------------------------------------------------------
- # Define "Coverage" Grid
- # ----------------------------------------------------------------------
- # Store grid as x-vector of grid vertices
- # and y-vector of grid vectices. Both of these are bookended
- # with their min & max values.
- # 0) Initialize with x-min,
- # 1) randomize position of first vertex
- # 2) lay down equally spaced grid until x.max reached
- # ** Repeate for y-axis
- # --------------------------------------------------
- # --------------------------------------------------
- # Randomize Coordinate for first grid cell boundary
- # --------------------------------------------------
- r.lat <- runif(1,min=0, max=grid.cell.min.lat)
- r.lon <- runif(1,min=0, max=grid.cell.min.lon)
- grid.ttt <- seq(from=(lon.min+r.lon),
- to=lon.max,
- by=grid.cell.min.lon)
- grid.xxx <- c(lon.min, grid.ttt, lon.max)
- grid.ttt <- seq(from=(lat.min+r.lat),
- to=lat.max,
- by=grid.cell.min.lat)
- grid.yyy <- c(lat.min, grid.ttt, lat.max)
- # incase of any duplicates!
- grid.xxx <- sort(unique(grid.xxx))
- grid.yyy <- sort(unique(grid.yyy))
- # -------------------------
- # Test Plot of Grid
- # -------------------------
- #plot(xxx,yyy, cex=0.25)
- #require(maps)
- #map("state", add=TRUE)
- #for (jjj in 1:length(grid.yyy)){
- # lines(c(lon.min,lon.max),rep(grid.yyy[jjj],2))
- # }
- #for (jjj in 1:length(grid.xxx)){
- # lines(rep(grid.xxx[jjj],2),c(lat.min,lat.max))
- # }
- # --------------------------------------------------------------
- # -------------------------------------------------------
- # Cycle over Columns(xxx_iii) within Given Row (yyy_jjj)
- # Sample Random Centers within Grid Cells
- # -------------------------------------------------------
- grid.centers.x <- NULL
- grid.centers.y <- NULL
- for (jjj in 1:(length(grid.yyy)-1)){
- for (iii in 1:(length(grid.xxx)-1)){
- ttt.index <- xxx >= grid.xxx[iii] & xxx < grid.xxx[iii+1] &
- yyy >= grid.yyy[jjj] & yyy < grid.yyy[jjj+1]
- ttt.df <- data.frame(xxx=xxx[ttt.index], yyy=yyy[ttt.index])
- #ttt.u <- unique(ttt.df)
- # Check for at least 1 data point in the coverage cell.
- # If so, then Sample Random Centers
- # ----------------------------------------
- if (NROW(ttt.df) > 0 ){
- n.centers <- n.centers.per.region
- grid.centers.x <-c(grid.centers.x,
- runif(n.centers,
- min=grid.xxx[iii],
- max=grid.xxx[iii+1]))
- grid.centers.y <-c(grid.centers.y,
- runif(n.centers,
- min=grid.yyy[jjj],
- max=grid.yyy[jjj+1]))
- } # endif
- # ---------------
- } #iii
- } #jjj
- grid.centers <- data.frame(x=grid.centers.x,
- y=grid.centers.y)
- rm(grid.centers.x)
- rm(grid.centers.y)
- #dim(grid.centers)
- # plot
- #points(grid.centers, cex=1.5, pch=19, col=2)
- # --------------------------------------------------
- # Filter Grid Centers to lie within Target Boundary
- # --------------------------------------------------
- ttt.index <- c(1:NROW(grid.centers))
- if (!is.null(spatial.extent.list)){
- if (spatial.extent.list$type == "shapefile"){
- ttt.index <- point.in.shapefile(
- sites = data.frame(lon=grid.centers$x,
- lat=grid.centers$y),
- shape.dir=spatial.extent.list$shape.dir,
- shape.filename=spatial.extent.list$shape.filename,
- att.selection.column.name=
- spatial.extent.list$att.selection.column.name,
- selected.shape.names=
- spatial.extent.list$selected.shape.names)
- }
- } # if (!is.null(spatial.extent.list)){
- # Use Convex Hull around ensemble.data to get approximate boundary
- # ------------------------------------------------------------
- if (!is.null(spatial.extent.list)){
- if (spatial.extent.list$type == "convexhull"){
- chull.index <- chull(ensemble.data.locs )
- ttt.index <- point.in.polygon(
- xxx = grid.centers$x,
- yyy = grid.centers$y,
- polygon.vertices = ensemble.data.locs[chull.index,])
- }}
- # -----------------------------------------
- grid.centers <- grid.centers[ttt.index,]
- # -----------------------------------------
- # plot check
- # -----------------------------------------
- #points(grid.centers, cex=1.0, pch=19, col=3)
- #cat(dim(grid.centers), "\n")
- #for (jjj in 1:length(grid.yyy)){
- # lines(c(lon.min,lon.max),rep(grid.yyy[jjj],2))
- # }
- #for (jjj in 1:length(grid.xxx)){
- # lines(rep(grid.xxx[jjj],2),c(lat.min,lat.max))
- # }
- # --------------
-# --------------------------------------------------------------------------------------------
-# Cycle over Regions - Check for minimum data & area requirements
-# Grow Rectanges as necessary
-# --------------------------------------------------------------------------------------------
- for (iii in 1:NROW(grid.centers)) {
- # Make Intial Rectangle
- # ----------------------
- center.lon <- grid.centers$x[iii]
- center.lat <- grid.centers$y[iii]
- r.lat <- regional.cell.min.lat/2
- r.lon <- regional.cell.min.lon/2
- regional.rectangle <- data.frame(
- x= c((center.lon-r.lon), (center.lon-r.lon),
- (center.lon+r.lon), (center.lon+r.lon), (center.lon- r.lon)),
- y= c((center.lat-r.lat), (center.lat+r.lat),
- (center.lat+r.lat), (center.lat-r.lat), (center.lat-r.lat)) )
- # Clip X & Y coordinates: maximum is
- # the rectangle bounding the data PLUS
- # an essential small (epsilon) boundary. This is essential
- # to include "boundary points" with the point in polygon
- # routines that I am using. They points that lie
- # on the lower polygon boundaries.
- # --------------------------------------------------
- epsilon <- 1e-10
- regional.rectangle$x[ regional.rectangle$x > max(xxx)] <- max(xxx)+epsilon
- regional.rectangle$x[ regional.rectangle$x < min(xxx)] <- min(xxx)-epsilon
- regional.rectangle$y[ regional.rectangle$y > max(yyy)] <- max(yyy)+epsilon
- regional.rectangle$y[ regional.rectangle$y < min(yyy)] <- min(yyy)-epsilon
- # --------------------------
- # Loop over all ST windows/extents/regions
- # Record vector of Regional-seasonal sample sizes
- # Test for minimum sample size requirements
- # --------------------------
- # Spatial Region Index
- rr.index <- point.in.rectangle(
- xxx = ensemble.data.locs$x,
- yyy = ensemble.data.locs$y,
- polygon.vertices = regional.rectangle )
- # Seasonal Index
- if ((begin.window[iii.interval] < end.window[iii.interval])) # non-Winter
- season.index <- ensemble.data.jdates >= begin.window[iii.interval] &
- ensemble.data.jdates <= end.window[iii.interval]
- if ((begin.window[iii.interval] > end.window[iii.interval])) # Winter
- season.index <-ensemble.data.jdates >= begin.window[iii.interval] |
- ensemble.data.jdates <= end.window[iii.interval]
- # regional & Seasonal indices
- ttt.index <- rr.index & season.index
- # Now see how many unique locations there
- # are among the selected/identified points
- # ------------------------------------------
- u.locs <- unique(data.frame(ensemble.data.locs$x[ttt.index],
- ensemble.data.locs$y[ttt.index]))
- # number of unique locs
- temp.samp.sizes <- NROW(u.locs) #sum(ttt.index)
- # -------------------------------
- # If minium data size is met for
- # ALL Temporal Windows in that region
- # Then we record its name in the book of
- # regional names. Otherwise, we ignore that region.
- # -------------------------------
- # 4) Summarize Regions
- # -------------------------------
- if (temp.samp.sizes > min.data.size) {
- iii.count <- iii.count + 1
- regional.polygons <- rbind(regional.polygons,
- data.frame(
- regional.rectangle,
- region.number=rep(iii.count, NROW(regional.rectangle)),
- region.mc = iii.mc.region,
- time.intervals=iii.interval))
- design.summary <- rbind(design.summary,
- data.frame(
- x.center=center.lon,
- y.center=center.lat,
- region.number=iii.count,
- region.mc=iii.mc.region,
- time.intervals=iii.interval,
- unique.locs = temp.samp.sizes))
- }
- # -------------------------------
- # 5) plot final region
- # -------------------------------
- #polygon(regional.rectangle, border=iii+3)
- #points(center.lon, center.lat, col=iii+3, pch=19)
- #cat("Region ",iii," :",sum(rr.index),"\n")
-# ------------------------------------------------
-} # end loop over regions iii
-# ------------------------------------------------
-iii.count <- 0
-# ------------------------------------------------
-}} # end loop over MC x Time Interval Combinations
-# --------------------------------------------------------------------------------------------
- #names(design.summary)
- #dim(design.summary)
- #names(regional.polygons)
- #dim(regional.polygons)
- # -----------------------------------------------------------------
- # -------------------------------------------------
- # Cleanup & Return
- # -------------------------------------------------
- return.list <- list(
- ensemble.data.locs=ensemble.data.locs, # <- data.frame(x=ensemble.data$X$x, y=ensemble.data$X$y)
- ensemble.data.jdates=ensemble.data.jdates, # "JDATE" = Julian date from 0 to 365
- # Spatial
- # --------
- n.ensemble.models = NROW(design.summary),
- regional.polygons=regional.polygons,
- design.summary = design.summary,
- spatial.region.par.list = spatial.region.par.list,
- # Temporal
- # ---------
- n.intervals=n.intervals, # Slice year into n.intervals prediction points
- begin.jdate = begin.jdate, #
- end.jdate = end.jdate,
- season.window.width=season.window.width, # Fitting/Training window width in days
- prediction.window.width=prediction.window.width, # Prediction window width in days
- begin.window=begin.window,
- end.window=end.window,
- begin.pred.window=begin.pred.window,
- end.pred.window=end.pred.window,
- # Sampling
- # -----------------------
- sample.ensemble.function = sample.ensemble.function,
- sampling.par.list = sampling.par.list,
- predict.ensemble.function = predict.ensemble.function)
-# ---------------------------------------- -----------------
- return(return.list)
-# ---------------------------------------- -----------------
-}# end Create STEM ensemble Function
-# ---------------------------------------------------------
-
-
-
-# ---------------------------------------------------------
-# sample.ST.ensemble
-# ---------------------------------------------------------
-# Generate a Sample from a SINGLE ST.ensemble model
-# 4.13.09 - modifications
-# ** if there are no data in stem cell, skip that cell.
-# ---------------------------------------------------------
-sample.ST.ensemble <- function(
- ensemble.model.number,
- ensemble.data,
- ensemble.par.list,
- diagnostic.plot = FALSE)
-{# -----------------------------------------------------------
-# -----------------------------------------------------------
-# Formal Parameter TEST Values
-# -----------------------------------------------------------
- #ensemble.model.number <- 100
- #ensemble.data <- train.data
-# -----------------------------------------------------------
-# Inits
-# -----------------------------------------------------------
- return.list <- NULL
- # -----------------
- n.ensemble.models <- ensemble.par.list$n.ensemble.models
- # Check ensemble.model.number
- if (ensemble.model.number > n.ensemble.models)
- stop(paste("Error: There are only ", n.ensemble.models,
- " ensemble models. "))
- # --------
- ensemble.data.locs <- ensemble.par.list$ensemble.data.locs
- ensemble.data.jdates <- ensemble.par.list$ensemble.data.jdates
-# -----------------------------------------------------------
-# Select Temporal Window
-# -----------------------------------------------------------
- iii.interval <-
- ensemble.par.list$design.summary$time.intervals[ensemble.model.number]
- sw.obj <- seasonal.window(
- begin.window = ensemble.par.list$begin.window[iii.interval],
- end.window = ensemble.par.list$end.window[iii.interval],
- p.data= ensemble.data)
-
-#cat(" iii.iterval=",iii.interval,
-# ensemble.par.list$begin.window[iii.interval],
-# ensemble.par.list$end.window[iii.interval],"\n")
-#readline()
-#print(
-# cbind(ensemble.par.list$begin.window, ensemble.par.list$end.window) )
-
-
-# -----------------------------------------------------------
-# Check that there are data!!!
-# -----------------------------------------------------------
- if (sum(sw.obj$season.index) > 0){
-# -----------------------------------------------------------
-# Select Region
-# -----------------------------------------------------------
- # Index into regional polygons
- region.number <- ensemble.par.list$design.summary$region.number[ensemble.model.number]
- region.mc <- ensemble.par.list$design.summary$region.mc[ensemble.model.number]
- #**** Requires temporal index
- # *** 4.13 Added temporal interval
- r.index <- (ensemble.par.list$regional.polygons$region.mc == region.mc &
- ensemble.par.list$regional.polygons$region.number == region.number &
- ensemble.par.list$regional.polygons$time.intervals == iii.interval )
- # Index into p.data Training set
- region.given.season.index <- point.in.rectangle(
- # = ttt.data$X$x
- xxx = ensemble.data.locs$x[sw.obj$season.index],
- # = ttt.data$X$y
- yyy = ensemble.data.locs$y[sw.obj$season.index],
- polygon.vertices = ensemble.par.list$regional.polygons[r.index,1:2])
-# -----------------------------------------------------------
-# Check that there are data!!!
-# -----------------------------------------------------------
- if (sum(region.given.season.index) > 0){
- # -----------------------------------------------------------
- # Indexing Verification
- # -----------------------------------------------------------
- # dim(ensemble.data$X) # size training data
- # # Seasonal index = logical index into training data
- # length(sw.obj$season.index)
- # sum( sw.obj$season.index)
- # # region.given.season.index = logical index into seasonal subset
- # length(region.given.season.index)
- # sum(region.given.season.index)
- # # sample.data$row.index = numeric index into regional-seasonal subset
- # length(sample.data$row.index)
- # -------------------------------------
- # numerical index from training data to
- # regional-seasonal OOB/IB samples
- # -------------------------------------
- seasonal.num.ind <- c(1:length(sw.obj$season.index))[sw.obj$season.index]
- #length(seasonal.num.ind)
- reg.sea.num.ind <- seasonal.num.ind[region.given.season.index]
-# -----------------------------------------------------------
-# Sampling and Data Transformations
-# -----------------------------------------------------------
- # Sample with rotate.ST.basis.sample()
- sample.data <- rotate.ST.basis.sample(
- train.data = list(
- X = ensemble.data$X[reg.sea.num.ind,],
- y = ensemble.data$y[reg.sea.num.ind]) ,
- train.locs =ensemble.data.locs[reg.sea.num.ind , ] ,
- train.jdates = ensemble.data.jdates[reg.sea.num.ind ],
- sampling.par.list = ensemble.par.list$sampling.par.list)
-
-# -----------------------------------------------------------
-# Check that there are data!!!
-if (length(sample.data$row.index) > 0){
-# ----------------------------------------------
- # ----------------------------------
- # Final Indexing Information
- # ----------------------------------
- #length(reg.sea.num.ind)
- ib.reg.sea.num.ind <- reg.sea.num.ind[sample.data$row.index]
- #length(oob.reg.sea.num.ind)
- # -----------------------
- oob.reg.sea.num.ind <- setdiff(reg.sea.num.ind,ib.reg.sea.num.ind)
- #length(ib.reg.sea.num.ind)
- #length(oob.reg.sea.num.ind)+ length(ib.reg.sea.num.ind)
-
-# -----------------------------------------
-# Visual Verification Plot
-# Illustrating some fancy sampling!
-# -----------------------------------------
- if (diagnostic.plot == TRUE) {
- #windows()
- # All training points
- plot( ensemble.data.locs$x, ensemble.data.locs$y, pch=19, cex=0.5)
- map('state',add=TRUE, lwd=2, col="yellow")
- map('state',add=TRUE, lwd=1, col="black")
- # -----------------------------------------------
- # Seasonal Points
- points(ensemble.data.locs$x[seasonal.num.ind],
- ensemble.data.locs$y[seasonal.num.ind],
- col="red", cex=1.0)
- # -----------------------------------------------
- # Regional-Seasonal Points
- points(ensemble.data.locs$x[reg.sea.num.ind],
- ensemble.data.locs$y[reg.sea.num.ind],
- col="blue", cex=1.5)
- polygon(ensemble.par.list$regional.polygons[r.index,1:2],
- border="blue")
- # ----------------------------------------------
- # IB/OOB points
- points(ensemble.data.locs$x[oob.reg.sea.num.ind],
- ensemble.data.locs$y[oob.reg.sea.num.ind],
- col="green", cex=2.0, lwd=2)
- points(ensemble.data.locs$x[ib.reg.sea.num.ind],
- ensemble.data.locs$y[ib.reg.sea.num.ind],
- col="purple", cex=2.0, lwd=2)
- }
- # -------------------------------------------------
- # Cleanup & Return
- # -------------------------------------------------
- return.list <- list(
- # These are the sampled ("in bag") data
- X = sample.data$X,
- y = sample.data$y,
- # Numerical IB & OOB Indices into formal parameter ensemble.data
- oob.num.ind = oob.reg.sea.num.ind,
- ib.num.ind = ib.reg.sea.num.ind,
- #unique.locs.split = sample.data$dsplit,
- realized.par = sample.data$realized.par)
-} # seasonal window check end ifs checking for data in stem cell
-} # #sw.obj$season.index
-} # bs - subsampling sampled
- return(return.list)
-# ---------------------------------------------------------
-}# end Function sample.ST.ensemble
-# ---------------------------------------------------------
-
-
-
-# ---------------------------------------------------------
-# Sample with ST Basis Rotation
-# ---------------------------------------------------------
-# This function is identical to simple.sample,
-# except for the rotation and the sister function
-# rotate.ST.basis.pred()
-# Note: I am going to start with hard coded
-# rotation code.
-#
-#
-# ---------------------------------------------------------
-rotate.ST.basis.sample <- function(
- train.data,
- train.locs,
- train.jdates,
- sampling.par.list=NULL){
- # ------------------------------------------------
- # Inits
- # ------------------------------------------------
- n <- NROW(train.data$X)
- realized.par <- NULL
- dsplit <- NULL
- # ------------------------------------------------
- # Check sampling.par.list for "RND.seed"
- # ------------------------------------------------
- if (!is.null(sampling.par.list)) {
- if (sum(names(sampling.par.list)=="RNG.seed") > 0)
- set.seed(sampling.par.list$RNG.seed)
- }
- # -----------------------------------------------------------
- # Check for Sampling with ST Basis Rotation
- # ----------------------------------
- # requires variables named
- # "x" - lon coordinate
- # "y" - lat coordinate
- # "JDATE" - julian date
- # --------------
- # ==> this is a way of introducing Data Transformations
- # or randomization into the model. perhaps this may be
- # a nice way of icncorporating latent structure???
- # -----------------------------------------------------------
- if (sampling.par.list$ST.basis.rotation == TRUE){
- # ------------------------------------------------
- # Random Rotation of "Cartesian" Lat-Lon Plane
- # and Random cutting of the Julian Date Circle
- # ------------------------------------------------
- theta.prime <- runif(1, min=0, max=2*pi)
- train.data$X$x <- train.data$X$x*cos(theta.prime) - train.data$X$y*sin(theta.prime)
- train.data$X$y <- train.data$X$x*sin(theta.prime) + train.data$X$y*cos(theta.prime)
- # ------------------------------------------
- # Random rotation of Julian Date line
- theta2.prime <- round(runif(1, min=0, max=365))
- train.data$X$JDATE <- train.data$X$JDATE + theta2.prime
- train.data$X$JDATE[train.data$X$JDATE > 365] <- train.data$X$JDATE[train.data$X$JDATE > 365] - 365
- realized.par <- c(theta.prime, theta2.prime)
- }
-
- # -------------------------------------------------
- # Split Data into Train:Test sets with Unique Locations
- # -------------------------------------------------
- if (!is.null(sampling.par.list$split.by.location)){
- if (sampling.par.list$split.by.location==TRUE){
- # ------------------------------------
- # train.locs = data.frame( x, y)
- # -----
- # m.frac
- if (is.null(sampling.par.list$m.frac))
- # Default ==> Use all available data for
- # test & training sets by including all replicate locations.
- m.frac <- 1.0
- if (!is.null(sampling.par.list$m.frac))
- m.frac <- sampling.par.list$m.frac
- # -------
- # p.train
- p.train <- NULL
- if (!is.null(sampling.par.list$p.train))
- p.train <- sampling.par.list$p.train
- if (is.null(sampling.par.list$p.train))
- # Bootstrap proportion as default
- p.train <- 0.63
- # --------
- dsplit <- unique.locs.splitting(
- locs=train.locs,
- p.train=p.train,
- m.frac=m.frac)
- bindex <- dsplit$train.locs.multiple
- # default is to pass back train.locs.multiple
- }}
-
- # -------------------------------------------------
- # Split Data Randomly - w/o respect to anything else
- # -------------------------------------------------
- if (is.null(sampling.par.list$split.by.location) |
- (!is.null(sampling.par.list$split.by.location) &
- sampling.par.list$split.by.location==FALSE)) {
- # ------------------------------------------------
- # -------------------------------------------------
- # Random Sampling
- # -------------------------------------------------
- if (!is.null(sampling.par.list$p.train)){
- bindex <- sample( c(1:n),
- round(n*sampling.par.list$p.train) ,
- replace=FALSE)
- }
- # Default is to sample with replacement
- if (is.null(sampling.par.list$p.train))
- bindex <- round(1 + (n-1)*runif(n))
- } # end random split
- # -------------------------------------------------
-
- # -------------------------------------------------
- # Cleanup & Return
- # -------------------------------------------------
- return.list <- list(
- X = train.data$X[bindex,],
- y = train.data$y[bindex],
- row.index = bindex,
- unique.locs.split = dsplit,
- realized.par = realized.par)
- return(return.list)
-# ---------------------------------------------------------
-}# end Function
-# ---------------------------------------------------------
-
-# ---------------------------------------------------------
-# Predict with ST Basis Rotation
-# ---------------------------------------------------------
-# The prediction-sampling functions need to
-# apply the same design transformations that were
-# used on the training data to subsequent prediction
-# designs. Here the "Cartesian" latxlon and Julian date
-# transformation are performed.
-#
-# INPUT:
-# X = (n x p) full design matrix (unrotated)
-# realized.par = c(theta.prime, theta2.prime)
-# rotation parameters
-#
-# OUTPUT:
-# X = (nnn x ppp) newly rotated prediction matrix
-#
-# NOTE
-# -----------
-# response could be made optional parameter,
-# This might be a nice way to deal with
-# response transformations??? Like
-# box-cox parameterization??
-# ----------------------------------------------
-
-
-# ---------------------------------------------------------
-rotate.ST.basis.pred <- function(X, realized.par){
- # ----------------------------------------------------------------------
- # Randomize(Rotate) the predictor.data
- # 7.17.08
- # ----------------------------------------------------------------------
- # Random rotation of "Cartesian" lat-lon plane
- theta.prime <-realized.par[1]
- # Random rotation of Julian Date line, Jan 1
- theta2.prime <- realized.par[2]
- # ---------------------------------
- X$x <- X$x*cos(theta.prime) - X$y*sin(theta.prime)
- X$y <- X$x*sin(theta.prime) + X$y*cos(theta.prime)
- # ------------------------------------------
- X$JDATE <- X$JDATE + theta2.prime
- ttt.ind <- (X$JDATE > 365)
- X$JDATE[ttt.ind] <- X$JDATE[ttt.ind] - 365
- # -------------------------------------------------
- # Cleanup & Return
- # -------------------------------------------------
- return(list(X = X))
-# ---------------------------------------------------------
-}# end Function
-# ---------------------------------------------------------
-
-
-
-
-
-# --------------------------------------------------------
-pop.rpart <- function(filename, ensemble.model.number,ttt.rpart){
- f.rpart <- ttt.rpart
- num.txt <- formatC(ensemble.model.number,format="fg", width=6)
- num.txt <- chartr(" ","0",num.txt)
- temp.filename <- paste(filename,".",num.txt,".RData",sep="")
- load( file=temp.filename) #rpart.parts
- # ----------------------------
- # Reassemble f.rpart from ttt.rpart stub
- # ----------------------------
- f.rpart$frame <- rpart.parts$frame
- f.rpart$where <- rpart.parts$where
- f.rpart$splits <- rpart.parts$splits
- f.rpart$cptable <- rpart.parts$cptable
- if (sum(names(rpart.parts) == "csplit") > 0)
- f.rpart$csplit <- rpart.parts$csplit
-
- return(f.rpart)
-}# end function
-
-
-# ---------------------------------------------------------
-# ---------------------------------------------------------
-# Notes: I need to check the resp.family
-# multiclass has not been added - I have not
-# how to handle the MATRIX of class probablities
-#
-# ** ensemble.pred.matrix - could be a VERY large
-# matrix. There are other strategies for dealing with
-# large data sets. This project is geared towards
-# "mid-sized" data sets.
-#
-#
-# # 3.18.09
-# ----------------------------
-# This the first revision to cut down on memory requirements
-# required when (naively) storing ALL ensmble predictions.
-# Here - store only the first two moments - mean & variance's
-# for baggged/ensemble predictions. There is a formal parameter
-# that can be set to store all predictions, if desired
-# matrix.flag = FALSE
-#
-#
-# ensemble.index = (not implemented yet)
-# optional ordered index of ensemble modelsto use for predictions)
-#
-# -----------------------------------------------------------
-# rpart.object$ frame
-# -----------------------------------------------------------
-# frame = data frame with one row for each node in the tree.
-# row.names of frame contain the (unique) node numbers that
-# follow a binary ordering indexed by node depth.
-# Elements of frame include
-# -----------------
-# * var = factor giving the variable used in the split at each node
-# (leaf nodes are denoted by the string <leaf>),
-# * n = size of each node,
-# * wt = sum of case weights for the node,
-# * dev = deviance of each node,
-# * yval = the fitted value of the response at each node, and
-# * splits = two column matrix of left and right split labels for each node.
-#Also included in the frame are
-# * complexity = complexity parameter at which this split will collapse,
-# * ncompete = number of competitor splits retained, and
-# * nsurrogate, the number of surrogate splits retained.
-# * yval2 = contains the number of events at the node (poisson),
-# or a matrix containing the fitted class, the class counts for
-# each node and the class probabilities (classification).
-# -----------------------------------------------------------
-# ---------------------------------------------------------
-# ---------------------------------------------------------
-# ---------------------------------------------------------
-predict.ST.ensemble <- function(
- filename, # filename of ensemble & index file
- ensemble.par.list,
- prediction.design,
- prediction.design.locs, # required for STEM
- prediction.design.jdates, # required for STEM
- matrix.flag = FALSE)
- #ensemble.index=NULL)
- #...) # pass through model.specific/predict.rpart parameters
-{
-
- # ---------------------------------------------------------
- # Formal Parameter Test Values
- # ---------------------------------------------------------
- # filename <- ensemble.model.filename
- # ensemble.index <- NULL
- # prediction.design <- train.data$X
- # matrix.flag <- FALSE
- # ---------------------------------------------------------
- # Inits
- # ---------------------------------------------------------
- function.call <- match.call()
- # ---------------------------
- # Load Ensemble Information
- # ---------------------------
- # * Number of models in ensemble
- # * ensemble resp.family
- # * realized.sample.par
- # ----------------------------
- n.ensemble.models <- ensemble.par.list$n.ensemble.models
- ensemble.index <- 1:n.ensemble.models
- ensemble.index <- sort(ensemble.index)
- # ------------------
- temp.filename <- paste(filename,".ensemble.index.RData",sep="")
- load(file=temp.filename) #return.list
- ens.realized.par <- return.list$realized.sample.par
- resp.family <- return.list$resp.family
- rm(return.list)
- ## KFW gc()
-# -------------------------
-# Extract Time Intervals
-# DMF - 3.17.10
-# added logic
-# -------------------------
- time.intervals <- sort(unique(ensemble.par.list$design.summary$time.intervals))
- time.interval.vect <- ensemble.par.list$design.summary$time.intervals
- # These two parametes define the time intervals
- # for each unique time interval in the ST ensemble
- # ==> vector of length(time.intervals)
- # ---------------------
- begin.pred.window <- ensemble.par.list$begin.pred.window
- end.pred.window <- ensemble.par.list$end.pred.window
- # -----------------------------------------------------------
- # 3.13.10
- # Instead of looping over all temporal intervals
- # I want to identify the subset of temporal intervals
- # that contain any of the prediction design!!!!
- #
- # This should result in speed ups for many predicitons
- # where the prediction design covers a relatively
- # small interval of times. Eg. ST matrix and ST PD predictions.
- # -----------------------------------------------------------
- ttt.intervals <- rep(FALSE, length(time.intervals))
- for (iii.time in time.intervals){
- winter <- begin.pred.window[iii.time] > end.pred.window[iii.time]
- if (!winter) {
- pd.season.index <- begin.pred.window[iii.time] <=
- prediction.design.jdates &
- prediction.design.jdates <= end.pred.window[iii.time]
- }
- else {
- pd.season.index <- begin.pred.window[iii.time] <=
- prediction.design.jdates |
- prediction.design.jdates <= end.pred.window[iii.time]
- }
- if (sum(pd.season.index) > 0) ttt.intervals[iii.time] <- TRUE
- }
- # Select only the time intervals needed to cover pred.design
- time.intervals <- time.intervals[ttt.intervals]
- # ----------------------------------------
- # Initialize Results/Prediction Vectors
- # ----------------------------------------
- ens.count <- rep(0, nrow(prediction.design))
- ens.moment1<- rep(0, nrow(prediction.design))
- ens.moment2<- rep(0, nrow(prediction.design))
- if (matrix.flag==TRUE){
- ensemble.pred.matrix <- matrix(NA, NROW(prediction.design), NROW(ensemble.par.list$design.summary))
- }
-
- # ----------------------------------------------------------
- # Init: Load First Ensemble Model
- # -----------------------------------------------------------
- iii <- 1
- num.txt <- formatC(iii,format="fg", width=6)
- num.txt <- chartr(" ","0",num.txt)
- temp.filename <- paste(filename,".",num.txt,".RData",sep="")
- load( file=temp.filename)
-
- # Save ensemble rpart.object stub
- ## f.rpart is coming from loaded(RData) objects
- ttt.rpart <- f.rpart
-
- # ----------------------------------------------------------
- # A) Loop Over All Seasons & ID Models within Given Season
- # -----------------------------------------------------------
- for (iii.time in time.intervals){
- seasonal.model.index <- c(1:length(time.interval.vect))[time.interval.vect == iii.time]
- # ----------------------------------------------------------
- # B) Loop over all MODELS in Specified Season &
- # Search for Subset of Data within Prediction Season
- # -----------------------------------------------------------
- for (ensemble.model.number in seasonal.model.index){
- winter <- begin.pred.window[iii.time] > end.pred.window[iii.time]
- if (!winter) {
- pd.season.index <- begin.pred.window[iii.time] <= prediction.design.jdates &
- prediction.design.jdates <= end.pred.window[iii.time]
- }
- else {
- pd.season.index <- begin.pred.window[iii.time] <= prediction.design.jdates |
- prediction.design.jdates <= end.pred.window[iii.time]
- }
- # --------------------------------------------------------
- # 1) Point in Polygon: Are seasonal data in Model Region?
- # --------------------------------------------------------
- if (sum(pd.season.index) > 0){
- # -----------------------------------------------------------
- # Select Region
- # -----------------------------------------------------------
- region.number <- ensemble.par.list$design.summary$region.number[ensemble.model.number]
- region.mc <- ensemble.par.list$design.summary$region.mc[ensemble.model.number]
- t.interval <- ensemble.par.list$design.summary$time.intervals[ensemble.model.number]
- r.index <- (ensemble.par.list$regional.polygons$region.mc == region.mc &
- ensemble.par.list$regional.polygons$region.number == region.number &
- ensemble.par.list$regional.polygons$time.intervals == t.interval )
- # Index into Prediction Design set
- region.given.season.index <- point.in.rectangle(xxx = prediction.design.locs$x[pd.season.index],
- yyy = prediction.design.locs$y[pd.season.index],
- polygon.vertices = ensemble.par.list$regional.polygons[r.index,1:2])
- # --------------------------------------------------------
- # 2) Are there data in ensemble.model.number's REGION-SEASON ?
- # -----------------------------------------------------------
- if (sum(region.given.season.index) > 0){
- # -------------------------------------------------
- # Numeric Indices:
- # superset/parent: Prediction.design
- # subset/child : Regional-Seaonal data set
- # -------------------------------------------------
- seasonal.num.ind <- c(1:length(pd.season.index))[pd.season.index]
- reg.sea.num.ind <- seasonal.num.ind[region.given.season.index]
- # -------------------------------
- # Regional-seasonal design
- # ------------------------------
- X.pred <- prediction.design[ reg.sea.num.ind, ]
- # -------------------------------------------------
- # check for Design Transformations, e.g. for basis rotation
- # -------------------------------------------------
- if (ensemble.par.list$sampling.par.list$ST.basis.rotation == TRUE){
- ttt <- rotate.ST.basis.pred(X = X.pred, realized.par=ens.realized.par[,ensemble.model.number])
- X.pred <- ttt$X
- rm(ttt)
- ## KFW gc()
- }
- # ----------------------------------------------------------
- # Load/Construct rpart.object
- # -----------------------------------------------------------
-
- if (ensemble.model.number != 1){
- # ---------------------------------
- # 5.20.09
- # Adding Error Trapping code
- # to deal with the following mysterious message
- # Error in f.rpart$frame <- rpart.parts$frame :
- # value of 'SET_ATTRIB' must be a pairlist or NULL, not a 'character'
- # ---------------------------------
- f.rpart <- try( pop.rpart(filename, ensemble.model.number, ttt.rpart) )
- # If there is an error, try it again
- if (class(f.rpart) == "try-error") {
- cat("rpart file read error \n")
- f.rpart <- try( pop.rpart(filename, ensemble.model.number, ttt.rpart) )
- }
- } # end ensemble.model.number != 1
- else {
- f.rpart <- ttt.rpart
- }
-
- # -------------------------------------------------
- # rpart Predict
- # ------------------
- # Note: the predict method for rpart will
- # not make a prediction on a root node only.
- # That is, if the rpart model is only a root node
- # then I need to skip the call to predict - will generate an error
- # and manually assign all pts the same prediction.
- # --------------------
- # 4.9.09
- # Separate out case when bernoulli because
- # it requires slightly different call to deal with two classes.
- # -------------------------------------------------
- #NROW(f.rpart$frame)
- if (NROW(f.rpart$frame) == 1) {
- if (resp.family == "bernoulli"){
- # yval is the predicted response
- # In the two class problem, the assumed coding is
- # a factor with levels "FALSE" and "TRUE".
- # rpart orders these alphabetically, so
- # The first class: FALSE
- # The second class: TRUE
- # So, if yval are predicted prob for the first class
- # i.e. FALSE, then I want to use 1-yval as the predicted value
- # -------------------------------------------------------------
- ttt.rpart.pred <- rep((1-f.rpart$frame$yval), NROW(X.pred))
- }
- if (resp.family =="gaussian"){
- ttt.rpart.pred <- rep(f.rpart$frame$yval, NROW(X.pred))
- }# end gaussian
- } #end stump predictions section
- # ------------------------------------------
- # If there is more than just the root node
- # ------------------------------------------
- if (NROW(f.rpart$frame) > 1) {
- if (resp.family=="gaussian"){
- ttt.rpart.pred <- predict(f.rpart,newdata=X.pred) # ...)
- }
- if (resp.family=="bernoulli"){
- ## ttt.rpart.pred.bern <- predict(f.rpart,newdata=X.pred, type="prob")
-
- tryCatch ({
- x.pred.attributes <- attributes(X.pred)
- f.rpart.attributes <- attributes(f.rpart)
-
- ## print("start of X.pred attributes")
- ## print(x.pred.attributes)
- ## print("end of X.pred attributes")
-
- if (is.null(x.pred.attributes)) {
- print("**** NULL X.pred attributes ***")
- }
-
- if (is.null(f.rpart.attributes)) {
- print("**** NULL X.pred attributes ***")
- }
-
-
- ## print("start of f.rpart attributes")
- ## print(f.rpart.attributes)
- ## print("end of f.rpart attributes")
- ## print(f.rpart)
- ## print("======= before predict() ==================================================")
-
- ttt.rpart.pred.bern <- predict(f.rpart,newdata=X.pred, type="prob");
-
- ## print("after predict()")
- },
- error = function(ex) {
- print("***** KFW start of catch block")
-
- x.pred.attributes <- attributes(X.pred)
- f.rpart.attributes <- attributes(f.rpart)
-
- print("start of X.pred attributes")
- print(x.pred.attributes)
- print("end of X.pred attributes")
- print("start of f.rpart attributes")
- print(f.rpart.attributes)
- print("end of f.rpart attributes")
- print(f.rpart)
- print("=========================================================")
-
- ##
- ## print("---- prediction.design ---")
- ##
- ## print(nrow(prediction.design))
- ## print(ncol(prediction.design))
- ##
- ## for (colIndex in 1:ncol(prediction.design)) {
- ## message <- paste(colIndex, class(prediction.design[,colIndex]), sep=" ")
- ## print(message)
- ## }
- ##
- ##
- stop("ERROR - bailing out!")
- },
- finally = {
- })
-
- ttt.rpart.pred <- ttt.rpart.pred.bern[,2]
- }
- if (resp.family=="poisson") {
- ttt.rpart.pred <- predict(f.rpart,newdata=X.pred,type="vector") #,...)
- }
- }
-
- #---------------------------------------------------------------
- # 3. Accumulate Predictions
- # --------------------------------------------------------------
- ens.count[reg.sea.num.ind] <- ens.count[reg.sea.num.ind] + 1
- ens.moment1[reg.sea.num.ind] <- ens.moment1[reg.sea.num.ind] + ttt.rpart.pred
- ens.moment2[reg.sea.num.ind] <- ens.moment2[reg.sea.num.ind] + ttt.rpart.pred^2
- # ----------------------------
- # nrow = NROW(prediction.design)
- # ncol = number models in ensemble models
- # ----------------------------
- if (matrix.flag == TRUE){
- ensemble.pred.matrix[reg.sea.num.ind,ensemble.model.number] <- ttt.rpart.pred
- }
-
- rm(X.pred)
- } # End REGION-SEASON Prediction
- } # if data in REGION-SEASON subset
-
- ## KFW gc()
- } # end loop over Seasonal ensemble models
- } # end time interval loop
-
- # ----------------------------------------------------------
- # Return Prediction Matrix
- # -----------------------------------------------------------
- # 3.18.09 Modifications
- # -----------------------------------
- ens.mean <- rep(NA, NROW(prediction.design))
- ens.var <- rep(NA, NROW(prediction.design))
- na.ind <- (ens.count > 0)
- ens.mean[na.ind] <- ens.moment1[na.ind]/ens.count[na.ind]
- na.ind2 <- (ens.count >= 2)
- ens.var[na.ind2] <- ens.moment2[na.ind2]/ (ens.count[na.ind2] -1) -
- (ens.mean[na.ind2]^2)*(ens.count[na.ind2])/(ens.count[na.ind2] -1)
-
- if (matrix.flag == TRUE) {
- return.list <- list(
- mean = ens.mean,
- sd = sqrt(ens.var),
- count = ens.count,
- matrix = ensemble.pred.matrix,
- function.call = function.call)
- }
- else {
- return.list <- list(
- mean = ens.mean,
- sd = sqrt(ens.var),
- count = ens.count,
- function.call = function.call)
- }
-
- if (matrix.flag==TRUE){
- rm(ensemble.pred.matrix)
- }
-
- ## kfw gc()
-
- return(return.list)
-}# End FUNCTION
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-
-
-
-
-
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-# BS.RPART Random Space-Time Prediction Function
-# --------------------------------------------------------------------------
-# 1.15.07
-# 7.16.08 - quick & dirty modifications to take into
-# account basis rotations performed in the function
-# ST.BDT.test (located in this file)
-# 1.8.09 - reorganization
-#
-# This function performs two related tasks:
-#
-# 1) Predictor Conditioning
-# 2) Time-Slice Predictions
-#
-# Predictor Conditioning:
-# -----------------------------
-# For many prediction tasks it is necessary to assign constant
-# values to certain predictors. E.g. constructing a prediction
-# design to control for observation effort - by seting effort constant.
-# The conditioning variables and corresponding values are defined
-# in the conditioning.vars list. If the conditioning variable is not
-# present in the predictor.design data frame, it will be added.
-#
-# Time-Slice predictions.
-# ----------------------------
-# We loop though all time slices (defined by julian date AND year)
-# and make the full set of (spatial) predictions. This simple looping
-# proceedure was designed to handle large prediction vectors.
-# For this reason, we decided to cycle throught each ensemble model
-# for EACH time slice. This takes more time to load and reload all
-# of the models, but requires less memory to hold the predictions
-# for ALL time slices simultaneously.
-#
-# The results, i.e. the prediction vectors, are saved into sequentially
-# numbered files, in the same order as the temporal sequence.
-#
-# Like the other functions I am writing, I will begin by keeping
-# this as simple as possible. KISS!!
-#
-# INPUT
-# ------------
-# predictor.design <- data frame of predictors. Including YEAR, JDATE,
-# and the conditioning variables, this should have
-# the same number of predictors are the
-# predictors used in the models.
-# --------------
-# information about the ensemble models
-# ------------------------------------
-# model.predictor.names,
-# bs.rpart.name,
-# bs.rpart.dir,
-# btrials,
-# Save Results to directory and name
-# # --------------
-# save.name,
-# save.dir,
-# Define Temporal Sequence
-# ** jdate.seq and year.seq must be of the same length
-# the code cycles through all pairs of values.
-# jdate.seq,
-# year.seq,
-# Conditioning Variable List - This is how we control for the Observation
-# process.
-# conditioning.vars = NULL
-#
-# OUTPUT
-# ------------
-# call = call,
-# # Saved predictions
-# save.name=save.name,
-# save.dir=save.dir,
-# # Temporal Sequence
-# jdate.seq=jdate.seq,
-# year.seq = year.seq)
-#
-# To do:
-# ---------
-# I need to describe the format of D.pred in detail so that I can
-# generate new sets. Part of this will be to point to/describe the
-# process that Roger and I went through to generate this data.
-#
-# A simple way to do this is to pass the dtm object which
-# should include the names of the predictors!
-# It will also include the bs.trial, and the bs.path and file
-# name information!!!
-#
-# ERROR occurs when there is a predictor.name in "model.predictor.names"
-# but that predictor does not occurr in predictor.design or the
-# conditioning variables. should this happen?
-# If so, I should pass a more intelligible error message to the user.
-#
-# NOTE:
-# When model predicts an NA (e.g. STEM does this when location
-# has no support , i.e. an extrapolation) then this function
-#will just pass NA's through $mean & $sd
-#
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-predict.st.matrix <- function(
- prediction.design,
- prediction.design.locs,
- #prediction.design.jdates = NULL, # required for STEM
- #--------------
- model.predictor.names,
- model.filename,
- ensemble.par.list,
- # --------------
- save.name,
- # Temporal Sequence
- jdate.seq,
- year.seq,
- # Conditioning Vars - Observation Process Design
- conditioning.vars = NULL){
-# ---------------------------------------------------
-# prediction.design = pred.data$D.pred
-# prediction.design.locs = pred.data$locs
-# #--------------
-# model.predictor.names = names(train.data$X)
-# model.filename = ensemble.model.filename
-# ensemble.par.list = ensemble.par.list
-# # --------------
-# save.name = st.pred.filename
-# # Temporal Sequence
-# jdate.seq =jdate.seq
-# year.seq =year.seq
-# # Conditioning Vars - Observation Process Design
-# conditioning.vars = conditioning.vars
-# ---------------------------------------------------------
-# Inits
-# ---------------------------------------------------------
- function.call <- match.call()
-## ------------------------------------------------------------------------
-# Assign and/or Add Conditioning variables as necessary
-# Verified for class numeric
-# Check to make sure that this works with factors -
-# especially if the conditioning value is a level
-# that has NOT been used for training!!!
-# ------------------------------------------------------------------------
- for (iii in 1:length(conditioning.vars)) {
- # When conditioning predictor is already in predictor.design
- if (names(conditioning.vars)[iii] %in% names(prediction.design) ) {
- pred.index <- names(prediction.design) %in% names(conditioning.vars)[iii]
- prediction.design[ , pred.index] <- conditioning.vars[[iii]]
- }
- # When conditioning predictor is NOT in predictor.design
- if (!(names(conditioning.vars)[iii] %in% names(prediction.design) )) {
- ttt.names <- names(prediction.design)
- ttt <- matrix(conditioning.vars[[iii]], NROW(prediction.design),1)
- prediction.design <- data.frame(prediction.design, ttt)
- names(prediction.design) <- c(ttt.names,
- names(conditioning.vars)[iii])
- }
- } # end iii
-
-# ------------------------------------------------------------------------
-# Check to see if any model.predictor.names are missing from predictor.design
-# ------------------------------------------------------------------------
- # ID predictors in the predictor.design but not in the model.predictors
- #setdiff(names(prediction.design), model.predictor.names)
- # These are OK, just extraneous
- # and the other way around
- #setdiff(model.predictor.names,names(prediction.design))
- # year and jdate are OK here, but anything else needs to be flagged
-
-# --------------------------------------------------------------------------
-# Loop over dates in design & make predicitons
-# --------------------------------------------------------------------------
- for (iii in 1:length(jdate.seq)){
- # Set prediction design jdate
- prediction.design.jdates <- rep(jdate.seq[iii],NROW(prediction.design))
- # Check for predictors called JDATES & YEARS
- # If so, then impute prediction design values
- # ----------------------------------------------
- if ( c("JDATE") %in% model.predictor.names )
- prediction.design$JDATE <- rep(jdate.seq[iii],NROW(prediction.design))
- if ( c("YEAR") %in% model.predictor.names )
- prediction.design$YEAR <- rep(year.seq[iii],NROW(prediction.design))
- # -----------------------------------------------
- # Ensemble predictions
- # -----------------------------------------------
- #pred.Xp <- ensemble.par.list$predict.ensemble.function(
- # filename = model.filename,
- # ensemble.par.list =ensemble.par.list,
- # prediction.design=predictor.design)
- # --------------------------------------
- pred.Xp <- predict.ST.ensemble(
- filename = model.filename,
- ensemble.par.list,
- prediction.design=prediction.design,
- prediction.design.locs=prediction.design.locs, # required for STEM
- prediction.design.jdates=prediction.design.jdates, # required for STEM
- matrix.flag = FALSE)
- # --------------------------------------------------------------------------
- # Save predictions to files
- # --------------------------------------------------------------------------
- save.filename <- paste(save.name,".",iii,".RData",sep="")
- st.pred <- data.frame(
- xxx = prediction.design.locs$x,
- yyy = prediction.design.locs$y,
- pred = pred.Xp$mean,
- sd = pred.Xp$sd)
- save(st.pred, file=save.filename) # st.pred
- # Compare to dput or other methods to see if
- # there is a size advantage
- # ----------------------------------------------------
- } # end iii loop
-
- # ------------------------------------------------------------
- # Return Values
- # ------------------------------------------------------------
- return(function.call)
-} # end function
-# --------------------------------------------------------------------------------------------
-# -------------------------------------------------------------------------------------------
-
-
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-# Modify predict.st.matrix from stem.library.8.18.09.R
-# by
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-predict.st.matrix.ebird.ref.data <- function(
- prediction.design,
- prediction.design.locs,
- #prediction.design.jdates = NULL, # required for STEM
- #--------------
- model.predictor.names,
- model.filename,
- ensemble.par.list,
- # --------------
- save.name,
- # Temporal Sequence
- jdate.seq,
- year.seq,
- # Conditioning Vars - Observation Process Design
- conditioning.vars = NULL){
-# ---------------------------------------------------
-# prediction.design = pred.data$D.pred
-# prediction.design.locs = pred.data$locs
-# #--------------
-# model.predictor.names = names(train.data$X)
-# model.filename = ensemble.model.filename
-# ensemble.par.list = ensemble.par.list
-# # --------------
-# save.name = st.pred.filename
-# # Temporal Sequence
-# jdate.seq =jdate.seq
-# year.seq =year.seq
-# # Conditioning Vars - Observation Process Design
-# conditioning.vars = conditioning.vars
-# ---------------------------------------------------------
-# Inits
-# ---------------------------------------------------------
- function.call <- match.call()
-# ------------------------------------------------------------------------
-# Assign and/or Add Conditioning variables as necessary
-# Verified for class numeric
-# Check to make sure that this works with factors -
-# especially if the conditioning value is a level
-# that has NOT been used for training!!!
-# ------------------------------------------------------------------------
- for (iii in 1:length(conditioning.vars)) {
- # When conditioning predictor is already in predictor.design
- if (names(conditioning.vars)[iii] %in% names(prediction.design) ) {
- pred.index <- names(prediction.design) %in% names(conditioning.vars)[iii]
- prediction.design[ , pred.index] <- conditioning.vars[[iii]]
- }
- # When conditioning predictor is NOT in predictor.design
- if (!(names(conditioning.vars)[iii] %in% names(prediction.design) )) {
- ttt.names <- names(prediction.design)
- ttt <- matrix(conditioning.vars[[iii]], NROW(prediction.design),1)
- prediction.design <- data.frame(prediction.design, ttt)
- names(prediction.design) <- c(ttt.names,
- names(conditioning.vars)[iii])
- }
- } # end iii
-
-# ------------------------------------------------------------------------
-# Check to see if any model.predictor.names are missing from predictor.design
-# ------------------------------------------------------------------------
- # ID predictors in the predictor.design but not in the model.predictors
- #setdiff(names(prediction.design), model.predictor.names)
- # These are OK, just extraneous
- # and the other way around
- #setdiff(model.predictor.names,names(prediction.design))
- # year and jdate are OK here, but anything else needs to be flagged
-
- ## KFW
- ## vegetationIndexData <- read.csv(file="ebird_reference_data/processed_VI_Data_SRD.csv", na.strings = c("NA", "?"))
- ## KFW
-
-# --------------------------------------------------------------------------
-# Loop over dates in design & make predicitons
-# --------------------------------------------------------------------------
- for (iii in 1:length(jdate.seq)){
- # Set prediction design jdate
- prediction.design.jdates <- rep(jdate.seq[iii],NROW(prediction.design))
- # Check for predictors called JDATES & YEARS
- # If so, then impute prediction design values
- # ----------------------------------------------
- if ( c("DAY") %in% model.predictor.names )
- prediction.design$DAY <- rep(jdate.seq[iii],NROW(prediction.design))
- if ( c("YEAR") %in% model.predictor.names )
- prediction.design$YEAR <- rep(year.seq[iii],NROW(prediction.design))
-
- # ----------------------------------------------------------------------------------------------------------------------
- # 8.18.09
- # -----------------
- # check for special ebird reference data predictors called
- # "caus_temp_avg" "caus_temp_min"
- #[15] "caus_temp_max" "caus_prec"
- #[17] "caus_snow"
- #each of these records the climate variable value ( e.g. snow depth )
- # for month in which observation was made. so, here i
- # will assume that the requisite us climate are available and then
- # select the approtiate month for the
- # corresponding prediction design "observation".
- # ----------------------------------------------
- if ( "CAUS_TEMP_AVG" %in% model.predictor.names ) {
- month.index <- floor(jdate.seq[iii] / (366/12))+1
- num.txt <- formatC(month.index, format="fg",width=2)
- num.txt <- chartr(" ","0",num.txt)
- ttt.pred.name <- paste("CAUS_TEMP_AVG", num.txt,sep="")
- ## KFW prediction.design$CAUS_TEMP_AVG <-
- ## KFW prediction.design[ , names(prediction.design) %in% ttt.pred.name]
-
- prediction.design$CAUS_TEMP_AVG <-
- as.numeric(prediction.design[ , names(prediction.design) %in% ttt.pred.name])
- } # end if
- if ( "CAUS_TEMP_MIN" %in% model.predictor.names ) {
- month.index <- floor(jdate.seq[iii] / (366/12))+1
- num.txt <- formatC(month.index, format="fg",width=2)
- num.txt <- chartr(" ","0",num.txt)
- ttt.pred.name <- paste("CAUS_TEMP_MIN", num.txt,sep="")
- ## KFW prediction.design$CAUS_TEMP_MIN <-
- ## KFW prediction.design[ , names(prediction.design) %in% ttt.pred.name]
-
- prediction.design$CAUS_TEMP_MIN <-
- as.numeric(prediction.design[ , names(prediction.design) %in% ttt.pred.name])
- } # end if
- if ( "CAUS_TEMP_MAX" %in% model.predictor.names ) {
- month.index <- floor(jdate.seq[iii] / (366/12))+1
- num.txt <- formatC(month.index, format="fg",width=2)
- num.txt <- chartr(" ","0",num.txt)
- ttt.pred.name <- paste("CAUS_TEMP_MAX", num.txt,sep="")
- ## KFW prediction.design$CAUS_TEMP_MAX <-
- ## KFW prediction.design[ , names(prediction.design) %in% ttt.pred.name]
-
- prediction.design$CAUS_TEMP_MAX <-
- as.numeric(prediction.design[ , names(prediction.design) %in% ttt.pred.name])
- } # end if
- if ( "CAUS_PREC" %in% model.predictor.names ) {
- month.index <- floor(jdate.seq[iii] / (366/12))+1
- num.txt <- formatC(month.index, format="fg",width=2)
- num.txt <- chartr(" ","0",num.txt)
- ttt.pred.name <- paste("CAUS_PREC", num.txt,sep="")
- ## KFW prediction.design$CAUS_PREC <-
- ## KFW prediction.design[ , names(prediction.design) %in% ttt.pred.name]
-
- prediction.design$CAUS_PREC <-
- as.numeric(prediction.design[ , names(prediction.design) %in% ttt.pred.name])
- } # end if
- if ( "CAUS_SNOW" %in% model.predictor.names ) {
- month.index <- floor(jdate.seq[iii] / (366/12))+1
- num.txt <- formatC(month.index, format="fg",width=2)
- num.txt <- chartr(" ","0",num.txt)
- ttt.pred.name <- paste("CAUS_SNOW", num.txt,sep="")
- # Check for Mean snow depth May - Sept
- snow.check <- month.index >=5 & month.index <=9
- if (snow.check) ttt.pred <- rep(0,NROW(prediction.design))
- if (!snow.check) ttt.pred <-
- prediction.design[ , names(prediction.design) %in% ttt.pred.name]
- ## KFW prediction.design$CAUS_SNOW <- ttt.pred
-
- prediction.design$CAUS_SNOW <- as.numeric(ttt.pred)
- } # end if
-
-
- ## KFW
- if ( "NDVI" %in% model.predictor.names ) {
- ## viDataRecordMask <- vegetationIndexData$YEAR == year.seq[iii] &
- ## vegetationIndexData$DAY == jdate.seq[iii]
-
- ## prediction.design$NDVI <- as.numeric(vegetationIndexData$NDVI[viDataRecordMask])
-
- viDataRecordMask <- vegetationIndexData[,3] == year.seq[iii] &
- vegetationIndexData[,4] == jdate.seq[iii]
-
- prediction.design$NDVI <- as.numeric(vegetationIndexData[viDataRecordMask, 5])
-
-
- ## print(year.seq[iii])
- ## print(jdate.seq[iii])
- ## print(prediction.design$NDVI)
-
- rm(viDataRecordMask)
- }
-
- if ( "EVI" %in% model.predictor.names ) {
- viDataRecordMask <- vegetationIndexData$YEAR == year.seq[iii] &
- vegetationIndexData$DAY == jdate.seq[iii]
-
- prediction.design$EVI <- as.numeric(vegetationIndexData$EVI[viDataRecordMask])
-
- rm(viDataRecordMask)
- }
- ## KFW
-
-
- # -----------------------------------------------
- # Ensemble predictions
- # -----------------------------------------------
- #pred.Xp <- ensemble.par.list$predict.ensemble.function(
- # filename = model.filename,
- # ensemble.par.list =ensemble.par.list,
- # prediction.design=predictor.design)
- # --------------------------------------
-
-
- ## print("predict.st.matrix.ebird.ref.data() calling predict.ST.ensemble()")
-
- pred.Xp <- predict.ST.ensemble(
- filename = model.filename,
- ensemble.par.list,
- prediction.design=prediction.design,
- prediction.design.locs=prediction.design.locs, # required for STEM
- prediction.design.jdates=prediction.design.jdates, # required for STEM
- matrix.flag = FALSE)
- # --------------------------------------------------------------------------
- # Save predictions to files
- # --------------------------------------------------------------------------
- save.filename <- paste(save.name,".",iii,".RData",sep="")
- st.pred <- data.frame(
- xxx = prediction.design.locs$x,
- yyy = prediction.design.locs$y,
- pred = pred.Xp$mean,
- sd = pred.Xp$sd)
- save(st.pred, file=save.filename) # st.pred
- # Compare to dput or other methods to see if
- # there is a size advantage
- # ----------------------------------------------------
- } # end iii loop
-
- # ------------------------------------------------------------
- # Return Values
- # ------------------------------------------------------------
- return(st.pred)
-} # end function
-# --------------------------------------------------------------------------------------------
-# -------------------------------------------------------------------------------------------
-
-
-
-# -------------------------------------------------------------------
-# Predict.pd.grid - Function to make Predictions over PD.grids
-# -------------------------------------------------------------------
-# Input
-# XX = DTM Design matrix
-# pd.quant.grids = create.pd.grid obejct
-# nn.sample = # of randomly selected samples from XX
-# Output
-# list of predictions for each member of the create.pd.grid.object
-#
-# 5.4.09
-# --------------------------------
-# ** Got rid of "matrix" object - only using mean
-# ** STEM additions
-# construct updated prediction.design.locs & prediction.design.jdate
-# ** break appart & sum over nn.sample
-# ** added logic to deal with PD of JDATE and (x,y) locs
-#
-# TO DO:
-# --------------------------------
-# ** collect PD sd estimates!
-# ** Need to Recode Categorical predictors
-# eg. if BCR was a predictor we would need to recode it
-# to its proper level labels !!!!!
-# Currently, BCR is coded as the number of the LEVEL
-# xxx.grid[,2] <- levels(train.data$X$BCR)[xxx.grid[,2]]
-# ** 2.26.10
-# I need to take a single random sample
-# of size nn.sample from an index of length == nrows(prediction.design)
-# then add to it over the batch "samples".
-# This instead of the multiple samples taken one batch at a time.
-# ------------------------------------------------------------------------------------------------------
-# ------------------------------------------------------------------------------------------------------
-STEM.partial.dependence <- function(
- filename,
- ensemble.par.list,
- prediction.design, #XX,
- prediction.design.locs, # required for STEM
- prediction.design.jdates, # required for STEM
- partial.dependence.list,
- continuous.resolution = 15,
- nn.sample = 200,
- batch.size =50 )
-{ # ----------------------------------------------------------------------------------------------------
-# ------------------------------------------------------------------------------------------------------
-# Test Formal Parameters
-# ------------------------------------------------------------------------------------------------------
-# pd.list <- list(
-# "NLCD01_N90A100R5", "JDATE",
-# # 2D Partials
-# c("x", "y"), # lat x lon interaction
-# c("JDATE", "NLCD01_N90A100R5")) # can we pick up change in time of sunrise?
-# filename = ensemble.model.filename
-# ensemble.par.list = ensemble.par.list
-# #XX = train.data$X,
-# prediction.design=train.data$X #XX,
-# prediction.design.locs=ensemble.par.list$ensemble.data.locs # required for STEM
-# prediction.design.jdates=ensemble.par.list$ensemble.data.jdates # required for STEM
-# partial.dependence.list=pd.list
-# continuous.resolution = 30
-# nn.sample = 500
-# batch.size = 50
-# ------------------------------------------------------------------------------------------------------
-# Inits Formal Parameters
-# ------------------------------------------------------------------------------------------------------
- #temp.filename <- paste(filename,".ensemble.index.RData",sep="")
- #load(file=temp.filename) #return.list
- #bs.trials <- NCOL(return.list$ib.sample.index)
- # Results
- XX <- prediction.design
- pd.means <- vector(mode="list", length=length(partial.dependence.list))
- pd.matrices <- vector(mode="list", length=length(partial.dependence.list))
-# ------------------------------------------------------------------------------------------------------
-# Compute Partial Dependence Quantile Grids
-# ------------------------------------------------------------------------------------------------------
- pd.quant.grids <- create.pd.grid(
- XX=XX,
- i.var.list=partial.dependence.list,
- continuous.resolution = continuous.resolution)
-# ------------------------------------------------------------------------------------------------------
-# Find factors in XX
-# Note : I can not use apply b/c XX is class data.frame
-# ------------------------------------------------------------------------------------------------------
- XX.factor.ind <- rep(FALSE, NCOL(XX))
- ttt <- XX[1,] # it is much faster to search a 1D data.frame!
- for (ii in 1:NCOL(XX)) XX.factor.ind[ii] <- is.factor(ttt[,ii])
- # Extract an index of column positions for factors (wo zeros!)
- factor.index <- as.numeric(XX.factor.ind)*seq(1,NCOL(XX))
- factor.index <- factor.index[factor.index > 0 ]
-# ------------------------------------------------------------------------------------------------------
-# Loop Over PD list elements
-# ------------------------------------------------------------------------------------------------------
-for (iii in 1:length(pd.quant.grids)){
- # Initialize Batch Result Vectors
- ppp.batch <- 0
- ppp.batch.count <- 0
- # Calculate # of Batch Loops
- nnn.batch <- floor(nn.sample/batch.size) +
- as.numeric(ceiling(nn.sample/batch.size) >
- floor(nn.sample/batch.size))
-# Begin Batch loop Here
-# -------------------------------
-for ( iii.batch in 1:nnn.batch){
-# -------------------------------
- batch.sample.size <- min(batch.size, (nn.sample - (iii.batch-1)*batch.size))
- # ------------------------------------------------------------------------------------------------------
- # Random Sample of Data Rows (same sample for all PD elements)
- # ------------------------------------------------------------------------------------------------------
- # Sample without replacement from data rows
- if (batch.sample.size >= NROW(XX))
- sample.index <- sample(1:NROW(XX), batch.sample.size, replace = TRUE)
- if (batch.sample.size < NROW(XX))
- sample.index <- sample(1:NROW(XX), batch.sample.size, replace = FALSE)
- #dim(XX.sample)
- # ------------------------------------
- # 1. Expand Quantile Grid into PD Prediction Design
- # 2. BDT Predictions
- # 3. Assemble Results
- # ------------------------------------
- i.var <- match( names(pd.quant.grids[[iii]]), names(XX))
- XX.sample <- XX[sample.index, setdiff(names(XX), names(XX)[i.var]) ]
- pd.grid <- pd.quant.grids[[iii]]
- # ----------------------------
- # NOTE** PD design can get big = batch.sample.size * length(pd.grid)
- # ------------------------------------------------------------------------------------------------------
- # Construct Partial Dependence Prediction Data Frame
- # NOTE: the use of data.matrix converts factors to numerics
- # ------------------------------------------------------------------------------------------------------
- # Stack Randomly Sampled Data Rows
- XX.stack <- kronecker( matrix(1, NROW(pd.grid), 1),
- data.matrix(XX.sample))
- XX.stack <- as.data.frame(XX.stack)
- names(XX.stack) <- names(XX.sample)
- # Stack Partial Dependence Grids
- pd.stack <- kronecker( data.matrix(pd.grid), matrix(1, batch.sample.size, 1))
- pd.stack <- as.data.frame(pd.stack)
- names(pd.stack) <- names(pd.grid)
- PD.prediction.frame <- cbind(pd.stack,XX.stack)
- # -------------------------------------------
- # Stack Location & JDATE indices
- # Stack Randomly Sampled Data Rows
- XX.locs.sample <- prediction.design.locs[sample.index,]
- XX.locs.stack <- kronecker( matrix(1, NROW(pd.grid), 1),
- data.matrix(XX.locs.sample))
- XX.locs.stack <- as.data.frame(XX.locs.stack)
- names(XX.locs.stack) <- names(XX.locs.sample)
- # -----------
- XX.jdates.sample <- prediction.design.jdates[sample.index]
- XX.jdates.stack <- kronecker( matrix(1, NROW(pd.grid), 1),
- data.matrix(XX.jdates.sample))
- # -------------------------------------------
- # **** Check to see if i.var is an index variable.
- # Currently the ST index variable names are hardcoded to " x, y, or JDATE "
- #
- # modified 10.20.09
- #
- # If so, then modify parameter indices accordingly
- # ** Check out the flexible logic - this will work
- # for any pd.list!
- # -------------------------------------------
- # if ("DAY" %in% names(XX)[i.var]) XX.jdates.stack <- pd.stack$DAY
- # if ("x" %in% names(XX)[i.var]) XX.locs.stack[,1] <- pd.stack$x
- # if ("y" %in% names(XX)[i.var]) XX.locs.stack[,2] <- pd.stack$y
- # modified 02.17.10
- # -------------------
- # With the separate index variables, there is no need to
- # treat them specially, whether or not the same index
- # variables are used as predictors.
- # Therefore, I removed the lines above.
-
-
- # ------------------------------------------------------------------------------------------------------
- # Reconstruct Factor structure for data.frame
- # ------------------------------------------------------------------------------------------------------
- # XX = original data frame that may include factors
- # PD.prediction.frame = the data.frame currently with numeric
- # values for all predictors. The prediction data.frame needs
- # to have the same column/predictor structure as XX
- # ------------------------------------------------
- # 1) Reorder PD.prediction.frame to match XX
- col.order <- match( names(XX), names(PD.prediction.frame))
- PD.prediction.frame <- PD.prediction.frame[,col.order]
- # 2) Convert PD.prediction.frame cols to factors
- for (i in factor.index) {
- PD.prediction.frame[,i] <-
- factor(levels(XX[,i])[PD.prediction.frame[,i]],
- levels=levels(XX[,i]))
- }
- # ------------------------------------------------------------------------------------------------------
- # Ensemble PD Predictions
- # ------------------------------------------------------------------------------------------------------
- ttt.pred <- predict.ST.ensemble(
- filename= filename, # filename of ensemble & index file
- ensemble.par.list = ensemble.par.list,
- prediction.design= PD.prediction.frame,
- prediction.design.locs=XX.locs.stack, # required for STEM
- prediction.design.jdates=XX.jdates.stack, # required for STEM
- matrix.flag = FALSE)
- pred.X <- ttt.pred$mean
- # --------------------------------------------
- # Average to get Ensemble average PD estimates
- # --------------------------------------------
- pred.index <- (rep(c(1:NROW(pd.grid)),each=batch.sample.size))
- ppp <- tapply(pred.X, pred.index, sum, na.rm=T)
- ppp.count <- tapply(!is.na(pred.X), pred.index, sum, na.rm=T)
- # ---------------------------------
- # Collect the mean (first moment + count)
- # across batch of partial prediction jobs
- # ---------------------------------
- ppp.batch <- ppp.batch + ppp
- ppp.batch.count <- ppp.batch.count + ppp.count
- # ---------------------------------
- # 2.26.10 Cleanup
- # (incomplete)
- # ---------------------------------
- rm(ttt.pred, XX.stack,pd.stack,PD.prediction.frame,
- XX.locs.stack, XX.jdates.stack)
- ## KFW gc()
-
-# end Batch loop Here
-# -------------------------
-} # end iii.batch
-# -------------------------
- if (sum(ppp.batch.count==0) > 0)
- warning(paste("STEM.partial.dependence: unsupported",
- "partial predictions, ppp.batch.count==0 "))
- # Calculate Mean Value and Final Count(support)
- ppp <- ppp.batch/ppp.batch.count
- # -------------------------------
- # recode pd.grid factors
- f.factor <- rep(FALSE, NCOL(pd.grid))
- for (i in 1:NCOL(pd.grid)) {
- col.index <- match( names(pd.grid)[i], names(XX))
- if (!is.numeric( XX[,col.index] )) {
- f.factor[i] <- TRUE
- #if (names(pd.grid[i]) %in% names(XX)[factor.index])
- pd.grid[,i] <-
- factor(levels(XX[,col.index])[pd.grid[,i]],
- levels=levels(XX[,col.index]))}
- } #end for i - search for factors
- # Reassociate pd.grid with predictions
- pdf.grid <- data.frame(pd.grid, pred=ppp)
- # -----------------------------------
- # Store results in PD.list
- # -----------------------------------
- # pd.means = the Partial Dependence Estimate averaged over bags
- # pd.matrices = the PD estimates, one col per bag/model
- pd.means[[iii]] <- pdf.grid
- #pd.matrices[[iii]] <- pdf.grid.matrix
- #names(pdf.grid)
- #dim(pdf.grid)
-} # end iii
-# -----------------
-return(list(
- pd.quant.grids=pd.quant.grids,
- pd.means=pd.means))
- #pd.matrices=pd.matrices))
-} # end function
-# -------------------------------------------------------------------
-# ---------------------------------------------------------------------
-
-
-
-
-# ---------------------------------------------------------------------------------------------------------------------
-# Plot STEM Temporal Design
-# ---------------------------------------------------------------------------------------------------------------------
-plot.STEM.temporal.design<- function(
- ensemble.par.list)
- #ensemble.data,
- #mc.region.x.time.index=1, # value of nnn.spatial.mc)
- #...) # pass through plotting parameters?
-{# ---------------------------------------------------------
- #ensemble.par.list
- p.min <- -1.5
- p.max <- 1.5
- # -----------------------------------------------------
- # Central Julian Calendar Circle
- # ------------------------------------------------------
- nnn <- 1000
- radian.seq <- seq(from=0, to=2*pi, length=nnn)
- plot( cos(radian.seq),
- sin(radian.seq),
- type="l",
- lwd=3.0,
- xlab=" ",
- ylab=" ",
- xlim = c(p.min,p.max),
- ylim = c(p.min, p.max),
- axes = FALSE)
- # ---------------------------------------------------------
- # Convert Temporal Sequence times to POSIX
- # ---------------------------------------------------------
- #text( -.25, .75,
- # pos=4, # text is to the left of location
- # cex = 1.5,
- # labels=c("Dec/Jan") )
- # Add notches at 3,6,9, & 12 o'clock
- n.notches <- 12
- radian.seq <- seq(from=pi/2, to=5*pi/2, length=(n.notches+1))
- jdate.ttt <- 365 - radian.seq/2/pi *365 + radian.seq[1]/2/pi *365 + 1
- jdate.ttt[jdate.ttt > 365] <- jdate.ttt[jdate.ttt > 365] -365
- jdate.ttt <- jdate.ttt[1:n.notches]
- p.time <- strptime( x=paste(round(jdate.ttt)), "%j")
- # Nice function to convert DateTime Classes
- month.text <- months(p.time, abbreviate = TRUE)
- date.names <- paste(month.text, " ",p.time$mday,sep="")
- #p.time
- #month.text
- #date.names
- ttt.min <- 1.0
- ttt.max <- 1.1
- inside.scale <- 0.9
- for (iii in 1:n.notches){
- lines( c(ttt.min*cos(radian.seq[iii]), ttt.max*cos(radian.seq[iii])),
- c(ttt.min*sin(radian.seq[iii]), ttt.max*sin(radian.seq[iii])),
- lwd=2.0)
- text( inside.scale* cos(radian.seq[iii]) ,
- inside.scale*sin(radian.seq[iii]),
- # pos=4, # text is to the left of location
- # cex = 1.5,
- labels=c(month.text[iii]) )
- }
- # ---------------------------------------------------------
- # Add Shingles
- # ---------------------------------------------------------
- nnn <- length(ensemble.par.list$begin.window)
- #nnn <- 1
- inner.radius <- 1.0
- outer.radius <- 1.5
- training.window.color <- "blue"
- inner.pred.radius <- inner.radius + 0.1
- outer.pred.radius <- outer.radius - 0.1
- pred.window.color <- "red"
- # Convert Julian dates into positions on Julian Calendar
- begin.window.radians <- ensemble.par.list$end.window/365*2*pi + pi/2
- end.window.radians <- ensemble.par.list$begin.window/365*2*pi + pi/2
- begin.pred.window.radians <- ensemble.par.list$begin.pred.window/365*2*pi + pi/2
- end.pred.window.radians <- ensemble.par.list$end.pred.window/365*2*pi + pi/2
- for (iii in 1:nnn){
- lines( c( inner.radius*cos(begin.window.radians [iii]),
- outer.radius*cos(end.window.radians [iii])),
- c( inner.radius*sin(begin.window.radians [iii]),
- outer.radius*sin(end.window.radians [iii])),
- lwd=2.0,
- col=training.window.color)
- #lines( c( inner.pred.radius*cos(begin.pred.window.radians [iii]),
- # outer.pred.radius*cos(end.pred.window.radians [iii])),
- # c( inner.pred.radius*sin(begin.pred.window.radians [iii]),
- # outer.pred.radius*sin(end.pred.window.radians [iii])),
- # lwd=2.0,
- # col=pred.window.color)
- }
- title(main = paste("STEM Temporal Design"),
- font.main=4, line=2, cex.main=2.0 )
-
-
- # ---------------------------------------------------------
- return()
-# ---------------------------------------------------------------------------------------------------------------------
-}# end plot ST ensemble Function
-# ---------------------------------------------------------------------------------------------------------------------
-# ---------------------------------------------------------------------------------------------------------------------
-
-
-
-
-# ---------------------------------------------------------------------------
-# FUNCTION: Plot STEM Spatial Design
-# --------------------------------------
-# Plots a sinlge realization of the STEM Spatial design
-# identified & indexed by its mc.region and time.interval values.
-#
-# # -------------------------------
-# regional.polygons <- rbind(regional.polygons,
-# data.frame(
-# regional.rectangle,
-# region.number=rep(iii, NROW(regional.rectangle)),
-# region.mc = iii.mc.region,
-# time.intervals=iii.interval))
-# ----------------------------------------------------------------------------
-plot.ST.ensemble <- function(
- ensemble.par.list,
- # Like JDATE-YEAR.SEQ's These two vectors
- # define an index PAIR into the ensemble
- # This means that these have to be the same length!!!!
- # ----------------------------------------------------
- mc.regions,
- time.intervals,
- ...) # pass through plotting parameters?
-{# ---------------------------------------------------------
- # mc.regions = c(1)
- # time.intervals = c(2)
-# -------------------------
-# Inits
-# ------------------------
- require(maps)
- regional.polygons <- ensemble.par.list$regional.polygons
- xxx <- regional.polygons$x
- yyy <- regional.polygons$y
- # -------------------------
- # Plot clusters
- # ------------------------
- # Divergent Colors from RColorBrewer
- col.names <- c( "#E41A1C", "#377EB8", "#4DAF4A",
- "#984EA3", "#FF7F00", #"#FFFF33", Remove yellow!!
- "#A65628", "#F781BF", "#999999",
- "#66C2A5", "#FC8D62", "#8DA0CB",
- "#E78AC3", "#A6D854", "#FFD92F",
- "#E5C494", "#B3B3B3")
- # Repeat colors for large sets of polygons
- col.names <- rep( col.names, times=1000)
- # Intialize Plotting Region
- plot(xxx, yyy, type="n", ...)
- map('state',add=TRUE, lwd=2, col="yellow")
- map('state',add=TRUE, lwd=1, col="black")
- # ------------------------------------------------
- for (jjj in length(time.intervals)){
- ttt.index <- regional.polygons$region.mc == mc.regions[jjj] &
- regional.polygons$time.intervals == time.intervals[jjj]
- ttt.poly <- regional.polygons[ttt.index,]
- n.region <- max(ttt.poly$region.number)
- for (iii in 1:n.region){
- polygon(ttt.poly[ttt.poly$region.number == iii,],
- border = col.names[iii],
- lwd=2.0,
- density=NULL)
- #cat("polygon=",iii," Enter to continue","\n") # prompt
- #ttt.scan <-scan(n=1,what="character")
- } # end iii
- } # end jjj
- # ------------------------------------------------
- #points(region.centers, col="white", cex=1.5)
- #points(ensemble.data$X$x,ensemble.data$X$y, col="black", cex=.25)
- #points(ensemble.data$X$x,ensemble.data$X$y, col="white", cex=.25)
-# ---------------------------------------------------------
- return()
-# ---------------------------------------------------------
-}# end plot ST ensemble Function
-# ---------------------------------------------------------
-
-
-
diff --git a/contrib/stem/code/stem.library.ST.R b/contrib/stem/code/stem.library.ST.R
deleted file mode 100644
index f795bad..0000000
--- a/contrib/stem/code/stem.library.ST.R
+++ /dev/null
@@ -1,2430 +0,0 @@
-
-
-
-# ------------------------------------------------------------------
-# 10.8.08
-# Adding
-# Point in ploygon Function
-# (This is a more basic/generic version of the
-# the point.in.polygon.contours() function in
-# rel.abundance.mapping.functions3.r.
-#
-#
-# 10.6.08
-# Adding Functions:
-# Point in ShapeFile Function
-# NOTE: This function is based on the NCEAS function XXXXXX
-# except that I needed to fix the donut hole problem with
-# the shape files. I need to finish documenting this and
-# send it back to those guys!
-# Initialize Map Gridding
-# Needed ==> a more generic regional.cluster.cloropleth.map()
-#
-# ------------------------------------------------------------------
-
-
-#------------------------------------------------------------------------------------------------------------
-#------------------------------------------------------------------------------------------------------------
-# SBT: Better ST Maps
-# -------------------------------------
-# 9.9.08
-#
-# Produce maps and save them to disk.
-# Based on "st.bdt.surface.maps.9.9.R"
-#
-# 10.20.08 Modifications
-# -----------------------------------------
-# 1) Added code include the leading zeros on the map.filename
-# This produces files that will be sequentially ordered in file browsers!
-# Small but important "convenience" modification.
-# 2) Also added call to the function initizalize.map.grid() in
-# st.clustering.functions.2.R format maps automatically
-# 3) Assumed additional parameters
-# begin.seq
-# end.seq
-#
-# 10/24/08
-# -------------------
-# * Added code & switch to deal with sqrt transform
-# # Response Transformation code: resp.transformation.code <- "sqrt"
-# * Excluded the extraneous spatial density contours
-#
-# 11/19/08
-# -------------
-# google earth maps - transparent & no margin plots.
-#
-#
-# REQUIRES
-# ------------------------
-#"eBird taxonomy file.csv",
-#"yelwar.East.travel.spatial.density.contours.RData",se
- #~ # ------------------------
- #~ # control.data
- #~ # ------------------------
- #~ # (spp.code, spatial.extent, exp.tag, ST.group)
- #~ # ST groups
- #~ # A - 156 - 1 per week 2004-06
- #~ # B - 36 - 1 per month 2004 -2006
- #~ # C -26 - 1per 2 weeks 2006
- #~ # ------------------------
- #~ "amekes", US, stbdt.8.19., B
- #~ "buffle",US, stbdt.8.19., C
- #~ "buwwar",East, stbdt.8.19., B
- #~ "barswa", US, stbdt.9.3.,C
- #~ "cavswa", SoTX, stbdt.9.3.,C
- #~ "cliswa", US, stbdt.9.3.,C
-#------------------------------------------------------------------------------------------------------------
-#------------------------------------------------------------------------------------------------------------
-
-
-
-## KFW
-require(fields)
-
-
-
-
-
-
-
-# These are legacy code for spatial contours
-# They will need to be intergrated with current functions
-# if this functions stays!
-# -------------------------------------------------------------------
-# Poisson Predictive Performance Measures
-# -------------------------------------------------------------------
-# yyy = observations
-# ppp = predicted value - response scale
-#
-# Verified - replicated GAM deviance calcuatlions for poisson
-poisson.deviance <- function(yyy,ppp){
- # if predictions (ppp) equal zero we will get underflow
- # problems from log function.
- # -------------
- # break deviance into two pieces - where obs == 0
- ttt.zero <- (yyy == 0)
- ttt.pos <- (yyy > 0)
- dev1 <- sum( (yyy[ttt.zero] - ppp[ttt.zero]) )
- dev2 <- sum( yyy[ttt.pos]*(log(yyy[ttt.pos])-log(ppp[ttt.pos])) -
- (yyy[ttt.pos] - ppp[ttt.pos]))
- dev <- 2*(dev2 - dev1)
- return(dev)
- }
-
-deviance.explained <- function(yyy,ppp){
- null.deviance <- poisson.deviance(yyy, rep(mean(yyy),length(yyy) ))
- obs.deviance <- poisson.deviance(yyy,ppp)
- deviance.explained <- (null.deviance - obs.deviance)/null.deviance
- de <- list(deviance.explained=deviance.explained,
- obs.deviance=obs.deviance,
- null.deviance=null.deviance)
- return(de)
- }
-
-poisson.pearson <- function(yyy,ppp){
- p <- sum( ((yyy - ppp)^2)/(ppp) )
- return(p)
- }
-
- # Accuracy of 0-1 Classification for Poisson Regression
- # ---------------------------------------------------------
- poisson.accuracy <- function(yyy, ppp, threshold=0.5){
- y.binary <- as.numeric(yyy > threshold)
- p.binary <- as.numeric(ppp > threshold)
- acc <- 1-sum(abs(y.binary - p.binary))/length(y.binary)
- return(acc)
- }
-# -------------------------------------------------------------------
-# -------------------------------------------------------------------
-
-
-
-
-
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-# Measure Predictive performance as a function of Spatial Scale
-# -----------------------------------------------------------------------------
-# Daniel Fink
-# 1.9.08
-# 2.7.08 modifications
-#
-# Description
-# -----------------
-# This function Measures the predictive performance as a function of
-# Spatial Scale. It takes the bs.model object from a single test/training
-# split and bins/grids this data across a range of scales. Performance
-# is computed and recorded at each scale and passed back to the user.
-# Predictive performance is computed on the test set.
-# Predictive performance may also be plotted as a function of scale.
-#
-# Currently, the function will take the entire spatial extent analyzed/
-# in the data set, p.data.
-#
-# Input
-# ----------
-# p.data,
-# dtm.obj,
-# grid.size.seq,
-# grid.size.units = "cells",
-# file.name=NULL,
-# plot.it=FALSE,
-# plot.height=600
-# plot.width=800
-#
-# Output
-# ----------
-# pred.performance[iii,1] <- perf.ttt$deviance.explained
-# pred.performance[iii,2] <- perf.ttt$obs.deviance
-# pred.performance[iii,3] <- poisson.pearson(zzz.size[ttt.ind],ppp.size[ttt.ind] )
-# # Total number of grid cells that have test-set observations
-# pred.performance[iii,4] <- NROW(image.pred$ind)
-# # Median # of observations/grid cell, in grid cells with observations
-# pred.performance[iii,5] <- median(image.pred$weights[image.pred$ind])
-# # Grid Size in units of cells
-# pred.performance[iii,6] <- grid.size[iii]
-# # Grid Size in units of (approximate) km^2
-# pred.performance[iii,7] <- grid.size[iii]
-#
-#
-# Notes:
-# ---------
-#
-# Further Development:
-# ----------------------------
-# * include km2 as units
-# Check out the web page at
-# http://www.movable-type.co.uk/scripts/latlong.html
-# for the Haversine formula
-# * inlcude control over spatial.extent
-# -----------------------------------------------------------------------------
-spatial.performance.plot <- function(
- xxx,
- yyy,
- ppp, # predicted
- zzz, #obs
- spatial.extent=NULL,
- #dtm.obj,
- grid.size.seq,
- grid.size.ratio = 2,
- grid.size.units = "cells",
- # ----------------------------
- file.name=NULL,
- plot.it=NULL,
- span=0.3,
- plot.height=600,
- plot.width=800){
-# ------------------------------------------
-# Dummy Values
-# ------------------------------------------
-# xxx = test.data$X$x[subset.index]
-# yyy = test.data$X$y[subset.index]
-# ppp = test.pred$mean[subset.index] predicted
-# zzz = test.data$y[subset.index] observed
-# spatial.extent = spatial.extent
-# grid.size.seq = grid.size.seq
-# grid.size.ratio = 1.0
-# file.name=NULL
-# plot.it=TRUE
-#
-# spatial.extent <- list(
-# # NE Region
-# lat.max = 50.0,
-# lat.min = 25.0,
-# lon.min= -100.0,
-# lon.max = -67.0 )
-# file.name <- FALSE
-# plot.it <- TRUE
-# n.sizes <- 50
-# grid.size.seq <- round(seq(from=5, to=120, length=n.sizes))
- # -----------------------------------
- # verification
- #length(xxx)
- #length(yyy)
- #length(ppp)
- #length(zzz)
- # image.pred <- as.image(ppp, x= data.frame(xxx,yyy),
- # nrow=40,
- # ncol=40, na.rm=TRUE)
- # image.plot(image.pred)
- # map('state',add=TRUE, lwd=1, col="grey")
-
-# ------------------------------------------
-# Initial Values
-# ------------------------------------------
- n.sizes <- length(grid.size.seq)
- pred.performance <- matrix(0, n.sizes, 20)
- # Covert grid sizes to both units
- # -----------------------------------------
-# ------------------------------------------
-# Compute Baseline-Point Performance
-# ------------------------------------------
- epsilon <- 1e-8
- #ppp <- ddd$pred.Xp
- #obs <- p.data$yp
- obs <- zzz
- ttt.index <- ppp == 0
- ppp[ttt.index] <- epsilon
- ttt.ind <- !is.na(ppp)
- test.dev <- deviance.explained(obs[ttt.ind],ppp[ttt.ind])$deviance.explained
- test.pearson <- poisson.pearson(obs[ttt.ind], ppp[ttt.ind])
-
-# ------------------------------------------
-# Compute Performance across scales
-# ------------------------------------------
- for (iii in 1:n.sizes){
-# -------------------------
-# if (!is.null(spatial.extent)){
-# # Add two points based on spatial extent
-# # Idea is to set spatial extent manually
-# # I should rewrite the binning myself!
-# # small bias caused in perf. metrics
-# ppp.ip <- c(ppp,0,0)
-# zzz.ip <- c(zzz,0,0)
-# xxx.ip <- c(xxx,spatial.extent$lon.min,spatial.extent$lon.max)
-# yyy.ip <- c(yyy,spatial.extent$lat.min,spatial.extent$lat.max)
-# image.pred <- as.image(ppp.ip, x= data.frame(xxx.ip,yyy.ip),
-# nrow=grid.size.seq[iii]*grid.size.ratio,
-# ncol=grid.size.seq[iii] , na.rm=TRUE)
-# image.obs <- as.image(zzz.ip, x= data.frame(xxx.ip,yyy.ip),
-# nrow=grid.size.seq[iii]*grid.size.ratio,
-# ncol=grid.size.seq[iii], na.rm=TRUE)
-# }
-# -----------------------
- #if (is.null(spatial.extent)){
- image.pred <- as.image(ppp, x= data.frame(xxx,yyy),
- nrow=grid.size.seq[iii]*grid.size.ratio,
- ncol=grid.size.seq[iii] , na.rm=TRUE)
- image.obs <- as.image(zzz, x= data.frame(xxx,yyy),
- nrow=grid.size.seq[iii]*grid.size.ratio,
- ncol=grid.size.seq[iii]) #, na.rm=TRUE)
- # Form a common na index
- # ---------------------------
- ddd.na.ind <- !is.na(image.pred$weights)
- d2.na.ind <- ddd.na.ind & !is.na(image.obs$weights)
-
- ppp.size <- image.pred$z[d2.na.ind ]
- zzz.size <- image.obs$z[d2.na.ind ]
- length(ppp.size)
- length(zzz.size)
-
- # -------------------------------------
- # Clean Predictions for Dev. Calcs
- # -------------------------------------
- # Substitute predicted zero's with small values
- ttt.index <- ppp.size == 0
- ppp.size[ttt.index] <- epsilon
- # Remove any NA's - several occurr with GAM models
- ttt.ind <- !is.na(ppp.size)
- # -------------------------------------
- perf.ttt <- deviance.explained(zzz.size[ttt.ind], ppp.size[ttt.ind])
- pred.performance[iii,1] <- perf.ttt$deviance.explained
- pred.performance[iii,2] <- perf.ttt$obs.deviance
- pred.performance[iii,3] <- poisson.pearson(zzz.size[ttt.ind],ppp.size[ttt.ind] )
- # Total number of grid cells that have test-set observations
- # This is the sample size at this scale
- ip.ind <- !is.na(image.pred$weight)
- pred.performance[iii,4] <- sum(ip.ind)
- # Mean Squared error and scaled RMSE
- pred.performance[iii,5] <- sqrt(
- mean((zzz.size[ttt.ind]-ppp.size[ttt.ind])^2))
- pred.performance[iii,6] <- sqrt(
- mean(((zzz.size[ttt.ind]-ppp.size[ttt.ind])/
- ppp.size[ttt.ind]) ))
- # -----------------------------
- # Add more
- # -------------------------
- #MSE
- pred.performance[iii,11] <- mean((ppp.size - zzz.size)^2)
-
- #R2
- pred.performance[iii,12] <- 1 - mean((ppp.size - zzz.size)^2)/
- mean((mean(zzz.size) - zzz.size)^2)
- #MSE.sqrt
- pred.performance[iii,13] <- mean((sqrt(ppp.size) - sqrt(zzz.size))^2)
- #R2.sqrt
- pred.performance[iii,14] <- 1 - mean((sqrt(ppp.size) - sqrt(zzz.size))^2)/
- mean((mean(sqrt(zzz.size)) - sqrt(zzz.size))^2)
- #MAD
- pred.performance[iii,15]<- mean(abs(ppp.size - zzz.size))
- #rho
- pred.performance[iii,16]<- cor(zzz.size,ppp.size)
- #rho.sqrt
- pred.performance[iii,17]<- cor(sqrt(zzz.size),sqrt(ppp.size))
-
- # --------------------------------
-
- # Median # of observations/grid cell, in grid cells with observations
- pred.performance[iii,7] <- median(image.pred$weights[ip.ind])
- pred.performance[iii,8] <- sd(image.pred$weights[ip.ind])
- # Grid Size in units of cells
- pred.performance[iii,9] <- grid.size.seq[iii]
- # Grid Size in units of (approximate) km^2
- # --------------------------------------------------
- # Great Circle Distance Formula using decimal degrees:
- # Where r is the radius of the earth in whatever units you desire.
- #r <-3437.74677 (nautical miles)
- r <- 6378.7 #(kilometers)
- #r<-3963.0 (statute miles)
- # Assume we are at centered at 40 Lat and 100 lon
- lat1 <- 40
- lon1 <- -100
- # Step size from image grid
- lat2 <- lat1 + (image.pred$y[2]- image.pred$y[1])
- lon2 <- lon1 #+ (image.pred$x[2]- image.pred$x[1])
- cell.height.km <- r * acos(sin(lat1/57.2958) * sin(lat2/57.2958) +
- cos(lat1/57.2958) * cos(lat2/57.2958) *
- cos(lon2/57.2958 -lon1/57.2958))
- lat2 <- lat1 #+ (image.pred$y[2]- image.pred$y[1])
- lon2 <- lon1 + (image.pred$x[2]- image.pred$x[1])
- cell.width.km <- r * acos(sin(lat1/57.2958) * sin(lat2/57.2958) +
- cos(lat1/57.2958) * cos(lat2/57.2958) *
- cos(lon2/57.2958 -lon1/57.2958))
- pred.performance[iii,10] <- cell.width.km*cell.height.km
- } # end for loop
- # ----------------------------------------------------------
-# pred.performance
-
-# ------------------------------------------
-# Plot Performance vs Spatial Scale
-# ------------------------------------------
- if (!is.null(file.name)){
- png(file=file.name,
- bg="white",
- width = plot.width,
- height = plot.height)
- }
- if (!is.null(file.name) | !is.null(plot.it)){
- # --------------------------------------
- # ** dual x-labels for # cells and km2 would be cool
- # ** draw Base-Line at point-level predictive performance
- # ** adaptively set maximum y-axis value?
- # ** plot smoothed performance trajectory??
- # --------------------------------------
- ymin <- min(c( 0.9*min(pred.performance[,1]), 0.9*test.dev) )
- ymax <- max( c( 1.1*max(pred.performance[,1]), 1.1*test.dev) )
- plot(pred.performance[,9],
- pred.performance[,1],
- ylim=c(ymin,ymax),
- type="p",
- lwd=2.0,
- col="red",
- xlab=" # latitude cells ",
- ylab=" Percent Deviance Explained",
- main="Performance vs Scale" )
- # Smoothed Performance
-
- # Smoothed Performance
- lines(lowess(pred.performance[,9], pred.performance[,1],
- f=span),
- lwd=2.0,
- col="red")
- # baseline performance
- lines(range(pred.performance[,9]),
- c(test.dev, test.dev),
- lwd=2.0,
- col="black")
-
- }
- if (!is.null(file.name)) dev.off()
-
-# ------------------------------------------
-# Return Values
-# ------------------------------------------
-return.list <- list(pred.performance=pred.performance,
- test.dev=test.dev,
- test.pearson=test.pearson)
-return(return.list)
-# --------------------------------------------------------------------------
-} # end function
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-
-
-
-
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-# Generate Contours for Spatial Density of Given Locations
-# -----------------------------------------------------------------------------
-# Daniel Fink
-# 2.7.08
-#
-# Description
-# -----------------
-# Objectives are to
-# ** estimate 2D KDE over lat & Lon
-# ** second: estimate the SD of prediction error
-# ** exclude/white out lowest level of density surface
-# ** estimate quantiles of density surface estimates
-
-# ----------------------------------------------------------------------
-#
-#
-# Input
-# ----------
-# xxx, yyy - locations
-# contours - vector of numbers
-# density.cutoff
-#
-# Output
-# ----------
-# ** draw contours
-# ** return zzz quantile hieghts that define the contours.
-# This will be a numeric vector with same length as contours
-#
-# Notes:
-# ---------
-#
-# Further Development:
-# ----------------------------
-# ** return density estimate
-# ** pass through to access options on density estimator
-# -----------------------------------------------------------------------------
-spatial.density.contours <- function(
- xxx, yyy,
- contours,
- density.cutoff = 0.1,
- xgridsize = 40,
- ygridsize = 40,
- # ----------------------------
- file.name =NULL,
- plot.it =FALSE,
- plot.height=600,
- plot.width=800){
-# ------------------------------------------
-# Dummy Values/Calls
-# ------------------------------------------
-
-# ------------------------------------------
-# Inits
-# ------------------------------------------
- require(GenKern)
- require(maps)
- require(fields)
-# -------------------------------------
-# GenKern: Estimate 2D KDE over lat & Lon
-# ----------------------------------
- # calculate and plot a surface with zero correlation
- # Notes that KernSur 2D KDE can change dramatically by
- # changing the bandwidths and correlation.
- # The selection of grid size determines spatial resoluation
- # of the contours. Which we want regional.
- # ------------------------------------------
- op <- KernSur(xxx,yyy,
- xgridsize=xgridsize,
- ygridsize=ygridsize)
- #correlation=0,
- #xbandwidth=1,
- #ybandwidth=1,
- # Plot level plot of the Density estimate
- #density.cutoff <- 0.1 # "Zero" Density cutoff
- # cleans up map and calculations
- #par(mfrow=c(1,2))
- image.plot(op$xords, op$yords,
- log(op$zden+1),
- zlim = c(density.cutoff, 7),
- col=terrain.colors(100),
- #col=heat.colors(100),
- axes=TRUE,
- xlab="Longitude",
- ylab="Latitude",
- main=" eBird Spatial Log Density " )
- # Compute quantiles of the Density estimate.
- # Note however, that this includes all the zeros that are
- # in the boundary area.
- # ---------------------------------------------------------
- # Quantiles for 2004 - 2007 Unique Locations (12008)
- zzz.quant <- quantile( op$zden[op$zden > density.cutoff],
- probs = contours) # Defines lower bound for data quality
- # Quantiles for 2004 - 2007 Unique Locations (12008)
- #zzz.quant <- quantile( op$zden[op$zden > density.cutoff],
- # probs =c(0.983, 0.88, 0.65))
- # Quantiles for 2006 Unique Locations (~6000) #c(0.85, 0.605))
- # Plot Contours at these levels
- # ------------------------------
- #contour(op$xords, op$yords, op$zden, add=TRUE,
- # levels=zzz.quant,
- # col=c(1:length(contours))+1,
- # lwd=2.0)
- box()
- # Add political Boundaries
- map('state',add=TRUE, lwd=2, col="yellow")
- map('state',add=TRUE, lwd=1, col="black")
- #points(xxx,yyy, cex=0.25)
-
- # Calculate All Contour Polygons using contourLines
- # contour.poly is a list where each element describes
- # one ploygon. Elements are
- # $level (this is one of the z.quantiles)
- # $x
- # $y (vectors defining boundary of polygon)
- # -------------------------------------------------
- contour.polygons <- contourLines(op$xords, op$yords, op$zden,
- levels=zzz.quant)
-# Return contours as polygons too!!!
-results.list <- list(
- contours = contours,
- xxx = xxx,
- yyy = yyy,
- log.density.quantiles = zzz.quant,
- contour.polygons = contour.polygons,
- density.KernSur.obj = op)
- return(results.list)
-}#---------------------------------------------------------------------
-#-----------------------------------------------------------------------
-#-----------------------------------------------------------------------
-
-
-
-
-
-
-# --------------------------------------------------------------------------
-# Plot Halloween Maps
-# -----------------------------
-#
-#
-# -------------------------------------
-# There may be a problem with the halloween.maps()
-# code when there are NO missing values and
-# this parameter is used: NA.col="grey20")
-# -------------------------------------
-#
-#
-# jdate.seq
-# year.seq
-# save.name
-# spp.name <- "Yellow Warbler"
-# z.min <-
-# z.max <-
-# If you use the mapping function for a single map, and
-# turn the add=TRUE parameter, then you can add
-# more stuff to the plot. You will need to end it with a call to
-# dev.off()
-#
-# # ----------------------------------------------------------------------
-# # Calculate Indices for Point.in.polygon for Contours
-# # ----------------------------------------------------------------------
-# # Do not filter locations
-# # ------------------------
-# contour.index <- rep(TRUE, length(st.pred$xxx))
-# # Filter locations using archived polygon
-# # --------------------------------
-# sdc.name <- paste(control.dir,
-# "yelwar.East.travel.spatial.density.contours.RData",sep="")
-# load( file=sdc.name) # sd.cont
-# pip.cont <- point.in.polygon.contours( st.pred$xxx, st.pred$yyy,
-# sd.cont$contour.polygons)
-# #contour.index <- pip.cont$contour.index[,1]
-# #
-##
-#
-# #~ # Eg.1. extract individual States
-# #~ #--------------------------------------------------------------
-# #~ sites <- data.frame(lon=st.pred$xxx, lat=st.pred$yyy)
-# #~ shape.dir <-"/mnt/data2/ST.BDT/BDT.shapefiles/"
-# #~ shape.filename <- "STATES.shp"
-# #~ selected.shape.names <- c("New York", "Georgia")
-# #~ att.selection.column.name <- "STATE_NAME"
-# #~ # --------------------------------------------------------------
-# #~ # Eg.2 extract individual BCRs
-# #~ #--------------------------------------------------------------
-# #~ sites <- data.frame(lon=st.pred$xxx, lat=st.pred$yyy)
-# #~ shape.dir <-"/mnt/data2/ST.BDT/BDT.shapefiles/"
-# #~ shape.filename <- "bcr.shp" # watch capitalization!
-# #~ att.selection.column.name <- "BCR"
-## #~ # -------------------------------------------------------------- #~ selected.shape.names <- c(13, 27) # class must match att.selection.column
-##
-#
-# --------------------------------------------------------------------------
-# DMF 3.19.10 modified from halloween.maps in stem.library.ST.R
-# dated 3.16.10
-#
-# I am going to add formal parameters so that
-# we can can specify separate input directories for st.matrix files
-# and separate directories for map sequence outputs
-# --------------------------------------------------------------------------
-st.matrix.maps <- function(
- st.matrix.directory,
- map.directory,
- # --------------
- #save.dir,
- #save.name,
- ## KFW resp.transformation.code = NULL,
- # ---------------
- jdate.seq,
- year.seq,
- begin.seq,
- end.seq=length(jdate.seq),
- # ------------------
- # output
- pred.grid.size=NULL,
- map.plot.width = 1000,
- spatial.extent.list = NULL,
- z.max = NULL,
- z.min = NULL,
- map.tag = NULL,
- google.maps=FALSE,
- add=FALSE,
- NA.col=NULL,
- halloween.colors=NULL,
- title.text = NULL,
- date.bar = TRUE,
- # -------------------------------------------
- # map args
- # -------------------------------------------
- county.map = FALSE,
- state.map=TRUE,
- world.map=FALSE,
- state.map.lwd = NULL,
- state.map.col = NULL,
- county.map.lwd = NULL,
- county.map.col = NULL,
- world.map.lwd = NULL,
- world.map.col = NULL,
- # -------------------------
- print.date=FALSE,
- # -------------------------
- ...) {
-# ------------------------------------------------
-
- if (is.null(state.map.lwd)) state.map.lwd <- 1.5
- if (is.null(state.map.col)) state.map.col <- "grey"
- if (is.null(county.map.lwd)) county.map.lwd <- 0.5
- if (is.null(county.map.col)) county.map.col <- "grey"
- if (is.null(world.map.lwd)) world.map.lwd <- 2.0
- if (is.null(world.map.col)) world.map.col <- "white"
-#---------------------------------------------
-
- if ("/" != substring(map.directory, nchar(map.directory), nchar(map.directory))) {
- map.directory <- paste(map.directory, "/", sep="")
- }
-
- if ("/" != substring(st.matrix.directory, nchar(st.matrix.directory), nchar(st.matrix.directory))) {
- st.matrix.directory <- paste(st.matrix.directory, "/", sep="")
- }
-
- system(paste("mkdir ", map.directory,sep=""), intern=TRUE)
- # Initialization Info Space-Time Predictions From file
- # ----------------------------------------------
- stp.name <- paste(st.matrix.directory,"st.matrix..1.RData",sep="")
- load(stp.name)
- # ----------------------------------------------------------------------
- # Limit Spatial Extent by Point in Polygon or ShapeFile
- # ----------------------------------------------------------------------
- contour.index <- rep(TRUE, length(st.pred$xxx))
- if (!is.null(spatial.extent.list)){
- if (spatial.extent.list$type == "rectangle"){
- ttt.index <- ( st.pred$yyy > spatial.extent.list$lat.min &
- st.pred$yyy < spatial.extent.list$lat.max &
- st.pred$xxx > spatial.extent.list$lon.min &
- st.pred$xxx < spatial.extent.list$lon.max )
- contour.index <- (ttt.index & contour.index)
- }
- if (spatial.extent.list$type == "polygon"){
- ttt.index <- point.in.polygon(
- xxx = st.pred$xxx,
- yyy = st.pred$yyy,
- polygon.vertices =
- spatial.extent.list$polygon.vertices)
- contour.index <- (ttt.index & contour.index)
- }
- if (spatial.extent.list$type == "shapefile"){
- ttt.index <- point.in.shapefile(
- sites = data.frame(lon=st.pred$xxx, lat=st.pred$yyy),
- shape.dir=spatial.extent.list$shape.dir,
- shape.filename=spatial.extent.list$shape.filename,
- att.selection.column.name=
- spatial.extent.list$att.selection.column.name,
- selected.shape.names=
- spatial.extent.list$selected.shape.names)
- contour.index <- (ttt.index & contour.index)
- }
- } # if (!is.null(spatial.extent.list)){
- # -------------------------------------------------------------------
- # initizalize.map.grid() formats maps automatically
- # -------------------------------------------------------------------
- mapping.spatial.extent <- list(
- lat.max = max( st.pred$yyy[contour.index]),
- lat.min = min( st.pred$yyy[contour.index]),
- lon.min = min( st.pred$xxx[contour.index]),
- lon.max = max( st.pred$xxx[contour.index]) )
- map.inits <- initizalize.map.grid(
- spatial.extent = mapping.spatial.extent,
- map.plot.width = map.plot.width,
- pred.grid.size = pred.grid.size)
- # ----------------------------------------------------------------------
- # Compute Surface Summaries
- # ----------------------------------------------------------------------
- st.summary <- matrix(0,(end.seq-begin.seq+1), 7)
- for (iii in begin.seq:end.seq){
- stp.name <- paste(st.matrix.directory,"st.matrix..",iii,".RData",sep="")
- load(stp.name)
- # ---------------------------------------------------------------------------
- # Un-tranform Responses
- # ---------------------------------------------------------------------------
- ## KFW if ( resp.transformation.code == "sqrt") {
- ## KFW st.pred$pred <- (st.pred$pred) ^2
- ## KFW }
- # ---------------------------------------------------------------------------
- st.summary[(iii-begin.seq +1),] <- quantile(st.pred$pred[contour.index],
- probs=c(0, .1,.25,.5,.75,.9,1),
- na.rm = TRUE)
- }
- # Set minium as min of 10th quantiles
- if (is.null(z.min)) z.min <- min(st.summary[,2])
- # Take max as max of 90th quantiles
- if (is.null(z.max)) z.max <- max(st.summary[,6])
- # ---------------------------------------------------------
- # Convert Temporal Sequence times to POSIX
- # ---------------------------------------------------------
- p.time <- strptime( x=paste(round(jdate.seq),year.seq), "%j %Y")
- # Nice function to convert DateTime Classes
- month.text <- months(p.time, abbreviate = FALSE)
- date.names <- paste(month.text, " ",p.time$mday,",", year.seq,sep="")
- # --------------------------------------------------------------
- # Lookup Common Name in eBird Taxonomy File
- # --------------------------------------------------------------
- # datafile <- paste(control.dir,"eBird taxonomy file.csv",sep="")
- # eBird.taxonomy <- read.csv(file=datafile)
- # #names(eBird.taxonomy)
- # spp.name <- eBird.taxonomy$PRIMARY_COM_NAME[
- # as.character(eBird.taxonomy$SPECIES_CODE) == spp.code ]
- # --------------------------------------------------------------
- # Will's Halloween Pallete
- # --------------------------------------------------------------
- if (is.null(halloween.colors)){
- n.red <- 100
- red.colors <- colorRampPalette(
- #-----------------------------------------------------------------------------------------
- # Traditional Halloweeen Map (black under 0.20)
- # -----------------------------------------------------------------------------------------
- # c("black","black","#FF7100","white"),
- # bias=1.9)
- # -----------------------------------------------------------------------------------------
- # Low Probability Halloween
- # -----------------------------------------------------------------------------------------
- # c("black","grey","#FF7100","yellow","white"),
- # bias=1.0)
- # -----------------------------------------------------------------------------------------
- # Low Probability Halloween 2
- # -----------------------------------------------------------------------------------------
- c("black","grey20","#FF7100","white"),
- bias=2.0)
- # -----------------------------------------------------------------------------------------
- # Green Halloween
- # -----------------------------------------------------------------------------------------
- #c("black","black","DarkGreen","Green4","Green"),
- #space = "rgb",
- }
- else {
- n.red <- 100
- red.colors <- halloween.colors
- }
-
- # --------------------------------------------------------------
- # Loop over Dates
- # --------------------------------------------------------------
- for (iii in begin.seq:end.seq){
- #---------------------------------------------
- # Load Space-Time Predictions From file
- # ----------------------------------------------
- #stp.name <- paste(save.dir,save.name,".",iii,".RData",sep="")
- stp.name <- paste(st.matrix.directory,"st.matrix..",iii,".RData",sep="")
- load(stp.name)
- # ---------------------------------------------------------------------------
- # Un-tranform Responses
- # ---------------------------------------------------------------------------
- ## KFW if ( resp.transformation.code== "sqrt")
- ## KFW st.pred$pred <- (st.pred$pred) ^2
- # ---------------------------------------------------------------------------
- #----------------------------
- # Surface Height Limits
- # ----------------------------
- st.pred$pred[st.pred$pred < z.min] <- z.min
- st.pred$pred[st.pred$pred > z.max] <- z.max
- # --------------
- # --------------
- num.txt <- formatC(iii,format="fg", width=5)
- num.txt <- chartr(" ","0",num.txt)
- map.file.name <- paste(map.directory,map.tag,
- num.txt,".",jdate.seq[iii],
- ".",year.seq[iii],".png" ,sep="")
-
- # --------------------------------------------------------------
- # "Google".maps == Transparent PNG's
- # --------------------------------------------------------------
- # if TRUE then background = Transparent
- # PNG margins are ajusted.
- # spatial.extent needs to be communicated to
- # Google.Earth so that it knows how to overlay image
- # --------------------------------------------------------------
- if (!google.maps) {
- png(file=map.file.name, bg="white",
- width=map.plot.width,
- height=map.inits$map.plot.height)
- par(mar = c(2,4,4,2), bg="black",fg="grey")
- }
- if (google.maps) {
- png(file=map.file.name, bg="transparent",
- width=map.plot.width,
- height=map.inits$map.plot.height)
- par(mar=c(0,0,0,0),bg="black",fg="grey",
- xpd=TRUE)
- }
- # --------------------------------------------------------------
- # Include Date Bar
- # --------------------------------------------------------------
- if (date.bar) {
- par(plt = c(0.10, 0.883, 0.25, 0.85) )
- # --------------------------------------------------------
- # Do not add NA's filled in with given color
- # --------------------------------------------------------
- if ( is.null(NA.col) ) {
- bs.rpart.maps(
- xxx = st.pred$xxx[contour.index],
- yyy = st.pred$yyy[contour.index],
- zzz = st.pred$pred[contour.index],
- zlim = c(z.min,z.max),
- pred.grid.size = map.inits$pred.grid.size ,
- grid.size.ratio = map.inits$grid.size.ratio,
- axis.args=list(fg="grey", col.axis="grey"),
- # Less than 1 reduces height,
- # greater than 1 increase height
- #for given width
- col.palette = red.colors(n.red),
- axes = FALSE,
- ...)
- }
- # --------------------------------------------------------
- # Add image plot with NA's filled in with given color
- # --------------------------------------------------------
- if ( !is.null(NA.col) ) {
- ttt.st.pred <- rep(NA,length(st.pred$pred))
- ttt.st.pred[is.na(st.pred$pred)] <- 1
- ttt.image <- as.image(
- ttt.st.pred[contour.index],
- x= data.frame( st.pred$xxx[contour.index],
- st.pred$yyy[contour.index]),
- nrow=round(map.inits$pred.grid.size*
- map.inits$grid.size.ratio), # nrow=X direction
- ncol=map.inits$pred.grid.size, # ncol=Y direction
- na.rm=TRUE)
- image(ttt.image,
- col=NA.col,
- # add=TRUE,
- axes = FALSE,...)
- if (!is.null(title.text)) {
- title(main=paste(title.text), col="white",line=0)
- }
- bs.rpart.maps(
- xxx = st.pred$xxx[contour.index],
- yyy = st.pred$yyy[contour.index],
- zzz = st.pred$pred[contour.index],
- zlim = c(z.min,z.max),
- pred.grid.size = map.inits$pred.grid.size ,
- grid.size.ratio = map.inits$grid.size.ratio,
- axis.args=list(fg="grey", col.axis="grey"),
- # Less than 1 reduces height,
- # greater than 1 increase height
- #for given width
- col.palette = red.colors(n.red),
- axes = FALSE,
- add=TRUE,
- ...)
- } # !is.null(NA.col)
- # -------------------------------------------------------------
- # Add Date Text
- # -------------------------------------------------------------
- if (print.date) {
- #mtext( paste(date.names[iii]), side=3, col="white")
- text( x= min(st.pred$xxx[contour.index]),
- y= min(st.pred$yyy[contour.index]),
- pos=4, #plot to the right
- labels= date.names[iii])
- }
- # -------------------------------------------------------------
- # Add Political Boundaries
- # -------------------------------------------------------------
- if (county.map) map('county',add=TRUE, lwd=county.map.lwd, col=county.map.col)
- if (state.map) map('state',add=TRUE, lwd=state.map.lwd, col=state.map.col)
- if (world.map) map('world',add=TRUE, lwd=world.map.lwd, col=world.map.col)
- # -------------------------------------------------------------
- # Bottom Date Legend Rectangle
- # -------------------------------------------------------------
- # Find the coordinate for the right boundary of
- # image.plot's "bigplot"
- right.corner <- image.plot.plt()$bigplot[2]
- par(plt = c(0.10, right.corner, 0.15, 0.22) )
- # Set user coordinates for this region
- par(usr=c(-1,366,0,1))
- box(lwd=2, col="grey")
- rect(xleft= (jdate.seq[iii]-2), ybottom=0, xright=(jdate.seq[iii]+2), ytop=2,
- col=red.colors(n.red)[n.red],
- border=NA )
- axis(1, at = c(5, 90, 180, 270, 360),
- labels = c("Jan", "Apr", "Jun", "Sep", "Dec"),
- cex=1.5,
- col="grey",
- col.axis="grey",
- font=1)
- # -------------------------------------------------------------
- } # end date.bar == TRUE
- # -------------------------------------------------------------
-
-
- # --------------------------------------------------------------
- # Exclude Date Bar
- # --------------------------------------------------------------
- if (!date.bar) {
- # --------------------------------------------------------
- # Do not add NA's filled in with given color
- # --------------------------------------------------------
- if ( is.null(NA.col) ) {
- bs.rpart.maps(
- xxx = st.pred$xxx[contour.index],
- yyy = st.pred$yyy[contour.index],
- zzz = st.pred$pred[contour.index],
- zlim = c(z.min,z.max),
- pred.grid.size = map.inits$pred.grid.size ,
- grid.size.ratio = map.inits$grid.size.ratio,
- axis.args=list(fg="grey", col.axis="grey"),
- # Less than 1 reduces height,
- # greater than 1 increase height
- #for given width
- col.palette = red.colors(n.red),
- axes = FALSE,
- ...)
- }
- # --------------------------------------------------------
- # Add image plot with NA's filled in with given color
- # --------------------------------------------------------
- if ( !is.null(NA.col) ) {
- ttt.st.pred <- rep(NA,length(st.pred$pred))
- ttt.st.pred[is.na(st.pred$pred)] <- 1
- ttt.image <- as.image(
- ttt.st.pred[contour.index],
- x= data.frame( st.pred$xxx[contour.index],
- st.pred$yyy[contour.index]),
- nrow=round(map.inits$pred.grid.size*
- map.inits$grid.size.ratio), # nrow=X direction
- ncol=map.inits$pred.grid.size, # ncol=Y direction
- na.rm=TRUE)
- image(ttt.image,
- col=NA.col,
- # add=TRUE,
- axes = FALSE,...)
- if (!is.null(title.text)) {
- title(main=paste(title.text), col="white",line=0)
- }
- bs.rpart.maps(
- xxx = st.pred$xxx[contour.index],
- yyy = st.pred$yyy[contour.index],
- zzz = st.pred$pred[contour.index],
- zlim = c(z.min,z.max),
- pred.grid.size = map.inits$pred.grid.size ,
- grid.size.ratio = map.inits$grid.size.ratio,
- axis.args=list(fg="grey", col.axis="grey"),
- # Less than 1 reduces height,
- # greater than 1 increase height
- #for given width
- col.palette = red.colors(n.red),
- axes = FALSE,
- add=TRUE,
- ...)
- } # !is.null(NA.col)
- # -------------------------------------------------------------
- # Add Date Text
- # -------------------------------------------------------------
- if (print.date) {
- #mtext( paste(date.names[iii]), side=3, col="white")
- text( x= min(st.pred$xxx[contour.index]),
- y= min(st.pred$yyy[contour.index]),
- pos=4, #plot to the right
- labels= date.names[iii])
- }
- # -------------------------------------------------------------
- # Add Political Boundaries
- # -------------------------------------------------------------
- if (county.map) map('county',add=TRUE, lwd=county.map.lwd, col=county.map.col)
- if (state.map) map('state',add=TRUE, lwd=state.map.lwd, col=state.map.col)
- if (world.map) map('world',add=TRUE, lwd=world.map.lwd, col=world.map.col)
- # -------------------------------------------------------------
- } # end plotting w/o date bar
- # -------------------------------------------------------------
- if (add==FALSE) dev.off()
- # ---------------------------------------------------------------------------
- } # iii - loop over dates
-# -----------------------------------------------------------------------------------
-}# end function
-#------------------------------------------------------------------------------------
-#------------------------------------------------------------------------------------
-#------------------------------------------------------------------------------------
-#------------------------------------------------------------------------------------
-
-
-
-# --------------------------------------------------------------------------
-# Plot Base Surface Maps
-# -----------------------------
-#
-#
-# Results:
-#
-#
-# jdate.seq
-# year.seq
-# save.name
-# spp.name <- "Yellow Warbler"
-# z.min <-
-# z.max <-
- #----------------------------
- # google.maps
- # ---------------------
- # if TRUE then background = Transparent
- # PNG margins are ajusted.
- # spatial.extent needs to be communicated to
- # Google.Earth so that it knows how to overlay image
- # ----------------------------
-# --------------------------------------------------------------------------
-surface.maps <- function(
- save.dir,
- save.name,
- jdate.seq,
- year.seq,
- begin.seq,
- end.seq=length(jdate.seq),
- ## KFW resp.transformation.code = NULL,
- # output
- pred.grid.size=NULL,
- z.max = NULL,
- z.min = NULL,
- map.tag,
- google.maps=FALSE,
- add=FALSE)
-{
-# ------------------------------------------
- # call to the function initizalize.map.grid() in
- # st.clustering.functions.2.R format maps automatically
- # ---------------------------------------------------------------------------------------------------
- map.inits <- initizalize.map.grid(spatial.extent=spatial.extent,
- map.plot.width=map.plot.width,
- pred.grid.size= pred.grid.size)
- # Reset this for slightly larger grid cells
- # Response Transformation code
- #resp.transformation.code <- "sqrt"
- # Map surface filename tag
- #map.tag <- paste(exp.name,"st.map.",sep="")
- #---------------------------------------------
- # Initialization Info Space-Time Predictions From file
- # ----------------------------------------------
- stp.name <- paste(save.dir,
- save.name,".",1,".RData",sep="")
- load(stp.name)
- # ----------------------------------------------------------------------
- # Calculate Indices for Point.in.polygon for Contours
- # ----------------------------------------------------------------------
- # Do not filter locations
- # ------------------------
- contour.index <- rep(TRUE, length(st.pred$xxx))
- # Filter locations using archived polygon
- # --------------------------------
- sdc.name <- paste(control.dir,
- "yelwar.East.travel.spatial.density.contours.RData",sep="")
- load( file=sdc.name) # sd.cont
- pip.cont <- point.in.polygon.contours( st.pred$xxx, st.pred$yyy,
- sd.cont$contour.polygons)
- #contour.index <- pip.cont$contour.index[,1]
- # ----------------------------------------------------------------------
- # Compute Surface Summaries
- # ----------------------------------------------------------------------
- st.summary <- matrix(0,(end.seq-begin.seq+1), 7)
- for (iii in begin.seq:end.seq){
- stp.name <- paste(save.dir,
- save.name,".",iii,".RData",sep="")
- load(stp.name)
- # ---------------------------------------------------------------------------
- # Un-tranform Responses
- # ---------------------------------------------------------------------------
- ## KFW if ( resp.transformation.code== "sqrt")
- ## KFW st.pred$pred <- (st.pred$pred) ^2
- # ---------------------------------------------------------------------------
- st.summary[iii,] <- quantile(st.pred$pred[contour.index],
- probs=c(0, .1,.25,.5,.75,.9,1))
- }
- # Set minium as min of 10th quantiles
- if (is.null(z.min)) z.min <- min(st.summary[,2])
- # Take max as max of 90th quantiles
- if (is.null(z.max)) z.max <- max(st.summary[,6])
-
- # Compute Slice Quantiles
- #pred.ecdf <- ecdf(st.pred$pred)+
- #qqq <- pred.ecdf(st.pred$pred)
- # ---------------------------------------------------------
- # Convert Temporal Sequence times to POSIX
- # ---------------------------------------------------------
- p.time <- strptime( x=paste(round(jdate.seq),year.seq), "%j %Y")
- # Nice function to convert DateTime Classes
- month.text <- months(p.time, abbreviate = FALSE)
- date.names <- paste(month.text, " ",p.time$mday,",", year.seq,sep="")
- # --------------------------------------------------------------
- # Lookup Common Name in eBird Taxonomy File
- # --------------------------------------------------------------
- datafile <- paste(control.dir,"eBird taxonomy file.csv",sep="")
- eBird.taxonomy <- read.csv(file=datafile)
- #names(eBird.taxonomy)
- spp.name <- eBird.taxonomy$PRIMARY_COM_NAME[
- as.character(eBird.taxonomy$SPECIES_CODE) == spp.code ]
- # ------------------------------------
- # My "Red" Pallete
- # ------------------------------------
- n.red <- 100
- red.colors <- colorRampPalette(
- c("white","red","#7F0000"),
- space = "rgb",
- bias=0.5)
- # ---------------------------------------
- for (iii in begin.seq:end.seq){
- #---------------------------------------------
- # Load Space-Time Predictions From file
- # ----------------------------------------------
- stp.name <- paste(save.dir,
- save.name,".",iii,".RData",sep="")
- load(stp.name)
- # ---------------------------------------------------------------------------
- # Un-tranform Responses
- # ---------------------------------------------------------------------------
- ## KFW if ( resp.transformation.code== "sqrt")
- ## KFW st.pred$pred <- (st.pred$pred) ^2
- # ---------------------------------------------------------------------------
- #----------------------------
- # Surface Height Limits
- # ----------------------------
- st.pred$pred[st.pred$pred < z.min] <- z.min
- st.pred$pred[st.pred$pred > z.max] <- z.max
- # --------------
- # --------------
- num.txt <- formatC(iii,format="fg", width=5)
- num.txt <- chartr(" ","0",num.txt)
- map.file.name <- paste(save.dir,map.tag,
- num.txt,".",jdate.seq[iii],
- ".",year.seq[iii],".png" ,sep="")
-
- #----------------------------
- # google.maps
- # ---------------------
- # if TRUE then background = Transparent
- # PNG margins are ajusted.
- # spatial.extent needs to be communicated to
- # Google.Earth so that it knows how to overlay image
- # ----------------------------
- if (!google.maps) {
- png(file=map.file.name, bg="white",
- width=map.plot.width,
- height=map.inits$map.plot.height)
- par(mfrow=c(1,1), cex=2.0, mar=c(5,4,4,5))
- }
- if (google.maps) {
- png(file=map.file.name, bg="transparent",
- width=map.plot.width,
- height=map.inits$map.plot.height)
- par(mfrow=c(1,1),
- cex=2.0,
- mar=c(0,0,0,0),
- xpd=TRUE)
- }
- # ---------------
- # Plot Surface
- # ---------------
- contour.index <- pip.cont$contour.index[,1]
- bs.rpart.maps(
- xxx = st.pred$xxx[contour.index],
- yyy = st.pred$yyy[contour.index],
- zzz = st.pred$pred[contour.index],
- zlim = c(z.min,z.max),
- pred.grid.size = map.inits$pred.grid.size ,
- grid.size.ratio = map.inits$grid.size.ratio,
- # Less than 1 reduces height,
- # greater than 1 increase height
- #for given width
- col.palette = red.colors(n.red),
- #spatial.extent = spatial.extent.map ,
- xlab= "Longitude",
- ylab= "Latitude")
- title(main = paste(spp.name, " ", date.names[iii]) ,
- font.main=4, line=1, cex.main=3.0 )
- # -------------------------------------------------------------
- # Add Polygon Boundaries
- # -------------------------------------------------------------
- kk <- 1 # first (lower) quantile
- hd.index <- pip.cont$contour.level.index ==
- sd.cont$log.density.quantiles[kk]
- hd.set <- (1:length(pip.cont$contour.level.index))[hd.index]
- # There are 9 polygons in this set, but only the first and fourth
- # are the big important regions
- for (kkk in c(1,4)){
- polygon(sd.cont$contour.polygons[[kkk]]) #$x,
- #sd.cont$contour.polygons[[jjj]]$y,
- # col= "black", #c.col[kk],
- #border=TRUE)
- }
- # -------------------------------------------------------------
- # Add Political Boundaries
- # -------------------------------------------------------------
- require(maps)
- map('county',add=TRUE, lwd=2, col="grey")
- map('state',add=TRUE, lwd=3, col="yellow")
- map('state',add=TRUE, lwd=2, col="black")
- # -----------------------------------------------------
- # -------------------------------------------------------------
- if (add==FALSE) dev.off()
- } # iii - st.pred index
-}# end fuction
-#------------------------------------------------------------------------------------
-#------------------------------------------------------------------------------------
-#------------------------------------------------------------------------------------
-#------------------------------------------------------------------------------------
-
-
-
-# ------------------------------------------------------------------------------------------------------
-# ------------------------------------------------------------------------------------------------------
-# Initialize Map Gridding
-# ------------------------------------------------------------
-# 10.7.08
-#
-# This needs to be cleaned up a bit
-#
-# Input:
-# -------------
-#
-# Output:
-# ----------
-#
-# Examples:
-# ------------------
-# --------------------------------------------------
- #~ spatial.extent <- list( lat.max = 45.0,
- #~ lat.min = 39.0,
- #~ lon.min= -82.5,
- #~ lon.max = -67.0 )
- #~ # ----------------------------------------
- #~ if (spatial.extent.code == "US") {
- #~ spatial.extent <- spatial.extent.US
- #~ map.plot.width <- 1800
- #~ #pred.grid.size <- 100 #height == lat
- #~ }
-# ------------------------------------------------------------------------------------------------------
-# ------------------------------------------------------------------------------------------------------
-
-
-initizalize.map.grid <- function(
- spatial.extent=NULL,
- lat=NULL,
- lon=NULL,
- map.plot.width,
- pred.grid.size=NULL ){
-# Needs either spatial.extent or lat & lon
-# -----------------------------------------------------------------------------
-# ST Surface Plots Inits
-# -----------------------------------------------------------------------------
-#~ Latitude and longitude can be used very simply for plotting
-#~ by setting up a rectangular grid (e.g. like a Simple Cylindrical Projection)
-#~ The question is how to scale the length:width of the rectangles.
-#~ At the equator a degree of latitude is roughly the same length
-#~ in miles as a degree of longitude - ignoring the asphericity of the
-#~ Earth's globe. Thus, at the equator, a square grid would be satisfactory
-#~ for a small map.
-#
-#~ As we move further away from the equator, e.g. where the continental US lies,
-#~ a degree of longitude is shorter in miles, though a degree of latitude
-#~ is much the same. Thus, a square lat-lon grid in the continental US distorts
-# distances, the map being stretched E-W. Using a rectangular lat-lon grid
-# gives a truer picture of everyday miles.
-#
-#~ The ratio of lengths for a degree latitude:longitude approximately corresponds
-#~ to the inverse of the cosine of the latitude. For example, at 40 degrees
-#~ latitude, the ratio of lat:lon is appriximately 1/cos(40 degrees) = 1.31.
-#~ This is the ratio for latitude of Denver,CO Springfield, IL, or Harrisburg, PA.
-#
-#~ This ratio of latitude:longitude is used to determine an appropriate
-#~ ratio of map image size (length & width in pixes) as well to determine
-# grid size ratio so that
-#~ grid cells plotted in the map surface have approximately equal length width & height in miles.
-#~ For simplicity, I use a fixed grid size for mapping. The ratio of
-#~ the length latitude:longitude length of the pixels is adjusted to
-#~ the inverse of the cosine of the latitude from the middle of the spatial
-#~ extent being plotted.
-# -----------------------------------------------------------------------------------------------------
- # user specified: Width of image (png file) in pixels
- #map.plot.width <- 1500
- middle.lat <- mean(spatial.extent$lat.max,spatial.extent$lat.min)
- pixels.per.degree.lon <- map.plot.width/
- (spatial.extent$lon.max - spatial.extent$lon.min)
- length.lat.to.length.lon.ratio <- 1/cos(middle.lat/360*2*pi)
- pixels.per.degree.lat <- length.lat.to.length.lon.ratio *
- pixels.per.degree.lon
- map.plot.height <- round(pixels.per.degree.lat *
- (spatial.extent$lat.max-spatial.extent$lat.min))
-
-# ------------------------------------------------------------------------
- # Discretization size
- # ------------------------------------------------------------------------
- # Calculate the maximum number of grid cells (minimum grid cell area)
- # to achieve the 10 random locations per cell from the prediction
- # grid design.
- #
- # NOTE: It appears that with these setting there are FAR more than
- # 10 random locs per cell!!!!
- #
- # The minimum Longitude grid side = . .14436 deg long
- # At 40 degrees Lat, a change of .14436 lon is 12km in length.
- # This number comes from the stratified design used to sample the
- # random locations based on extent and 400 equally spaced lon cells:
- # .14436 deg long = (-124.72839 - -66.98426)/400
- #
- # The minimum Latitude grid side = ..12210 deg lat
- # At 40 degrees Lat, a change of .12210 lat is 14 km in length.
- # This number comes from the stratified design used to sample the
- # random locations based on extent and 200 equally spaced lat cells:
- # .12210 deg lat= (48.97630 - 24.55572)/200
- #------------------------------------------------------------------------
- if (is.null(pred.grid.size)) {
- # Calculate Maximum pred.grid.size for this region
- pred.grid.size.max.xxx <-
- floor( (spatial.extent$lon.max - spatial.extent$lon.min)/.145)
- pred.grid.size.max.yyy <-
- floor( (spatial.extent$lat.max - spatial.extent$lat.min)/.123 )
- if (pred.grid.size.max.xxx < pred.grid.size.max.yyy)
- pred.grid.size <- floor(pred.grid.size.max.xxx)
- if (pred.grid.size.max.xxx > pred.grid.size.max.yyy)
- pred.grid.size <- floor(pred.grid.size.max.yyy)
- #pred.grid.size
- }
- # -------------------------------------------------------------------
- # User specified: number of latitude cells across spatial.extent
- #pred.grid.size <- 100
- # --------------------------------------------------------------------------
- # longitude cells = pred.grid.size * grid.size.ratio
- # Note that this ratio really takes into account two
- # quantities, the ratio of the lat:lon distances on the
- # surface of the Earth as well as the lat:lon ratio of
- # the spatial extent.
- # -------------------------------------------------------------------------
- cells.per.degree.lat <- pred.grid.size/
- (spatial.extent$lat.max - spatial.extent$lat.min)
- cells.per.degree.lon <- cells.per.degree.lat /
- length.lat.to.length.lon.ratio
- grid.cell.plot.width <- cells.per.degree.lon *
- (spatial.extent$lon.max-spatial.extent$lon.min)
- grid.size.ratio <- grid.cell.plot.width/pred.grid.size
- #grid.size.ratio
- #pred.grid.size
- #grid.cell.plot.width
-
- # ---------------------------------------------------------------------------------
- # How long are the sides of a grid cell?
- # ----------------------------------------------------------------------------------
- # Assume a grid cell centered at 40 degrees lat
- # ----------------------------------------------------------------------------------
- # Formula for distance between two points on a great circle
- # Each point needs to be expressed in radians
- # ---------------------------------------------------------------------------------------------
- lat1<- (40)*pi/180
- lon1 <- 70*pi/180
- lat2 <- (40 + 1/cells.per.degree.lat)*pi/180
- lon2 <- lon1
- d <- 2*asin(sqrt((sin((lat1-lat2)/2))^2 +
- cos(lat1)*cos(lat2)*(sin((lon1-lon2)/2))^2))
- radius.km <- 6371.0
- lat.distance.km <- radius.km * d
- # ---------------------------------------------------------------------------------------------
- lat1<- (40)*pi/180
- lon1 <- 70*pi/180
- lon2 <- (70 + 1/cells.per.degree.lon)*pi/180
- lat2 <- lat1
- d <- 2*asin(sqrt((sin((lat1-lat2)/2))^2 +
- cos(lat1)*cos(lat2)*(sin((lon1-lon2)/2))^2))
- radius.km <- 6371.0
- lon.distance.km <- radius.km * d
- # ----------------------------
-
-return(list(
- pixels.per.degree.lon=pixels.per.degree.lon,
- pixels.per.degree.lat=pixels.per.degree.lat,
- map.plot.height=map.plot.height,
- length.lat.to.length.lon.ratio=length.lat.to.length.lon.ratio,
- cells.per.degree.lat =cells.per.degree.lat ,
- cells.per.degree.lon=cells.per.degree.lon,
- grid.cell.plot.width=grid.cell.plot.width,
- grid.size.ratio =grid.size.ratio,
- pred.grid.size=pred.grid.size,
- lon.distance.km=lon.distance.km,
- lat.distance.km=lat.distance.km))
-} # end function
-# ------------------------------------------------------------------------------------------------------
-# ------------------------------------------------------------------------------------------------------
-
-# ------------------------------------------------------------------------------------------------------
-# ------------------------------------------------------------------------------------------------------
-# Point in Shapefile Polygon Operation
-# ------------------------------------------------------------
-# 6.3.08
-# 10.6.08
-#
-# This function performs the "Point in shapefile" operation
-# for BCRs and Statenames for a specific set of shapefiles.
-# Because each shape file has its own attr data frame, there are two
-# steps to select shapes:
-# 1) find the att.selection.column of the att.data data.frame
-# 2) search for selected.shape.names in the att.selection.column
-#
-# NOTE: This function is based on the NCEAS function XXXXXX
-# except that I needed to fix the donut hole problem with
-# the shape files. I need to finish documenting this and
-# send it back to those guys!
-#
-# NOTE: 1.9.09
-# ---------------
-# I changed the way that I access attributes -
-# I ran into problems not having S4 objects
-#
-# Input:
-# -------------
-# shape.dir
-# shape.filename
-# sites = data.frame with lat & lon vectors for spatial extent/universe
-# att.selection.column.name = the name of the att.data column
-# selected.shape.names = vector of region/shape names from shape file
-#
-# Output:
-# ----------
-# location.pip - T/F vector the length of the sites
-#
-# Examples:
-# ------------------
- #~ # --------------------------------------------------------------
- #~ # Eg.1. extract individual States
- #~ #--------------------------------------------------------------
- #~ sites <- data.frame(lon=st.pred$xxx, lat=st.pred$yyy)
- #~ shape.dir <-"/mnt/data2/ST.BDT/BDT.shapefiles/"
- #~ shape.filename <- "STATES.shp"
- #~ selected.shape.names <- c("New York", "Georgia")
- #~ att.selection.column.name <- "STATE_NAME"
- #~ # --------------------------------------------------------------
- #~ # Eg.2 extract individual BCRs
- #~ #--------------------------------------------------------------
- #~ sites <- data.frame(lon=st.pred$xxx, lat=st.pred$yyy)
- #~ shape.dir <-"/mnt/data2/ST.BDT/BDT.shapefiles/"
- #~ shape.filename <- "bcr.shp" # watch capitalization!
- #~ att.selection.column.name <- "BCR"
- #~ selected.shape.names <- c(13, 27) # class must match att.selection.column
-
- #~ # ------------------------------------------------------------
- #~ location.pip <- point.in.shapefile(
- #~ sites,
- #~ shape.dir,
- #~ shape.filename,
- #~ att.selection.column.name,
- #~ selected.shape.names)
- #~ plot(sites)
- #~ points(sites[location.pip,], col="red",cex=0.25)
-# ------------------------------------------------------------------------------------------------------
-# ------------------------------------------------------------------------------------------------------
-point.in.shapefile <- function(
- sites,
- shape.dir,
- shape.filename,
- att.selection.column.name,
- selected.shape.names
- ) {
-# ------------------------------------------------------------------------------------------------------
- require(maptools)
- require(splancs)
- #require(maps)
- # --------------------------------------------------------------
- # Read Shape File & Create Map object (using Maptools package)
- #--------------------------------------------------------------
- #shape.dir <-"c:\\users\\Research.AKN\\BDT\\Data\\point.in.polygon\\"
- #shape.dir <- data.dir
- #shape.filename <- "STATES.shp"
- #shape.data <- read.shape(paste(shape.dir,shape.filename,sep=""))
-
- # 2.24.10 Theo Damoulas
- # The map tools library was "updated"
- # !!!!!!! function read.shape deprecated use internal ::: to find
- shape.data <- maptools:::read.shape(paste(shape.dir,shape.filename,sep=""))
- #maptools:::getinfo.shape(paste(shape.dir,shape.filename,sep=""))
-
- # --------------------------------------------------------------------------------
- # Because each shape file has its own attr data frame,
- # 1) find the att.selection.column.name of the att.data data.frame
- # 2) search for selected.shape.names in the att.selection.column
- # --------------------------------------------------------------------------------
- att.col.index <-( names(shape.data$att.data) %in%
- att.selection.column.name )
- #selected.regions <- subset(Map2poly(shape.data),
- # shape.data$att.data[, att.col.index] %in% selected.shape.names )
- selected.regions <- subset(maptools:::Map2poly(shape.data),
- shape.data$att.data[, att.col.index] %in% selected.shape.names )
-
- # ----------------------------------------------
- # PIP function
- # ----------------------------------------------
- selected.sites <- NULL
- nnn.regions <- length(selected.regions[])
- point.in.poly.ind <- NULL
- for (iii in 1:nnn.regions){
- # --------------------------------------------------
- temp.region <- selected.regions[[iii]]
- # cycle through individual parts within each polygon region
- # performing the PinP operation one part at a time
- # instead of one region at a time
- # ------------------------------------------------
- attr.temp <- attributes(temp.region)
- #nParts <- temp.region at nParts
- nParts <- attr.temp$nParts
- for (jjj in 1:nParts) {
- #begin.ttt <- temp.region at pstart$from[jjj]
- #end.ttt <- temp.region at pstart$to[jjj]
- begin.ttt <- attr.temp$pstart$from[jjj]
- end.ttt <- attr.temp$pstart$to[jjj]
- ttt <- temp.region[begin.ttt:end.ttt,]
- res <- try(inpip(sites[c("lon","lat")], ttt))
- # If no errors, collect indices of sites that
- # are within the set of polygons.
- if (class(res)=="integer")
- point.in.poly.ind <- c(point.in.poly.ind,res)
- } # end for jjj
- } #end for iii
- # --------------------------------------------------------
- # Collect all point in Polygon set
- # --------------------------------------------------------
- location.pip <- rep(FALSE, NROW(sites))
- location.pip[point.in.poly.ind] <- TRUE
- return(location.pip)
-} # end function
-# ----------------------------------------------------------------------
-# ----------------------------------------------------------------------
-
-
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-# Point-in-Polygon Function
-# -----------------------------------------------------------------------------
-# Daniel Fink
-# 10.08.08
-# 03.17.10
-#
-# Description
-# -----------------
-# For a given set of locations determine if they fall into
-# a sinlge Polygon. Return one index (length of locations).
-#
-# Input
-# ----------
-# xxx, yyy - locations
-# polygon.vertices - data.frame with named vertices x and y
-# corresponding to xxx and yyy coordinates, resp.
-#
-# Output
-# ----------
-# index vector the length of locations
-#
-# Notes:
-# ---------
-#
-# Examples:
-# ----------
-#nnn <- 1000
-#xxx <- rnorm(nnn, mean=0, sd=1)
-#yyy <- rnorm(nnn, mean=0, sd=1)
-#unit.sq.polygon <- data.frame( x=c(0,0,1,1),y=c(0,1,1,0))
-#pip.index <- point.in.polygon(
-# xxx = xxx,
-# yyy = yyy,
-# polygon.vertices = unit.sq.polygon)
-#plot(xxx, yyy, type="n")
-#polygon(unit.sq.polygon, col="blue")
-#points(xxx,yyy)
-#points(xxx[pip.index], yyy[pip.index], pch=19, col="yellow")
-#
-# -----------------------------------------------------------------------------
-point.in.polygon <- function(
- xxx, yyy,
- polygon.vertices){
-# ------------------------------------------
- require(splancs)
- ttt.index <- inpip(cbind(xxx,yyy),
- cbind(polygon.vertices$x,
- polygon.vertices$y))
- data.index <- rep(FALSE, length(xxx))
- data.index[ttt.index] <- TRUE
- return(data.index)
-}#---------------------------------------------------------------------
-#-----------------------------------------------------------------------
-# Drew, Kevin, and the Point in Polygon requires a lot
-# DF: is very general - allows very flexible spatial partions
-# Drew: is computationally intensive
-# Kevin: is easily replaced
-#
-# I have changed the name because point.in.polygon is
-# used LEGITIMATELY used in many other routines.
-# This new function expedites the logic that selects
-# stixels (ST ensemble extents/subsets)
-# predict.ST.ensemble
-# sample.ST.ensemble
-# and create.ST.ensemble
-#
-#
-# ------------------------------------------
-# ------------------------------------------
-## For North America
-##
-## min(x), max(y)
-## -----------------------
-## | |
-## | |
-## | |
-## | |
-## | |
-## | |
-## -----------------------
-## max(x), min(y)
-##
-## This means that even if the base model extents
-## were indeed non-rectangular polgons, then
-## this logic will simply cover each polygon with
-## the smallest covering retangle.
-## This is an interesting idea.
-##
-##
-## Here is another way to do it:
-# The order of the vertices written by create.ST.ensemble is:
-# 1) Lower Left corner
-# 2) Upper Left
-# 3) Upper Right
-# 4) Lower Right
-# ttt.index <- rep(FALSE, length(xxx))
-# ttt.index <- xxx >= polygon.vertices$x[1] &
-# xxx <= polygon.vertices$x[4] &
-# yyy >= polygon.vertices$y[1] &
-# xxx <= polygon.vertices$y[2]
-#
-#-----------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-point.in.rectangle <- function(
- xxx, yyy,
- polygon.vertices){
-# ------------------------------------------
- maxX <- max(polygon.vertices$x)
- minX <- min(polygon.vertices$x)
- maxY <- max(polygon.vertices$y)
- minY <- min(polygon.vertices$y)
- newDataIndex <- rep(FALSE, length(xxx))
- locationMask <- xxx <= maxX & xxx >= minX & yyy <= maxY & yyy >= minY
- newDataIndex[locationMask] <- TRUE
-#### if (isTRUE(all.equal(data.index,newDataIndex)) == FALSE) {
-#### print("~~~~~ point.in.polygon FALSE")
-#### }
- return(newDataIndex)
-}#---------------------------------------------------------------------
-#-----------------------------------------------------------------------
-#-----------------------------------------------------------------------
-
-
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-# BS.RPART Mapping Plot Function
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-# 1.2.08
-#
-# Description:
-# ----------------
-# This function produces a single map image using fields.
-# No smoothing.
-# Primitive (i.e. rectangular) control of spatial extent
-#
-# INPUT
-# ------------
-# xxx
-# yyy
-# zzz
-#
-# OUTPUT
-# ------------
-#
-# To do:
-# ---------
-#
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-bs.rpart.maps <- function(
- # Data
- xxx,
- yyy,
- zzz,
- pred.grid.size = NULL,
- grid.size.ratio = 2,
- spatial.extent = NULL,
- # Save File
- save.name = NULL,
- plot.width = 800,
- plot.height = 600,
- main.text = NULL,
- # Pass in other plotting parameters
- col.palette=NULL,
- ... )
-{ #begin function
-
-# ------------------------------------------------------
-# Inits
-# ------------------------------------------------------
- call <- match.call()
- require(maps)
- require(fields)
-
- if (is.null(col.palette)){
- # Color scheme stolen from sp library
- col.palette<- c(
- "#000033FF", "#00003CFF", "#000046FF", "#00004FFF", "#000058FF", "#000061FF",
- "#00006BFF", "#000074FF", "#00007DFF", "#000086FF", "#000090FF", "#000099FF",
- "#0000A2FF", "#0000ACFF", "#0000B5FF", "#0000BEFF", "#0000C7FF", "#0000D1FF",
- "#0000DAFF", "#0000E3FF", "#0000ECFF", "#0000F6FF", "#0000FFFF", "#0700FFFF",
- "#0E00FFFF", "#1600FFFF", "#1D00FFFF", "#2400FFFF", "#2B00FFFF", "#3300FFFF",
- "#3A00FFFF", "#4100FFFF", "#4800FFFF", "#5000FFFF", "#5700FFFF", "#5E00FFFF",
- "#6500FFFF", "#6D00FFFF", "#7400FFFF", "#7B00FFFF", "#8200FFFF", "#8A01FEFF",
- "#9106F9FF", "#980BF4FF", "#9F0FF0FF", "#A714EBFF", "#AE19E6FF", "#B51DE2FF",
- "#BC22DDFF", "#C426D9FF", "#CB2BD4FF", "#D230CFFF", "#D934CBFF", "#E139C6FF",
- "#E83EC1FF", "#EF42BDFF", "#F647B8FF", "#FE4CB3FF", "#FF50AFFF", "#FF55AAFF",
- "#FF59A6FF", "#FF5EA1FF", "#FF639CFF", "#FF6798FF", "#FF6C93FF", "#FF718EFF",
- "#FF758AFF", "#FF7A85FF", "#FF7F80FF", "#FF837CFF", "#FF8877FF", "#FF8C73FF",
- "#FF916EFF", "#FF9669FF", "#FF9A65FF", "#FF9F60FF", "#FFA45BFF", "#FFA857FF",
- "#FFAD52FF", "#FFB24DFF", "#FFB649FF", "#FFBB44FF", "#FFBF40FF", "#FFC43BFF",
- "#FFC936FF", "#FFCD32FF", "#FFD22DFF", "#FFD728FF", "#FFDB24FF", "#FFE01FFF",
- "#FFE51AFF", "#FFE916FF", "#FFEE11FF", "#FFF20DFF", "#FFF708FF", "#FFFC03FF",
- "#FFFF09FF", "#FFFF26FF", "#FFFF43FF", "#FFFF60FF")}
-
-# ----------------------------------------------
-# Set Spatial Extent
-# ----------------------------------------------
- if (!is.null(spatial.extent)) {
- if (is.null(spatial.extent$lat.max)) spatial.extent$lat.max <- max(yyy)
- if (is.null(spatial.extent$lat.min)) spatial.extent$lat.min <- min(yyy)
- if (is.null(spatial.extent$lon.min)) spatial.extent$lon.min <- min(xxx)
- if (is.null(spatial.extent$lon.max)) spatial.extent$lon.max <- max(xxx)
- x.zoom.ind <- (xxx < spatial.extent$lon.max & xxx > spatial.extent$lon.min)
- y.zoom.ind <- (yyy < spatial.extent$lat.max & yyy > spatial.extent$lat.min)
- zoom.ind <- as.logical( x.zoom.ind & y.zoom.ind)
- #sum(zoom.ind)
- zzz <- zzz[zoom.ind]
- xxx <- xxx[zoom.ind]
- yyy <- yyy[zoom.ind]
- }
-
- # ------------------------------------------------------------------------
- # Discretization size
- # ------------------------------------------------------------------------
- # Calculate the maximum number of grid cells(minimum grid cell area)
- # to achieve the 10 random locations per cell from the prediction
- # grid design.
- #
- # The minimum Longitude grid side = .28872 deg long
- # This number comes from the stratified design used to sample the
- # random locations based on extent and 200 equally spaced lon cells:
- # .28872 deg long = (-124.72839 - -66.98426)/200
- #
- # The minimum Latitude grid side = .24421 deg lat
- # This number comes from the stratified design used to sample the
- # random locations based on extent and 100 equally spaced lat cells:
- # .24421 deg lat= (48.97630 - 24.55572)/100
- #------------------------------------------------------------------------
- if (is.null(pred.grid.size)) {
- # Calculate Maximum pred.grid.size for this region
- pred.grid.size.max.xxx <- floor( (max(xxx) - min(xxx))/.28872 )
- pred.grid.size.max.yyy <- floor( (max(yyy) - min(yyy))/.24421 )
- if (pred.grid.size.max.xxx/2 < pred.grid.size.max.yyy)
- pred.grid.size <- floor(pred.grid.size.max.xxx/2)
- if (pred.grid.size.max.xxx > pred.grid.size.max.yyy*2)
- pred.grid.size <- floor(pred.grid.size.max.yyy)
- #pred.grid.size
- }
-
- # ----------------------------------------------
- # Create Prediction Grid with as.image
- # ----------------------------------------------
- ttt.image <- as.image(zzz,
- x= data.frame(xxx,yyy),
- nrow=round(pred.grid.size*grid.size.ratio), # nrow=X direction
- ncol=pred.grid.size, # ncol=Y direction
- na.rm=TRUE)
-
- if (!is.null(save.name)){
- png(file=save.name,
- bg="white",
- width = plot.width,
- height = plot.height)
- }
- image.plot(ttt.image,
- col = col.palette, ...)
- # zlim=c(0,5))
- if (!is.null(main.text)){
- title(main = main.text , font.main=4, line=2)
- title(main = paste("Spatial Grid:",pred.grid.size,"x",
- pred.grid.size*2), font.main=4, line=1, cex.main=0.75)}
-
- # Add political Boundaries
- # ----------------------------
- #map('state',add=TRUE, lwd=2, col="yellow")
- #map('state',add=TRUE, lwd=1.5, col="black")
-
-if (!is.null(save.name)){
- dev.off()
- }
-
-# --------------------------------------------------------------------------
-} # end function
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-
-
-# -----------------------------------------------------------------------------
-# -----------------------------------------------------------------------------
-# Point-in-Polygon Contours
-# -----------------------------------------------------------------------------
-# Daniel Fink
-# 2.7.08
-#
-# Description
-# -----------------
-# For a given set of locations determine if they fall into
-# a set of Polygon contours. Return one index (lenght of locations)
-# for each unique level of polygon contours.
-#
-# Also compute quantiles for locations and make a pretty picture.
-#
-# Input
-# ----------
-# xxx, yyy - locations
-# contour.polygons - list of polygon contours from contourLines
-# function
-#
-# Output
-# ----------
-# Return one index (lenght of locations)
-# for each unique level of polygon contours.
-#
-# Notes:
-# ---------
-#
-# Further Development:
-# ----------------------------
-# -----------------------------------------------------------------------------
-point.in.polygon.contours <- function(
- xxx, yyy,
- contour.polygons){
-# ------------------------------------------
-# Dummy Values/Calls
-# ------------------------------------------
- #contour.polygons <- sd.cont$contour.polygons
-# ------------------------------------------
-# Inits
-# ------------------------------------------
- require(splancs)
-
-# ------------------------------------------
-# Identify unique polygon levels
-# ------------------------------------------
- level.index <- rep(0,length(contour.polygons))
- for (iii in 1:length(contour.polygons))
- level.index[iii] <- contour.polygons[[iii]]$level
- unique.levels <- sort(unique(level.index))
- # Matrix of Contour indices
- contour.index <- matrix(FALSE,length(xxx),length(unique.levels))
-
- # Cycle through all Polygons in order
- # ** Do point-in-polygon operations
- # ** store indices according to polygon level
- # ----------------------------------------------------------
- #sum.points <- 0
- for (jjj in 1:length(contour.polygons)) {
- ttt.ind <- inpip(cbind(yyy,xxx),
- cbind(contour.polygons[[jjj]]$y,
- contour.polygons[[jjj]]$x))
- # Construct/store contour indices
- col.index <- (contour.polygons[[jjj]]$level == unique.levels)
- contour.index[ ttt.ind, col.index] <- TRUE
- }
- # -----------------------
- # Empirical Quantiles
- empirical.quant <- apply(contour.index, 2, mean)
-
- # ---------------------------------------------------------
- # Construct Indices into nonoverlapping contours
- # ---------------------------------------------------------
- non.olap.index <- matrix(FALSE, NROW(contour.index),
- NCOL(contour.index))
- # Begin with smallest contour
- non.olap.index[,NCOL(contour.index)] <-
- contour.index[,NCOL(contour.index)]
- # Sequentially subtract
- for (iii in NCOL(contour.index):2){
- non.olap.index[,(iii-1)] <- (contour.index[,(iii-1)] &
- !contour.index[,iii])
- }
- # % of data in each contour
- n.contour <- apply(non.olap.index, 2, sum)
- # ---------------------------------------------------------
-
-# Return contours as polygons too!!!
-results.list <- list(
- xxx = xxx,
- yyy = yyy,
- empirical.quant = empirical.quant,
- contour.polygons = contour.polygons,
- contour.index = contour.index,
- contour.level.index = level.index,
- non.olap.index = non.olap.index,
- n.contour = n.contour)
- return(results.list)
-}#---------------------------------------------------------------------
-#-----------------------------------------------------------------------
-
-
-#-----------------------------------------------------------------------
-# -------------------------------------------------------------------------------
-# Smooth ST Predictions
-#
-# -------------------------------------------------------------------------------
-smooth.st.predictions <- function(
- kkk, # Single Time slice
- pred.grid.size, # roughly twice desired plotting resolution
- gam.smoothing.knots=25,
- st.rough.dir,
- st.rough.name ,
- st.smooth.dir ,
- st.smooth.name){
- # ----------------
- #shape.dir, # <- "C:\\users\\Research.STBDT\\Data\\BDT.shapefiles\\"
- #shape.filename, # <- "STATES.shp"
- #selected.state.names = NULL) {
- # -----------------------------------------------
- stp.name <- paste(st.rough.dir,st.rough.name,".",kkk,".RData",sep="")
- load(stp.name) #st.pred
- require(mgcv)
- # -----------------------------------------------
- xxx <- st.pred$xxx
- yyy <- st.pred$yyy
- #xxx.name <- "Lon"
- #yyy.name <- "Lat"
- zzz <- st.pred$pred
- # -----------------------------------------------
- require(mgcv)
- d.gam <- gam( zzz ~ s(xxx,yyy, k=gam.smoothing.knots))
- nnn.xxx <- pred.grid.size
- nnn.yyy <- pred.grid.size
- xxx.pred <- seq(from=min(xxx),to=max(xxx),length=nnn.xxx)
- yyy.pred <- seq(from=min(yyy),to=max(yyy),length=nnn.yyy)
- pred.design <- expand.grid(xxx=xxx.pred, yyy=yyy.pred)
- # "Fuzz up" Prediction Grid to better fill in image.plot
- pred.design$xxx <- pred.design$xxx + runif(NROW(pred.design),
- min = -(abs(xxx.pred[2] - xxx.pred[1]))/2.,
- max = (abs(xxx.pred[2] - xxx.pred[1]))/2.)
- pred.design$yyy <- pred.design$yyy + runif(NROW(pred.design),
- min = -(abs(yyy.pred[2] - yyy.pred[1]))/2.,
- max = (abs(yyy.pred[2] - yyy.pred[1]))/2.)
-# # -------------------------------------------------------
-# # Cutout US States to reduce prediction time!
-# # --------------------------------------------------------------
-# if (!is.null(selected.state.names)){
-# sites <- data.frame(lon=pred.design$xxx, lat=pred.design$yyy)
-# #shape.dir <- "C:\\users\\Research.STBDT\\Data\\BDT.shapefiles\\"
-# #shape.filename <- "STATES.shp"
-# #selected.shape.names <-
-# # c("New York", "Pennsylvania", "New Jersey",
-# # "Ohio", "West Virginia", "Delaware", "Connecticut",
-# # "Rhode Island", "Massachusetts",
-# # "Vermont", "New Hampshire", "Maine",
-# # "Maryland", "Virginia")
-# att.selection.column.name <- "STATE_NAME"
-# location.pip <- point.in.shapefile(
-# sites,
-# shape.dir,
-# shape.filename,
-# att.selection.column.name,
-# selected.shape.names=selected.state.names)
-# #plot(sites)
-# #points(sites[location.pip,], col="red",cex=0.25)
-# pred.design <- pred.design[ location.pip, ]
-# }
-# # -------------------------------
- pred.gam <- predict(d.gam,
- newdata=pred.design,
- se.fit=FALSE, type="response")
- st.pred <- data.frame(pred.design, pred=pred.gam)
- names(st.pred)
- dim(st.pred)
- # -----------------------------------------------
- smooth.filename <- paste(st.smooth.dir,st.smooth.name,".",kkk,".RData",sep="")
- save(st.pred, file=smooth.filename)
- # For initialization in Halloween.maps()
- #smooth.filename <- paste(st.smooth.dir,st.smooth.name,".",1,".RData",sep="")
- #save(st.pred, file=smooth.filename)
- # -----------------------------------------------
- # ------------------------------------------------------------
- # Return Values
- # ------------------------------------------------------------
-} # end function
-# --------------------------------------------------------------------------------------------
-# -------------------------------------------------------------------------------------------
-
-
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-# Load & Process SPAT_COVAR Data for Spatial Prediction
-# --------------------------------------------------------------------------
-# This function will load, subsample, and process the Spatial
-# prediction data.
-#
-# Like the other functions I am writing, I will begin by keeping
-# this as simple as possible. KISS!!
-#
-# INPUT
-# ------------
-# INPUT
-# ------------
-# pred.data.file <- character string for file location including directory
-# pred.dir <- "~/norcar.temp/USA Prediction Grid/"
-# pred.data.file <- paste(pred.dir,"Random.locations.NE.10.31.07.csv",sep="")
-#
-#
-# This file is assumed to contain the following fields/information
-#
-# what happens if a field is missing?
-# Should these fields be compared/match to the p.data$X fields used to
-# develop the model?
-#
-#
-# NNN.pred <- (sub)sample size of prediction data file. Defalult = NULL
-# (defaults to whole data set)
-# NNN <- 5000
-# spatial.extent <- list( # NE Region
-# lat.max <- 45.0,
-# lat.min <- 39.0,
-# lon.min <- -82.5,
-# lon.max <- -67.0 )
-#
-# OUTPUT
-# ------------
-# D.pred - prediction data frame
-# locs - locations corresponding to D.pred
-#
-# To do:
-# ---------
-# I need to describe the format of D.pred in detail so that I can
-# generate new sets. Part of this will be to point to/describe the
-# process that Roger and I went through to generate this data.
-#
-# Currently, I have hard coded the list of predictor variables that
-# to be added to D.pred. I would like to add logic to match and
-# keep only those predictors that match a list of predictor names
-# target.var <- names(p.data$X)
-# possibly matching the classes of the variables too. That would
-# be very useful.
-#
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-make.SPAT.COVAR.pred.data <- function(
- pred.data.file,
- NNN.pred = NULL,
- spatial.extent = NULL) {
-# ---------------------------------------------------
- call <- match.call()
-# ----------------------------------------------
-# Load Data
-# ----------------------------------------------
- D.pred <- read.csv(file=pred.data.file)
- #dim(D.pred) #27933 67
-# ----------------------------------------------
-# Set Spatial Extent
-# ----------------------------------------------
- if (!is.null(spatial.extent)) {
- xxx <- D.pred$DECIMAL_LONGITUDE
- yyy <- D.pred$DECIMAL_LATITUDE
- if (is.null(spatial.extent$lat.max)) spatial.extent$lat.max <- max(yyy)
- if (is.null(spatial.extent$lat.min)) spatial.extent$lat.min <- min(yyy)
- if (is.null(spatial.extent$lon.min)) spatial.extent$lon.min <- min(xxx)
- if (is.null(spatial.extent$lon.max)) spatial.extent$lon.max <- max(xxx)
- x.zoom.ind <- (xxx < spatial.extent$lon.max & xxx > spatial.extent$lon.min)
- y.zoom.ind <- (yyy < spatial.extent$lat.max & yyy > spatial.extent$lat.min)
- zoom.ind <- as.logical( x.zoom.ind & y.zoom.ind)
- #sum(zoom.ind)
- D.pred <- D.pred[zoom.ind, ]
- rm(xxx,yyy)
- }
-
-# ---------------------------------------------------------------------
-# Convert regional NCLD classes counts to proportions
-# ---------------------------------------------------------------------
- # Currently, Rogers NLCD neighborhood variables in SPATCOVAR
- # contain the counts of each landcover class within the given neighborhood.
- # i.e percentages x 100
- # # of cells = (a*r)^2
- #
- # This was only for earlier version ==>
- # It should be a non-issue with the "new" version of
- # "ebird.data.processing.12.03.07.R"
- # ----------------------------------------------------
- # NLCD01_CMN" "NLCD01_IMN", are already stored as %'s
- # However, I am going to include them so that these
- # predictors are 100% compatible with the ebird predictors.
- # I need to fix the ebird data!!!
- # ------------------------------------------------------------
- nbhd.size <- c("A10R15", "A10R5", "A100R5")
- nbhd.cell.size <- c(22500,2500,250000)
- nlcd.vars <- c(
- "NLCD01_N11", "NLCD01_N12",
- "NLCD01_N21", "NLCD01_N22",
- "NLCD01_N23", "NLCD01_N24",
- "NLCD01_N31", "NLCD01_N41",
- "NLCD01_N42", "NLCD01_N43",
- "NLCD01_N52", "NLCD01_N71",
- "NLCD01_N81", "NLCD01_N82",
- "NLCD01_N90", "NLCD01_N95")
- for (iii in 1:3) {
- regional.nlcd.vars <- paste(nlcd.vars, nbhd.size[iii] ,sep="")
- D.pred[,names(D.pred) %in% regional.nlcd.vars] <-
- D.pred[,names(D.pred) %in%
- regional.nlcd.vars]/nbhd.cell.size[iii]*100
- }
-# ------------------------------------------------------------
-# Subsampling
-# ------------------------------------------------------------
- subsample.index <- NULL
- if (!is.null(NNN.pred)) {
- if (NNN.pred < NROW(D.pred)){
- subsample.index <- sample(1:NROW(D.pred), NNN.pred)
- D.pred <- D.pred[subsample.index, ]
- }}
-
-# ------------------------------------------------------------
-# Predictor Processing
-# ------------------------------------------------------------
- y <- D.pred$DECIMAL_LATITUDE
- x <- D.pred$DECIMAL_LONGITUDE
- # List of D.NE predictors that need to be removed
- remove.var <- c( "X", "DECIMAL_LATITUDE_CS", "DECIMAL_LONGITUDE_CS",
- "NED48_ELEVATION", "BLOCKGROUP_FIPS_ESRI04" ,
- "DECIMAL_LATITUDE", "DECIMAL_LONGITUDE")
- # "NLCD01_IMPERV" , "NLCD01_LANDCOVER" )
- D.pred <- D.pred[ , !(names(D.pred) %in% remove.var) ]
- # BCR Processing: BCR == 0 occurs at coastline locations
- # ---------------------------------------------------------------------
- #points( loc.x[ D.pred$BCR == 0],
- # loc.y[ D.pred$BCR == 0],
- # col=4,
- # cex=3.0,
- # pch=5)
- D.pred$BCR[ D.pred$BCR == 0] <- NA
- D.pred$BCR <- as.factor(D.pred$BCR)
- D.pred$NLCD01_LANDCOVER <- as.factor(D.pred$NLCD01_LANDCOVER)
- # Append Lat & lon
- # ------------------------------------------
- D.pred <- cbind(D.pred, x, y)
-# ------------------------------------------------------------
-# Return Values
-# ------------------------------------------------------------
- locs <- data.frame(x = x, y=y)
- data.list <- list(
- call = call,
- locs = locs,
- D.pred = D.pred,
- subsample.index=subsample.index)
- return(data.list)
-} # end function
-
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-
-
-
-
-
-# -----------------------------------------------------------------------------------------------------------
-# Plot Monthly Training Data Map
-# -----------------------------------------------------------------------------------------------------------
-monthly.maps <- function(
- xxx,
- yyy,
- jdates,
- zzz, # same length as (xxx, yyy, jdates)
- zzz.index.1, #red obs > pred ===> Predictions too BIG
- zzz.index.2)
-{# ----------------------------------------
- mo.txt <- c("Jan","Feb","Mar","Apr","May","Jun",
- "Jul","Aug","Sep","Oct","Nov","Dec")
- require(maps)
- par(mfrow=c(3,4),mar=c(0,0,1,0),cex=1.0)
- n.period <- 12
- for (iii in 1:n.period) {
- #Subseting Criterion
- # -------------------------------------
- #ll <- min(jdates)
- #ul <- max(jdates)
- #ttt.index <- jdates >= ll & jdates <= ul
- ll <- (365/n.period)*(iii-1)
- ul <- (365/n.period)*(iii)
- ttt.index <- jdates > ll & jdates < ul
- # --------------------------------------
- plot( xxx[ttt.index],
- yyy[ttt.index],
- #type="n",
- cex=0.25,
- pch=19,
- col="grey",
- axes = FALSE,
- main=paste( mo.txt[iii], " ", format(ll, digits=3),":",
- format(ul, digits=3)," + propor = ",
- format(sum(zzz[ttt.index] > 0)/ sum(ttt.index),
- digits=3)))
- box()
- # ---------------------------------------
- # Add negative residuals in blue
- # RED, neg res ==> ppp> yyy ==> almost all occur when yyy == 0)
- # ----------------------------------------
- ttt.index <- jdates > ll & jdates < ul & zzz.index.1
- points( xxx[ttt.index],
- yyy[ttt.index],
- cex=sqrt(abs(zzz[ttt.index])),
- col="red",
- #cex=0.25,
- pch=1)
- # BLUE ==> ppp < yyy
- ttt.index <- jdates > ll & jdates < ul & zzz.index.2
- points( xxx[ttt.index],
- yyy[ttt.index],
- cex=sqrt(abs(zzz[ttt.index])),
- col="blue",
- #cex=0.25,
- pch=4)
- # Add political Boundaries
- # ----------------------------
- map('state',add=TRUE, lwd=2, col="yellow")
- map('state',add=TRUE, lwd=1.5, col="black")
- } # end iii = months
-
- # ------------------------------------------------------------
- # Return Values
- # ------------------------------------------------------------
- return()
-} # end function
-# --------------------------------------------------------------------------------------------
-# -------------------------------------------------------------------------------------------
-
-
-# ------------------------------------------------------------------
-# FOR LOOP over time slices (within season)
-# * Load Predicted Surface
-# * Pixelate it
-# * Stack pixelated surface into Clustering design
-# row = pixel/locations, cols= times
-# ==> group trajectories
-# Q: rows come from stack/unstack(ttt.image) ??
-# * END FOR
-#
-# Then cluster the Clustering design
-# Output: each row, i.e. pixel/location will get a cluster
-# label and a silhoullette number
-#
-# Plot these on a map, perhaps one color at a time.
-#
-#
-# Inputs:
-# ---------
-# stp.save.name, #bs.stp.save.name
-# temporal.index,
-# pred.grid.size,
-# grid.size.ratio,
-# spatial.index=NULL This is an index on the prediction vector,
-# usually used to select regions (BCR's or states)
-# Outputs:
-# ---------
-#return.list <- list(call=call,
-# X=X.cluster,
-# X.image = ttt.image)
-# ------------------------------------------------------------------
-make.functional.data.design.matrix <- function(
- stp.save.dir, #bs.stp.save.dir
- stp.save.name, #bs.stp.save.name
- temporal.index,
- pred.grid.size,
- grid.size.ratio,
- spatial.index=NULL){
- # ----------------------------------
- call <- match.call()
- # ------------------------------------------------------------
- X.cluster <- NULL
- # ------------------------------------------------
- for (iii in (temporal.index)){
- # ----------------------------------------------
- # Load Space-Time Predictions From file
- # ----------------------------------------------
- stp.name <- paste(stp.save.dir,stp.save.name,".",iii,".RData",sep="")
- load(stp.name) # st.pred
- # ----------------------------------------------
- # Spatial Index
- # ----------------------------------------------
- if (is.null(spatial.index))
- spatial.index <- rep(TRUE, length(st.pred$xxx))
- # ----------------------------------------------
- # Create Prediction Grid with as.image
- # ----------------------------------------------
- xxx <- st.pred$xxx[spatial.index]
- yyy <- st.pred$yyy[spatial.index]
- zzz <- st.pred$pred[spatial.index]
- # ----------------------------------------------
- # Stack/Unstack using as.image
- # ----------------------------------------------
- ttt.image <- as.image(zzz,
- x= data.frame(xxx,yyy),
- nrow=round(pred.grid.size*grid.size.ratio), # nrow=X direction
- ncol=pred.grid.size,
- na.rm=TRUE) # ncol=Y direction
- #names(ttt.image)
- # ---------------------
- zzz.vector <- rep(0, length( ttt.image$ind[,1] ))
- for (jjj in 1:length( ttt.image$ind[,1] ))
- zzz.vector[jjj] <- ttt.image$z[ ttt.image$ind[jjj,1],
- ttt.image$ind[jjj,2]]
- #zzz.loc.x <- ttt.image$x[ttt.image$ind[,1]]
- #zzz.loc.y <- ttt.image$y[ttt.image$ind[,2]]
- # ---------------------
- #hist(zzz.vector)
- #image.plot(ttt.image)
- #points(ttt.image$x[ttt.image$ind[,1]],
- # ttt.image$y[ttt.image$ind[,2]],
- # cex=0.5*zzz.vector ,
- # col="yellow")
- # ---------------------
- # ----------------------------------------------
- # Add to cluster design
- # ----------------------------------------------
- X.cluster <- cbind(X.cluster, zzz.vector)
- } # end iii
-# ------------------------------------------
-# Return Values
-# ------------------------------------------
-return.list <- list(call=call,
- X=X.cluster,
- X.image = ttt.image)
-return(return.list)
-# --------------------------------------------------------------------------
-} # end function
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-# --------------------------------------------------------------------------
-
diff --git a/contrib/stem/current.vt b/contrib/stem/current.vt
deleted file mode 100644
index 9a86095..0000000
Binary files a/contrib/stem/current.vt and /dev/null differ
diff --git a/contrib/stem/init.py b/contrib/stem/init.py
deleted file mode 100644
index efacabb..0000000
--- a/contrib/stem/init.py
+++ /dev/null
@@ -1,646 +0,0 @@
-import os
-
-from core.modules.basic_modules import File, Directory, new_constant
-from core.modules.module_registry import get_module_registry
-from core.modules.vistrails_module import Module, ModuleError, ModuleConnector
-
-reg = get_module_registry()
-RSource = \
- reg.get_descriptor_by_name('edu.utah.sci.vistrails.rpy', 'RSource').module
-RFigure = reg.get_descriptor_by_name('edu.utah.sci.vistrails.rpy',
- 'RFigure', 'Figures').module
-
-def create_file_module(fname, f=None):
- if f is None:
- f = File()
- f.name = fname
- f.upToDate = True
- return f
-
-def create_dir_module(dname, d=None):
- if d is None:
- d = Directory()
- d.name = dname
- d.upToDate = True
- return d
-
-def get_path(fname=''):
- return os.path.join(os.path.dirname(__file__), fname)
-
-def build_params(input_ports, remap={}):
- def get_name(port):
- if port in remap:
- return remap[port]
- return port
- params = ",\n".join(["%s=%s" % (get_name(port[0]), get_name(port[0]))
- for port in input_ports
- if port[0] not in remap.keys() or (port[0] in remap.keys() and remap[port[0]] is not None)])
- return params
-
-
-
-def processActivePortData(inputPorts, object):
- portData = []
-
- if object.hasInputFromPort('stem.globals'):
- stemGlobals = object.getInputFromPort('stem.globals')
- else :
- stemGlobals = None
-
- for port in inputPorts:
- if port[0] != 'stem.globals' and object.hasInputFromPort(port[0]) and object.getInputFromPort(port[0]) is not None:
- portData.append((port[0], port[0]))
- if port[1] == '(edu.utah.sci.vistrails.basic:Directory)' or port[1] == '(edu.utah.sci.vistrails.basic:File)':
- object.set_variable(port[0], object.getInputFromPort(port[0]).name)
- else:
- object.set_variable(port[0], object.getInputFromPort(port[0]))
- elif stemGlobals:
- if stemGlobals.global_vars.has_key(port[0]) and stemGlobals.global_vars[port[0]] is not None:
- portData.append((port[0], port[0]))
-
- return portData
-
-class STEMConfiguration(RSource):
- _input_ports = []
- _output_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)')]
- def compute(self):
- self.chdir(get_path())
- self.run_file(get_path('STEM_Configuration.R'),
- excluded_outputs=set(['config']))
- self.setResult('config', self)
-
-class RunModels(RSource):
- _input_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)'),
- ('spp.name', '(edu.utah.sci.vistrails.basic:String)'),
- ('spp.common', '(edu.utah.sci.vistrails.basic:String)')]
- _output_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)')]
- def compute(self):
- self.chdir(get_path())
- self.set_variable('spp.dir.name', self.getInputFromPort('spp.name'))
- self.run_file(get_path('STEM_ModelingEngine.R'),
- excluded_inputs=set(['source', 'config']),
- excluded_outputs=set(['config']))
- self.setResult('config', self.getInputFromPort('config'))
-
-class BuildVisualizations(RSource):
- _input_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)')]
- _output_ports = [('results.dir',
- '(edu.utah.sci.vistrails.basic:Directory)')]
- def compute(self):
- self.chdir(get_path())
- self.run_file(get_path('STEM.nfold.pp.comp_2.12.10.R'),
- excluded_inputs=set(['source', 'config']),
- excluded_outputs=set(['results.dir']))
- dname = list(self.get_variable('results.dir'))[0]
- self.setResult('results.dir', create_dir_module(dname))
-
-class STEMFigure(RFigure):
- """Write only the R figure code. You do not need the png or pdf
- graphics setup code or the dev.off calls"""
- _input_ports = [('results.dir',
- '(edu.utah.sci.vistrails.basic:Directory)', ),
- ('pp.metric', '(edu.utah.sci.vistrails.basic:String)')]
- def compute(self):
- self.chdir(get_path())
- self.set_variable('results.dir',
- self.getInputFromPort('results.dir').name)
- self.run_figure_file(get_path('STEM_Figure.R'), 'png', 800, 600,
- excluded_inputs=set(['source',
- 'results.dir']))
-
-# class STEMCreateData(Module):
-# """Data preparation"""
-# def compute(self):
-# self.run_file(get_path('STEM.erd.data.creation.R'))
-
-class STEMGlobals(RSource):
- _input_ports = [('debugOutput', '(edu.utah.sci.vistrails.basic:Boolean)'),
- ('platform', '(edu.utah.sci.vistrails.basic:String)'),
- ('parent.dir', '(edu.utah.sci.vistrails.basic:Directory)'),
- ('code.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
- ('species.name', '(edu.utah.sci.vistrails.basic:String)'),
- ('common.name', '(edu.utah.sci.vistrails.basic:String)'),
- ('erd.data.file', '(edu.utah.sci.vistrails.basic:File)'),
- ('srd.pred.design.file', '(edu.utah.sci.vistrails.basic:File)')]
- _output_ports = [('self', '(edu.cornell.birds.stem:STEMGlobals)')]
- def compute(self):
- # run the requires and the loading of STEM libs
- parent_dir = self.getInputFromPort('parent.dir')
- self.chdir(self.getInputFromPort('code.directory').name)
- self.set_variable('parent.dir', parent_dir.name)
- # FIXME code.directory defaults to parent.dir
- if not self.hasInputFromPort('code.directory'):
- self.set_variable('code.directory', parent_dir.name)
- else:
- self.set_variable('code.directory',
- self.getInputFromPort('code.directory').name)
- self.set_variable('erd.data.filename',
- ''.join([parent_dir.name, "Data/", self.getInputFromPort('erd.data.file').name]))
- self.set_variable('srd.pred.design.filename',
- ''.join([parent_dir.name, "Data/", self.getInputFromPort('srd.pred.design.file').name]))
- species_name = self.getInputFromPort('species.name')
- stem_directory = create_dir_module(os.path.join(parent_dir.name, species_name))
- self.set_variable('stem.directory', stem_directory.name)
- self.set_variable('species.name', species_name)
- self.set_variable('common.name', self.getInputFromPort('common.name'))
-
- # FIXME add erd.data.filename and srd.pred.design.filename
- # No tags needed, then
-
- self.run_code(''.join(["source(\"", "STEM_Globals.R", "\")"]),
- excluded_inputs=set(['source', 'parent.dir',
- 'code.directory', 'erd.data.file',
- 'srd.pred.design.file']))
-
- # FIXME need to actually use and output the globals
- global_var_list = ['debugOutput',
- 'platform',
- 'parent.dir',
- 'code.directory',
- 'species.name',
- 'common.name',
- 'erd.data.filename',
- 'srd.pred.design.filename',
- 'stem.directory',
- 'spatial.extent.list',
- 'temporal.extent.list',
- 'predictor.names',
- 'response.family',
- 'cv.folds',
- 'cv.folds.par.list',
- 'cv.list',
- 'stem.init.par.list',
- 'base.model.par.list',
- 'srd.max.sample.size',
- 'split.par.list',
- 'st.matrix.name',
- 'jdate.seq',
- 'year.seq',
- 'conditioning.vars',
- 'st.matrix.ave.maps',
- 'begin.seq',
- 'end.seq',
- 'pred.grid.size',
- 'map.plot.width',
- 'spatial.extent.list',
- 'z.max',
- 'z.min',
- 'map.tag',
- 'date.bar',
- 'print.date',
- 'county.map',
- 'county.map.lwd',
- 'state.map',
- 'state.map.lwd']
- self.global_vars = dict((name, self.get_variable(name))
- for name in global_var_list)
-
-
-class InitERDMapAnalysis(RSource):
- _input_ports = [('project.directory', '(edu.utah.sci.vistrails.basic:String)'),
- ('species.directory.nametag', '(edu.utah.sci.vistrails.basic:String)'),
- ('map.directory.nametag', '(edu.utah.sci.vistrails.basic:String)'),
- ('map.file.nametag', '(edu.utah.sci.vistrails.basic:String)'),
- ('map.rows', '(edu.utah.sci.vistrails.basic:Integer)'),
- ('z.max', '(edu.utah.sci.vistrails.basic:Float)'),
- ('z.min', '(edu.utah.sci.vistrails.basic:Float)'),
- ('map.number', '(edu.utah.sci.vistrails.basic:Integer)'),
- ('lat.max', '(edu.utah.sci.vistrails.basic:Float)'),
- ('lat.min', '(edu.utah.sci.vistrails.basic:Float)'),
- ('lon.max', '(edu.utah.sci.vistrails.basic:Float)'),
- ('lon.min', '(edu.utah.sci.vistrails.basic:Float)')]
- _output_ports = [('self', '(edu.cornell.birds.stem:InitERDMapAnalysis)')]
- def compute(self):
- # run the requires and the loading of STEM libs
- self.chdir(self.getInputFromPort('project.directory'))
-
- self.set_variable('project.directory', self.getInputFromPort('project.directory'))
- self.set_variable('species.directory.nametag', self.getInputFromPort('species.directory.nametag'))
- self.set_variable('map.directory.nametag', self.getInputFromPort('map.directory.nametag'))
- self.set_variable('map.file.nametag', self.getInputFromPort('map.file.nametag'))
- self.set_variable('map.rows', self.getInputFromPort('map.rows'))
- self.set_variable('z.max', self.getInputFromPort('z.max'))
- self.set_variable('z.min', self.getInputFromPort('z.min'))
- self.set_variable('map.number', self.getInputFromPort('map.number'))
-
- latMax = self.getInputFromPort('lat.max')
- if latMax:
- self.set_variable('lat.max', latMax)
- else:
- ## self.set_variable('lat.max', "as.null(lat.max)")
- self.run_code("lat.max <- NULL")
-
- latMin = self.getInputFromPort('lat.min')
- if latMin:
- self.set_variable('lat.min', latMin)
- else :
- self.run_code("lat.min <- NULL")
-
- lonMax = self.getInputFromPort('lon.max')
- if lonMax:
- self.set_variable('lon.max', lonMax)
- else:
- self.run_code("lon.max <- NULL")
-
- lonMin = self.getInputFromPort('lon.min')
- if lonMin:
- self.set_variable('lon.min', lonMin)
- else:
- self.run_code("lon.min <- NULL")
-
- self.run_code(''.join(["source(\"", self.getInputFromPort('project.directory'), '/code/stem.vt.erd.map.function.R', "\")"]))
-
- global_var_list = ['project.directory',
- 'species.directory.nametag',
- 'map.directory.nametag',
- 'map.file.nametag',
- 'map.rows',
- 'z.max',
- 'z.min',
- 'map.number',
- 'lat.max',
- 'lat.min',
- 'lon.max',
- 'lon.min']
-
- self.global_vars = dict((name, self.get_variable(name))
- for name in global_var_list if name is not None)
-
-class PlotERDMaps(RSource):
- _input_ports = [('stem.globals', '(edu.cornell.birds.stem:InitERDMapAnalysis)'),
- ('project.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
- ('species.directory.nametag', '(edu.utah.sci.vistrails.basic:String)'),
- ('map.directory.nametag', '(edu.utah.sci.vistrails.basic:Directory)'),
- ('map.file.nametag', '(edu.utah.sci.vistrails.basic:File)'),
- ('map.rows', '(edu.utah.sci.vistrails.basic:Integer)'),
- ('z.max', '(edu.utah.sci.vistrails.basic:Float)'),
- ('z.min', '(edu.utah.sci.vistrails.basic:Float)'),
- ('map.number', '(edu.utah.sci.vistrails.basic:Integer)'),
- ('lat.max', '(edu.utah.sci.vistrails.basic:Float)'),
- ('lat.min', '(edu.utah.sci.vistrails.basic:Float)'),
- ('lon.max', '(edu.utah.sci.vistrails.basic:Float)'),
- ('lon.min', '(edu.utah.sci.vistrails.basic:Float)')]
- _output_ports = [('map_file', '(edu.utah.sci.vistrails.basic:File)')]
-
- def compute(self):
- ## stem_globals = self.getInputFromPort('stem.globals')
- ## for k, v in stem_globals.global_vars.iteritems():
- ## self.set_variable(k,v)
-
- activePorts = processActivePortData(PlotERDMaps._input_ports, self)
-
- remap = {'stem.globals': None}
- params = build_params(activePorts, remap)
- code_str = "mapFile <-stem.erd.maps(%s)" % params
-
- self.run_code(code_str)
-
- self.setResult('map_file', create_file_module(str(list(self.get_variable('mapFile'))[0])))
-
-
-class ERDDataCreation(RSource):
- _input_ports = [('protocol.tag', '(edu.utah.sci.vistrails.basic:String)'),
- ('max.effort.hours',
- '(edu.utah.sci.vistrails.basic:Float)'),
- ('max.effort.distance.fm',
- '(edu.utah.sci.vistrails.basic:Float)'),
- ('min.obs.time', '(edu.utah.sci.vistrails.basic:Float)'),
- ('max.obs.time', '(edu.utah.sci.vistrails.basic:Float)'),
- ('response.type', '(edu.utah.sci.vistrails.basic:String)'),
- ('ebird.data.dir',
- '(edu.utah.sci.vistrails.basic:Directory)'),
- ('erd.data.tag', '(edu.utah.sci.vistrails.basic:String)'),
- ('spatial.erd.tag',
- '(edu.utah.sci.vistrails.basic:String)'),
- ('checklist.covariate.names',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('core.covariate.names',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('NLCD.class.neighborhood.size',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('NLCD.names',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('class.level.fragstats',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('landscape.fragstat.tags',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('landscape.neighborhood.size',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)')]
- _output_ports = [('srd.pred.design.file',
- '(edu.utah.sci.vistrails.basic:File)'),
- ('erd.design.file',
- '(edu.utah.sci.vistrails.basic:File)')]
- def compute(self):
- self.chdir(get_path())
- self.set_variable('ebird.data.dir',
- self.getInputFromPort('ebird.data.dir').name)
- self.run_file(get_path('STEM_Globals.R'),
- excluded_inputs=set(['source', 'ebird.data.dir']))
- srd_fname = list(self.get_variable('srd.pred.design.filename'))[0]
- erd_fname = list(self.get_variable('erd.design.filename'))[0]
- self.setResult('srd.pred.design.file', create_file_module(srd_fname))
- self.setResult('erd.design.file', create_file_module(erd_fname))
-
-
-class ERDDataSubsetting(RSource):
- _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
- ('erd.data.filename', '(edu.utah.sci.vistrails.basic:File)'),
- ('srd.pred.design.filename', '(edu.utah.sci.vistrails.basic:File)'),
- ('spatial.extent.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('temporal.extent.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('species.name', '(edu.utah.sci.vistrails.basic:String)'),
- ('predictor.names', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('response.family', '(edu.utah.sci.vistrails.basic:String)'),
- ('srd.max.sample.size', '(edu.utah.sci.vistrails.basic:Integer)'),
- ('split.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)')]
- _output_ports = [('train.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('test.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('pred.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('stem.predictor.names', '(edu.utah.sci.vistrails.rpy:RVector:Types)')]
- # Get train.data, test.data, srd.data from eBird.data and expose
- # these three as the output ports
- def compute(self):
- ## stem_globals = self.getInputFromPort('stem.globals')
- ## for k, v in stem_globals.global_vars.iteritems():
- ## self.set_variable(k,v)
-
- activePorts = processActivePortData(ERDDataSubsetting._input_ports, self)
-
- remap = {'srd.pred.design.file': 'srd.pred.design.filename',
- 'stem.globals': None}
- params = build_params(activePorts, remap)
- code_str = "eBird.data <- erd.srd.data.subsetting(%s)" % params
-
- self.run_code(code_str,
- excluded_inputs=set(['source', 'srd.pred.design.file']),
- excluded_outputs=set(['eBird.data']))
-
- train = self.get_variable('eBird.data$train.data')
- test = self.get_variable('eBird.data$test.data')
- srd = self.get_variable('eBird.data$srd.data')
-
- self.run_code("stem.predictor.names <- names(eBird.data$train.data$X)")
- stem_predictor_names = self.get_variable('stem.predictor.names')
-
- self.setResult('train.data', train)
- self.setResult('test.data', test)
- self.setResult('pred.data', srd)
- self.setResult('stem.predictor.names', stem_predictor_names)
-
-class FitSTEM(RSource):
- _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
- ('train.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('stem.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
- ('response.family', '(edu.utah.sci.vistrails.basic:String)'),
- ('cv.folds', '(edu.utah.sci.vistrails.basic:Integer)'),
- ('cv.folds.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('stem.init.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('base.model.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)')]
- _output_ports = [('models.directory', '(edu.utah.sci.vistrails.basic:Directory)')]
-
- def compute(self):
- # use a single models dir with a variable number of
- # subdirectories depending on the cv.folds value
- # same for results, now -- models/stem.models.[1-10]
- ## stem_globals = self.getInputFromPort('stem.globals')
- ## for k, v in stem_globals.global_vars.iteritems():
- ## self.set_variable(k,v)
-
- activePorts = processActivePortData(FitSTEM._input_ports, self)
-
- remap = {'stem.globals': None}
- params = build_params(activePorts, remap)
- code_str = "stem(%s)" % params
-
- self.run_code(code_str)
-
-
-class ERDPredictivePerformance(RSource):
- _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
- ('test.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('stem.directory',
- '(edu.utah.sci.vistrails.basic:Directory)'),
- ('pp.directory',
- '(edu.utah.sci.vistrails.basic:Directory)'),
- ('cv.list',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('n.mc',
- '(edu.utah.sci.vistrails.basic:Integer)'),
- ('grid.cell.min.lat',
- '(edu.utah.sci.vistrails.basic:Float)'),
- ('grid.cell.min.lon',
- '(edu.utah.sci.vistrails.basic:Float)'),
- ('min.val.cell.locs',
- '(edu.utah.sci.vistrails.basic:Integer)'),
- ('threshold',
- '(edu.utah.sci.vistrails.basic:Float)'),
- ('min.testset.sample.size',
- '(edu.utah.sci.vistrails.basic:Integer)'),
- ('plot.it',
- '(edu.utah.sci.vistrails.basic:Boolean)')]
- # pp.directory specifies where, but we can move this, i think
- _output_ports = [('pp.directory',
- '(edu.utah.sci.vistrails.basic:Directory)')]
- def compute(self):
- self.set_variable('stem.directory',
- self.getInputFromPort('stem.directory').name)
- pp_directory = self.getInputFromPort('pp.directory')
- self.set_variable('pp.directory', pp_directory.name)
- self.run_file('')
- self.setResult('pp.directory', pp_directory)
-
-class PredictSTEM(RSource):
- _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
- ('stem.directory',
- '(edu.utah.sci.vistrails.basic:Directory)'),
- ('pred.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('st.pred.tag', '(edu.utah.sci.vistrails.basic:String)'),
- ('st.prediction.filename',
- '(edu.utah.sci.vistrails.basic:File)')]
- _output_ports = [('st.pred', '(edu.utah.sci.vistrails.rpy:RList:Types)')]
- def compute(self):
- pas
-
-class ERDPredictSTMatrix(RSource):
- _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
- ('stem.directory',
- '(edu.utah.sci.vistrails.basic:Directory)'),
- ('pred.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('stem.predictor.names',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('st.matrix.name',
- '(edu.utah.sci.vistrails.basic:String)'),
- ('jdate.seq',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('year.seq',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('conditioning.vars',
- '(edu.utah.sci.vistrails.rpy:RList:Types)')]
- _output_ports = [('st.matrix.directory',
- '(edu.utah.sci.vistrails.basic:Directory)')]
- def compute(self):
- stem_globals = self.getInputFromPort('stem.globals')
- ## for k, v in stem_globals.global_vars.iteritems():
- ## self.set_variable(k,v)
-
- activePorts = processActivePortData(ERDPredictSTMatrix._input_ports, self)
-
- remap = {'stem.globals': None}
- params = build_params(activePorts, remap)
- code_str = "predict.erd.st.matrix(%s)" % params
-
- self.run_code(code_str)
-
- if self.hasInputFromPort('stem.directory'):
- if self.hasInputFromPort('st.matrix.name'):
- self.setResult('st.matrix.directory', create_dir_module(os.path.join(self.getInputFromPort('stem.directory').name,
- self.getInputFromPort('st.matrix.name'))))
- else:
- self.setResult('st.matrix.directory', create_dir_module(os.path.join(self.getInputFromPort('stem.directory').name,
- str(list(stem_globals.global_vars['st.matrix.name'])[0]))))
- else:
- if self.hasInputFromPort('st.matrix.name'):
- self.setResult('st.matrix.directory', create_dir_module(os.path.join(str(list(stem_globals.global_vars['stem.directory'])[0]),
- self.getInputFromPort('st.matrix.name'))))
- else:
- self.setResult('st.matrix.directory', create_dir_module(os.path.join(str(list(stem_globals.global_vars['stem.directory'])[0]),
- str(list(stem_globals.global_vars['st.matrix.name'])[0]))))
-
-
-class STMatrixCVAvg(RSource):
- _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
- ('stem.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
- ('st.matrix.input.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
- ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('jdate.seq', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('year.seq', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('st.matrix.output.directory', '(edu.utah.sci.vistrails.basic:Directory)')]
- _output_ports = [('st.matrix.directory', '(edu.utah.sci.vistrails.basic:Directory)'),
- ('map.directory', '(edu.utah.sci.vistrails.basic:Directory)')]
- def compute(self):
- self.set_variable('st.matrix.input.directory', self.getInputFromPort('st.matrix.input.directory').name)
- st_matrix_output_directory = self.getInputFromPort('st.matrix.input.directory')
- self.set_variable('st.matrix.output.directory', st_matrix_output_directory.name)
-
- stem_globals = self.getInputFromPort('stem.globals')
- ## for k, v in stem_globals.global_vars.iteritems():
- ## self.set_variable(k,v)
-
- activePorts = processActivePortData(STMatrixCVAvg._input_ports, self)
-
- remap = {'stem.globals': None}
- params = build_params(activePorts, remap)
- code_str = "st.matrix.cv.average(%s)" % params
-
- self.run_code(code_str)
-
- self.setResult('st.matrix.directory', st_matrix_output_directory)
- self.setResult('map.directory', create_dir_module(os.path.join(str(list(stem_globals.global_vars['stem.directory'])[0]),
- str(list(stem_globals.global_vars['st.matrix.ave.maps'])[0]))))
-
-
-
-class STMatrixMaps(RSource):
- _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
- ('st.matrix.directory',
- '(edu.utah.sci.vistrails.basic:Directory)'),
- ('map.directory',
- '(edu.utah.sci.vistrails.basic:Directory)'),
- ('jdate.seq',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('year.seq',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('begin.seq',
- '(edu.utah.sci.vistrails.basic:Integer)'),
- ('end.seq',
- '(edu.utah.sci.vistrails.basic:Integer)'),
- ('pred.grid.size',
- '(edu.utah.sci.vistrails.basic:Integer)'),
- ('map.plot.width',
- '(edu.utah.sci.vistrails.basic:Integer)'),
- ('spatial.extent.list',
- '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('z.max',
- '(edu.utah.sci.vistrails.basic:Float)'),
- ('z.min',
- '(edu.utah.sci.vistrails.basic:Float)'),
- ('map.tag',
- '(edu.utah.sci.vistrails.basic:String)'),
- ('date.bar',
- '(edu.utah.sci.vistrails.basic:Boolean)'),
- ('print.date',
- '(edu.utah.sci.vistrails.basic:Boolean)'),
- ('county.map',
- '(edu.utah.sci.vistrails.basic:Boolean)'),
- ('county.map.lwd',
- '(edu.utah.sci.vistrails.basic:Float)'),
- ('state.map',
- '(edu.utah.sci.vistrails.basic:Boolean)'),
- ('state.map.lwd',
- '(edu.utah.sci.vistrails.basic:Float)')]
- _output_ports = [('map.directory',
- '(edu.utah.sci.vistrails.basic:Directory)'),
- ('map_file_1',
- '(edu.utah.sci.vistrails.basic:File)')]
- def compute(self):
- self.set_variable('st.matrix.directory', ''.join([self.getInputFromPort('st.matrix.directory').name]))
- map_directory = self.getInputFromPort('map.directory')
- self.set_variable('map.directory', map_directory.name)
-
- ## stem_globals = self.getInputFromPort('stem.globals')
- ## for k, v in stem_globals.global_vars.iteritems():
- ## self.set_variable(k,v)
-
- activePorts = processActivePortData(STMatrixMaps._input_ports, self)
-
- remap = {'stem.globals': None}
- params = build_params(activePorts, remap)
- code_str = "st.matrix.maps(%s)" % params
-
- self.run_code(code_str)
-
- self.setResult('map.directory', map_directory)
-
-
-
-class ERD_CV_Avg_Maps(RSource):
- _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'),
- ('stem.directory',
- '(edu.utah.sci.vistrails.basic:Directory)'),
- ('st.matrix.file.tag',
- '(edu.utah.sci.vistrails.basic:String)'),
- ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'),
- ('maps.directory',
- '(edu.utah.sci.vistrails.basic:Directory)'),
- ('map.file.tag', '(edu.utah.sci.vistrails.basic:String)'),
- ('ns.rows', '(edu.utah.sci.vistrails.basic:Integer)'),
- ('map.plot.pixel.width',
- '(edu.utah.sci.vistrails.basic:Integer)'),
- ('mapping.spatial.extent',
- '(edu.utah.sci.vistrails.rpy:RList:Types)'),
- ('z.max', '(edu.utah.sci.vistrails.basic:Float)')]
- _output_ports = [('erd.cv.avg.maps.directory',
- '(edu.utah.sci.vistrails.basic:Directory)')]
- def compute(self):
- pass
-
-# _modules = [STEMConfiguration,
-# RunModels,
-# BuildVisualizations,
-# STEMFigure]
-
-_modules = [ERDDataCreation,
- ERDDataSubsetting,
- FitSTEM,
- ERDPredictivePerformance,
- PredictSTEM,
- ERDPredictSTMatrix,
- STMatrixCVAvg,
- STMatrixMaps,
- # ERD_CV_Avg_Maps,
- STEMGlobals,
- InitERDMapAnalysis,
- PlotERDMaps
- ]
diff --git a/contrib/stem/mycurrent.vt b/contrib/stem/mycurrent.vt
deleted file mode 100644
index 1b3d0d0..0000000
Binary files a/contrib/stem/mycurrent.vt and /dev/null differ
diff --git a/contrib/stem/mycurrent2.vt b/contrib/stem/mycurrent2.vt
deleted file mode 100644
index 208e254..0000000
Binary files a/contrib/stem/mycurrent2.vt and /dev/null differ
diff --git a/contrib/titan/__init__.py b/contrib/titan/__init__.py
deleted file mode 100644
index 546fd3f..0000000
--- a/contrib/titan/__init__.py
+++ /dev/null
@@ -1,59 +0,0 @@
-###########################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-################################################################################
-# Titan Package for VisTrails (Sandia National Laboratories)
-################################################################################
-
-"""The Titan Informatics Toolkit is a collaborative effort between
-Sandia National Laboratories and Kitware Inc. It represents a
-significant expansion of the Visualization ToolKit (VTK) to support
-the ingestion, processing, and display of informatics data. By
-leveraging the VTK engine, Titan provides a flexible, component
-based, pipeline architecture for the integration and deployment of
-algorithms in the fields of intelligence, semantic graph and
-information analysis.
-
-https://www.kitware.com/InfovisWiki/"""
-
-identifier = 'edu.utah.sci.vistrails.titan'
-name = 'Titan'
-version = '0.1.2'
-
-def package_dependencies():
- import core.packagemanager
- manager = core.packagemanager.get_package_manager()
-
- ret = []
- #if manager.has_package('edu.utah.sci.vistrails.vtk'):
- ret.append('edu.utah.sci.vistrails.vtk')
- #if manager.has_package('edu.utah.sci.vistrails.spreadsheet'):
- ret.append('edu.utah.sci.vistrails.spreadsheet')
- return ret
-
-def package_requirements():
- import core.requirements
- if not core.requirements.python_module_exists('titan'):
- raise core.requirements.MissingRequirement('titan')
- if not core.requirements.python_module_exists('PyQt4'):
- print 'PyQt4 is not available. There will be no interaction',
- print 'between Titan and the spreadsheet.'
- import titan
diff --git a/contrib/titan/base_module.py b/contrib/titan/base_module.py
deleted file mode 100644
index 0b74737..0000000
--- a/contrib/titan/base_module.py
+++ /dev/null
@@ -1,203 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-################################################################################
-# This describes basic modules used by other VTK module
-################################################################################
-import vtk
-from core.modules.module_registry import registry
-from core.modules.vistrails_module import Module, ModuleError
-from itertools import izip
-
-################################################################################
-
-class vtkBaseModule(Module):
- """
- vtkBaseModule is the base class for all VTK modules in VisTrails, it acts
- as a wrapper to direct all input/output ports to appropriate VTK function
- calls
-
- """
-
- def __init__(self):
- """ vtkBaseModule() -> vtkBaseModule
- Instantiate an emptt VTK Module with real VTK instance
-
- """
- Module.__init__(self)
- self.vtkInstance = None
-
- def is_cacheable(self):
- # VTK objects are by default cacheable only if they're subclasses
- # of vtkAlgorithm
- return (issubclass(self.vtkClass, vtk.vtkAlgorithm)
- and (not issubclass(self.vtkClass, vtk.vtkAbstractMapper)))
-
- def call_input_function(self, function, params):
- """self.call_input_function(function, params) -> None
- Calls the input function on the vtkInstance, or a special
- input function if one exists in the class."""
- if hasattr(self, '_special_input_function_' + function):
- attr = getattr(self, '_special_input_function_' + function)
- else:
- try:
- attr = getattr(self.vtkInstance, function)
- except AttributeError:
- # Compensates for overload by exploiting the fact that
- # no VTK method has underscores.
- f = function.find('_')
- if f != -1:
- function = function[:f]
- attr = getattr(self.vtkInstance, function)
- attr(*params)
- # print "Called ",attr,function,params
-
- @classmethod
- def _provide_doc(cls, port_name):
- f = port_name.find('_')
- if f != -1:
- name = port_name[:f]
- else:
- name = port_name
- return getattr(cls.vtkClass, name).__doc__
-
- @classmethod
- def provide_input_port_documentation(cls, port_name):
- return cls._provide_doc(port_name)
-
- @classmethod
- def provide_output_port_documentation(cls, port_name):
- return cls._provide_doc(port_name)
-
- def compute(self):
- """ compute() -> None
- Actually perform real VTK task by directing all input/output ports
- to VTK function calls
-
- """
-
- def call_it(function, p):
- # Translate between VisTrails objects and VTK objects
- if p is None:
- # None indicates a call with no parameters
- params = []
- elif type(p) == tuple:
- # A tuple indicates a call with many parameters
- params = list(p)
- else:
- # Otherwise, it's a single parameter
- params = [p]
-
- # Unwraps VTK objects
- for i in xrange(len(params)):
- if hasattr(params[i], 'vtkInstance'):
- params[i] = params[i].vtkInstance
- try:
- self.call_input_function(function, params)
- except Exception, e:
- msg = 'VTK Exception: '
- raise ModuleError(self, msg + str(type(e)) + ': ' + str(e))
-
- # Always re-create vtkInstance module, no caching here
- if self.vtkInstance:
- del self.vtkInstance
- self.vtkInstance = self.vtkClass()
-
- # We need to call method ports before anything else, and in
- # the right order.
-
- # FIXME: This does not belong here, it belongs in the main class
- # No time for that now
- methods = self.is_method.values()
- methods.sort()
- for value in methods:
- (_, port) = value
- conn = self.is_method.inverse[value]
- p = conn()
- call_it(port, p)
-
- # Make sure all input ports are called correctly
- for (function, connector_list) in self.inputPorts.iteritems():
- paramList = self.forceGetInputListFromPort(function)
- if function[:18]=='SetInputConnection':
- paramList = zip([int(function[18:])]*len(paramList),
- paramList)
- function = 'SetInputConnection'
- if function=='AddInputConnection':
- desc = registry.get_descriptor_by_name(
- 'edu.utah.sci.vistrails.vtk',
- 'vtkAlgorithmOutput')
- for i in xrange(len(paramList)):
- if type(paramList[i])==desc.module:
- paramList[i] = (0, paramList[i])
- for p,connector in izip(paramList, connector_list):
- # Don't call method
- if connector in self.is_method:
- continue
- call_it(function, p)
-
- # Call update if appropriate
- if hasattr(self.vtkInstance, 'Update'):
- def ProgressEvent(obj, event):
- self.logging.update_progress(self, obj.GetProgress())
- isAlgorithm = issubclass(self.vtkClass, vtk.vtkAlgorithm)
- if isAlgorithm:
- cbId = self.vtkInstance.AddObserver('ProgressEvent', ProgressEvent)
- self.vtkInstance.Update()
- if isAlgorithm:
- self.vtkInstance.RemoveObserver(cbId)
-
- # Then update the output ports also with appropriate function calls
- for function in self.outputPorts.keys():
- if function[:13]=='GetOutputPort':
- i = int(function[13:])
- vtkOutput = self.vtkInstance.GetOutputPort(i)
- output = vtkBaseModule.wrapperModule('vtkAlgorithmOutput',
- vtkOutput)
- self.setResult(function, output)
- elif hasattr(self.vtkInstance, function):
- retValues = getattr(self.vtkInstance, function)()
- if issubclass(retValues.__class__, vtk.vtkObject):
- className = retValues.GetClassName()
- output = vtkBaseModule.wrapperModule(className, retValues)
- self.setResult(function, output)
- elif (type(retValues) in [tuple, list]):
- result = list(retValues)
- for i in xrange(len(result)):
- if issubclass(result[i].__class__, vtk.vtkObject):
- className = result[i].GetClassName()
- result[i] = vtkBaseModule.wrapperModule(className,
- result[i])
- self.setResult(function, type(retValues)(result))
- else:
- self.setResult(function, retValues)
-
- @staticmethod
- def wrapperModule(classname, instance):
- """ wrapperModule(classname: str, instance: vtk class) -> Module
- Create a wrapper module in VisTrails with a vtk instance
-
- """
- result = registry.get_descriptor_by_name(
- 'edu.utah.sci.vistrails.vtk',
- classname).module()
- result.vtkInstance = instance
- return result
diff --git a/contrib/titan/class_tree.py b/contrib/titan/class_tree.py
deleted file mode 100644
index c9f53ff..0000000
--- a/contrib/titan/class_tree.py
+++ /dev/null
@@ -1,268 +0,0 @@
-# Author: Prabhu Ramachandran
-# Copyright (c) 2004, Enthought, Inc.
-# License: BSD Style.
-
-"""This module generates the class hierarchy for any given Python
-modules. This can be used (among other things) to generate the
-traitified VTK classes in the correct order.
-
-"""
-
-import __builtin__
-
-
-class TreeNode(object):
- """Represents a node in the class tree.
-
- Stores information on the sub and super classes of a particular
- class. It also stores the inheritance level of the class inside
- the inheritance tree (essentially how many levels of inheritance
- are there below this class). This inheritance level is computed
- when the `get_level` method is called. The `get_level` method
- works only when the parent information is complete.
-
- """
-
- def __init__(self, klass):
- """Given a class, create a node in the tree.
-
- Parameters
- ----------
- - klass : `class`
-
- The class which is represented as a node in the tree.
-
- """
- self.klass = klass
- self.name = klass.__name__
- self.children = []
- self.parents = []
- # Uninitialized level is set to None
- self.level = None
-
- def add_parent(self, parent):
- """Add a parent node."""
- assert isinstance(parent, TreeNode)
- if parent not in self.parents:
- self.parents.append(parent)
-
- def add_child(self, child):
- """Add a child node. """
- assert isinstance(child, TreeNode)
- if child not in self.children:
- self.children.append(child)
-
- def get_level(self):
- """Returns the inheritance level of the node (an int). If the
- level has not been set, the method computes it. Note however,
- that this computation will fail if the parent information is
- incorrect.
-
- """
- if not self.level:
- if self.parents:
- self.level = max([x.get_level() for x in self.parents]) + 1
- else:
- self.level = 0
- return self.level
-
- def get_ancestors(self):
- """Returns a list of ancestor nodes from which this class has
- descended.
-
- """
- def _get_ancestors(node, ancestors):
- ancestors.extend(node.parents)
- for p in node.parents:
- _get_ancestors(p, ancestors)
- ancestors = []
- _get_ancestors(self, ancestors)
- return ancestors
-
-
-class ClassTree(object):
- """Contains and generates all the class tree information.
-
- On initialization of the instance, nothing is done. The classes
- are obtained using the list of modules (or a single module) that
- is used to initialize the instance. One must then call the
- `create` method to generate the tree structure. The instance of
- the class also can be treated as an iterator which iterates over
- the nodes of the tree.
-
- There are two ways in which the tree hierarchy is stored. A
- dictionary mapping class names to the tree node and a tree
- represented as a list of lists containing the nodes. The tree is
- organized based on a concept of an inheritance level. A class
- that has no parent classes (no base classes) is said to be at
- level zero. If a class inherits successively from 7 classes, it
- is at level 6. An example of inheritance for a vtkFoo class is
- given below:
-
- vtkFoo -> vtkBar -> vtkObject -> vtkObjectBase
-
- Here, vtkObjectBase has an inheritance level of 0 and vtkFoo a
- level of 3. One can traverse the tree by using the level as an
- index and find all the classes at a particular level.
-
- Here is some example usage of this class::
-
- >>> import vtk
- >>> t = ClassTree(vtk)
- >>> t.create()
- >>> print t.get_node('vtkObject').name
- vtkObject
- >>> print t.get_node('vtkObject').parents[0].name
- vtkObjectBase
- >>> print len(t.tree[0])
- 1
- >>> t.tree[0][0].name
- vtkObjectBase
-
- """
-
- def __init__(self, modules):
- """Initialize the instance with the given modules.
-
- Parameters
- ----------
-
- - modules : `sequence` of modules or a module
-
- This is either a single module or a sequence of modules.
- The instance uses these list of modules to generate the
- class tree.
-
- """
- self.nodes = {}
- self.tree = [[]]
- if not hasattr(modules, '__iter__'):
- self.modules = [modules]
- else:
- self.modules = modules
-
- def __iter__(self):
- return iter(self.nodes.values())
-
- def _generate_hierarchy(self, klass):
- """Does the hard work of generating the class hierarchy."""
- node = self.get_node(klass.__name__, create=1)
- for base in klass.__bases__:
- base_node = self.get_node_from_class(base, create=1)
- node.add_parent(base_node)
- base_node.add_child(node)
- self._generate_hierarchy(base)
-
- def get_class(self, name):
- """Given a class name in the given modules returns the class."""
- klass = None
- for m in self.modules:
- if hasattr(m, name):
- return getattr(m, name)
- if hasattr(__builtin__, name):
- klass = getattr(__builtin__, name)
- if not klass:
- try:
- klass = self.nodes[name].klass
- except KeyError:
- raise KeyError, "Cannot find class of name %s"%name
- return klass
-
- def add_node(self, klass):
- """Create a node for the given class."""
- name = klass.__name__
- if not self.nodes.has_key(name):
- node = TreeNode(klass)
- self.nodes[name] = node
- return node
-
- def get_node(self, name, create=0):
- """Get a node of the given name.
-
- Parameters
- ----------
-
- - name : `str`
-
- Name of the node to get.
-
- - create : `boolean`
-
- If True, a new node will be added if no node of the given
- name is available. Defaults to False.
-
- Returns
- -------
-
- - `TreeNode`
-
- """
- if self.nodes.has_key(name):
- return self.nodes[name]
- elif create:
- return self.add_node(self.get_class(name))
-
- def get_node_from_class(self, cls, create=0):
- """Get a node of the given class.
-
- Parameters
- ----------
-
- - cls : `class`
-
- Class of the node to get.
-
- - create : `boolean`
-
- If True, a new node will be added if no node of the given
- name is available. Defaults to False.
-
- Returns
- -------
-
- - `TreeNode`
-
- """
- name = cls.__name__
- if self.nodes.has_key(name):
- return self.nodes[name]
- elif create:
- return self.add_node(cls)
-
- def create(self, class_names=None):
- """This method generates the class tree given an optional list
- of class names.
-
- Parameters
- ----------
-
- - class_names - `list` of `str`
-
- An optional list of names of the classes to generate the
- tree for. Defaults to None where the class list is computed
- from the modules.
-
- """
- if class_names is None:
- class_names = []
- for m in self.modules:
- class_names.extend(dir(m))
-
- # Generate the nodes.
- for name in class_names:
- klass = self.get_class(name)
- if klass and hasattr(klass, '__bases__'):
- self._generate_hierarchy(klass)
-
- # Compute the inheritance level and store the nodes in the tree.
- for node in self:
- d = node.get_level()
- while len(self.tree) <= d:
- self.tree.append([])
- self.tree[d].append(node)
-
- # Sort the nodes alphabetically.
- def _comp(x, y):
- return cmp(x.name, y.name)
- for nodes in self.tree:
- nodes.sort(_comp)
diff --git a/contrib/titan/fix_classes.py b/contrib/titan/fix_classes.py
deleted file mode 100644
index 8181458..0000000
--- a/contrib/titan/fix_classes.py
+++ /dev/null
@@ -1,51 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-import vtk
-
-################################################################################
-# Some fixed classes that solve a few VTK API issues
-
-# This dictionary stores the patched class to vtk class mapping.
-# This would be naturally better stored as an attribute directly on the
-# patched class. VTK, however, doesn't like class attributes.
-description = {}
-
-# http://www.vtk.org/doc/nightly/html/classvtkImagePlaneWidget.html
-# SetUserControlledLookupTable needs to be set before calling
-# SetLookupTable. VTK should do it automatically, so let's fix it
-
-
-# This fix seems to break on VTK versions larger than 5.0.3. It might also
-# be because of an interaction with python 2.6, but I haven't checked that.
-class vtkImagePlaneWidget_fixed(vtk.vtkImagePlaneWidget):
- def SetLookupTable(self, lookup_table):
- self.UserControlledLookupTableOn()
- vtk.vtkImagePlaneWidget.SetLookupTable(self, lookup_table)
-
-if tuple(vtk.vtkVersion().GetVTKVersion().split('.')) < ('5', '0', '4'):
- description[vtkImagePlaneWidget_fixed] = vtk.vtkImagePlaneWidget
-else:
- description[id(vtkImagePlaneWidget_fixed)] = vtk.vtkImagePlaneWidget
-
-# Set docstring to wrap it correctly
-vtkImagePlaneWidget_fixed.SetLookupTable.__doc__ = vtk.vtkImagePlaneWidget.SetLookupTable.__doc__
diff --git a/contrib/titan/hasher.py b/contrib/titan/hasher.py
deleted file mode 100644
index 34909ec..0000000
--- a/contrib/titan/hasher.py
+++ /dev/null
@@ -1,36 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-# This is the user-defined hasher for VTK, that takes into account
-# incoming and outgoing connections
-from core.cache.hasher import Hasher
-
-def vtk_hasher(pipeline, module, chm):
- outgoing_connections = pipeline.graph.edges_from(module.id)
- incoming_connections = pipeline.graph.edges_to(module.id)
- current_hash = Hasher.module_signature(module, chm)
- chashes = [Hasher.connection_signature(pipeline.connections[c_id])
- for (_, c_id) in outgoing_connections]
- chashes += [Hasher.connection_signature(pipeline.connections[c_id])
- for (_, c_id) in incoming_connections]
- compound_hash = Hasher.compound_signature(chashes)
- return Hasher.compound_signature([current_hash, compound_hash])
diff --git a/contrib/titan/init.py b/contrib/titan/init.py
deleted file mode 100644
index 070661a..0000000
--- a/contrib/titan/init.py
+++ /dev/null
@@ -1,1132 +0,0 @@
-###########################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-################################################################################
-# Titan Package for VisTrails (Sandia National Laboratories)
-################################################################################
-from core.bundles import py_import
-
-pkgs = [ "titan.Antiword",
-#"titan.Clustering",
-"titan.Common",
-"titan.DataAnalysis",
-"titan.GMeans",
-"titan.HDF5",
-#"titan.JSON",
-#"titan.LsaLib",
-"titan.MPIDataAnalysis",
-"titan.MPITextAnalysis",
-"titan.MTGLGraphAnalysis",
-"titan.OWL",
-#"titan.QtGui",
-"titan.StanfordNER",
-"titan.TextAnalysis",
-"titan.Trilinos",
-"titan.Web",
-#"titan.uBLAS",
-"titan.XPDF"]
-
-import sys
-titan2 = []
-for i in pkgs:
- __import__(i)
- titan2.append(sys.modules[i])
-
-titan = sys.modules["titan"]
-
-import vtk
-
-in_out_table = {
-
-}
-
-
-from core.utils import all, any, VistrailsInternalError, InstanceObject
-from core.debug import debug
-from core.modules.basic_modules import Integer, Float, String, File, \
- Variant, Color
-from core.modules.module_registry import get_module_registry
-from core.modules.vistrails_module import new_module, ModuleError
-from base_module import vtkBaseModule
-from class_tree import ClassTree
-from vtk_parser import VTKMethodParser
-import re
-import os.path
-from itertools import izip
-from vtkcell import VTKCell
-import tf_widget
-import offscreen
-import fix_classes
-import inspectors
-from hasher import vtk_hasher
-import sys
-
-################################################################################
-
-# filter some deprecation warnings coming from the fact that vtk calls
-# range() with float parameters
-
-import warnings
-warnings.filterwarnings("ignore",
- message="integer argument expected, got float")
-
-################################################################################
-
-if tuple(vtk.vtkVersion().GetVTKVersion().split('.')) < ('5', '0', '4'):
- def get_description_class(klass):
- """Because sometimes we need to patch VTK classes, the klass that
- has the methods is different than the klass we want to
- instantiate. get_description_class makes sure that for patched
- classes we get the correct one."""
- try:
- return fix_classes.description[klass]
- except KeyError:
- return klass
-else:
- # On VTK 5.0.4, we use the id of the class to hash, because it
- # seems that VTK hasn't implemented hash() correctly for their
- # classes.
- def get_description_class(klass):
- """Because sometimes we need to patch VTK classes, the klass that
- has the methods is different than the klass we want to
- instantiate. get_description_class makes sure that for patched
- classes we get the correct one."""
- try:
- return fix_classes.description[id(klass)]
- except KeyError:
- return klass
-
-parser = VTKMethodParser()
-
-typeMapDict = {'int': Integer,
- 'long': Integer,
- 'float': Float,
- 'char*': String,
- 'char *': String,
- 'string': String,
- 'char': String,
- 'const char*': String,
- 'const char *': String}
-typeMapDictValues = [Integer, Float, String]
-
-file_name_pattern = re.compile('.*FileName$')
-set_file_name_pattern = re.compile('Set.*FileName$')
-
-def resolve_overloaded_name(name, ix, signatures):
- # VTK supports static overloading, VisTrails does not. The
- # solution is to check whether the current function has
- # overloads and change the names appropriately.
- if len(signatures) == 1:
- return name
- else:
- return name + '_' + str(ix+1)
-
-def typeMap(name, package=None):
- """ typeMap(name: str) -> Module
- Convert from C/C++ types into VisTrails Module type
-
- """
-
- if package is None:
- package = identifier
- if type(name) == tuple:
- return [typeMap(x, package) for x in name]
- if name in typeMapDict:
- return typeMapDict[name]
- else:
- registry = get_module_registry()
-
- if registry.has_descriptor_with_name('edu.utah.sci.vistrails.vtk', name):
- return registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', name).module
- elif not registry.has_descriptor_with_name(package, name):
- return None
- else:
- return registry.get_descriptor_by_name(package, name).module
-
-def get_method_signature(method):
- """ get_method_signature(method: vtkmethod) -> [ret, arg]
- Re-wrap Prabu's method to increase performance
-
- """
- doc = method.__doc__
- tmptmp = doc.split('\n')
- tmp = []
- for l in tmptmp:
- l = l.strip('\n \t')
- if l.startswith('V.') or l.startswith('C++:'):
- tmp.append(l)
- #else:
- # tmp[-1] = tmp[-1] + l
- tmp.append('')
- sig = []
- pat = re.compile(r'\b')
-
- # Remove all the C++ function signatures and V.<method_name> field
- offset = 2+len(method.__name__)
- for i in xrange(len(tmp)):
- s = tmp[i]
- if s=='': break
- if i%2==0:
- x = s.split('->')
- arg = x[0].strip()[offset:]
- if len(x) == 1: # No return value
- ret = None
- else:
- ret = x[1].strip()
-
- # Remove leading and trailing parens for arguments.
- arg = arg[1:-1]
- if not arg:
- arg = None
- if arg and arg[-1] == ')':
- arg = arg + ','
-
- # Now quote the args and eval them. Easy!
- if ret and ret[:3]!='vtk':
- try:
- ret = eval(pat.sub('\"', ret))
- except:
- continue
- if arg:
- if arg.find('(')!=-1:
- try:
- arg = eval(pat.sub('\"', arg))
- except:
- continue
- else:
- arg = arg.split(', ')
- if len(arg)>1:
- arg = tuple(arg)
- else:
- arg = arg[0]
- if type(arg) == str:
- arg = [arg]
-
- sig.append(([ret], arg))
- return sig
-
-def prune_signatures(module, name, signatures, output=False):
- """prune_signatures tries to remove redundant signatures to reduce
- overloading. It _mutates_ the given parameter.
-
- It does this by performing several operations:
-
- 1) It compares a 'flattened' version of the types
- against the other 'flattened' signatures. If any of them match, we
- keep only the 'flatter' ones.
-
- A 'flattened' signature is one where parameters are not inside a
- tuple.
-
- 2) We explicitly forbid a few signatures based on modules and names
-
- """
- # yeah, this is Omega(n^2) on the number of overloads. Who cares?
-
- def flatten(type_):
- if type_ is None:
- return []
- def convert(entry):
- if type(entry) == tuple:
- return list(entry)
- else:
- assert(type(entry) == str)
- return [entry]
- result = []
- for entry in type_:
- result.extend(convert(entry))
- return result
-
- flattened_entries = [flatten(sig[1]) for
- sig in signatures]
- def hit_count(entry):
- result = 0
- for entry in flattened_entries:
- if entry in flattened_entries:
- result += 1
- return result
- hits = [hit_count(entry) for entry in flattened_entries]
-
- def forbidden(flattened, hit_count, original):
- if (issubclass(get_description_class(module.vtkClass), vtk.vtk3DWidget) and
- name == 'PlaceWidget' and
- flattened == []):
- return True
- # We forbid this because addPorts hardcodes this but
- # SetInputArrayToProcess is an exception for the InfoVis
- # package
- if (get_description_class(module.vtkClass) == vtk.vtkAlgorithm and
- name!='SetInputArrayToProcess'):
- return True
- return False
-
- # This is messy: a signature is only allowed if there's no
- # explicit disallowing of it. Then, if it's not overloaded,
- # it is also allowed. If it is overloaded and not the flattened
- # version, it is pruned. If these are output ports, there can be
- # no parameters.
-
- def passes(flattened, hit_count, original):
- if forbidden(flattened, hit_count, original):
- return False
- if hit_count == 1:
- return True
- if original[1] is None:
- return True
- if output and len(original[1]) > 0:
- return False
- if hit_count > 1 and len(original[1]) == len(flattened):
- return True
- return False
-
- signatures[:] = [original for (flattened, hit_count, original)
- in izip(flattened_entries,
- hits,
- signatures)
- if passes(flattened, hit_count, original)]
-
- #then we remove the duplicates, if necessary
- unique_signatures = []
- [unique_signatures.append(s) for s in signatures if not unique_signatures.count(s)]
- signatures[:] = unique_signatures
-
-disallowed_classes = set(
- [
- 'vtkCriticalSection',
- 'vtkDataArraySelection',
- 'vtkDebugLeaks',
- 'vtkDirectory',
- 'vtkDynamicLoader',
- 'vtkFunctionParser',
- 'vtkGarbageCollector',
- 'vtkHeap',
- 'vtkInformationKey',
- 'vtkInstantiator',
- 'vtkLogLookupTable', # VTK: use vtkLookupTable.SetScaleToLog10() instead
- 'vtkMath',
- 'vtkModelMetadata',
- 'vtkMultiProcessController',
- 'vtkMutexLock',
- 'vtkOutputWindow',
- 'vtkPriorityQueue',
- 'vtkReferenceCount',
- 'vtkRenderWindowCollection',
- 'vtkRenderWindowInteractor',
- 'vtkTesting',
- 'vtkWindow',
- 'vtkVersion',
- 'vtkDiffFilter',
- 'vtkDocumentM3MetaData',
- 'vtkPPointwiseMutualInformation'
- #'vtkXMLUtilities',
- #'vtkXMLShader',
- #'vtkXMLMaterialReader',
- #'vtkXMLMaterial',
- #'vtkXMLDataElement'
- ])
-
-def is_class_allowed(module):
- if module is None:
- return False
- try:
- name = module.__name__
- return not (name in disallowed_classes)
- except AttributeError:
- return True
-
-def addAlgorithmPorts(module):
- """ addAlgorithmPorts(module: Module) -> None
- If module is a subclass of vtkAlgorithm, this function will add all
- SetInputConnection([id],[port]) and GetOutputPort([id]) as
- SetInputConnection{id}([port]) and GetOutputPort{id}.
-
- """
- if issubclass(get_description_class(module.vtkClass), vtk.vtkAlgorithm):
- if get_description_class(module.vtkClass)!=vtk.vtkStructuredPointsGeometryFilter:
- # We try to instantiate the class here to get the number of
- # ports and to avoid abstract classes
- try:
- instance = module.vtkClass()
- except TypeError:
- pass
- else:
- registry = get_module_registry()
- des = registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk',
- 'vtkAlgorithmOutput')
- for i in xrange(0,instance.GetNumberOfInputPorts()):
- registry.add_input_port(module, 'SetInputConnection%d'%i,
- des.module)
- for i in xrange(0,instance.GetNumberOfOutputPorts()):
- registry.add_output_port(module, 'GetOutputPort%d'%i,
- des.module)
-
-disallowed_set_get_ports = set(['ReferenceCount',
- 'InputConnection',
- 'OutputPort',
- 'Progress',
- 'ProgressText',
- 'InputArrayToProcess',
- ])
-def addSetGetPorts(module, get_set_dict, delayed):
- """ addSetGetPorts(module: Module, get_set_dict: dict) -> None
- Convert all Setxxx methods of module into input ports and all Getxxx
- methods of module into output ports
-
- Keyword arguments:
- module --- Module
- get_set_dict --- the Set/Get method signatures returned by vtk_parser
-
- """
-
- klass = get_description_class(module.vtkClass)
- registry = get_module_registry()
- for name in get_set_dict.iterkeys():
- if name in disallowed_set_get_ports: continue
- getterMethod = getattr(klass, 'Get%s'%name)
- setterMethod = getattr(klass, 'Set%s'%name)
- getterSig = get_method_signature(getterMethod)
- setterSig = get_method_signature(setterMethod)
-
- if len(getterSig) > 1:
- prune_signatures(module, 'Get%s'%name, getterSig, output=True)
- for order, getter in enumerate(getterSig):
- if getter[1]:
- debug("Can't handle getter %s (%s) of class %s: Needs input to "
- "get output" % (order+1, name, klass))
- continue
- if len(getter[0]) != 1:
- debug("Can't handle getter %s (%s) of class %s: More than a "
- "single output" % (order+1, name, str(klass)))
- continue
- class_ = typeMap(getter[0][0])
- if is_class_allowed(class_):
- registry.add_output_port(module, 'Get'+name, class_, True)
- if len(setterSig) > 1:
- prune_signatures(module, 'Set%s'%name, setterSig)
- for ix, setter in enumerate(setterSig):
- if setter[1]==None: continue
- n = resolve_overloaded_name('Set' + name, ix, setterSig)
- if len(setter[1]) == 1 and is_class_allowed(typeMap(setter[1][0])):
- registry.add_input_port(module, n,
- typeMap(setter[1][0]),
- setter[1][0] in typeMapDict)
- else:
- classes = [typeMap(i) for i in setter[1]]
- if all(is_class_allowed(x) for x in classes):
- registry.add_input_port(module, n, classes, True)
- # Wrap SetFileNames for VisTrails file access
- if file_name_pattern.match(name):
- registry.add_input_port(module, 'Set' + name[:-4],
- (File, 'input file'), False)
- # Wrap SetRenderWindow for exporters
- elif name == 'RenderWindow':
- # cscheid 2008-07-11 This is messy: VTKCell isn't
- # registered yet, so we can't use it as a port
- # However, we can't register VTKCell before these either,
- # because VTKCell requires vtkRenderer. The "right" way would
- # be to add all modules first, then all ports. However, that would
- # be too slow.
- # Workaround: delay the addition of the port by storing
- # the information in a list
- if registry.has_module('edu.utah.sci.vistrails.spreadsheet',
- 'SpreadsheetCell'):
- delayed.add_input_port.append((module, 'SetVTKCell', VTKCell, False))
- # Wrap color methods for VisTrails GUI facilities
- elif name == 'DiffuseColor':
- registry.add_input_port(module, 'SetDiffuseColorWidget',
- (Color, 'color'), True)
- elif name == 'Color':
- registry.add_input_port(module, 'SetColorWidget',
- (Color, 'color'), True)
- elif name == 'AmbientColor':
- registry.add_input_port(module, 'SetAmbientColorWidget',
- (Color, 'color'), True)
- elif name == 'SpecularColor':
- registry.add_input_port(module, 'SetSpecularColorWidget',
- (Color, 'color'), True)
- elif name == 'EdgeColor':
- registry.add_input_port(module, 'SetEdgeColorWidget',
- (Color, 'color'), True)
- elif name == 'Background' :
- registry.add_input_port(module, 'SetBackgroundWidget',
- (Color, 'color'), True)
- elif name == 'Background2' :
- registry.add_input_port(module, 'SetBackground2Widget',
- (Color, 'color'), True)
-
-disallowed_toggle_ports = set(['GlobalWarningDisplay',
- 'Debug',
- ])
-def addTogglePorts(module, toggle_dict):
- """ addTogglePorts(module: Module, toggle_dict: dict) -> None
- Convert all xxxOn/Off methods of module into input ports
-
- Keyword arguments:
- module --- Module
- toggle_dict --- the Toggle method signatures returned by vtk_parser
-
- """
- registry = get_module_registry()
- for name in toggle_dict.iterkeys():
- if name in disallowed_toggle_ports:
- continue
- registry.add_input_port(module, name+'On', [], True)
- registry.add_input_port(module, name+'Off', [], True)
-
-disallowed_state_ports = set(['SetInputArrayToProcess'])
-def addStatePorts(module, state_dict):
- """ addStatePorts(module: Module, state_dict: dict) -> None
- Convert all SetxxxToyyy methods of module into input ports
-
- Keyword arguments:
- module --- Module
- state_dict --- the State method signatures returned by vtk_parser
-
- """
- klass = get_description_class(module.vtkClass)
- registry = get_module_registry()
- for name in state_dict.iterkeys():
- for mode in state_dict[name]:
- # Creates the port Set foo to bar
- field = 'Set'+name+'To'+mode[0]
- if field in disallowed_state_ports:
- continue
- if not registry.has_input_port(module, field):
- registry.add_input_port(module, field, [], True)
-
- # Now create the port Set foo with parameter
- if hasattr(klass, 'Set%s'%name):
- setterMethod = getattr(klass, 'Set%s'%name)
- setterSig = get_method_signature(setterMethod)
- # if the signature looks like an enum, we'll skip it, it shouldn't
- # be necessary
- if len(setterSig) > 1:
- prune_signatures(module, 'Set%s'%name, setterSig)
- for ix, setter in enumerate(setterSig):
- n = resolve_overloaded_name('Set' + name, ix, setterSig)
- tm = typeMap(setter[1][0])
- if len(setter[1]) == 1 and is_class_allowed(tm):
- registry.add_input_port(module, n, tm,
- setter[1][0] in typeMapDict)
- else:
- classes = [typeMap(i) for i in setter[1]]
- if all(is_class_allowed(x) for x in classes):
- registry.add_input_port(module, n, classes, True)
-
-disallowed_other_ports = set(
- [
- 'BreakOnError',
- 'DeepCopy',
- 'FastDelete',
- 'HasObserver',
- 'HasExecutive',
- 'INPUT_ARRAYS_TO_PROCESS',
- 'INPUT_CONNECTION',
- 'INPUT_IS_OPTIONAL',
- 'INPUT_IS_REPEATABLE',
- 'INPUT_PORT',
- 'INPUT_REQUIRED_DATA_TYPE',
- 'INPUT_REQUIRED_FIELDS',
- 'InvokeEvent',
- 'IsA',
- 'Modified',
- 'NewInstance',
- 'PrintRevisions',
- 'RemoveAllInputs',
- 'RemoveObserver',
- 'RemoveObservers',
-# 'SafeDownCast',
-# 'SetInputArrayToProcess',
- 'ShallowCopy',
- 'Update',
- 'UpdateInformation',
- 'UpdateProgress',
- 'UpdateWholeExtent',
- ])
-
-force_not_optional_port = set(
- ['ApplyViewTheme',
- ])
-
-
-def addOtherPorts(module, other_list):
- """ addOtherPorts(module: Module, other_list: list) -> None
- Convert all other ports such as Insert/Add.... into input/output
-
- Keyword arguments:
- module --- Module
- other_dict --- any other method signatures that is not
- Algorithm/SetGet/Toggle/State type
-
- """
- klass = get_description_class(module.vtkClass)
- registry = get_module_registry()
- for name in other_list:
- if name[:3] in ['Add','Set'] or name[:6]=='Insert':
- if name in disallowed_other_ports:
- continue
- method = getattr(klass, name)
- signatures = ""
- if not isinstance(method, int):
- signatures = get_method_signature(method)
- if len(signatures) > 1:
- prune_signatures(module, name, signatures)
- for (ix, sig) in enumerate(signatures):
- ([result], params) = sig
- types = []
- if params:
- for p in params:
- t = typeMap(p)
- if not t:
- types = None
- break
- else: types.append(t)
- else:
- types = [[]]
- if types:
- if not all(is_class_allowed(x) for x in types):
- continue
- n = resolve_overloaded_name(name, ix, signatures)
- if len(types)<=1:
- registry.add_input_port(module, n, types[0],
- types[0] in typeMapDictValues)
- else:
- registry.add_input_port(module, n, types, True)
- else:
- if name in disallowed_other_ports:
- continue
- method = getattr(klass, name)
- signatures = ""
- if not isinstance(method, int):
- signatures = get_method_signature(method)
- if len(signatures) > 1:
- prune_signatures(module, name, signatures)
- for (ix, sig) in enumerate(signatures):
- ([result], params) = sig
- types = []
- if params:
- types = [typeMap(p) for p in params]
- else:
- types = []
- if not all(is_class_allowed(x) for x in types):
- continue
- if types==[] or (result==None):
- n = resolve_overloaded_name(name, ix, signatures)
- registry.add_input_port(module, n, types,
- not (n in force_not_optional_port))
-
-disallowed_get_ports = set([
- 'GetClassName',
- 'GetErrorCode',
- 'GetNumberOfInputPorts',
- 'GetNumberOfOutputPorts',
- 'GetOutputPortInformation',
- 'GetTotalNumberOfInputConnections',
- ])
-
-def addGetPorts(module, get_list):
- klass = get_description_class(module.vtkClass)
- registry = get_module_registry()
- for name in get_list:
- if name in disallowed_get_ports:
- continue
- method = getattr(klass, name)
- signatures = get_method_signature(method)
- if len(signatures) > 1:
- prune_signatures(module, name, signatures, output=True)
- for ix, getter in enumerate(signatures):
- if getter[1] or len(getter[0]) > 1:
- continue
- class_ = typeMap(getter[0][0])
- if is_class_allowed(class_):
- if len(signatures) > 1:
- n = name + "_" + str(ix+1)
- else:
- n = name
- registry.add_output_port(module, n, class_, True)
-
-def addPorts(module, delayed):
- """ addPorts(module: VTK module inherited from Module,
- delayed: object with add_input_port slot
- ) -> None
-
- Search all metamethods of module and add appropriate ports
-
- ports that cannot be added immediately should be appended to
- the delayed object that is passed. see the SetRenderWindow cases.
-
- """
- klass = get_description_class(module.vtkClass)
- registry = get_module_registry()
- registry.add_output_port(module, 'self', module)
- parser.parse(klass)
- addAlgorithmPorts(module)
- addGetPorts(module, parser.get_get_methods())
- addSetGetPorts(module, parser.get_get_set_methods(), delayed)
- addTogglePorts(module, parser.get_toggle_methods())
- addStatePorts(module, parser.get_state_methods())
- addOtherPorts(module, parser.get_other_methods())
-
- # CVS version of VTK doesn't support AddInputConnect(vtkAlgorithmOutput)
- if klass==vtk.vtkAlgorithm:
- registry.add_input_port(module, 'AddInputConnection',
- typeMap('vtkAlgorithmOutput'))
- # vtkWriters have a custom File port
- elif klass==vtk.vtkWriter:
- registry.add_output_port(module, 'file',
- typeMap('File','edu.utah.sci.vistrails.basic'))
- elif klass==vtk.vtkImageWriter:
- registry.add_output_port(module, 'file',
- typeMap('File','edu.utah.sci.vistrails.basic'))
- elif klass==vtk.vtkVolumeProperty:
- registry.add_input_port(module, 'SetTransferFunction',
- typeMap('TransferFunction'))
- elif klass==vtk.vtkDataSet:
- registry.add_input_port(module, 'SetPointData', typeMap('vtkPointData'))
- registry.add_input_port(module, 'SetCallData', typeMap('vtkCellData'))
- elif klass==vtk.vtkCell:
- registry.add_input_port(module, 'SetPointIds', typeMap('vtkIdList'))
-
-def setAllPorts(descriptor, delayed):
- """ setAllPorts(descriptor: ModuleDescriptor) -> None
- Traverse descriptor and all of its children/grand-children to add all ports
-
- """
- addPorts(descriptor.module, delayed)
- for child in descriptor.children:
- setAllPorts(child, delayed)
-
-def class_dict(base_module, node):
- """class_dict(base_module, node) -> dict
- Returns the class dictionary for the module represented by node and
- with base class base_module"""
-
- class_dict_ = {}
- def update_dict(name, callable_):
- if class_dict_.has_key(name):
- class_dict_[name] = callable_(class_dict_[name])
- elif hasattr(base_module, name):
- class_dict_[name] = callable_(getattr(base_module, name))
- else:
- class_dict_[name] = callable_(None)
-
- def guarded_SimpleScalarTree_wrap_compute(old_compute):
- # This builds the scalar tree and makes it cacheable
-
- def compute(self):
- self.is_cacheable = lambda *args, **kwargs: True
- old_compute(self)
- self.vtkInstance.BuildTree()
- return compute
-
- def guarded_SetFileName_wrap_compute(old_compute):
- # This checks for the presence of file in VTK readers
- def compute(self):
-
- # Skips the check if it's a vtkImageReader or vtkPLOT3DReader, because
- # it has other ways of specifying files, like SetFilePrefix for
- # multiple files
- if any(issubclass(self.vtkClass, x)
- for x in
- [vtk.vtkBYUReader,
- vtk.vtkImageReader,
- vtk.vtkPLOT3DReader,
- vtk.vtkDICOMImageReader,
- vtk.vtkTIFFReader]):
- old_compute(self)
- return
- if self.hasInputFromPort('SetFileName'):
- name = self.getInputFromPort('SetFileName')
- elif self.hasInputFromPort('SetFile'):
- name = self.getInputFromPort('SetFile').name
- else:
- raise ModuleError(self, 'Missing filename')
- if not os.path.isfile(name):
- raise ModuleError(self, 'File does not exist')
- old_compute(self)
- return compute
-
- def compute_SetDiffuseColorWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetDiffuseColorWidget(self, color):
- self.vtkInstance.SetDiffuseColor(color.tuple)
- return call_SetDiffuseColorWidget
-
- def compute_SetAmbientColorWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetAmbientColorWidget(self, color):
- self.vtkInstance.SetAmbientColor(color.tuple)
- return call_SetAmbientColorWidget
-
- def compute_SetSpecularColorWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetSpecularColorWidget(self, color):
- self.vtkInstance.SetSpecularColor(color.tuple)
- return call_SetSpecularColorWidget
-
- def compute_SetColorWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetColorWidget(self, color):
- self.vtkInstance.SetColor(color.tuple)
- return call_SetColorWidget
-
- def compute_SetEdgeColorWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetEdgeColorWidget(self, color):
- self.vtkInstance.SetEdgeColor(color.tuple)
- return call_SetEdgeColorWidget
-
- def compute_SetBackgroundWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetBackgroundWidget(self, color):
- self.vtkInstance.SetBackground(color.tuple)
- return call_SetBackgroundWidget
-
- def compute_SetBackground2Widget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetBackground2Widget(self, color):
- self.vtkInstance.SetBackground2(color.tuple)
- return call_SetBackground2Widget
-
- def compute_SetVTKCell(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetRenderWindow(self, cellObj):
- if cellObj.cellWidget:
- self.vtkInstance.SetRenderWindow(cellObj.cellWidget.mRenWin)
- return call_SetRenderWindow
-
- def compute_SetTransferFunction(old_compute):
- # This sets the transfer function
- if old_compute != None:
- return old_compute
- def call_SetTransferFunction(self, tf):
- tf.set_on_vtk_volume_property(self.vtkInstance)
- return call_SetTransferFunction
-
- def compute_SetPointData(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetPointData(self, pd):
- self.vtkInstance.GetPointData().ShallowCopy(pd)
- return call_SetPointData
-
- def compute_SetCellData(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetCellData(self, cd):
- self.vtkInstance.GetCellData().ShallowCopy(cd)
- return call_SetCellData
-
- def compute_SetPointIds(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetPointIds(self, point_ids):
- self.vtkInstance.GetPointIds().SetNumberOfIds(point_ids.GetNumberOfIds())
- for i in xrange(point_ids.GetNumberOfIds()):
- self.vtkInstance.GetPointIds().SetId(i, point_ids.GetId(i))
- return call_SetPointIds
-
- def guarded_Writer_wrap_compute(old_compute):
- # The behavior for vtkWriter subclasses is to call Write()
- # If the user sets a name, we will create a file with that name
- # If not, we will create a temporary file from the file pool
- def compute(self):
- old_compute(self)
- fn = self.vtkInstance.GetFileName()
- if not fn:
- o = self.interpreter.filePool.create_file(suffix='.vtk')
- self.vtkInstance.SetFileName(o.name)
- else:
- o = File()
- o.name = fn
- self.vtkInstance.Write()
- self.setResult('file', o)
- return compute
-
- for var in dir(node.klass):
- # Everyone that has a Set.*FileName should have a Set.*File port too
- if set_file_name_pattern.match(var):
- def get_compute_SetFile(method_name):
- def compute_SetFile(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetFile(self, file_obj):
- getattr(self.vtkInstance, method_name)(file_obj.name)
- return call_SetFile
- return compute_SetFile
- update_dict('_special_input_function_' + var[:-4],
- get_compute_SetFile(var))
-
- if hasattr(node.klass, 'SetFileName'):
- # ... BUT we only want to check existence of filenames on
- # readers. VTK is nice enough to be consistent with names, but
- # this is brittle..
- if node.klass.__name__.endswith('Reader'):
- if not node.klass.__name__.endswith('TiffReader'):
- update_dict('compute', guarded_SetFileName_wrap_compute)
- if hasattr(node.klass, 'SetRenderWindow'):
- update_dict('_special_input_function_SetVTKCell',
- compute_SetVTKCell)
- #color gui wrapping
- if hasattr(node.klass, 'SetDiffuseColor'):
- update_dict('_special_input_function_SetDiffuseColorWidget',
- compute_SetDiffuseColorWidget)
- if hasattr(node.klass, 'SetAmbientColor'):
- update_dict('_special_input_function_SetAmbientColorWidget',
- compute_SetAmbientColorWidget)
- if hasattr(node.klass, 'SetSpecularColor'):
- update_dict('_special_input_function_SetSpecularColorWidget',
- compute_SetSpecularColorWidget)
- if hasattr(node.klass, 'SetEdgeColor'):
- update_dict('_special_input_function_SetEdgeColorWidget',
- compute_SetEdgeColorWidget)
- if hasattr(node.klass, 'SetColor'):
- update_dict('_special_input_function_SetColorWidget',
- compute_SetColorWidget)
-
- if (issubclass(node.klass, vtk.vtkRenderer) and
- hasattr(node.klass, 'SetBackground')):
- update_dict('_special_input_function_SetBackgroundWidget',
- compute_SetBackgroundWidget)
- if (issubclass(node.klass, vtk.vtkRenderer) and
- hasattr(node.klass, 'SetBackground2')):
- update_dict('_special_input_function_SetBackground2Widget',
- compute_SetBackground2Widget)
- if issubclass(node.klass, vtk.vtkWriter):
- update_dict('compute', guarded_Writer_wrap_compute)
-
- if issubclass(node.klass, vtk.vtkScalarTree):
- update_dict('compute', guarded_SimpleScalarTree_wrap_compute)
-
- if issubclass(node.klass, vtk.vtkVolumeProperty):
- update_dict('_special_input_function_SetTransferFunction',
- compute_SetTransferFunction)
- if issubclass(node.klass, vtk.vtkDataSet):
- update_dict('_special_input_function_SetPointData',
- compute_SetPointData)
- update_dict('_special_input_function_SetCellData',
- compute_SetCellData)
- if issubclass(node.klass, vtk.vtkCell):
- update_dict('_special_input_function_SetPointIds',
- compute_SetPointIds)
- return class_dict_
-
-disallowed_modules = set([
-# 'vtkGeoAlignedImageCache',
-# 'vtkGeoTerrainCache',
-# 'vtkMimeTypeStrategy',
-# 'vtkMPIGroup',
- 'vtkPlotWriter', # Segfaults when being destroyed (when created without a reference, or when last reference is removed)
- 'vtkRenderedLandscapeRepresentation' # Segfaults when calling: GetPeakLabelStopWords()
- ])
-def createModule(baseModule, node):
- """ createModule(baseModule: a Module subclass, node: TreeNode) -> None
- Construct a module inherits baseModule with specification from node
-
- """
- if node.name in disallowed_modules: return
- def obsolete_class_list():
- lst = []
- items = ['vtkInteractorStyleTrackball',
- 'vtkStructuredPointsGeometryFilter',
- 'vtkConstrainedPointHandleRepresentation',
- 'vtkTypePromotion']
- def try_to_add_item(item):
- try:
- lst.append(getattr(titan, item))
- except AttributeError:
- pass
- for item in items:
- try_to_add_item(item)
- return lst
-
- obsolete_list = obsolete_class_list()
-
- pack1 = vtk
- for i in titan2:
- if getattr(i, node.name, None) != None:
- pack1 = i
-
- def is_abstract():
- """is_abstract tries to instantiate the class. If it's
- abstract, this will raise."""
- # Consider obsolete classes abstract
- if node.klass in obsolete_list:
- return True
- try:
- getattr(pack1, node.name)()
- except TypeError: # VTK raises type error on abstract classes
- return True
- return False
-
- module = new_module(baseModule, node.name,
- class_dict(baseModule, node),
- docstring=getattr(pack1, node.name).__doc__
- )
-
- # This is sitting on the class
- if hasattr(fix_classes, node.klass.__name__ + '_fixed'):
- module.vtkClass = getattr(fix_classes, node.klass.__name__ + '_fixed')
- else:
- module.vtkClass = node.klass
- registry = get_module_registry()
- registry.add_module(module, abstract=is_abstract(),
- signatureCallable=vtk_hasher)
- for child in node.children:
- if child.name in disallowed_classes:
- continue
- createModule(module, child)
-
-def createAllModules(g):
- """ createAllModules(g: ClassTree) -> None
- Traverse the VTK class tree and add all modules into the module registry
-
- """
- if tuple(vtk.vtkVersion().GetVTKVersion().split('.')) < ('5', '7', '0'):
- assert len(g.tree[0]) == 1
- base = g.tree[0][0]
- assert base.name == 'vtkObjectBase'
-
- vtkObjectBase = new_module(vtkBaseModule, 'vtkObjectBase')
- vtkObjectBase.vtkClass = vtk.vtkObjectBase
- registry = get_module_registry()
- registry.add_module(vtkObjectBase)
- if tuple(vtk.vtkVersion().GetVTKVersion().split('.')) < ('5', '7', '0'):
- for child in base.children:
- if child.name in disallowed_classes:
- continue
- createModule(vtkObjectBase, child)
- else:
- for base in g.tree[0]:
- for child in base.children:
- if child.name in disallowed_classes:
- continue
- createModule(vtkObjectBase, child)
-
-##############################################################################
-# Convenience methods
-
-def extract_vtk_instance(vistrails_obj):
- """extract_vtk_instance(vistrails_obj) -> vtk_object
-
- takes an instance of a VisTrails module that is a subclass
- of the vtkObjectBase module and returns the corresponding
- instance."""
- global identifier
- vtkObjectBase = registry.get_descriptor_by_name(identifier,
- 'vtkObjectBase').module
- assert isinstance(vistrails_obj, vtkObjectBase)
- return vistrails_obj.vtkInstance
-
-def wrap_vtk_instance(vtk_obj):
- """wrap_vtk_instance(vtk_object) -> VisTrails module
-
- takes a vtk instance and returns a corresponding
- wrapped instance of a VisTrails module"""
- global identifier
-
- assert isinstance(vtk_obj, vtk.vtkObjectBase)
- m = registry.get_descriptor_by_name(identifier,
- vtk_obj.GetClassName())
- result = m.module()
- result.vtkInstance = vtk_obj
- return result
-
-################################################################################
-
-def initialize():
- """ initialize() -> None
- Package-entry to initialize the package
-
- """
- # Check VTK version
- v = vtk.vtkVersion()
- version = [v.GetVTKMajorVersion(),
- v.GetVTKMinorVersion(),
- v.GetVTKBuildVersion()]
- if version < [5, 0, 0]:
- raise Exception("You need to upgrade your VTK install to version \
- > >= 5.0.0")
- inheritanceGraph = ClassTree(titan2)
- inheritanceGraph.create()
-
- # Transfer Function constant
- tf_widget.initialize()
-
- delayed = InstanceObject(add_input_port=[])
- # Add VTK modules
- registry = get_module_registry()
- registry.add_module(vtkBaseModule)
- createAllModules(inheritanceGraph)
- setAllPorts(registry.get_descriptor_by_name(identifier,
- 'vtkObjectBase'),
- delayed)
-
-# # Register the VTKCell and VTKHandler type if the spreadsheet is up
-# if registry.has_module('edu.utah.sci.vistrails.spreadsheet',
-# 'SpreadsheetCell'):
-# import vtkhandler
-# import vtkcell
-# import vtkviewcell
-# vtkhandler.registerSelf()
-# vtkcell.registerSelf()
-# vtkviewcell.registerSelf()
-
- # register offscreen rendering module
- offscreen.register_self()
-
- # Now add all "delayed" ports - see comment on addSetGetPorts
- for args in delayed.add_input_port:
-
- registry.add_input_port(*args)
-
- # register Transfer Function adjustment
- # This can't be reordered -- TransferFunction needs to go before
- # vtkVolumeProperty, but vtkScaledTransferFunction needs
- # to go after vtkAlgorithmOutput
-
- getter = registry.get_descriptor_by_name
- registry.add_module(tf_widget.vtkScaledTransferFunction)
- registry.add_input_port(tf_widget.vtkScaledTransferFunction,
- 'Input', getter('edu.utah.sci.vistrails.vtk',
- 'vtkAlgorithmOutput').module)
- registry.add_input_port(tf_widget.vtkScaledTransferFunction,
- 'Dataset', getter ('edu.utah.sci.vistrails.vtk',
- 'vtkDataObject').module)
- registry.add_input_port(tf_widget.vtkScaledTransferFunction,
- 'Range', [Float, Float])
- registry.add_input_port(tf_widget.vtkScaledTransferFunction,
- 'TransferFunction',
- tf_widget.TransferFunctionConstant)
- registry.add_output_port(tf_widget.vtkScaledTransferFunction,
- 'TransferFunction',
- tf_widget.TransferFunctionConstant)
-
-
-################################################################################
diff --git a/contrib/titan/inspectors.py b/contrib/titan/inspectors.py
deleted file mode 100644
index f94e2b5..0000000
--- a/contrib/titan/inspectors.py
+++ /dev/null
@@ -1,232 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-##############################################################################
-# Data inspectors for VTK
-import vtk
-
-from core.modules.vistrails_module import ModuleError
-from core.utils import VistrailsInternalError
-from core.modules.basic_modules import Module, Float, Integer
-from core.modules.module_registry import get_module_registry
-from base_module import vtkBaseModule
-from hasher import vtk_hasher
-
-class vtkBaseInspector(Module):
-
- @classmethod
- def register_self(cls, **kwargs):
- registry = get_module_registry()
- def resolve_type(t):
- if type(t) == tuple:
- return registry.get_descriptor_by_name(*t).module
- elif type(t) == type:
- return t
- else:
- assert False, ("Unknown type " + str(type(t)))
-
- registry.add_module(cls, **kwargs)
- try:
- ips = cls.input_ports
- except AttributeError:
- pass
- else:
- for (port_name, types) in ips:
- registry.add_input_port(cls,
- port_name,
- list(resolve_type(t) for t in types))
-
- try:
- ops = cls.output_ports
- except AttributeError:
- pass
- else:
- for (port_name, types) in ops:
- registry.add_output_port(cls,
- port_name,
- list(resolve_type(t) for t in types))
-
- def auto_set_results(self, vtk_object):
- for function in self.outputPorts.keys():
- if hasattr(vtk_object, function):
- retValues = getattr(vtk_object, function)()
- if issubclass(retValues.__class__, vtk.vtkObject):
- className = retValues.GetClassName()
- output = vtkBaseModule.wrapperModule(className, retValues)
- self.setResult(function, output)
- elif type(retValues) in [tuple, list]:
- result = list(retValues)
- for i in xrange(len(result)):
- if issubclass(result[i].__class__, vtk.vtkObject):
- className = result[i].GetClassName()
- result[i] = vtkBaseModule.wrapperModule(className,
- result[i])
- self.setResult(function, type(retValues)(result))
- else:
- self.setResult(function, retValues)
-
-class vtkDataSetInspector(vtkBaseInspector):
-
- def compute(self):
- vtk_object = None
- if self.hasInputFromPort("SetInputConnection0"):
- ic = self.getInputFromPort("SetInputConnection0")
- port_object = ic.vtkInstance
- ix = port_object.GetIndex()
- producer = port_object.GetProducer()
- try:
- vtk_object = producer.GetOutput()
- except AttributeError:
- raise ModuleError(self,
- "expected a module that supports GetOutput")
- elif self.hasInputFromPort("SetInput"):
- port_object = self.getInputFromPort("SetInput")
- if hasattr(port_object, "vtkInstance"):
- vtk_object = port_object.vtkInstance
- else:
- raise ModuleError(self, "expected a vtk module")
- if vtk_object:
- self.auto_set_results(vtk_object)
-
- input_ports = [('SetInputConnection0',
- [('edu.utah.sci.vistrails.vtk', 'vtkAlgorithmOutput')]),
- ('SetInput',
- [('edu.utah.sci.vistrails.vtk', 'vtkDataSet')]),
- ]
- output_ports = [('GetBounds', [Float] * 6),
- ('GetScalarRange', [Float] * 2),
- ('GetLength', [Float]),
- ('GetCenter', [Float] * 3),
- ('GetNumberOfPoints', [Integer]),
- ('GetNumberOfCells', [Integer]),
- ('GetPointData',
- [('edu.utah.sci.vistrails.vtk', 'vtkPointData')]),
- ('GetCellData',
- [('edu.utah.sci.vistrails.vtk', 'vtkCellData')]),
- ]
-
-class vtkDataSetAttributesInspector(vtkBaseInspector):
-
- def compute(self):
- vtk_object = None
- if self.hasInputFromPort("SetInput"):
- port_object = self.getInputFromPort("SetInput")
- if hasattr(port_object, "vtkInstance"):
- vtk_object = port_object.vtkInstance
- else:
- raise ModuleError(self, "expected a vtk module")
- if vtk_object:
- self.auto_set_results(vtk_object)
-
- input_ports = [('SetInput',
- [('edu.utah.sci.vistrails.vtk', 'vtkDataSetAttributes')]),
- ]
- output_ports = [('GetScalars',
- [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
- ('GetVectors',
- [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
- ('GetNormals',
- [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
- ('GetTCoords',
- [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
- ('GetTensors',
- [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
- ('GetGlobalIds',
- [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')]),
- ('GetPedigreeIds',
- [('edu.utah.sci.vistrails.vtk', 'vtkAbstractArray')]),
- ]
-
-class vtkDataArrayInspector(vtkBaseInspector):
-
- def compute(self):
- vtk_object = None
- if self.hasInputFromPort("SetInput"):
- port_object = self.getInputFromPort("SetInput")
- if hasattr(port_object, "vtkInstance"):
- vtk_object = port_object.vtkInstance
- else:
- raise ModuleError(self, "expected a vtk module")
- if vtk_object:
- self.auto_set_results(vtk_object)
-
- input_ports = [('SetInput',
- [('edu.utah.sci.vistrails.vtk', 'vtkDataArray')])]
- output_ports = [('GetMaxNorm', [Float]),
- ('GetRange', [Float] * 2)]
-
-class vtkPolyDataInspector(vtkDataSetInspector):
-
- def compute(self):
- vtk_object = None
- if self.hasInputFromPort("SetInputConnection0"):
- ic = self.getInputFromPort("SetInputConnection0")
- port_object = ic.vtkInstance
- ix = port_object.GetIndex()
- producer = port_object.GetProducer()
- try:
- vtk_object = producer.GetOutput()
- except AttributeError:
- raise ModuleError(self,
- "expected a module that supports GetOutput")
- elif self.hasInputFromPort("SetInput"):
- port_object = self.getInputFromPort("SetInput")
- if hasattr(port_object, "vtkInstance"):
- vtk_object = port_object.vtkInstance
- else:
- raise ModuleError(self, "expected a vtk module")
- if vtk_object:
- self.auto_set_results(vtk_object)
-
-# Wendel
- input_ports = [('SetInputConnection0',
- [('edu.utah.sci.vistrails.vtk', 'vtkAlgorithmOutput')]),
- ('SetInput',
- [('edu.utah.sci.vistrails.vtk', 'vtkDataSet')]),
- ]
- output_ports = [('GetVerts',
- [('edu.utah.sci.vistrails.vtk', 'vtkCellArray')]),
- ('GetLines',
- [('edu.utah.sci.vistrails.vtk', 'vtkCellArray')]),
- ('GetPolys',
- [('edu.utah.sci.vistrails.vtk', 'vtkCellArray')]),
- ('GetStrips',
- [('edu.utah.sci.vistrails.vtk', 'vtkCellArray')]),
- ('GetPoints',
- [('edu.utah.sci.vistrails.vtk', 'vtkPoints')]),
- ('GetNumberOfVerts', [Integer]),
- ('GetNumberOfLines', [Integer]),
- ('GetNumberOfPolys', [Integer]),
- ('GetNumberOfStrips', [Integer]),
- ]
-
-def initialize():
- vtkBaseInspector.register_self(abstract=True, signatureCallable=vtk_hasher)
- vtkDataSetInspector.register_self(abstract=False,
- signatureCallable=vtk_hasher)
- vtkDataSetAttributesInspector.register_self(abstract=False,
- signatureCallable=vtk_hasher)
- vtkDataArrayInspector.register_self(abstract=False,
- signatureCallable=vtk_hasher)
- vtkPolyDataInspector.register_self(abstract=False,
- signatureCallable=vtk_hasher)
-
diff --git a/contrib/titan/offscreen.py b/contrib/titan/offscreen.py
deleted file mode 100644
index 127ba57..0000000
--- a/contrib/titan/offscreen.py
+++ /dev/null
@@ -1,62 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-from core.modules.module_registry import get_module_registry
-from core.modules.vistrails_module import Module
-from core.modules.basic_modules import File, Integer
-
-class VTKRenderOffscreen(Module):
-
- def compute(self):
- r = self.getInputFromPort("renderer").vtkInstance
- window = vtk.vtkRenderWindow()
- w = self.forceGetInputFromPort("width", 512)
- h = self.forceGetInputFromPort("height", 512)
- window.OffScreenRenderingOn()
- window.SetSize(w, h)
- # r.ResetCamera()
- window.AddRenderer(r)
- window.Start()
- window.Render()
- win2image = vtk.vtkWindowToImageFilter()
- win2image.SetInput(window)
- win2image.Update()
- writer = vtk.vtkPNGWriter()
- writer.SetInput(win2image.GetOutput())
- output = self.interpreter.filePool.create_file(suffix='.png')
- writer.SetFileName(output.name)
- writer.Write()
- window.Finalize()
- self.setResult("image", output)
-
-def register_self():
- registry = get_module_registry()
- r = registry.get_descriptor_by_name(
- 'edu.utah.sci.vistrails.vtk',
-# Wendel
- 'vtkRenderer').module
- registry.add_module(VTKRenderOffscreen)
- registry.add_input_port(VTKRenderOffscreen, 'renderer', r)
- registry.add_input_port(VTKRenderOffscreen, 'width', Integer)
- registry.add_input_port(VTKRenderOffscreen, 'height', Integer)
- registry.add_output_port(VTKRenderOffscreen, 'image', File)
-
diff --git a/contrib/titan/tf_widget.py b/contrib/titan/tf_widget.py
deleted file mode 100644
index 0c52e73..0000000
--- a/contrib/titan/tf_widget.py
+++ /dev/null
@@ -1,575 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-##############################################################################
-# Transfer Function Widget for VTK
-
-from PyQt4 import QtCore, QtGui
-from core.modules.constant_configuration import ConstantWidgetMixin
-from core.modules.basic_modules import new_constant, init_constant, Module
-from core.utils.color import ColorByName
-import vtk
-import math
-import pickle
-import copy
-
-################################################################################
-# etc
-
-def clamp(v, mn, mx, eps=0.0):
- mn += eps
- mx -= eps
- if v < mn: return mn
- if v > mx: return mx
- return v
-
-##############################################################################
-# Transfer Function object
-
-class TransferFunction(object):
-
- def __init__(self):
- self._min_range = 0.0
- self._max_range = 1.0
- self._pts = []
-
- def set_range(self, mn, mx):
- self._min_range = mn
- self._max_range = mx
-
- def set_on_vtk_volume_property(self, vtk_volume_property):
- # Builds the opacity and color functions
- of = vtk.vtkPiecewiseFunction()
- cf = vtk.vtkColorTransferFunction()
- vp = vtk_volume_property
- for pt in self._pts:
- (scalar, opacity, color) = pt
- # Map scalar to tf range
- s = self._min_range + (self._max_range - self._min_range) * scalar
- of.AddPoint(s, opacity)
- cf.AddRGBPoint(s, color[0], color[1], color[2])
- vp.SetScalarOpacity(of)
- vp.SetColor(cf)
-
- def add_point(self, scalar, opacity, color):
- self._pts.append((scalar, opacity, color))
- self._pts.sort()
-
- def get_value(self, scalar):
- """get_value(scalar): returns the opacity and color
- linearly interpolated at the value. Useful for
- adding knots."""
- ix = 0
- while ix < len(self._pts) and self._pts[ix][0] > scalar:
- ix += 1
- if ix == 0:
- return (self._pts[0][1], self._pts[0][2])
- elif ix == len(self._pts):
- return (self._pts[-1][1], self._pts[-1][2])
- else:
- u = ((self._pts[ix][0] - scalar) /
- (self._pts[ix][0] - self._pts[ix-1][0]))
- do = self._pts[ix][1] - self._pts[ix-1][1]
- dr = self._pts[ix][2][0] - self._pts[ix-1][2][0]
- dg = self._pts[ix][2][1] - self._pts[ix-1][2][1]
- db = self._pts[ix][2][2] - self._pts[ix-1][2][2]
- return (self._pts[ix-1][1] + u * do,
- (self._pts[ix-1][2][0] + u * dr,
- self._pts[ix-1][2][1] + u * dg,
- self._pts[ix-1][2][2] + u * db))
-
- def __copy__(self):
- result = TransferFunction()
- result._min_range = self._min_range
- result._max_range = self._max_range
- result._pts = copy.copy(self._pts)
- return result
-
- def __eq__(self, other):
- if type(other) != type(self):
- return False
- if self._min_range != other._min_range:
- return False
- if self._max_range != other._max_range:
- return False
- for my_pt, other_pt in zip(self._pts, other._pts):
- if my_pt != other_pt:
- return False
- return True
-
- def __ne__(self, other):
- return not self.__eq__(other)
-
-##############################################################################
-# Graphics Items
-
-class TransferFunctionPoint(QtGui.QGraphicsEllipseItem):
-
- selection_pens = { True: QtGui.QPen(QtGui.QBrush(
- QtGui.QColor(*(ColorByName.get_int('goldenrod_medium')))),0.012),
- False: QtGui.QPen() }
-
- def __init__(self, scalar, opacity, color, parent=None):
- QtGui.QGraphicsEllipseItem.__init__(self, parent)
- self._scalar = scalar
- self._opacity = opacity
- self._color = QtGui.QColor(color[0]*255,
- color[1]*255,
- color[2]*255)
- self.setPen(QtGui.QPen(QtGui.QColor(0,0,0)))
- self.setFlag(QtGui.QGraphicsItem.ItemIsMovable)
- self.setFlag(QtGui.QGraphicsItem.ItemIsSelectable)
- self.setFlag(QtGui.QGraphicsItem.ItemIsFocusable)
- self.setZValue(2.0)
-
- self._sx = 1.0
- self._sy = 1.0
- self._left_line = None
- self._right_line = None
- self._point = QtCore.QPointF(scalar, opacity)
- self.refresh()
-
- self.setToolTip("Double-click to change color\n"
- "Right-click to remove point\n"
- "Scalar: %.5f, Opacity: %.5f" % (self._scalar,
- self._opacity))
- # This sets up the linked list of Lines
-
- def keyPressEvent(self, event):
- if event.key() == QtCore.Qt.Key_Backspace or \
- event.key() == QtCore.Qt.Key_Delete:
- self.remove_self()
-
- def refresh(self):
- dx = 0.025 / self._sx
- dy = 0.025 / self._sy
- # this is the setup
- self.setBrush(QtGui.QBrush(self._color))
- self.setRect(-dx,
- -dy,
- 2 * dx, 2 * dy)
- self.setPos(self._scalar,
- self._opacity)
-
- def update_scale(self, sx, sy):
- self._sx = sx
- self._sy = sy
- self.refresh()
-
- def itemChange(self, change, value):
- if change == QtGui.QGraphicsItem.ItemSelectedChange:
- self.setPen(self.selection_pens[value.toBool()])
- if change == QtGui.QGraphicsItem.ItemPositionChange:
- # moves point
- pt = value.toPointF()
- pt.setY(clamp(pt.y(), 0.0, 1.0))
- self._opacity = pt.y()
- self._point.setY(pt.y())
- if not self._left_line:
- pt.setX(0.0)
- elif not self._right_line:
- pt.setX(1.0)
- else:
- assert self._left_line._point_right == self
- assert self._right_line._point_left == self
- pt.setX(clamp(pt.x(),
- self._left_line._point_left._point.x(),
- self._right_line._point_right._point.x(),
- 1e-6))
- self._point.setX(pt.x())
- self._scalar = pt.x()
- if self._left_line:
- self._left_line.refresh()
- if self._right_line:
- self._right_line.refresh()
- if self.scene():
- self.scene()._tf_poly.setup()
- self.setToolTip("Double-click to change color\n"
- "Right-click to remove point\n"
- "Scalar: %.5f, Opacity: %.5f" % (self._scalar,
- self._opacity))
- return QtGui.QGraphicsItem.itemChange(self, change,
- QtCore.QVariant(pt))
- return QtGui.QGraphicsItem.itemChange(self, change, value)
-
- def remove_self(self):
- if not self._left_line or not self._right_line:
- # Ignore, self is a corner node that can't be removed
- return
-
- # Removes the right line and self, re-ties data structure
- self._left_line._point_right = self._right_line._point_right
- self._left_line._point_right._left_line = self._left_line
-
- # be friends with garbage collector
- self._right_line._point_left = None
- self._right_line._point_right = None
- self.scene()._tf_poly.setup()
- self.scene().removeItem(self._right_line)
- self.scene().removeItem(self)
- self._left_line.refresh()
-
- def mouseDoubleClickEvent(self, event):
- new_color = QtGui.QColorDialog.getColor(self._color)
- if not new_color.isValid():
- return
- self._color = new_color
- if self._left_line:
- self._left_line.refresh()
- if self._right_line:
- self._right_line.refresh()
- self.refresh()
- self.scene()._tf_poly.setup()
-
- def mousePressEvent(self, event):
- if event.button() == QtCore.Qt.RightButton:
- event.accept()
- self.remove_self()
- else:
- QtGui.QGraphicsEllipseItem.mousePressEvent(self, event)
-
- def add_self_to_transfer_function(self, tf):
- tf.add_point(self._scalar,
- self._opacity,
- (self._color.redF(),
- self._color.greenF(),
- self._color.blueF()))
-
-class TransferFunctionPolygon(QtGui.QGraphicsPolygonItem):
-
- def __init__(self):
- QtGui.QGraphicsPolygonItem.__init__(self)
-
- def setup(self):
- # This inspects the scene, finds the left-most point, and
- # then builds the polygon traversing the linked list structure
- if not self.scene():
- return
- pt = self.scene().get_leftmost_point()
- first_pt = pt
- self.setZValue(1.25)
- g = QtGui.QLinearGradient()
- g.setStart(0.0, 0.5)
- g.setFinalStop(1.0, 0.5)
- p = QtGui.QPen()
- p.setStyle(QtCore.Qt.NoPen)
- pts = [QtCore.QPointF(pt.x(), 0)]
- self.setPen(p)
-
- while 1:
- c = QtGui.QColor(pt._color)
- c.setAlphaF(pt._opacity)
- g.setColorAt(pt._scalar, c)
- pts.append(pt._point)
- # move cursor fwd
- if pt._right_line:
- pt = pt._right_line._point_right
- else:
- break
- self.setBrush(QtGui.QBrush(g))
- pts.append(QtCore.QPointF(pt.x(), 0))
- self.setPolygon(QtGui.QPolygonF(pts))
-
-class TransferFunctionLine(QtGui.QGraphicsPolygonItem):
-
- def __init__(self, point_left, point_right, parent=None):
- assert point_right._scalar >= point_left._scalar
- QtGui.QGraphicsPolygonItem.__init__(self, parent)
- self._point_left = point_left
- self._point_right = point_right
- self._point_left._right_line = self
- self._point_right._left_line = self
- self.setup(1.0, 1.0)
- self._sx = 1.0
- self._sy = 1.0
-
- def setup(self, sx, sy):
- d = self._point_right._point - self._point_left._point
- d_normal = QtCore.QPointF(d.y(), -d.x())
- l = math.sqrt(d.x() * d.x() + d.y() * d.y())
- if l != 0.0:
- d_normal /= l
- d_normal *= 0.010
- d_normal.setX(d_normal.x() / sx)
- d_normal.setY(d_normal.y() / sy)
- ps = [self._point_left._point + d_normal,
- self._point_right._point + d_normal,
- self._point_right._point - d_normal,
- self._point_left._point - d_normal]
- self.setPolygon(QtGui.QPolygonF(ps))
- self.setZValue(1.5)
- # Gradient for filling
- g = QtGui.QLinearGradient()
- g.setStart(self._point_left._point)
- g.setFinalStop(self._point_right._point)
- g.setColorAt(0.0, self._point_left._color)
- g.setColorAt(1.0, self._point_right._color)
- self.setBrush(QtGui.QBrush(g))
- # Gradient for outlining
- g = QtGui.QLinearGradient()
- g.setStart(self._point_left._point)
- g.setFinalStop(self._point_right._point)
- dark_pl = QtGui.QColor(self._point_left._color.red() * 0.5,
- self._point_left._color.green() * 0.5,
- self._point_left._color.blue() * 0.5)
- dark_pr = QtGui.QColor(self._point_right._color.red() * 0.5,
- self._point_right._color.green() * 0.5,
- self._point_right._color.blue() * 0.5)
- g.setColorAt(0.0, dark_pl)
- g.setColorAt(1.0, dark_pr)
- p = QtGui.QPen()
- p.setBrush(QtGui.QBrush(g))
- self.setPen(p)
-
- def update_scale(self, sx, sy):
- self._sx = sx
- self._sy = sy
- self.refresh()
-
- def refresh(self):
- self.setup(self._sx, self._sy)
-
- def mouseDoubleClickEvent(self, event):
- p = event.scenePos()
- c_left = self._point_left._color
- c_right = self._point_right._color
- u = ((p.x() - self._point_left._point.x()) /
- (self._point_right._point.x() - self._point_left._point.x()))
- new_c = (u * c_right.redF() + (1-u) * c_left.redF(),
- u * c_right.greenF() + (1-u) * c_left.greenF(),
- u * c_right.blueF() + (1-u) * c_left.blueF())
- new_point = TransferFunctionPoint(p.x(), p.y(), new_c)
- new_line = TransferFunctionLine(new_point, self._point_right)
- new_point._left_line = self
- self._point_right = new_point
- self.scene().addItem(new_line)
- self.scene().addItem(new_point)
- new_line.update_scale(self._point_left._sx,
- self._point_left._sy)
- new_point.update_scale(self._point_left._sx,
- self._point_left._sy)
- new_point.refresh()
- self.refresh()
-
- def mousePressEvent(self, event):
- # This needs to be here, otherwise mouseDoubleClickEvent does
- # not get called.
- event.accept()
-
-
-##############################################################################
-# Scene, view, widget
-
-class TransferFunctionScene(QtGui.QGraphicsScene):
-
- def __init__(self, tf, parent=None):
- QtGui.QGraphicsScene.__init__(self, parent)
- self._tf_items = []
- poly = TransferFunctionPolygon()
- poly.setup()
- self._tf_poly = poly
- self.addItem(poly)
- self.create_tf_items(tf)
- #current scale
- self._sx = 1.0
- self._sy = 1.0
- # Add outlines
- line_color = QtGui.QColor(200, 200, 200)
- pen = QtGui.QPen(line_color)
- ps = [QtCore.QPointF(0.0, 0.0),
- QtCore.QPointF(1.0, 0.0),
- QtCore.QPointF(1.0, 1.0),
- QtCore.QPointF(0.0, 1.0)]
- outline = QtGui.QPolygonF(ps)
- self.addPolygon(outline, pen)
-
- for i in xrange(51):
- u = float(i) / 50.0
- self.addLine(QtCore.QLineF(u, 0.0, u, 1.0), pen)
- self.addLine(QtCore.QLineF(0.0, u, 1.0, u), pen)
-
- def reset_transfer_function(self, tf):
- self.create_tf_items(tf)
- self.update_scale(self._sx, self._sy)
- self._tf_poly.setup()
-
- def removeItem(self, item):
- if item in self._tf_items:
- self._tf_items.remove(item)
- QtGui.QGraphicsScene.removeItem(self, item)
-
- def addItem(self, item):
- # Ugly, but hey
- if isinstance(item, TransferFunctionLine) or \
- isinstance(item, TransferFunctionPoint):
- self._tf_items.append(item)
- QtGui.QGraphicsScene.addItem(self, item)
-
- def create_tf_items(self, tf):
- items = copy.copy(self._tf_items)
- for item in items:
- self.removeItem(item)
- self._tf_items = []
- if len(tf._pts) == 0:
- pt_left = TransferFunctionPoint(0.0, 0.0, (0.0, 0.0, 0.0))
- pt_right = TransferFunctionPoint(1.0, 0.0, (0.0, 0.0, 0.0))
- line = TransferFunctionLine(pt_left, pt_right)
-
- self.addItem(pt_left)
- self.addItem(pt_right)
- self.addItem(line)
-
- else:
- pts = [TransferFunctionPoint(*pt)
- for pt in tf._pts]
- lines = [TransferFunctionLine(pt_l, pt_r)
- for (pt_l, pt_r) in zip(pts[:-1], pts[1:])]
- for pt in pts:
- self.addItem(pt)
- for line in lines:
- self.addItem(line)
-
- def add_knot(self, scalar, opacity):
- pass
-
- def update_scale(self, sx, sy):
- for item in self._tf_items:
- item.update_scale(sx, sy)
- self._sx = sx
- self._sy = sy
-
- def get_leftmost_point(self):
- pt = None
-
- for item in self._tf_items:
- if hasattr(item, '_left_line') and not item._left_line:
- pt = item
- break
- assert pt
- return pt
-
- def get_transfer_function(self):
- result = TransferFunction()
- pt = self.get_leftmost_point()
- while 1:
- pt.add_self_to_transfer_function(result)
- if pt._right_line:
- pt = pt._right_line._point_right
- else:
- break
- return result
-
-class TransferFunctionView(QtGui.QGraphicsView):
- def __init__(self, parent=None):
- QtGui.QGraphicsView.__init__(self, parent)
- self.setRenderHint(QtGui.QPainter.Antialiasing)
- self.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
- self.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
-
- def resizeEvent(self, event):
- self.setMatrix(QtGui.QMatrix(event.size().width() / (10.0/9), 0,
- 0, -event.size().height() / (10.0/9), 0, 0))
- self.scene().update_scale(event.size().width()/(2000.0/9), event.size().height()/(2000.0/9))
-
- def focusOutEvent(self, event):
- self.parent().update_parent()
- QtGui.QGraphicsView.focusOutEvent(self, event)
-
-default_tf = TransferFunction()
-default_tf.add_point(0.0, 0.0, (0.0, 0.0, 0.0))
-default_tf.add_point(1.0, 0.0, (0.0, 0.0, 0.0))
-
-class TransferFunctionWidget(QtGui.QWidget, ConstantWidgetMixin):
-
- def __init__(self, param, parent=None):
- QtGui.QWidget.__init__(self, parent)
- ConstantWidgetMixin.__init__(self, param.strValue)
- if not param.strValue:
- self._tf = copy.copy(default_tf)
- else:
- self._tf = pickle.loads(param.strValue.decode('hex'))
- self._scene = TransferFunctionScene(self._tf, self)
- layout = QtGui.QVBoxLayout()
- self.setLayout(layout)
- self._view = TransferFunctionView()
- self._view.setScene(self._scene)
- self._view.setMinimumSize(200,200)
- self._view.show()
- self._view.setSizePolicy(QtGui.QSizePolicy.Expanding,
- QtGui.QSizePolicy.Expanding)
- self._view.setMatrix(QtGui.QMatrix(180, 0, 0, -180, 0, 0))
- self.setMinimumSize(200,200)
- caption = QtGui.QLabel("Double-click on the line to add a point")
- font = QtGui.QFont('Arial', 11)
- font.setItalic(True)
- caption.setFont(font)
- layout.addWidget(self._view)
- layout.addWidget(caption)
-
- def contents(self):
- return pickle.dumps(self._scene.get_transfer_function()).encode('hex')
-
- def setContents(self, strValue, silent=True):
- if not strValue:
- self._tf = copy.copy(default_tf)
- else:
- self._tf = pickle.loads(strValue.decode('hex'))
- self._scene.reset_transfer_function(self._tf)
- if not silent:
- self.update_parent()
-
-##############################################################################
-# Helper module to adjust range
-
-class vtkScaledTransferFunction(Module):
-
- def compute(self):
- tf = self.getInputFromPort('TransferFunction')
- new_tf = copy.copy(tf)
- if self.hasInputFromPort('Input'):
- port = self.getInputFromPort('Input')
- algo = port.vtkInstance.GetProducer()
- output = algo.GetOutput(port.vtkInstance.GetIndex())
- (new_tf._min_range, new_tf._max_range) = output.GetScalarRange()
- elif self.hasInputFromPort('Dataset'):
- algo = self.getInputFromPort('Dataset').vtkInstance
- output = algo
- (new_tf._min_range, new_tf._max_range) = output.GetScalarRange()
- else:
- (new_tf._min_range, new_tf._max_range) = self.getInputFromPort('Range')
-
- self.setResult('TransferFunction', new_tf)
-
-string_conversion = staticmethod(lambda x: pickle.dumps(x).encode('hex'))
-conversion = staticmethod(lambda x: pickle.loads(x.decode('hex')))
-validation = staticmethod(lambda x: isinstance(x, TransferFunction))
-TransferFunctionConstant = new_constant('TransferFunction',
- conversion,
- default_tf,
- validation,
- TransferFunctionWidget)
-TransferFunctionConstant.translate_to_string = string_conversion
-
-##############################################################################
-
-def initialize():
- init_constant(TransferFunctionConstant)
diff --git a/contrib/titan/vtk_parser.py b/contrib/titan/vtk_parser.py
deleted file mode 100644
index c0479c9..0000000
--- a/contrib/titan/vtk_parser.py
+++ /dev/null
@@ -1,528 +0,0 @@
-# Author: Prabhu Ramachandran
-# Copyright (c) 2004, Enthought, Inc.
-# License: BSD Style.
-
-# Modified for VisTrails by the VisTrails team.
-
-"""This module parses the VTK methods, obtains the argument and return
-type information, and organizes them.
-
-"""
-
-pkgs = [ "titan.Antiword", "titan.Common", "titan.DataAnalysis",
-"titan.GMeans", "titan.HDF5", "titan.MPIDataAnalysis", "titan.MPITextAnalysis",
-"titan.MTGLGraphAnalysis", "titan.OWL",
-#"titan.StanfordNER",
-"titan.TextAnalysis", "titan.Trilinos", "titan.Web", "titan.XPDF"]
-titan2 = []
-for i in pkgs:
- titan2.append(__import__(i))
-
-import vtk
-
-import re
-import class_tree
-import core.debug
-
-log = core.debug.log
-warning = core.debug.warning
-critical = core.debug.critical
-debug = core.debug.debug
-
-class VTKMethodParser(object):
- """This class provides useful methods for parsing methods of a VTK
- class or instance.
-
- The class allows one to categorize the methods of the VTK class
- and also obtain the method signatures in a form that is easy to
- use. When the `parse` method is called, it in turn calls the
- `_organize_methods` method. This method organizes the VTK methods
- into different instance variables described in the following.
- `self.toggle_meths` contains a dictionary of all the boolean
- methods of the form <Value>On/Off. The dictionary keys are
- strings with the <Value>'s and the value of each item is the
- default value (0/1) of the item (the example below will clarify
- this). `self.state_meths` contains a dictionary which collects
- the Set<Prop>To<Value> type of methods. The key is the <Prop> and
- the value is a list containing the different string <Value>'s and
- their corresponding mapped value. The first value in these is the
- default value of the <Prop>. `self.get_set_meths` will contain a
- dictionary which collects all the methods of the form
- Set/Get<Prop> that are not already specified in
- `self.toggle_meths` or `self.state_meths`. The default value of
- the Get<Prop> is stored. If the value accepted by the method has
- a range (via the methods `Get<Prop>MinValue` and
- `Get<Prop>MaxValue`), then that range is computed and stored.
- `self.get_meths` stores the methods that are of the form
- `Get<Prop>`. `self.other_meths` stores the remaining methods.
- The parsing is quite fast. Parsing every class in the VTK API
- takes a couple of seconds (on a Pentium III @ 450Mhz).
-
- Here is an example::
-
- >>> import vtk
- >>> p = VTKMethodParser()
- >>> p.parse(vtk.vtkProperty)
- >>> print p.get_toggle_methods()
- {'EdgeVisibility': 0, 'BackfaceCulling': 0, 'FrontfaceCulling': 0}
- >>> print p.get_state_methods()['Representation']
- [['Surface', 2], ['Points', 0], ['Surface', 2], ['Wireframe', 1]]
- >>> print p.get_get_set_methods()['Opacity']
- (1.0, (0.0, 1.0))
- >>> print p.get_get_methods()
- ['GetClassName']
- >>> print p.get_other_methods()[:3]
- ['BackfaceRender', 'DeepCopy', 'IsA']
-
-
- The class also provides a method called `get_method_signature`
- that obtains the Python method signature given the VTK method
- object. Here is an example::
-
- >>> import vtk
- >>> p = VTKMethodParser()
- >>> o = vtk.vtkProperty
- >>> print p.get_method_signature(o.GetClassName)
- [(['string'], None)]
- >>> print p.get_method_signature(o.GetColor)[0]
- ([('float', 'float', 'float')], None)
- >>> print p.get_method_signature(o.GetColor)[1]
- ([None], (('float', 'float', 'float'),))
-
- The `get_method_signature` is fairly efficient and obtaining the
- signature for every method in every class in the VTK API takes
- around 6 seconds (on a Pentium III @ 450Mhz).
-
- """
-
- def __init__(self, use_tree=True):
- """Initializes the object.
-
- Parameters
- ----------
-
- - use_tree : `bool`
-
- If True (default), use a ClassTree instance to obtain a
- concrete subclass for an abstract base class. This is used
- only to find the range and default values for some of the
- methods. If False, no ClassTree instance is created.
-
- This is optional because, creating a ClassTree is expensive.
- The parser functionality can be very useful even without the
- use of a ClassTree. For example, if one wants to save the
- state of a VTK object one only needs to know the names of
- the methods and not their default values, ranges etc. In
- that case using a parser should be cheap.
-
- """
- # The ClassTree is needed to find an instantiable child class
- # for an abstract VTK parent class. This instance is used to
- # obtain the state values and the ranges of the arguments
- # accepted by the Get/Set methods that have a
- # Get<Prop>{MaxValue,MinValue} method.
- if use_tree:
- self._tree = class_tree.ClassTree(titan2)
- self._tree.create()
- else:
- self._tree = None
- self._state_patn = re.compile('To[A-Z0-9]')
- self._initialize()
-
- #################################################################
- # 'VTKMethodParser' interface.
- #################################################################
-
- def parse(self, obj, no_warn=True):
- """Parse the methods for a given VTK object/class.
-
- Given a VTK class or object, this method parses the methods
- and orgaizes them into useful categories. The categories and
- their usage is documented in the documentation for the class.
-
- Parameters
- ----------
-
- - obj : VTK class or instance
-
- - no_warn : `bool` (default: True)
-
- If True (default), it suppresses any warnings generated by
- the VTK object when parsing the methods. This is safe to
- use.
-
- """
- if not hasattr(obj, '__bases__'):
- klass = obj.__class__
- else:
- klass = obj
-
- methods = self.get_methods(klass)
-
-# Wendel
- if no_warn:
- # Save warning setting and shut it off before parsing.
- warn = vtk.vtkObject.GetGlobalWarningDisplay()
- if klass.__name__ <> 'vtkObject':
- vtk.vtkObject.GlobalWarningDisplayOff()
-
- self._organize_methods(klass, methods)
-
- if no_warn:
- # Reset warning status.
- vtk.vtkObject.SetGlobalWarningDisplay(warn)
-
- def get_methods(self, klass):
- """Returns all the relevant methods of the given VTK class."""
- methods = dir(klass)[:]
- if hasattr(klass, '__members__'):
- # Only VTK versions < 4.5 have these.
- for m in klass.__members__:
- methods.remove(m)
-
- return methods
-
- def get_toggle_methods(self):
- """Returns a dictionary of the parsed <Value>On/Off methods
- along with the default value.
-
- """
- return self.toggle_meths
-
- def get_state_methods(self):
- """Returns a dict of the parsed Set<Prop>To<Value>.
-
- The keys are the <Prop> string with a list of the different
- <Value> strings along with their corresponding value (if
- obtainable). The first value is the default value of the
- state.
-
- """
- return self.state_meths
-
- def get_get_set_methods(self):
- """Returns a dict of the parsed Get/Set<Value> methods.
-
- The keys of the dict are the <Value> strings and contain a
- two-tuple containing the default value (or None if it is not
- obtainable for some reason) and a pair of numbers specifying
- an acceptable range of values (or None if not obtainable).
-
- """
- return self.get_set_meths
-
- def get_get_methods(self):
- """Return a list of parsed Get<Value> methods.
-
- All of these methods do NOT have a corresponding Set<Value>.
-
- """
- return self.get_meths
-
- def get_other_methods(self):
- """Return list of all other methods, that are not
- categorizable.
-
- """
- return self.other_meths
-
- def get_method_signature(self, method):
- """Returns information on the Python method signature given
- the VTK method.
-
- The doc string of the given method object to get the method
- signature. The method returns a list of tuples, each of which
- contains 2 items, the first is a list representing the return
- value the second represents the arguments to be passed to the
- function. If the method supports different return values and
- arguments, this function returns all of their signatures.
-
- Parameters
- ----------
-
- - method : `method`
-
- A VTK method object.
-
- """
- doc = method.__doc__
- doc = doc[:doc.find('\n\n')]
- sig = doc.split('\n')
- sig = [x.strip() for x in sig]
-
- # Remove all the C++ function signatures.
- for i in sig[:]:
- if i[:4] == 'C++:':
- sig.remove(i)
-
- # Remove the V.<method_name>
- sig = [x.replace('V.' + method.__name__, '') for x in sig]
-
- pat = re.compile(r'\b')
-
- # Split into [return_value, arguments] after processing them.
- tmp = list(sig)
- sig = []
- for i in tmp:
- # Split to get return values.
- x = i.split('->')
- # Strip each part.
- x = [y.strip() for y in x]
-
- if len(x) == 1: # No return value
- x = [None, x[0]]
- else:
- x.reverse()
-
- ret, arg = x
-
- # Remove leading and trailing parens for arguments.
- arg = arg[1:-1]
- if not arg:
- arg = None
- if arg and arg[-1] == ')':
- arg = arg + ','
-
- # Now quote the args and eval them. Easy!
- if ret:
- ret = eval(pat.sub('\"', ret))
- if arg:
- arg = eval(pat.sub('\"', arg))
- if type(arg) == type('str'):
- arg = [arg]
-
- sig.append(([ret], arg))
-
- return sig
-
- def get_tree(self):
- """Return the ClassTree instance used by this class."""
- return self._tree
-
- #################################################################
- # Non-public interface.
- #################################################################
-
- def _initialize(self):
- """Initializes the method categories."""
- # Collects the <Value>On/Off methods.
- self.toggle_meths = {}
- # Collects the Set<Prop>To<Value> methods.
- self.state_meths = {}
- # Collects the Set/Get<Value> pairs.
- self.get_set_meths = {}
- # Collects the Get<Value> methods.
- self.get_meths = []
- # Collects all the remaining methods.
- self.other_meths = []
-
- def _organize_methods(self, klass, methods):
- """Organizes the given methods of a VTK class into different
- categories.
-
- Parameters
- ----------
-
- - klass : A VTK class
-
- - methods : `list` of `str`
-
- A list of the methods to be categorized.
-
- """
- self._initialize()
- meths = methods[:]
- meths = self._find_toggle_methods(klass, meths)
- meths = self._find_state_methods(klass, meths)
- meths = self._find_get_set_methods(klass, meths)
- meths = self._find_get_methods(klass, meths)
- self.other_meths = [x for x in meths if '__' not in x]
-
- def _remove_method(self, meths, method):
- try:
- meths.remove(method)
- except ValueError:
- pass
-
- def _find_toggle_methods(self, klass, methods):
- """Find/store methods of the form <Value>{On,Off} in the given
- `methods`. Returns the remaining list of methods.
-
- """
- meths = methods[:]
- tm = self.toggle_meths
- for method in meths[:]:
- if method[-2:] == 'On':
- key = method[:-2]
- if (key + 'Off') in meths and ('Get' + key) in meths:
- tm[key] = None
- meths.remove(method)
- meths.remove(key + 'Off')
- self._remove_method(meths, 'Set' + key)
- self._remove_method(meths, 'Get' + key)
- # get defaults
- if tm:
- obj = self._get_instance(klass)
- if obj:
- for key in tm:
- try:
- tm[key] = getattr(obj, 'Get%s'%key)()
- except TypeError, e:
- log("Type error during parsing: class %s will not expose method %s " % (klass.__name__, key))
- except AttributeError, e:
- log("Attribute error during parsing: class %s will not expose method %s " % (klass.__name__, key))
- return meths
-
- def _find_state_methods(self, klass, methods):
- """Find/store methods of the form Set<Prop>To<Value> in the
- given `methods`. Returns the remaining list of methods. The
- method also computes the mapped value of the different
- <Values>.
-
- """
- # These ignored ones are really not state methods.
- ignore = ['SetUpdateExtentToWholeExtent']
- meths = methods[:]
- sm = self.state_meths
- for method in meths[:]:
- if method not in ignore and method[:3] == 'Set':
- # Methods of form Set<Prop>To<Value>
- match = self._state_patn.search(method)
- # Second cond. ensures that this is not an accident.
- if match and (('Get'+method[3:]) not in meths):
- key = method[3:match.start()] # The <Prop> part.
- if (('Get' + key) in methods):
- val = method[match.start()+2:] # <Value> part.
- meths.remove(method)
- if sm.has_key(key):
- sm[key].append([val, None])
- else:
- sm[key] = [[val, None]]
- meths.remove('Get'+ key)
- self._remove_method(meths, 'Set'+ key)
- if ('Get' + key + 'MaxValue') in meths:
- meths.remove('Get' + key + 'MaxValue')
- meths.remove('Get' + key + 'MinValue')
- try:
- meths.remove('Get' + key + 'AsString')
- except ValueError:
- pass
-
- # Find the values for each of the states, i.e. find that
- # vtkProperty.SetRepresentationToWireframe() corresponds to
- # vtkProperty.SetRepresentation(1).
- if sm:
- obj = self._get_instance(klass)
- if obj:
- for key, values in sm.items():
- default = getattr(obj, 'Get%s'%key)()
- for x in values[:]:
- try:
- getattr(obj, 'Set%sTo%s'%(key, x[0]))()
- except:
- continue
- val = getattr(obj, 'Get%s'%key)()
- x[1] = val
- if val == default:
- values.insert(0, [x[0], val])
- return meths
-
- def _find_get_set_methods(self, klass, methods):
- """Find/store methods of the form {Get,Set}Prop in the given
- `methods` and returns the remaining list of methods.
-
- Note that it makes sense to call this *after*
- `_find_state_methods` is called in order to avoid incorrect
- duplication. This method also computes the default value and
- the ranges of the arguments (when possible) by using the
- Get<Prop>{MaxValue,MinValue} methods.
-
- """
- meths = methods[:]
- gsm = self.get_set_meths
-
- for method in meths[:]:
- # Methods of the Set/Get form.
- if method in ['Get', 'Set']:
- # This occurs with the vtkInformation class.
- continue
- elif (method[:3] == 'Set') and ('Get' + method[3:]) in methods:
- key = method[3:]
- meths.remove('Set' + key)
- meths.remove('Get' + key)
- if ('Get' + key + 'MaxValue') in meths:
- meths.remove('Get' + key + 'MaxValue')
- meths.remove('Get' + key + 'MinValue')
- gsm[key] = 1
- else:
- gsm[key] = None
-
- # Find the default and range of the values.
- if gsm:
- obj = self._get_instance(klass)
- if obj:
- klass_name = klass.__name__
- for key, value in gsm.items():
- if klass_name == 'vtkPolyData':
- # Evil hack, this class segfaults!
- default = None
- else:
- try:
- default = getattr(obj, 'Get%s'%key)()
- except TypeError:
- default = None
- if value:
- low = getattr(obj, 'Get%sMinValue'%key)()
- high = getattr(obj, 'Get%sMaxValue'%key)()
- gsm[key] = (default, (low, high))
- else:
- gsm[key] = (default, None)
- else:
- # We still might have methods that have a default range.
- for key, value in gsm.items():
- if value == 1:
- gsm[key] = None
-
- return meths
-
- def _find_get_methods(self, klass, methods):
- """Find/store methods of the form Get<Value> in the given
- `methods` and returns the remaining list of methods.
-
- """
- meths = methods[:]
- gm = self.get_meths
- for method in meths[:]:
- if method == 'Get':
- # Occurs with vtkInformation
- continue
- elif method[:3] == 'Get':
- gm.append(method)
- meths.remove(method)
- return meths
-
- def _get_instance(self, klass):
- """Given a VTK class, `klass`, returns an instance of the
- class.
-
- If the class is abstract, it uses the class tree to return an
- instantiable subclass. This is necessary to get the values of
- the 'state' methods and the ranges for the Get/Set methods.
-
- """
- obj = None
- try:
- obj = klass()
- except TypeError:
- if self._tree:
- t = self._tree
- n = t.get_node(klass.__name__)
-# Wendel
- if n == None:
- return False
- for c in n.children:
- obj = self._get_instance(t.get_class(c.name))
- if obj:
- break
- return obj
-
diff --git a/contrib/titan/vtkcell.py b/contrib/titan/vtkcell.py
deleted file mode 100644
index 429c77a..0000000
--- a/contrib/titan/vtkcell.py
+++ /dev/null
@@ -1,1094 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-################################################################################
-# File QVTKWidget.py
-# File for displaying a vtkRenderWindow in a Qt's QWidget ported from
-# VTK/GUISupport/QVTK. Combine altogether to a single class: QVTKWidget
-################################################################################
-import vtk
-from PyQt4 import QtCore, QtGui
-import sip
-from core import system
-from core.modules.module_registry import get_module_registry
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
-import vtkcell_rc
-import gc
-from gui.qt import qt_super
-import core.db.action
-from core.vistrail.action import Action
-from core.vistrail.port import Port
-from core.vistrail import module
-from core.vistrail import connection
-from core.vistrail.module_function import ModuleFunction
-from core.vistrail.module_param import ModuleParam
-from core.vistrail.location import Location
-from core.modules.vistrails_module import ModuleError
-import copy
-
-################################################################################
-
-class VTKCell(SpreadsheetCell):
- """
- VTKCell is a VisTrails Module that can display vtkRenderWindow inside a cell
-
- """
-
- def __init__(self):
- SpreadsheetCell.__init__(self)
- self.cellWidget = None
-
- def compute(self):
- """ compute() -> None
- Dispatch the vtkRenderer to the actual rendering widget
- """
- renderers = self.forceGetInputListFromPort('AddRenderer')
- renderViews = self.forceGetInputListFromPort('SetRenderView')
- if len(renderViews)>1:
- raise ModuleError(self, 'There can only be one vtkRenderView '
- 'per cell')
- if len(renderViews)==1 and len(renderers)>0:
- raise ModuleError(self, 'Cannot set both vtkRenderView '
- 'and vtkRenderer to a cell')
- renderView = self.forceGetInputFromPort('SetRenderView')
- iHandlers = self.forceGetInputListFromPort('InteractionHandler')
- iStyle = self.forceGetInputFromPort('InteractorStyle')
- picker = self.forceGetInputFromPort('AddPicker')
- self.cellWidget = self.displayAndWait(QVTKWidget, (renderers, renderView, iHandlers, iStyle, picker))
-
-AsciiToKeySymTable = ( None, None, None, None, None, None, None,
- None, None,
- "Tab", None, None, None, None, None, None,
- None, None, None, None, None, None,
- None, None, None, None, None, None,
- None, None, None, None,
- "space", "exclam", "quotedbl", "numbersign",
- "dollar", "percent", "ampersand", "quoteright",
- "parenleft", "parenright", "asterisk", "plus",
- "comma", "minus", "period", "slash",
- "0", "1", "2", "3", "4", "5", "6", "7",
- "8", "9", "colon", "semicolon", "less", "equal",
- "greater", "question",
- "at", "A", "B", "C", "D", "E", "F", "G",
- "H", "I", "J", "K", "L", "M", "N", "O",
- "P", "Q", "R", "S", "T", "U", "V", "W",
- "X", "Y", "Z", "bracketleft",
- "backslash", "bracketright", "asciicircum",
- "underscore",
- "quoteleft", "a", "b", "c", "d", "e", "f", "g",
- "h", "i", "j", "k", "l", "m", "n", "o",
- "p", "q", "r", "s", "t", "u", "v", "w",
- "x", "y", "z", "braceleft", "bar", "braceright",
- "asciitilde", "Delete",
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None)
-
-class QVTKWidget(QCellWidget):
- """
- QVTKWidget is the actual rendering widget that can display
- vtkRenderer inside a Qt QWidget
-
- """
- def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
- """ QVTKWidget(parent: QWidget, f: WindowFlags) -> QVTKWidget
- Initialize QVTKWidget with a toolbar with its own device
- context
-
- """
- QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
-
- self.interacting = None
- self.mRenWin = None
- self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
- self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
- self.setMouseTracking(True)
- self.setFocusPolicy(QtCore.Qt.StrongFocus)
- self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
- QtGui.QSizePolicy.Expanding))
- self.toolBarType = QVTKWidgetToolBar
- self.iHandlers = []
- self.setAnimationEnabled(True)
- self.renderer_maps = {}
-
- def removeObserversFromInteractorStyle(self):
- """ removeObserversFromInteractorStyle() -> None
- Remove all python binding from interactor style observers for
- safely freeing the cell
-
- """
- iren = self.mRenWin.GetInteractor()
- if iren:
- style = iren.GetInteractorStyle()
- style.RemoveObservers("InteractionEvent")
- style.RemoveObservers("EndPickEvent")
- style.RemoveObservers("CharEvent")
- style.RemoveObservers("MouseWheelForwardEvent")
- style.RemoveObservers("MouseWheelBackwardEvent")
-
- def addObserversToInteractorStyle(self):
- """ addObserversToInteractorStyle() -> None
- Assign observer to the current interactor style
-
- """
- iren = self.mRenWin.GetInteractor()
- if iren:
- style = iren.GetInteractorStyle()
- style.AddObserver("InteractionEvent", self.interactionEvent)
- style.AddObserver("EndPickEvent", self.interactionEvent)
- style.AddObserver("CharEvent", self.charEvent)
- style.AddObserver("MouseWheelForwardEvent", self.interactionEvent)
- style.AddObserver("MouseWheelBackwardEvent", self.interactionEvent)
-
- def deleteLater(self):
- """ deleteLater() -> None
- Make sure to free render window resource when
- deallocating. Overriding PyQt deleteLater to free up
- resources
-
- """
- self.renderer_maps = {}
- for ren in self.getRendererList():
- self.mRenWin.RemoveRenderer(ren)
-
- self.removeObserversFromInteractorStyle()
-
- self.updateContents(([], None, [], None, None))
-
- self.SetRenderWindow(None)
-
- QCellWidget.deleteLater(self)
-
- def updateContents(self, inputPorts):
- """ updateContents(inputPorts: tuple)
- Updates the cell contents with new vtkRenderer
-
- """
- renWin = self.GetRenderWindow()
- for iHandler in self.iHandlers:
- if iHandler.observer:
- iHandler.observer.vtkInstance.SetInteractor(None)
- iHandler.clear()
-
- # Remove old renderers first
- oldRenderers = self.getRendererList()
- for renderer in oldRenderers:
- renWin.RemoveRenderer(renderer)
- renderer.SetRenderWindow(None)
- del oldRenderers
-
- (renderers, renderView, self.iHandlers, iStyle, picker) = inputPorts
- if renderView:
- renderView.vtkInstance.SetupRenderWindow(renWin)
- renderers = [renderView.vtkInstance.GetRenderer()]
- self.renderer_maps = {}
- for renderer in renderers:
- if renderView==None:
- vtkInstance = renderer.vtkInstance
- renWin.AddRenderer(vtkInstance)
- self.renderer_maps[vtkInstance] = renderer.moduleInfo['moduleId']
- else:
- vtkInstance = renderer
- if hasattr(vtkInstance, 'IsActiveCameraCreated'):
- if not vtkInstance.IsActiveCameraCreated():
- vtkInstance.ResetCamera()
- else:
- vtkInstance.ResetCameraClippingRange()
-
- iren = renWin.GetInteractor()
- if picker:
- iren.SetPicker(picker.vtkInstance)
-
- # Update interactor style
- self.removeObserversFromInteractorStyle()
- if renderView==None:
- if iStyle==None:
- iStyleInstance = vtk.vtkInteractorStyleTrackballCamera()
- else:
- iStyleInstance = iStyle.vtkInstance
- iren.SetInteractorStyle(iStyleInstance)
- self.addObserversToInteractorStyle()
-
- for iHandler in self.iHandlers:
- if iHandler.observer:
- iHandler.observer.vtkInstance.SetInteractor(iren)
- renWin.Render()
-
- # Capture window into history for playback
- # Call this at the end to capture the image after rendering
- QCellWidget.updateContents(self, inputPorts)
-
- def GetRenderWindow(self):
- """ GetRenderWindow() -> vtkRenderWindow
- Return the associated vtkRenderWindow
-
- """
- if not self.mRenWin:
- win = vtk.vtkRenderWindow()
- win.DoubleBufferOn()
- self.SetRenderWindow(win)
- del win
-
- return self.mRenWin
-
- def SetRenderWindow(self,w):
- """ SetRenderWindow(w: vtkRenderWindow)
- Set a new render window to QVTKWidget and initialize the
- interactor as well
-
- """
- if w == self.mRenWin:
- return
-
- if self.mRenWin:
- if system.systemType!='Linux':
- self.mRenWin.SetInteractor(None)
- if self.mRenWin.GetMapped():
- self.mRenWin.Finalize()
-
- self.mRenWin = w
-
- if self.mRenWin:
- self.mRenWin.Register(None)
- if self.mRenWin.GetMapped():
- self.mRenWin.Finalize()
- if system.systemType=='Linux':
- try:
- vp = '_%s_void_p' % (hex(int(QtGui.QX11Info.display()))[2:])
- except TypeError:
- #This was change for PyQt4.2
- if isinstance(QtGui.QX11Info.display(),QtGui.Display):
- display = sip.unwrapinstance(QtGui.QX11Info.display())
- vp = '_%s_void_p' % (hex(display)[2:])
- self.mRenWin.SetDisplayId(vp)
- self.resizeWindow(1,1)
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- if self.isVisible():
- self.mRenWin.Start()
-
- if not self.mRenWin.GetInteractor():
- iren = vtk.vtkRenderWindowInteractor()
- if system.systemType=='Darwin':
- iren.InstallMessageProcOff()
- iren.SetRenderWindow(self.mRenWin)
- iren.Initialize()
- if system.systemType=='Linux':
- system.XDestroyWindow(self.mRenWin.GetGenericDisplayId(),
- self.mRenWin.GetGenericWindowId())
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- self.resizeWindow(self.width(), self.height())
- self.mRenWin.SetPosition(self.x(), self.y())
-
- def GetInteractor(self):
- """ GetInteractor() -> vtkInteractor
- Return the vtkInteractor control this QVTKWidget
- """
- return self.GetRenderWindow().GetInteractor()
-
- def event(self, e):
- """ event(e: QEvent) -> depends on event type
- Process window and interaction events
-
- """
- if e.type()==QtCore.QEvent.ParentAboutToChange:
- if self.mRenWin:
- if self.mRenWin.GetMapped():
- self.mRenWin.Finalize()
- else:
- if e.type()==QtCore.QEvent.ParentChange:
- if self.mRenWin:
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- if self.isVisible():
- self.mRenWin.Start()
-
- if QtCore.QObject.event(self,e):
- return 1
-
- if e.type() == QtCore.QEvent.KeyPress:
- self.keyPressEvent(e)
- if e.isAccepted():
- return e.isAccepted()
-
- return qt_super(QVTKWidget, self).event(e)
-
- # return QtGui.QWidget.event(self,e)
- # Was this right? Wasn't this supposed to be QCellWidget.event()?
-
- def resizeWindow(self, width, height):
- """ resizeWindow(width: int, height: int) -> None
- Work around vtk bugs for resizing window
-
- """
- ########################################################
- # VTK - BUGGGGGGGGG - GRRRRRRRRR
- # This is a 'bug' in vtkWin32OpenGLRenderWindow(.cxx)
- # If a render window is mapped to screen, the actual
- # window size is the client area of the window in Win32.
- # However, this real window size is only updated through
- # vtkWin32OpenGLRenderWindow::GetSize(). So this has to
- # be called here to get the cell size correctly. This
- # invalidates the condition in the next SetSize().
- # We can use self.mRenWin.SetSize(0,0) here but it will
- # cause flickering and decrease performance!
- # SetPosition(curX,curY) also works here but slower.
- self.mRenWin.GetSize()
-
- self.mRenWin.SetSize(width, height)
- if self.mRenWin.GetInteractor():
- self.mRenWin.GetInteractor().SetSize(width, height)
-
- def resizeEvent(self, e):
- """ resizeEvent(e: QEvent) -> None
- Re-adjust the vtkRenderWindow size then QVTKWidget resized
-
- """
- qt_super(QVTKWidget, self).resizeEvent(e)
- if not self.mRenWin:
- return
-
- self.resizeWindow(self.width(), self.height())
- self.mRenWin.Render()
-
- def moveEvent(self,e):
- """ moveEvent(e: QEvent) -> None
- Echo the move event into vtkRenderWindow
-
- """
- qt_super(QVTKWidget, self).moveEvent(e)
- if not self.mRenWin:
- return
-
- self.mRenWin.SetPosition(self.x(),self.y())
-
- def paintEvent(self, e):
- """ paintEvent(e: QPaintEvent) -> None
- Paint the QVTKWidget with vtkRenderWindow
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- if hasattr(self.mRenWin, 'UpdateGLRegion'):
- self.mRenWin.UpdateGLRegion()
- self.mRenWin.Render()
-
- def SelectActiveRenderer(self,iren):
- """ SelectActiveRenderer(iren: vtkRenderWindowIteractor) -> None
- Only make the vtkRenderer below the mouse cursor active
-
- """
- epos = iren.GetEventPosition()
- rens = iren.GetRenderWindow().GetRenderers()
- rens.InitTraversal()
- for i in xrange(rens.GetNumberOfItems()):
- ren = rens.GetNextItem()
- ren.SetInteractive(ren.IsInViewport(epos[0], epos[1]))
-
- def mousePressEvent(self,e):
- """ mousePressEvent(e: QMouseEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- isDoubleClick = e.type()==QtCore.QEvent.MouseButtonDblClick
- iren.SetEventInformationFlipY(e.x(),e.y(),
- ctrl,
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),
- isDoubleClick,
- None)
- invoke = {QtCore.Qt.LeftButton:"LeftButtonPressEvent",
- QtCore.Qt.MidButton:"MiddleButtonPressEvent",
- QtCore.Qt.RightButton:"RightButtonPressEvent"}
-
- self.SelectActiveRenderer(iren)
-
- if ctrl:
- e.ignore()
- return
-
- self.interacting = self.getActiveRenderer(iren)
-
- if e.button() in invoke:
- iren.InvokeEvent(invoke[e.button()])
-
- def mouseMoveEvent(self,e):
- """ mouseMoveEvent(e: QMouseEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0), 0, None)
-
- iren.InvokeEvent("MouseMoveEvent")
-
- def enterEvent(self,e):
- """ enterEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.InvokeEvent("EnterEvent")
-
- def leaveEvent(self,e):
- """ leaveEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.InvokeEvent("LeaveEvent")
-
- def mouseReleaseEvent(self,e):
- """ mouseReleaseEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),0,None)
-
- invoke = {QtCore.Qt.LeftButton:"LeftButtonReleaseEvent",
- QtCore.Qt.MidButton:"MiddleButtonReleaseEvent",
- QtCore.Qt.RightButton:"RightButtonReleaseEvent"}
-
- self.interacting = None
-
- if e.button() in invoke:
- iren.InvokeEvent(invoke[e.button()])
-
- def keyPressEvent(self,e):
- """ keyPressEvent(e: QKeyEvent) -> None
- Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ascii_key = None
- if e.text().length()>0:
- ascii_key = e.text().toLatin1()[0]
- else:
- ascii_key = chr(0)
-
- keysym = self.ascii_to_key_sym(ord(ascii_key))
-
- if not keysym:
- keysym = self.qt_key_to_key_sym(e.key())
-
- # Ignore 'q' or 'e' or Ctrl-anykey
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
- if (keysym in ['q', 'e'] or ctrl):
- e.ignore()
- return
-
- iren.SetKeyEventInformation(ctrl,shift,ascii_key, e.count(), keysym)
-
- iren.InvokeEvent("KeyPressEvent")
-
- if ascii_key:
- iren.InvokeEvent("CharEvent")
-
-
- def keyReleaseEvent(self,e):
- """ keyReleaseEvent(e: QKeyEvent) -> None
- Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ascii_key = None
- if e.text().length()>0:
- ascii_key = e.text().toLatin1()[0]
- else:
- ascii_key = chr(0)
-
- keysym = self.ascii_to_key_sym(ord(ascii_key))
-
- if not keysym:
- keysym = self.qt_key_to_key_sym(e.key())
-
- # Ignore 'q' or 'e' or Ctrl-anykey
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
- if (keysym in ['q','e'] or ctrl):
- e.ignore()
- return
-
- iren.SetKeyEventInformation(ctrl, shift, ascii_key, e.count(), keysym)
-
- iren.InvokeEvent("KeyReleaseEvent")
-
- def wheelEvent(self,e):
- """ wheelEvent(e: QWheelEvent) -> None
- Zoom in/out while scrolling the mouse
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),0,None)
-
- self.SelectActiveRenderer(iren)
-
- if e.delta()>0:
- iren.InvokeEvent("MouseWheelForwardEvent")
- else:
- iren.InvokeEvent("MouseWheelBackwardEvent")
-
- def focusInEvent(self,e):
- """ focusInEvent(e: QFocusEvent) -> None
- Ignore focus event
-
- """
- pass
-
- def focusOutEvent(self,e):
- """ focusOutEvent(e: QFocusEvent) -> None
- Ignore focus event
-
- """
- pass
-
- def contextMenuEvent(self,e):
- """ contextMenuEvent(e: QContextMenuEvent) -> None
- Make sure to get the right mouse position for the context menu
- event, i.e. also the right click
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ctrl = int(e.modifiers()&QtCore.Qt.ControlModifier)
- shift = int(e.modifiers()&QtCore.Qt.ShiftModifier)
- iren.SetEventInformationFlipY(e.x(),e.y(),ctrl,shift,chr(0),0,None)
- iren.InvokeEvent("ContextMenuEvent")
-
- def ascii_to_key_sym(self,i):
- """ ascii_to_key_sym(i: int) -> str
- Convert ASCII code into key name
-
- """
- global AsciiToKeySymTable
- return AsciiToKeySymTable[i]
-
- def qt_key_to_key_sym(self,i):
- """ qt_key_to_key_sym(i: QtCore.Qt.Keycode) -> str
- Convert Qt key code into key name
-
- """
- handler = {QtCore.Qt.Key_Backspace:"BackSpace",
- QtCore.Qt.Key_Tab:"Tab",
- QtCore.Qt.Key_Backtab:"Tab",
- QtCore.Qt.Key_Return:"Return",
- QtCore.Qt.Key_Enter:"Return",
- QtCore.Qt.Key_Shift:"Shift_L",
- QtCore.Qt.Key_Control:"Control_L",
- QtCore.Qt.Key_Alt:"Alt_L",
- QtCore.Qt.Key_Pause:"Pause",
- QtCore.Qt.Key_CapsLock:"Caps_Lock",
- QtCore.Qt.Key_Escape:"Escape",
- QtCore.Qt.Key_Space:"space",
- QtCore.Qt.Key_End:"End",
- QtCore.Qt.Key_Home:"Home",
- QtCore.Qt.Key_Left:"Left",
- QtCore.Qt.Key_Up:"Up",
- QtCore.Qt.Key_Right:"Right",
- QtCore.Qt.Key_Down:"Down",
- QtCore.Qt.Key_SysReq:"Snapshot",
- QtCore.Qt.Key_Insert:"Insert",
- QtCore.Qt.Key_Delete:"Delete",
- QtCore.Qt.Key_Help:"Help",
- QtCore.Qt.Key_0:"0",
- QtCore.Qt.Key_1:"1",
- QtCore.Qt.Key_2:"2",
- QtCore.Qt.Key_3:"3",
- QtCore.Qt.Key_4:"4",
- QtCore.Qt.Key_5:"5",
- QtCore.Qt.Key_6:"6",
- QtCore.Qt.Key_7:"7",
- QtCore.Qt.Key_8:"8",
- QtCore.Qt.Key_9:"9",
- QtCore.Qt.Key_A:"a",
- QtCore.Qt.Key_B:"b",
- QtCore.Qt.Key_C:"c",
- QtCore.Qt.Key_D:"d",
- QtCore.Qt.Key_E:"e",
- QtCore.Qt.Key_F:"f",
- QtCore.Qt.Key_G:"g",
- QtCore.Qt.Key_H:"h",
- QtCore.Qt.Key_I:"i",
- QtCore.Qt.Key_J:"h",
- QtCore.Qt.Key_K:"k",
- QtCore.Qt.Key_L:"l",
- QtCore.Qt.Key_M:"m",
- QtCore.Qt.Key_N:"n",
- QtCore.Qt.Key_O:"o",
- QtCore.Qt.Key_P:"p",
- QtCore.Qt.Key_Q:"q",
- QtCore.Qt.Key_R:"r",
- QtCore.Qt.Key_S:"s",
- QtCore.Qt.Key_T:"t",
- QtCore.Qt.Key_U:"u",
- QtCore.Qt.Key_V:"v",
- QtCore.Qt.Key_W:"w",
- QtCore.Qt.Key_X:"x",
- QtCore.Qt.Key_Y:"y",
- QtCore.Qt.Key_Z:"z",
- QtCore.Qt.Key_Asterisk:"asterisk",
- QtCore.Qt.Key_Plus:"plus",
- QtCore.Qt.Key_Minus:"minus",
- QtCore.Qt.Key_Period:"period",
- QtCore.Qt.Key_Slash:"slash",
- QtCore.Qt.Key_F1:"F1",
- QtCore.Qt.Key_F2:"F2",
- QtCore.Qt.Key_F3:"F3",
- QtCore.Qt.Key_F4:"F4",
- QtCore.Qt.Key_F5:"F5",
- QtCore.Qt.Key_F6:"F6",
- QtCore.Qt.Key_F7:"F7",
- QtCore.Qt.Key_F8:"F8",
- QtCore.Qt.Key_F9:"F9",
- QtCore.Qt.Key_F10:"F10",
- QtCore.Qt.Key_F11:"F11",
- QtCore.Qt.Key_F12:"F12",
- QtCore.Qt.Key_F13:"F13",
- QtCore.Qt.Key_F14:"F14",
- QtCore.Qt.Key_F15:"F15",
- QtCore.Qt.Key_F16:"F16",
- QtCore.Qt.Key_F17:"F17",
- QtCore.Qt.Key_F18:"F18",
- QtCore.Qt.Key_F19:"F19",
- QtCore.Qt.Key_F20:"F20",
- QtCore.Qt.Key_F21:"F21",
- QtCore.Qt.Key_F22:"F22",
- QtCore.Qt.Key_F23:"F23",
- QtCore.Qt.Key_F24:"F24",
- QtCore.Qt.Key_NumLock:"Num_Lock",
- QtCore.Qt.Key_ScrollLock:"Scroll_Lock"}
- if i in handler:
- return handler[i]
- else:
- return "None"
-
- def getRendererList(self):
- """ getRendererList() -> list
- Return a list of vtkRenderer running in this QVTKWidget
- """
- result = []
- renWin = self.GetRenderWindow()
- renderers = renWin.GetRenderers()
- renderers.InitTraversal()
- for i in xrange(renderers.GetNumberOfItems()):
- result.append(renderers.GetNextItem())
- return result
-
- def getActiveRenderer(self, iren):
- """ getActiveRenderer(iren: vtkRenderWindowwInteractor) -> vtkRenderer
- Return the active vtkRenderer under mouse
-
- """
- epos = list(iren.GetEventPosition())
- if epos[1]<0:
- epos[1] = -epos[1]
- rens = iren.GetRenderWindow().GetRenderers()
- rens.InitTraversal()
- for i in xrange(rens.GetNumberOfItems()):
- ren = rens.GetNextItem()
- if ren.IsInViewport(epos[0], epos[1]):
- return ren
- return None
-
- def findSheetTabWidget(self):
- """ findSheetTabWidget() -> QTabWidget
- Find and return the sheet tab widget
-
- """
- p = self.parent()
- while p:
- if hasattr(p, 'isSheetTabWidget'):
- if p.isSheetTabWidget()==True:
- return p
- p = p.parent()
- return None
-
- def getRenderersInCellList(self, sheet, cells):
- """ isRendererIn(sheet: spreadsheet.StandardWidgetSheet,
- cells: [(int,int)]) -> bool
- Get the list of renderers in side a list of (row, column)
- cells.
-
- """
- rens = []
- for (row, col) in cells:
- cell = sheet.getCell(row, col)
- if hasattr(cell, 'getRendererList'):
- rens += cell.getRendererList()
- return rens
-
- def getSelectedCellWidgets(self):
- sheet = self.findSheetTabWidget()
- if sheet:
- iren = self.mRenWin.GetInteractor()
- ren = self.interacting
- if not ren: ren = self.getActiveRenderer(iren)
- if ren:
- cells = sheet.getSelectedLocations()
- if (ren in self.getRenderersInCellList(sheet, cells)):
- return [sheet.getCell(row, col)
- for (row, col) in cells
- if hasattr(sheet.getCell(row, col),
- 'getRendererList')]
- return []
-
- def interactionEvent(self, istyle, name):
- """ interactionEvent(istyle: vtkInteractorStyle, name: str) -> None
- Make sure interactions sync across selected renderers
-
- """
- if name=='MouseWheelForwardEvent':
- istyle.OnMouseWheelForward()
- if name=='MouseWheelBackwardEvent':
- istyle.OnMouseWheelBackward()
- ren = self.interacting
- if not ren:
- ren = self.getActiveRenderer(istyle.GetInteractor())
- if ren:
- cam = ren.GetActiveCamera()
- cpos = cam.GetPosition()
- cfol = cam.GetFocalPoint()
- cup = cam.GetViewUp()
- for cell in self.getSelectedCellWidgets():
- if cell!=self and hasattr(cell, 'getRendererList'):
- rens = cell.getRendererList()
- for r in rens:
- if r!=ren:
- dcam = r.GetActiveCamera()
- dcam.SetPosition(cpos)
- dcam.SetFocalPoint(cfol)
- dcam.SetViewUp(cup)
- r.ResetCameraClippingRange()
- cell.update()
-
- def charEvent(self, istyle, name):
- """ charEvent(istyle: vtkInteractorStyle, name: str) -> None
- Make sure key presses also sync across selected renderers
-
- """
- iren = istyle.GetInteractor()
- ren = self.interacting
- if not ren: ren = self.getActiveRenderer(iren)
- if ren:
- keyCode = iren.GetKeyCode()
- if keyCode in ['w','W','s','S','r','R','p','P']:
- for cell in self.getSelectedCellWidgets():
- if hasattr(cell, 'GetInteractor'):
- selectedIren = cell.GetInteractor()
- selectedIren.SetKeyCode(keyCode)
- selectedIren.GetInteractorStyle().OnChar()
- selectedIren.Render()
- istyle.OnChar()
-
- def saveToPNG(self, filename):
- """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
-
- Save the current widget contents to an image file. If
- str==None, then it returns the vtkUnsignedCharArray containing
- the PNG image. Otherwise, the filename is returned.
-
- """
- w2i = vtk.vtkWindowToImageFilter()
- w2i.ReadFrontBufferOff()
- w2i.SetInput(self.mRenWin)
- # Render twice to get a clean image on the back buffer
- self.mRenWin.Render()
- self.mRenWin.Render()
- w2i.Update()
- writer = vtk.vtkPNGWriter()
- writer.SetInputConnection(w2i.GetOutputPort())
- if filename!=None:
- writer.SetFileName(filename)
- else:
- writer.WriteToMemoryOn()
- writer.Write()
- if filename:
- return filename
- else:
- return writer.GetResult()
-
- def captureWindow(self):
- """ captureWindow() -> None
- Capture the window contents to file
-
- """
- fn = QtGui.QFileDialog.getSaveFileName(None,
- "Save file as...",
- "screenshot.png",
- "Images (*.png)")
- if fn.isNull():
- return
- self.saveToPNG(str(fn))
-
- def grabWindowPixmap(self):
- """ grabWindowImage() -> QPixmap
- Widget special grabbing function
-
- """
- uchar = self.saveToPNG(None)
-
- ba = QtCore.QByteArray()
- buf = QtCore.QBuffer(ba)
- buf.open(QtCore.QIODevice.WriteOnly)
- for i in xrange(uchar.GetNumberOfTuples()):
- c = uchar.GetValue(i)
- buf.putChar(chr(c))
- buf.close()
-
- pixmap = QtGui.QPixmap()
- pixmap.loadFromData(ba, 'PNG')
- return pixmap
-
- def dumpToFile(self, filename):
- """dumpToFile() -> None
- Dumps itself as an image to a file, calling saveToPNG
- """
- self.saveToPNG(filename)
-
-class QVTKWidgetCapture(QtGui.QAction):
- """
- QVTKWidgetCapture is the action to capture the vtk rendering
- window to an image
-
- """
- def __init__(self, parent=None):
- """ QVTKWidgetCapture(parent: QWidget) -> QVTKWidgetCapture
- Setup the image, status tip, etc. of the action
-
- """
- QtGui.QAction.__init__(self,
- QtGui.QIcon(":/images/camera.png"),
- "&Capture image to file",
- parent)
- self.setStatusTip("Capture the rendered image to a file")
-
- def triggeredSlot(self, checked=False):
- """ toggledSlot(checked: boolean) -> None
- Execute the action when the button is clicked
-
- """
- cellWidget = self.toolBar.getSnappedWidget()
- cellWidget.captureWindow()
-
-class QVTKWidgetSaveCamera(QtGui.QAction):
- """
- QVTKWidgetSaveCamera is the action to capture the current camera
- of the vtk renderers and save it back to the pipeline
-
- """
- def __init__(self, parent=None):
- """ QVTKWidgetSaveCamera(parent: QWidget) -> QVTKWidgetSaveCamera
- Setup the image, status tip, etc. of the action
-
- """
- QtGui.QAction.__init__(self,
- "Save &Camera",
- parent)
- self.setStatusTip("Save current camera views to the pipeline")
-
- def setCamera(self, controller):
- ops = []
- pipeline = controller.current_pipeline
- cellWidget = self.toolBar.getSnappedWidget()
- renderers = cellWidget.getRendererList()
- for ren in renderers:
- cam = ren.GetActiveCamera()
- cpos = cam.GetPosition()
- cfol = cam.GetFocalPoint()
- cup = cam.GetViewUp()
- rendererId = cellWidget.renderer_maps[ren]
- # Looking for SetActiveCamera()
- camera = None
- renderer = pipeline.modules[rendererId]
- for c in pipeline.connections.values():
- if c.destination.moduleId==rendererId:
- if c.destination.name=='SetActiveCamera':
- camera = pipeline.modules[c.source.moduleId]
- break
-
- if not camera:
- # Create camera
- vtk_package = 'edu.utah.sci.vistrails.vtk'
- camera = controller.create_module(vtk_package, 'vtkCamera', '',
- 0.0, 0.0)
- ops.append(('add', camera))
-
- # Connect camera to renderer
- camera_conn = controller.create_connection(camera, 'self',
- renderer,
- 'SetActiveCamera')
- ops.append(('add', camera_conn))
- # update functions
- def convert_to_str(arglist):
- new_arglist = []
- for arg in arglist:
- new_arglist.append(str(arg))
- return new_arglist
- functions = [('SetPosition', convert_to_str(cpos)),
- ('SetFocalPoint', convert_to_str(cfol)),
- ('SetViewUp', convert_to_str(cup))]
- ops.extend(controller.update_functions_ops(camera, functions))
-
- action = core.db.action.create_action(ops)
- controller.add_new_action(action)
- controller.perform_action(action)
- controller.select_latest_version()
-
- def triggeredSlot(self, checked=False):
- """ toggledSlot(checked: boolean) -> None
- Execute the action when the button is clicked
-
- """
- visApp = QtCore.QCoreApplication.instance()
- if hasattr(visApp, 'builderWindow'):
- builderWindow = visApp.builderWindow
- if builderWindow:
- info = self.toolBar.sheet.getCellPipelineInfo(
- self.toolBar.row, self.toolBar.col)
- if info:
- info = info[0]
- viewManager = builderWindow.viewManager
- view = viewManager.ensureVistrail(info['locator'])
- if view:
- controller = view.controller
- controller.change_selected_version(info['version'])
- self.setCamera(controller)
-
-
-class QVTKWidgetToolBar(QCellToolBar):
- """
- QVTKWidgetToolBar derives from QCellToolBar to give the VTKCell
- a customizable toolbar
-
- """
- def createToolBar(self):
- """ createToolBar() -> None
- This will get call initiallly to add customizable widgets
-
- """
- self.appendAction(QVTKWidgetCapture(self))
- self.addAnimationButtons()
- self.appendAction(QVTKWidgetSaveCamera(self))
-
-def registerSelf():
- """ registerSelf() -> None
- Registry module with the registry
- """
- identifier = 'edu.utah.sci.vistrails.vtk'
- registry = get_module_registry()
- registry.add_module(VTKCell)
- registry.add_input_port(VTKCell, "Location", CellLocation)
- import core.debug
- for (port,module) in [("AddRenderer",'vtkRenderer'),
- ("SetRenderView",'vtkRenderView'),
- ("InteractionHandler",'vtkInteractionHandler'),
- ("InteractorStyle", 'vtkInteractorStyle'),
- ("AddPicker",'vtkAbstractPicker')]:
- try:
- registry.add_input_port(VTKCell, port,'(%s:%s)'%(identifier,module))
-
- except Exception, e:
- core.debug.warning(str(e))
-
- registry.add_output_port(VTKCell, "self", VTKCell)
diff --git a/contrib/titan/vtkcell_rc.py b/contrib/titan/vtkcell_rc.py
deleted file mode 100644
index 8aa8cbf..0000000
--- a/contrib/titan/vtkcell_rc.py
+++ /dev/null
@@ -1,793 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-# Resource object code
-#
-# Created: Fri Sep 22 09:09:40 2006
-# by: The Resource Compiler for PyQt (Qt v4.1.3)
-#
-# WARNING! All changes made in this file will be lost!
-
-from PyQt4 import QtCore
-
-qt_resource_data = "\
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-"
-
-qt_resource_name = "\
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-"
-
-qt_resource_struct = "\
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-"
-
-def qInitResources():
- QtCore.qRegisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
-
-def qCleanupResources():
- QtCore.qUnregisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
-
-qInitResources()
diff --git a/contrib/titan/vtkhandler.py b/contrib/titan/vtkhandler.py
deleted file mode 100644
index b6703a3..0000000
--- a/contrib/titan/vtkhandler.py
+++ /dev/null
@@ -1,292 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-"""Modules for handling vtkRenderWindowInteractor events"""
-from PyQt4 import QtCore, QtGui
-from core.modules.basic_modules import String
-from core.modules.vistrails_module import Module, NotCacheable
-from core.modules.module_registry import get_module_registry
-from core.modules.module_configure import StandardModuleConfigurationWidget
-from core.modules.python_source_configure import PythonEditor
-from core.vistrail.module_function import ModuleFunction, ModuleParam
-import urllib
-
-################################################################################
-class vtkInteractionHandler(NotCacheable, Module):
- """
- vtkInteractionHandler allow users to insert callback code for interacting
- with the vtkRenderWindowInteractor InteractionEvent
-
- """
-
- # Since vtkCommand is not wrapped in Python, we need to hardcoded all events
- # string from vtkCommand.h
- vtkEvents = [
- 'AnyEvent',
- 'DeleteEvent',
- 'StartEvent',
- 'EndEvent',
- 'RenderEvent',
- 'ProgressEvent',
- 'PickEvent',
- 'StartPickEvent',
- 'EndPickEvent',
- 'AbortCheckEvent',
- 'ExitEvent',
- 'LeftButtonPressEvent',
- 'LeftButtonReleaseEvent',
- 'MiddleButtonPressEvent',
- 'MiddleButtonReleaseEvent',
- 'RightButtonPressEvent',
- 'RightButtonReleaseEvent',
- 'EnterEvent',
- 'LeaveEvent',
- 'KeyPressEvent',
- 'KeyReleaseEvent',
- 'CharEvent',
- 'ExposeEvent',
- 'ConfigureEvent',
- 'TimerEvent',
- 'MouseMoveEvent',
- 'MouseWheelForwardEvent',
- 'MouseWheelBackwardEvent',
- 'ResetCameraEvent',
- 'ResetCameraClippingRangeEvent',
- 'ModifiedEvent',
- 'WindowLevelEvent',
- 'StartWindowLevelEvent',
- 'EndWindowLevelEvent',
- 'ResetWindowLevelEvent',
- 'SetOutputEvent',
- 'ErrorEvent',
- 'WarningEvent',
- 'StartInteractionEvent',
- 'InteractionEvent',
- 'EndInteractionEvent',
- 'EnableEvent',
- 'DisableEvent',
- 'CreateTimerEvent',
- 'DestroyTimerEvent',
- 'PlacePointEvent',
- 'PlaceWidgetEvent',
- 'CursorChangedEvent',
- 'ExecuteInformationEvent',
- 'RenderWindowMessageEvent',
- 'WrongTagEvent',
- 'StartAnimationCueEvent',
- 'AnimationCueTickEvent',
- 'EndAnimationCueEvent',
- 'VolumeMapperRenderEndEvent',
- 'VolumeMapperRenderProgressEvent',
- 'VolumeMapperRenderStartEvent',
- 'VolumeMapperComputeGradientsEndEvent',
- 'VolumeMapperComputeGradientsProgressEvent',
- 'VolumeMapperComputeGradientsStartEvent',
- 'WidgetModifiedEvent',
- 'WidgetValueChangedEvent',
- 'WidgetActivateEvent',
- 'ConnectionCreatedEvent',
- 'ConnectionClosedEvent',
- 'DomainModifiedEvent',
- 'PropertyModifiedEvent',
- 'UpdateEvent',
- 'RegisterEvent',
- 'UnRegisterEvent',
- 'UpdateInformationEvent']
-
- def __init__(self):
- Module.__init__(self)
- self.observer = None
- self.handler = None
- self.shareddata = None
-
- def compute(self):
- """ compute() -> None
- Actually compute nothing
- """
- self.observer = self.forceGetInputFromPort('Observer')
- self.handler = self.forceGetInputFromPort('Handler', '')
- self.shareddata = self.forceGetInputListFromPort('SharedData')
- if len(self.shareddata)==1:
- self.shareddata = self.shareddata[0]
- if self.observer:
- source = urllib.unquote(self.handler)
- observer = self.observer.vtkInstance
- for e in vtkInteractionHandler.vtkEvents:
- f = e[0].lower() + e[1:]
- f = f.replace('Event', 'Handler')
- source += ('\nif locals().has_key("%s"):\n' % f +
- '\tobserver.AddObserver("%s", ' % e +
- 'self.eventHandler)\n')
- exec(source)
- if hasattr(self.observer.vtkInstance, 'PlaceWidget'):
- self.observer.vtkInstance.PlaceWidget()
-
- def eventHandler(self, obj, event):
- """ eventHandler(obj: vtkObject, event: str) -> None
- A proxy for all vtk events to direct to the correct calls
-
- """
- if self.handler!='':
- source = urllib.unquote(self.handler)
- f = event[0].lower() + event[1:]
- f = f.replace('Event', 'Handler')
- myGlobals = globals()
- myGlobals.update({'self':self})
- exec(source + ('\nif locals().has_key("%s"):\n' % f)+
- ('\t%s(obj, self.shareddata)' % f)) in myGlobals, locals()
-
- def clear(self):
- """ clear() -> None
- Remove event handler so the object can be freed correctly
-
- """
- # Remove all observers
- if self.observer:
- for e in vtkInteractionHandler.vtkEvents:
- self.observer.vtkInstance.RemoveObservers(e)
- Module.clear(self)
-
- def repaintCells(self):
- """ repaintCells() -> None
- Redraw all cells on the current sheet
-
- """
- from packages.spreadsheet.spreadsheet_controller \
- import spreadsheetController
- from packages.spreadsheet.spreadsheet_event \
- import RepaintCurrentSheetEvent
- spreadsheetController.postEventToSpreadsheet(RepaintCurrentSheetEvent())
-
-class HandlerConfigurationWidget(StandardModuleConfigurationWidget):
- """
- HandlerConfigurationWidget is simialr to PythonSource
- configuration widget except that it doesn't allow add/remove
- ports. In this configuration widget, the user will enter their
- python code to handle a specifc event
-
- """
- def __init__(self, module, controller, parent=None):
- """ HandlerConfigurationWidget(module: Module,
- controller: VistrailController,
- parent: QWidget)
- -> HandlerConfigurationWidget
- Setup the dialog to have a single python source editor and 2
- buttons
-
- """
- StandardModuleConfigurationWidget.__init__(self, module,
- controller, parent)
- self.setWindowTitle('Handler Python Script Editor')
- self.setLayout(QtGui.QVBoxLayout())
- self.layout().setMargin(0)
- self.layout().setSpacing(0)
- self.createEditor()
- self.createButtonLayout()
-
- def findHandlerFunction(self):
- """ findHandlerFunction() -> int
- Return the function id associated with input port 'source'
-
- """
- fid = -1
- for i in xrange(self.module.getNumFunctions()):
- if self.module.functions[i].name=='Handler':
- fid = i
- break
- return fid
-
- def createEditor(self):
- """ createEditor() -> None
- Add a python editor into the widget layout
-
- """
- self.codeEditor = PythonEditor(self)
- fid = self.findHandlerFunction()
- if fid!=-1:
- f = self.module.functions[fid]
- self.codeEditor.setPlainText(urllib.unquote(f.params[0].strValue))
- self.codeEditor.document().setModified(False)
- self.layout().addWidget(self.codeEditor, 1)
-
- def createButtonLayout(self):
- """ createButtonLayout() -> None
- Construct Ok & Cancel button
-
- """
- self.buttonLayout = QtGui.QHBoxLayout()
- self.buttonLayout.setMargin(5)
- self.okButton = QtGui.QPushButton('&OK', self)
- self.okButton.setAutoDefault(False)
- self.okButton.setFixedWidth(100)
- self.buttonLayout.addWidget(self.okButton)
- self.cancelButton = QtGui.QPushButton('&Cancel', self)
- self.cancelButton.setAutoDefault(False)
- self.cancelButton.setShortcut('Esc')
- self.cancelButton.setFixedWidth(100)
- self.buttonLayout.addWidget(self.cancelButton)
- self.layout().addLayout(self.buttonLayout)
- self.connect(self.okButton, QtCore.SIGNAL('clicked(bool)'), self.okTriggered)
- self.connect(self.cancelButton, QtCore.SIGNAL('clicked(bool)'), self.close)
-
- def sizeHint(self):
- """ sizeHint() -> QSize
- Return the recommendation size of this widget
-
- """
- return QtCore.QSize(512, 512)
-
- def updateController(self, controller):
- """ updateController() -> None
- Based on the input of the python editor, update the vistrail
- controller appropriately
-
- """
- if self.codeEditor.document().isModified():
- code = urllib.quote(str(self.codeEditor.toPlainText()))
- functions = [('Handler', [code])]
- self.controller.update_functions(self.module, functions)
-
- def okTriggered(self, checked = False):
- """ okTriggered(checked: bool) -> None
- Update vistrail controller (if neccesssary) then close the widget
-
- """
- self.updateController(self.controller)
- self.emit(QtCore.SIGNAL('doneConfigure()'))
- self.close()
-
-
-def registerSelf():
- """ registerSelf() -> None
- Registry module with the registry
- """
- registry = get_module_registry()
- vIO = registry.get_descriptor_by_name(
- 'edu.utah.sci.vistrails.vtk',
-# Wendel
- 'vtkInteractorObserver').module
- registry.add_module(vtkInteractionHandler, configureWidgetType=HandlerConfigurationWidget)
- registry.add_input_port(vtkInteractionHandler, 'Observer', vIO)
- registry.add_input_port(vtkInteractionHandler, 'Handler', String, True)
- registry.add_input_port(vtkInteractionHandler, 'SharedData', Module)
- registry.add_output_port(vtkInteractionHandler, 'self',
- vtkInteractionHandler)
diff --git a/contrib/titan/vtkviewcell.py b/contrib/titan/vtkviewcell.py
deleted file mode 100644
index a4826d0..0000000
--- a/contrib/titan/vtkviewcell.py
+++ /dev/null
@@ -1,1032 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-################################################################################
-# File QVTKViewWidget.py
-# File for displaying a vtkRenderWindow in a Qt's QWidget ported from
-# VTK/GUISupport/QVTK. Combine altogether to a single class: QVTKViewWidget
-################################################################################
-import vtk
-from PyQt4 import QtCore, QtGui
-import sip
-from core import system
-from core.modules.module_registry import get_module_registry
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
-import vtkcell_rc
-import gc
-from gui.qt import qt_super
-import core.db.action
-from core.vistrail.action import Action
-from core.vistrail.port import Port
-from core.vistrail import module
-from core.vistrail import connection
-from core.vistrail.module_function import ModuleFunction
-from core.vistrail.module_param import ModuleParam
-from core.vistrail.location import Location
-from core.modules.vistrails_module import ModuleError
-import copy
-
-################################################################################
-
-class VTKViewCell(SpreadsheetCell):
- """
- VTKViewCell is a VisTrails Module that can display vtkRenderWindow inside a cell
-
- """
-
- def __init__(self):
- SpreadsheetCell.__init__(self)
- self.cellWidget = None
-
- def compute(self):
- """ compute() -> None
- Dispatch the vtkRenderer to the actual rendering widget
- """
- renderView = self.forceGetInputFromPort('SetRenderView')
- if renderView==None:
- raise ModuleError(self, 'A vtkRenderView input is required.')
- self.cellWidget = self.displayAndWait(QVTKViewWidget, (renderView,))
-
-AsciiToKeySymTable = ( None, None, None, None, None, None, None,
- None, None,
- "Tab", None, None, None, None, None, None,
- None, None, None, None, None, None,
- None, None, None, None, None, None,
- None, None, None, None,
- "space", "exclam", "quotedbl", "numbersign",
- "dollar", "percent", "ampersand", "quoteright",
- "parenleft", "parenright", "asterisk", "plus",
- "comma", "minus", "period", "slash",
- "0", "1", "2", "3", "4", "5", "6", "7",
- "8", "9", "colon", "semicolon", "less", "equal",
- "greater", "question",
- "at", "A", "B", "C", "D", "E", "F", "G",
- "H", "I", "J", "K", "L", "M", "N", "O",
- "P", "Q", "R", "S", "T", "U", "V", "W",
- "X", "Y", "Z", "bracketleft",
- "backslash", "bracketright", "asciicircum",
- "underscore",
- "quoteleft", "a", "b", "c", "d", "e", "f", "g",
- "h", "i", "j", "k", "l", "m", "n", "o",
- "p", "q", "r", "s", "t", "u", "v", "w",
- "x", "y", "z", "braceleft", "bar", "braceright",
- "asciitilde", "Delete",
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None)
-
-class QVTKViewWidget(QCellWidget):
- """
- QVTKViewWidget is the actual rendering widget that can display
- vtkRenderer inside a Qt QWidget
-
- """
- def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
- """ QVTKViewWidget(parent: QWidget, f: WindowFlags) -> QVTKViewWidget
- Initialize QVTKViewWidget with a toolbar with its own device
- context
-
- """
- QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
-
- self.interacting = None
- self.mRenWin = None
- self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
- self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
- self.setMouseTracking(True)
- self.setFocusPolicy(QtCore.Qt.StrongFocus)
- self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
- QtGui.QSizePolicy.Expanding))
- self.toolBarType = QVTKViewWidgetToolBar
- self.setAnimationEnabled(True)
-
- def removeObserversFromInteractorStyle(self):
- """ removeObserversFromInteractorStyle() -> None
- Remove all python binding from interactor style observers for
- safely freeing the cell
-
- """
- iren = self.mRenWin.GetInteractor()
- if iren:
- style = iren.GetInteractorStyle()
- style.RemoveObservers("InteractionEvent")
- style.RemoveObservers("EndPickEvent")
- style.RemoveObservers("CharEvent")
- style.RemoveObservers("MouseWheelForwardEvent")
- style.RemoveObservers("MouseWheelBackwardEvent")
-
- def addObserversToInteractorStyle(self):
- """ addObserversToInteractorStyle() -> None
- Assign observer to the current interactor style
-
- """
- iren = self.mRenWin.GetInteractor()
- if iren:
- style = iren.GetInteractorStyle()
- style.AddObserver("InteractionEvent", self.interactionEvent)
- style.AddObserver("EndPickEvent", self.interactionEvent)
- style.AddObserver("CharEvent", self.charEvent)
- style.AddObserver("MouseWheelForwardEvent", self.interactionEvent)
- style.AddObserver("MouseWheelBackwardEvent", self.interactionEvent)
-
- def deleteLater(self):
- """ deleteLater() -> None
- Make sure to free render window resource when
- deallocating. Overriding PyQt deleteLater to free up
- resources
-
- """
- self.renderer_maps = {}
- for ren in self.getRendererList():
- self.mRenWin.RemoveRenderer(ren)
- self.removeObserversFromInteractorStyle()
- self.SetRenderWindow(None)
- QCellWidget.deleteLater(self)
-
- def updateContents(self, inputPorts):
- """ updateContents(inputPorts: tuple)
- Updates the cell contents with new vtkRenderer
-
- """
- (renderView, ) = inputPorts
- renWin = renderView.vtkInstance.GetRenderWindow()
- renWin.DoubleBufferOn()
- self.SetRenderWindow(renWin)
- renderView.vtkInstance.ResetCamera()
- self.addObserversToInteractorStyle()
-
-# renWin = self.GetRenderWindow()
-# renderers = [renderView.vtkInstance.GetRenderer()]
-# iren = renWin.GetInteractor()
- # Update interactor style
-# self.removeObserversFromInteractorStyle()
-# if renderView==None:
-# if iStyle==None:
-# iStyleInstance = vtk.vtkInteractorStyleTrackballCamera()
-# else:
-# iStyleInstance = iStyle.vtkInstance
-# iren.SetInteractorStyle(iStyleInstance)
-# self.addObserversToInteractorStyle()
- # Capture window into history for playback
- # Call this at the end to capture the image after rendering
- QCellWidget.updateContents(self, inputPorts)
-
- def GetRenderWindow(self):
- """ GetRenderWindow() -> vtkRenderWindow
- Return the associated vtkRenderWindow
-
- """
- if not self.mRenWin:
- win = vtk.vtkRenderWindow()
- win.DoubleBufferOn()
- self.SetRenderWindow(win)
- del win
-
- return self.mRenWin
-
- def SetRenderWindow(self,w):
- """ SetRenderWindow(w: vtkRenderWindow)
- Set a new render window to QVTKViewWidget and initialize the
- interactor as well
-
- """
- if w == self.mRenWin:
- return
-
- if self.mRenWin:
- if self.mRenWin.GetMapped():
- self.mRenWin.Finalize()
-
- self.mRenWin = w
-
- if self.mRenWin:
- self.mRenWin.Register(None)
- if system.systemType=='Linux':
- try:
- vp = '_%s_void_p' % (hex(int(QtGui.QX11Info.display()))[2:])
- except TypeError:
- #This was change for PyQt4.2
- if isinstance(QtGui.QX11Info.display(),QtGui.Display):
- display = sip.unwrapinstance(QtGui.QX11Info.display())
- vp = '_%s_void_p' % (hex(display)[2:])
- self.mRenWin.SetDisplayId(vp)
- if not self.mRenWin.GetMapped():
- self.mRenWin.GetInteractor().Initialize()
- system.XDestroyWindow(self.mRenWin.GetGenericDisplayId(),
- self.mRenWin.GetGenericWindowId())
- self.mRenWin.Finalize()
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- else:
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- if self.isVisible():
- self.mRenWin.Start()
-
- def GetInteractor(self):
- """ GetInteractor() -> vtkInteractor
- Return the vtkInteractor control this QVTKViewWidget
- """
- return self.GetRenderWindow().GetInteractor()
-
- def event(self, e):
- """ event(e: QEvent) -> depends on event type
- Process window and interaction events
-
- """
- if e.type()==QtCore.QEvent.ParentAboutToChange:
- if self.mRenWin:
- if self.mRenWin.GetMapped():
- self.mRenWin.Finalize()
- else:
- if e.type()==QtCore.QEvent.ParentChange:
- if self.mRenWin:
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- if self.isVisible():
- self.mRenWin.Start()
-
- if QtCore.QObject.event(self,e):
- return 1
-
- if e.type() == QtCore.QEvent.KeyPress:
- self.keyPressEvent(e)
- if e.isAccepted():
- return e.isAccepted()
-
- return qt_super(QVTKViewWidget, self).event(e)
-
- # return QtGui.QWidget.event(self,e)
- # Was this right? Wasn't this supposed to be QCellWidget.event()?
-
- def resizeWindow(self, width, height):
- """ resizeWindow(width: int, height: int) -> None
- Work around vtk bugs for resizing window
-
- """
- ########################################################
- # VTK - BUGGGGGGGGG - GRRRRRRRRR
- # This is a 'bug' in vtkWin32OpenGLRenderWindow(.cxx)
- # If a render window is mapped to screen, the actual
- # window size is the client area of the window in Win32.
- # However, this real window size is only updated through
- # vtkWin32OpenGLRenderWindow::GetSize(). So this has to
- # be called here to get the cell size correctly. This
- # invalidates the condition in the next SetSize().
- # We can use self.mRenWin.SetSize(0,0) here but it will
- # cause flickering and decrease performance!
- # SetPosition(curX,curY) also works here but slower.
- self.mRenWin.GetSize()
-
- self.mRenWin.SetSize(width, height)
- if self.mRenWin.GetInteractor():
- self.mRenWin.GetInteractor().SetSize(width, height)
-
- def resizeEvent(self, e):
- """ resizeEvent(e: QEvent) -> None
- Re-adjust the vtkRenderWindow size then QVTKViewWidget resized
-
- """
- qt_super(QVTKViewWidget, self).resizeEvent(e)
- if not self.mRenWin:
- return
-
- self.resizeWindow(self.width(), self.height())
- self.mRenWin.Render()
-
- def moveEvent(self,e):
- """ moveEvent(e: QEvent) -> None
- Echo the move event into vtkRenderWindow
-
- """
- qt_super(QVTKViewWidget, self).moveEvent(e)
- if not self.mRenWin:
- return
-
- self.mRenWin.SetPosition(self.x(),self.y())
-
- def paintEvent(self, e):
- """ paintEvent(e: QPaintEvent) -> None
- Paint the QVTKViewWidget with vtkRenderWindow
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- if hasattr(self.mRenWin, 'UpdateGLRegion'):
- self.mRenWin.UpdateGLRegion()
- self.mRenWin.Render()
-
- def SelectActiveRenderer(self,iren):
- """ SelectActiveRenderer(iren: vtkRenderWindowIteractor) -> None
- Only make the vtkRenderer below the mouse cursor active
-
- """
- epos = iren.GetEventPosition()
- rens = iren.GetRenderWindow().GetRenderers()
- rens.InitTraversal()
- for i in xrange(rens.GetNumberOfItems()):
- ren = rens.GetNextItem()
- ren.SetInteractive(ren.IsInViewport(epos[0], epos[1]))
-
- def mousePressEvent(self,e):
- """ mousePressEvent(e: QMouseEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- isDoubleClick = e.type()==QtCore.QEvent.MouseButtonDblClick
- iren.SetEventInformationFlipY(e.x(),e.y(),
- ctrl,
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),
- isDoubleClick,
- None)
- invoke = {QtCore.Qt.LeftButton:"LeftButtonPressEvent",
- QtCore.Qt.MidButton:"MiddleButtonPressEvent",
- QtCore.Qt.RightButton:"RightButtonPressEvent"}
-
- self.SelectActiveRenderer(iren)
-
- if ctrl:
- e.ignore()
- return
-
- self.interacting = self.getActiveRenderer(iren)
-
- if e.button() in invoke:
- iren.InvokeEvent(invoke[e.button()])
-
- def mouseMoveEvent(self,e):
- """ mouseMoveEvent(e: QMouseEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0), 0, None)
-
- iren.InvokeEvent("MouseMoveEvent")
-
- def enterEvent(self,e):
- """ enterEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.InvokeEvent("EnterEvent")
-
- def leaveEvent(self,e):
- """ leaveEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.InvokeEvent("LeaveEvent")
-
- def mouseReleaseEvent(self,e):
- """ mouseReleaseEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),0,None)
-
- invoke = {QtCore.Qt.LeftButton:"LeftButtonReleaseEvent",
- QtCore.Qt.MidButton:"MiddleButtonReleaseEvent",
- QtCore.Qt.RightButton:"RightButtonReleaseEvent"}
-
- self.interacting = None
-
- if e.button() in invoke:
- iren.InvokeEvent(invoke[e.button()])
-
- def keyPressEvent(self,e):
- """ keyPressEvent(e: QKeyEvent) -> None
- Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ascii_key = None
- if e.text().length()>0:
- ascii_key = e.text().toLatin1()[0]
- else:
- ascii_key = chr(0)
-
- keysym = self.ascii_to_key_sym(ord(ascii_key))
-
- if not keysym:
- keysym = self.qt_key_to_key_sym(e.key())
-
- # Ignore 'q' or 'e' or Ctrl-anykey
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
- if (keysym in ['q', 'e'] or ctrl):
- e.ignore()
- return
-
- iren.SetKeyEventInformation(ctrl,shift,ascii_key, e.count(), keysym)
-
- iren.InvokeEvent("KeyPressEvent")
-
- if ascii_key:
- iren.InvokeEvent("CharEvent")
-
-
- def keyReleaseEvent(self,e):
- """ keyReleaseEvent(e: QKeyEvent) -> None
- Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ascii_key = None
- if e.text().length()>0:
- ascii_key = e.text().toLatin1()[0]
- else:
- ascii_key = chr(0)
-
- keysym = self.ascii_to_key_sym(ord(ascii_key))
-
- if not keysym:
- keysym = self.qt_key_to_key_sym(e.key())
-
- # Ignore 'q' or 'e' or Ctrl-anykey
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
- if (keysym in ['q','e'] or ctrl):
- e.ignore()
- return
-
- iren.SetKeyEventInformation(ctrl, shift, ascii_key, e.count(), keysym)
-
- iren.InvokeEvent("KeyReleaseEvent")
-
- def wheelEvent(self,e):
- """ wheelEvent(e: QWheelEvent) -> None
- Zoom in/out while scrolling the mouse
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),0,None)
-
- self.SelectActiveRenderer(iren)
-
- if e.delta()>0:
- iren.InvokeEvent("MouseWheelForwardEvent")
- else:
- iren.InvokeEvent("MouseWheelBackwardEvent")
-
- def focusInEvent(self,e):
- """ focusInEvent(e: QFocusEvent) -> None
- Ignore focus event
-
- """
- pass
-
- def focusOutEvent(self,e):
- """ focusOutEvent(e: QFocusEvent) -> None
- Ignore focus event
-
- """
- pass
-
- def contextMenuEvent(self,e):
- """ contextMenuEvent(e: QContextMenuEvent) -> None
- Make sure to get the right mouse position for the context menu
- event, i.e. also the right click
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ctrl = int(e.modifiers()&QtCore.Qt.ControlModifier)
- shift = int(e.modifiers()&QtCore.Qt.ShiftModifier)
- iren.SetEventInformationFlipY(e.x(),e.y(),ctrl,shift,chr(0),0,None)
- iren.InvokeEvent("ContextMenuEvent")
-
- def ascii_to_key_sym(self,i):
- """ ascii_to_key_sym(i: int) -> str
- Convert ASCII code into key name
-
- """
- global AsciiToKeySymTable
- return AsciiToKeySymTable[i]
-
- def qt_key_to_key_sym(self,i):
- """ qt_key_to_key_sym(i: QtCore.Qt.Keycode) -> str
- Convert Qt key code into key name
-
- """
- handler = {QtCore.Qt.Key_Backspace:"BackSpace",
- QtCore.Qt.Key_Tab:"Tab",
- QtCore.Qt.Key_Backtab:"Tab",
- QtCore.Qt.Key_Return:"Return",
- QtCore.Qt.Key_Enter:"Return",
- QtCore.Qt.Key_Shift:"Shift_L",
- QtCore.Qt.Key_Control:"Control_L",
- QtCore.Qt.Key_Alt:"Alt_L",
- QtCore.Qt.Key_Pause:"Pause",
- QtCore.Qt.Key_CapsLock:"Caps_Lock",
- QtCore.Qt.Key_Escape:"Escape",
- QtCore.Qt.Key_Space:"space",
- QtCore.Qt.Key_End:"End",
- QtCore.Qt.Key_Home:"Home",
- QtCore.Qt.Key_Left:"Left",
- QtCore.Qt.Key_Up:"Up",
- QtCore.Qt.Key_Right:"Right",
- QtCore.Qt.Key_Down:"Down",
- QtCore.Qt.Key_SysReq:"Snapshot",
- QtCore.Qt.Key_Insert:"Insert",
- QtCore.Qt.Key_Delete:"Delete",
- QtCore.Qt.Key_Help:"Help",
- QtCore.Qt.Key_0:"0",
- QtCore.Qt.Key_1:"1",
- QtCore.Qt.Key_2:"2",
- QtCore.Qt.Key_3:"3",
- QtCore.Qt.Key_4:"4",
- QtCore.Qt.Key_5:"5",
- QtCore.Qt.Key_6:"6",
- QtCore.Qt.Key_7:"7",
- QtCore.Qt.Key_8:"8",
- QtCore.Qt.Key_9:"9",
- QtCore.Qt.Key_A:"a",
- QtCore.Qt.Key_B:"b",
- QtCore.Qt.Key_C:"c",
- QtCore.Qt.Key_D:"d",
- QtCore.Qt.Key_E:"e",
- QtCore.Qt.Key_F:"f",
- QtCore.Qt.Key_G:"g",
- QtCore.Qt.Key_H:"h",
- QtCore.Qt.Key_I:"i",
- QtCore.Qt.Key_J:"h",
- QtCore.Qt.Key_K:"k",
- QtCore.Qt.Key_L:"l",
- QtCore.Qt.Key_M:"m",
- QtCore.Qt.Key_N:"n",
- QtCore.Qt.Key_O:"o",
- QtCore.Qt.Key_P:"p",
- QtCore.Qt.Key_Q:"q",
- QtCore.Qt.Key_R:"r",
- QtCore.Qt.Key_S:"s",
- QtCore.Qt.Key_T:"t",
- QtCore.Qt.Key_U:"u",
- QtCore.Qt.Key_V:"v",
- QtCore.Qt.Key_W:"w",
- QtCore.Qt.Key_X:"x",
- QtCore.Qt.Key_Y:"y",
- QtCore.Qt.Key_Z:"z",
- QtCore.Qt.Key_Asterisk:"asterisk",
- QtCore.Qt.Key_Plus:"plus",
- QtCore.Qt.Key_Minus:"minus",
- QtCore.Qt.Key_Period:"period",
- QtCore.Qt.Key_Slash:"slash",
- QtCore.Qt.Key_F1:"F1",
- QtCore.Qt.Key_F2:"F2",
- QtCore.Qt.Key_F3:"F3",
- QtCore.Qt.Key_F4:"F4",
- QtCore.Qt.Key_F5:"F5",
- QtCore.Qt.Key_F6:"F6",
- QtCore.Qt.Key_F7:"F7",
- QtCore.Qt.Key_F8:"F8",
- QtCore.Qt.Key_F9:"F9",
- QtCore.Qt.Key_F10:"F10",
- QtCore.Qt.Key_F11:"F11",
- QtCore.Qt.Key_F12:"F12",
- QtCore.Qt.Key_F13:"F13",
- QtCore.Qt.Key_F14:"F14",
- QtCore.Qt.Key_F15:"F15",
- QtCore.Qt.Key_F16:"F16",
- QtCore.Qt.Key_F17:"F17",
- QtCore.Qt.Key_F18:"F18",
- QtCore.Qt.Key_F19:"F19",
- QtCore.Qt.Key_F20:"F20",
- QtCore.Qt.Key_F21:"F21",
- QtCore.Qt.Key_F22:"F22",
- QtCore.Qt.Key_F23:"F23",
- QtCore.Qt.Key_F24:"F24",
- QtCore.Qt.Key_NumLock:"Num_Lock",
- QtCore.Qt.Key_ScrollLock:"Scroll_Lock"}
- if i in handler:
- return handler[i]
- else:
- return "None"
-
- def getRendererList(self):
- """ getRendererList() -> list
- Return a list of vtkRenderer running in this QVTKViewWidget
- """
- result = []
- renWin = self.GetRenderWindow()
- renderers = renWin.GetRenderers()
- renderers.InitTraversal()
- for i in xrange(renderers.GetNumberOfItems()):
- result.append(renderers.GetNextItem())
- return result
-
- def getActiveRenderer(self, iren):
- """ getActiveRenderer(iren: vtkRenderWindowwInteractor) -> vtkRenderer
- Return the active vtkRenderer under mouse
-
- """
- epos = list(iren.GetEventPosition())
- if epos[1]<0:
- epos[1] = -epos[1]
- rens = iren.GetRenderWindow().GetRenderers()
- rens.InitTraversal()
- for i in xrange(rens.GetNumberOfItems()):
- ren = rens.GetNextItem()
- if ren.IsInViewport(epos[0], epos[1]):
- return ren
- return None
-
- def findSheetTabWidget(self):
- """ findSheetTabWidget() -> QTabWidget
- Find and return the sheet tab widget
-
- """
- p = self.parent()
- while p:
- if hasattr(p, 'isSheetTabWidget'):
- if p.isSheetTabWidget()==True:
- return p
- p = p.parent()
- return None
-
- def getRenderersInCellList(self, sheet, cells):
- """ isRendererIn(sheet: spreadsheet.StandardWidgetSheet,
- cells: [(int,int)]) -> bool
- Get the list of renderers in side a list of (row, column)
- cells.
-
- """
- rens = []
- for (row, col) in cells:
- cell = sheet.getCell(row, col)
- if hasattr(cell, 'getRendererList'):
- rens += cell.getRendererList()
- return rens
-
- def getSelectedCellWidgets(self):
- sheet = self.findSheetTabWidget()
- if sheet:
- iren = self.mRenWin.GetInteractor()
- ren = self.interacting
- if not ren: ren = self.getActiveRenderer(iren)
- if ren:
- cells = sheet.getSelectedLocations()
- if (ren in self.getRenderersInCellList(sheet, cells)):
- return [sheet.getCell(row, col)
- for (row, col) in cells
- if hasattr(sheet.getCell(row, col),
- 'getRendererList')]
- return []
-
- def interactionEvent(self, istyle, name):
- """ interactionEvent(istyle: vtkInteractorStyle, name: str) -> None
- Make sure interactions sync across selected renderers
-
- """
- if name=='MouseWheelForwardEvent':
- istyle.OnMouseWheelForward()
- if name=='MouseWheelBackwardEvent':
- istyle.OnMouseWheelBackward()
- ren = self.interacting
- if not ren:
- ren = self.getActiveRenderer(istyle.GetInteractor())
- if ren:
- cam = ren.GetActiveCamera()
- cpos = cam.GetPosition()
- cfol = cam.GetFocalPoint()
- cup = cam.GetViewUp()
- for cell in self.getSelectedCellWidgets():
- if cell!=self and hasattr(cell, 'getRendererList'):
- rens = cell.getRendererList()
- for r in rens:
- if r!=ren:
- dcam = r.GetActiveCamera()
- dcam.SetPosition(cpos)
- dcam.SetFocalPoint(cfol)
- dcam.SetViewUp(cup)
- r.ResetCameraClippingRange()
- cell.update()
-
- def charEvent(self, istyle, name):
- """ charEvent(istyle: vtkInteractorStyle, name: str) -> None
- Make sure key presses also sync across selected renderers
-
- """
- iren = istyle.GetInteractor()
- ren = self.interacting
- if not ren: ren = self.getActiveRenderer(iren)
- if ren:
- keyCode = iren.GetKeyCode()
- if keyCode in ['w','W','s','S','r','R','p','P']:
- for cell in self.getSelectedCellWidgets():
- if hasattr(cell, 'GetInteractor'):
- selectedIren = cell.GetInteractor()
- selectedIren.SetKeyCode(keyCode)
- selectedIren.GetInteractorStyle().OnChar()
- selectedIren.Render()
- istyle.OnChar()
-
- def saveToPNG(self, filename):
- """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
-
- Save the current widget contents to an image file. If
- str==None, then it returns the vtkUnsignedCharArray containing
- the PNG image. Otherwise, the filename is returned.
-
- """
- w2i = vtk.vtkWindowToImageFilter()
- w2i.ReadFrontBufferOff()
- w2i.SetInput(self.mRenWin)
- # Render twice to get a clean image on the back buffer
- self.mRenWin.Render()
- self.mRenWin.Render()
- w2i.Update()
- writer = vtk.vtkPNGWriter()
- writer.SetInputConnection(w2i.GetOutputPort())
- if filename!=None:
- writer.SetFileName(filename)
- else:
- writer.WriteToMemoryOn()
- writer.Write()
- if filename:
- return filename
- else:
- return writer.GetResult()
-
- def captureWindow(self):
- """ captureWindow() -> None
- Capture the window contents to file
-
- """
- fn = QtGui.QFileDialog.getSaveFileName(None,
- "Save file as...",
- "screenshot.png",
- "Images (*.png)")
- if fn.isNull():
- return
- self.saveToPNG(str(fn))
-
- def grabWindowPixmap(self):
- """ grabWindowImage() -> QPixmap
- Widget special grabbing function
-
- """
- uchar = self.saveToPNG(None)
-
- ba = QtCore.QByteArray()
- buf = QtCore.QBuffer(ba)
- buf.open(QtCore.QIODevice.WriteOnly)
- for i in xrange(uchar.GetNumberOfTuples()):
- c = uchar.GetValue(i)
- buf.putChar(chr(c))
- buf.close()
-
- pixmap = QtGui.QPixmap()
- pixmap.loadFromData(ba, 'PNG')
- return pixmap
-
- def dumpToFile(self, filename):
- """dumpToFile() -> None
- Dumps itself as an image to a file, calling saveToPNG
- """
- self.saveToPNG(filename)
-
-class QVTKViewWidgetCapture(QtGui.QAction):
- """
- QVTKViewWidgetCapture is the action to capture the vtk rendering
- window to an image
-
- """
- def __init__(self, parent=None):
- """ QVTKViewWidgetCapture(parent: QWidget) -> QVTKViewWidgetCapture
- Setup the image, status tip, etc. of the action
-
- """
- QtGui.QAction.__init__(self,
- QtGui.QIcon(":/images/camera.png"),
- "&Capture image to file",
- parent)
- self.setStatusTip("Capture the rendered image to a file")
-
- def triggeredSlot(self, checked=False):
- """ toggledSlot(checked: boolean) -> None
- Execute the action when the button is clicked
-
- """
- cellWidget = self.toolBar.getSnappedWidget()
- cellWidget.captureWindow()
-
-class QVTKViewWidgetSaveCamera(QtGui.QAction):
- """
- QVTKViewWidgetSaveCamera is the action to capture the current camera
- of the vtk renderers and save it back to the pipeline
-
- """
- def __init__(self, parent=None):
- """ QVTKViewWidgetSaveCamera(parent: QWidget) -> QVTKViewWidgetSaveCamera
- Setup the image, status tip, etc. of the action
-
- """
- QtGui.QAction.__init__(self,
- "Save &Camera",
- parent)
- self.setStatusTip("Save current camera views to the pipeline")
-
- def setCamera(self, controller):
- ops = []
- pipeline = controller.current_pipeline
- cellWidget = self.toolBar.getSnappedWidget()
- renderers = cellWidget.getRendererList()
- for ren in renderers:
- cam = ren.GetActiveCamera()
- cpos = cam.GetPosition()
- cfol = cam.GetFocalPoint()
- cup = cam.GetViewUp()
- rendererId = cellWidget.renderer_maps[ren]
- # Looking for SetActiveCamera()
- camera = None
- renderer = pipeline.modules[rendererId]
- for c in pipeline.connections.values():
- if c.destination.moduleId==rendererId:
- if c.destination.name=='SetActiveCamera':
- camera = pipeline.modules[c.source.moduleId]
- break
-
- if not camera:
- # Create camera
- vtk_package = 'edu.utah.sci.vistrails.vtk'
- camera = controller.create_module(vtk_package, 'vtkCamera', '',
- 0.0, 0.0)
- ops.append(('add', camera))
-
- # Connect camera to renderer
- camera_conn = controller.create_connection(camera, 'self',
- renderer,
- 'SetActiveCamera')
- ops.append(('add', camera_conn))
- # update functions
- def convert_to_str(arglist):
- new_arglist = []
- for arg in arglist:
- new_arglist.append(str(arg))
- return new_arglist
- functions = [('SetPosition', convert_to_str(cpos)),
- ('SetFocalPoint', convert_to_str(cfol)),
- ('SetViewUp', convert_to_str(cup))]
- ops.extend(controller.update_functions_ops(camera, functions))
-
- action = core.db.action.create_action(ops)
- controller.add_new_action(action)
- controller.perform_action(action)
- controller.select_latest_version()
-
- def triggeredSlot(self, checked=False):
- """ toggledSlot(checked: boolean) -> None
- Execute the action when the button is clicked
-
- """
- visApp = QtCore.QCoreApplication.instance()
- if hasattr(visApp, 'builderWindow'):
- builderWindow = visApp.builderWindow
- if builderWindow:
- info = self.toolBar.sheet.getCellPipelineInfo(
- self.toolBar.row, self.toolBar.col)
- if info:
- info = info[0]
- viewManager = builderWindow.viewManager
- view = viewManager.ensureVistrail(info['locator'])
- if view:
- controller = view.controller
- controller.change_selected_version(info['version'])
- self.setCamera(controller)
-
-
-class QVTKViewWidgetToolBar(QCellToolBar):
- """
- QVTKViewWidgetToolBar derives from QCellToolBar to give the VTKViewCell
- a customizable toolbar
-
- """
- def createToolBar(self):
- """ createToolBar() -> None
- This will get call initiallly to add customizable widgets
-
- """
- self.appendAction(QVTKViewWidgetCapture(self))
- self.addAnimationButtons()
- self.appendAction(QVTKViewWidgetSaveCamera(self))
-
-def registerSelf():
- """ registerSelf() -> None
- Registry module with the registry
- """
- identifier = 'edu.utah.sci.vistrails.vtk'
- registry = get_module_registry()
- registry.add_module(VTKViewCell)
- registry.add_input_port(VTKViewCell, "Location", CellLocation)
- import core.debug
- for (port,module) in [("SetRenderView",'vtkRenderView')]:
- try:
- registry.add_input_port(VTKViewCell, port,'(%s:%s)'%(identifier,module))
-
- except Exception, e:
- core.debug.warning(str(e))
-
- registry.add_output_port(VTKViewCell, "self", VTKViewCell)
diff --git a/contrib/trimesh2.py b/contrib/trimesh2.py
deleted file mode 100644
index f00638a..0000000
--- a/contrib/trimesh2.py
+++ /dev/null
@@ -1,123 +0,0 @@
-# VisTrails package for trimesh2 support
-# Copyright Carlos Eduardo Scheidegger, 2007
-# Get trimesh2 at www.cs.princeton.edu/gfx/proj/trimesh2/
-# or a patched version with more available file formats
-# at www.sci.utah.edu/~cscheid/software
-
-# License: GPLv2 or later
-
-# ChangeLog:
-
-# 2007-03-13 Carlos Scheidegger <cscheid at juggernaut>
-# * uses core.system.list2cmd to generate command lines.
-# 2007-03-12 Carlos Scheidegger <cscheid at juggernaut>
-# * First release
-##############################################################################
-
-import core.modules
-import core.modules.module_registry
-from core.modules.vistrails_module import Module, ModuleError
-from core.system import list2cmdline
-import os
-
-_mesh_filter_path = None
-
-identifier = 'edu.utah.sci.cscheid.trimesh2'
-version = '0.1'
-name = 'trimesh2'
-
-##############################################################################
-# MeshFilter
-class MeshFilter(Module):
-
- def guess_input_format(self, input_file_name):
- i = input_file_name.rfind('.')
- if i == -1:
- return None
- else:
- return input_file_name[i:]
-
- def compute(self):
- self.checkInputPort('input_file')
- input_file = self.getInputFromPort('input_file')
- if self.hasInputFromPort('output_format'):
- output_suffix = self.getInputFromPort('output_format')
- else:
- output_suffix = self.guess_input_format(input_file.name)
- if not output_suffix:
- output_suffix = '.off'
- output_file = self.interpreter.filePool.create_file(suffix=output_suffix)
- values = [_mesh_filter_path,
- input_file.name,
- output_file.name]
- cmdline = list2cmdline(values)
- print cmdline
- result = os.system(cmdline)
- if result != 0:
- raise ModuleError(self, 'Execution failed')
- self.setResult('output_file', output_file)
-
-##############################################################################
-# PlanarSubdiv
-class PlanarSubdiv(MeshFilter):
-
- def compute(self):
- self.checkInputPort('input_file')
- self.checkInputPort('iterations')
- iters = self.getInputFromPort('iterations')
- if iters < 1:
- raise ModuleError(self, 'iterations must be >=1')
- input_file = self.getInputFromPort('input_file')
- if self.hasInputFromPort('output_format'):
- output_suffix = self.getInputFromPort('output_format')
- else:
- output_suffix = self.guess_input_format(input_file.name)
- if not output_suffix:
- output_suffix = '.off'
- output_file = self.interpreter.filePool.create_file(suffix=output_suffix)
-
- values = [_mesh_filter_path,
- input_file.name,
- '-subdiv',
- output_file.name]
- cmdline = list2cmdline(values)
- print cmdline
- result = os.system(cmdline)
- if result != 0:
- raise ModuleError(self, 'Execution failed')
-
- for i in xrange(iters-1):
- cmdline = '%s %s -subdiv %s' % (_mesh_filter_path,
- output_file.name,
- output_file.name)
- print cmdline
- result = os.system(cmdline)
- if result != 0:
- raise ModuleError(self, 'Execution failed')
-
- self.setResult('output_file', output_file)
-
-
-def initialize(executable_path=None):
- global _mesh_filter_path
- if not executable_path:
- print "Assuming mesh_filter is in path"
- _mesh_filter_path = 'mesh_filter'
- else:
- print "Assuming mesh_filter is in '%s'" % executable_path
- _mesh_filter_path = executable_path + '/mesh_filter'
-
- reg = core.modules.module_registry
-
- reg.add_module(MeshFilter)
-
- reg.add_input_port(MeshFilter, 'input_file',
- core.modules.basic_modules.File)
- reg.add_input_port(MeshFilter, 'output_format',
- core.modules.basic_modules.String)
- reg.add_output_port(MeshFilter, 'output_file',
- core.modules.basic_modules.File)
-
- reg.add_module(PlanarSubdiv)
- reg.add_input_port(PlanarSubdiv, 'iterations',
- core.modules.basic_modules.Integer)
diff --git a/contrib/vtksnl/__init__.py b/contrib/vtksnl/__init__.py
deleted file mode 100644
index 03508a3..0000000
--- a/contrib/vtksnl/__init__.py
+++ /dev/null
@@ -1,53 +0,0 @@
-###########################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-################################################################################
-# VTK-SNL Package for VisTrails (Sandia National Laboratories)
-################################################################################
-
-"""The Visualization ToolKit (VTK) is an open source, freely available
-software system for 3D computer graphics, image processing, and
-visualization used by thousands of researchers and developers around
-the world. This version of the VTK package requires the Sandia
-National Laboratories version of the VTK libraries.
-
-http://www.vtk.org"""
-
-identifier = 'edu.utah.sci.vistrails.vtksnl'
-name = 'VTKSNL'
-version = '0.9.1'
-
-def package_dependencies():
- import core.packagemanager
- manager = core.packagemanager.get_package_manager()
- if manager.has_package('edu.utah.sci.vistrails.spreadsheet'):
- return ['edu.utah.sci.vistrails.spreadsheet']
- else:
- return []
-
-def package_requirements():
- import core.requirements
- if not core.requirements.python_module_exists('vtksnl'):
- raise core.requirements.MissingRequirement('vtksnl')
- if not core.requirements.python_module_exists('PyQt4'):
- print 'PyQt4 is not available. There will be no interaction',
- print 'between VTK and the spreadsheet.'
- import vtksnl
diff --git a/contrib/vtksnl/base_module.py b/contrib/vtksnl/base_module.py
deleted file mode 100644
index e9cadac..0000000
--- a/contrib/vtksnl/base_module.py
+++ /dev/null
@@ -1,203 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-################################################################################
-# This describes basic modules used by other VTK module
-################################################################################
-import vtksnl
-from core.modules.module_registry import registry
-from core.modules.vistrails_module import Module, ModuleError
-from itertools import izip
-
-################################################################################
-
-class vtkBaseModule(Module):
- """
- vtkBaseModule is the base class for all VTK modules in VisTrails, it acts
- as a wrapper to direct all input/output ports to appropriate VTK function
- calls
-
- """
-
- def __init__(self):
- """ vtkBaseModule() -> vtkBaseModule
- Instantiate an emptt VTK Module with real VTK instance
-
- """
- Module.__init__(self)
- self.vtkInstance = None
-
- def is_cacheable(self):
- # VTK objects are by default cacheable only if they're subclasses
- # of vtkAlgorithm
- return (issubclass(self.vtkClass, vtksnl.vtkAlgorithm)
- and (not issubclass(self.vtkClass, vtksnl.vtkAbstractMapper)))
-
- def call_input_function(self, function, params):
- """self.call_input_function(function, params) -> None
- Calls the input function on the vtkInstance, or a special
- input function if one exists in the class."""
- if hasattr(self, '_special_input_function_' + function):
- attr = getattr(self, '_special_input_function_' + function)
- else:
- try:
- attr = getattr(self.vtkInstance, function)
- except AttributeError:
- # Compensates for overload by exploiting the fact that
- # no VTK method has underscores.
- f = function.find('_')
- if f != -1:
- function = function[:f]
- attr = getattr(self.vtkInstance, function)
- attr(*params)
- # print "Called ",attr,function,params
-
- @classmethod
- def _provide_doc(cls, port_name):
- f = port_name.find('_')
- if f != -1:
- name = port_name[:f]
- else:
- name = port_name
- return getattr(cls.vtkClass, name).__doc__
-
- @classmethod
- def provide_input_port_documentation(cls, port_name):
- return cls._provide_doc(port_name)
-
- @classmethod
- def provide_output_port_documentation(cls, port_name):
- return cls._provide_doc(port_name)
-
- def compute(self):
- """ compute() -> None
- Actually perform real VTK task by directing all input/output ports
- to VTK function calls
-
- """
-
- def call_it(function, p):
- # Translate between VisTrails objects and VTK objects
- if p is None:
- # None indicates a call with no parameters
- params = []
- elif type(p) == tuple:
- # A tuple indicates a call with many parameters
- params = list(p)
- else:
- # Otherwise, it's a single parameter
- params = [p]
-
- # Unwraps VTK objects
- for i in xrange(len(params)):
- if hasattr(params[i], 'vtkInstance'):
- params[i] = params[i].vtkInstance
- try:
- self.call_input_function(function, params)
- except Exception, e:
- msg = 'VTK Exception: '
- raise ModuleError(self, msg + str(type(e)) + ': ' + str(e))
-
- # Always re-create vtkInstance module, no caching here
- if self.vtkInstance:
- del self.vtkInstance
- self.vtkInstance = self.vtkClass()
-
- # We need to call method ports before anything else, and in
- # the right order.
-
- # FIXME: This does not belong here, it belongs in the main class
- # No time for that now
- methods = self.is_method.values()
- methods.sort()
- for value in methods:
- (_, port) = value
- conn = self.is_method.inverse[value]
- p = conn()
- call_it(port, p)
-
- # Make sure all input ports are called correctly
- for (function, connector_list) in self.inputPorts.iteritems():
- paramList = self.forceGetInputListFromPort(function)
- if function[:18]=='SetInputConnection':
- paramList = zip([int(function[18:])]*len(paramList),
- paramList)
- function = 'SetInputConnection'
- if function=='AddInputConnection':
- desc = registry.get_descriptor_by_name(
- 'edu.utah.sci.vistrails.vtksnl',
- 'vtkAlgorithmOutput')
- for i in xrange(len(paramList)):
- if type(paramList[i])==desc.module:
- paramList[i] = (0, paramList[i])
- for p,connector in izip(paramList, connector_list):
- # Don't call method
- if connector in self.is_method:
- continue
- call_it(function, p)
-
- # Call update if appropriate
- if hasattr(self.vtkInstance, 'Update'):
- def ProgressEvent(obj, event):
- self.logging.update_progress(self, obj.GetProgress())
- isAlgorithm = issubclass(self.vtkClass, vtksnl.vtkAlgorithm)
- if isAlgorithm:
- cbId = self.vtkInstance.AddObserver('ProgressEvent', ProgressEvent)
- self.vtkInstance.Update()
- if isAlgorithm:
- self.vtkInstance.RemoveObserver(cbId)
-
- # Then update the output ports also with appropriate function calls
- for function in self.outputPorts.keys():
- if function[:13]=='GetOutputPort':
- i = int(function[13:])
- vtkOutput = self.vtkInstance.GetOutputPort(i)
- output = vtkBaseModule.wrapperModule('vtkAlgorithmOutput',
- vtkOutput)
- self.setResult(function, output)
- elif hasattr(self.vtkInstance, function):
- retValues = getattr(self.vtkInstance, function)()
- if issubclass(retValues.__class__, vtksnl.vtkObject):
- className = retValues.GetClassName()
- output = vtkBaseModule.wrapperModule(className, retValues)
- self.setResult(function, output)
- elif (type(retValues) in [tuple, list]):
- result = list(retValues)
- for i in xrange(len(result)):
- if issubclass(result[i].__class__, vtksnl.vtkObject):
- className = result[i].GetClassName()
- result[i] = vtkBaseModule.wrapperModule(className,
- result[i])
- self.setResult(function, type(retValues)(result))
- else:
- self.setResult(function, retValues)
-
- @staticmethod
- def wrapperModule(classname, instance):
- """ wrapperModule(classname: str, instance: vtk class) -> Module
- Create a wrapper module in VisTrails with a vtk instance
-
- """
- result = registry.get_descriptor_by_name(
- 'edu.utah.sci.vistrails.vtksnl',
- classname).module()
- result.vtkInstance = instance
- return result
diff --git a/contrib/vtksnl/class_tree.py b/contrib/vtksnl/class_tree.py
deleted file mode 100644
index 75f8566..0000000
--- a/contrib/vtksnl/class_tree.py
+++ /dev/null
@@ -1,268 +0,0 @@
-# Author: Prabhu Ramachandran
-# Copyright (c) 2004, Enthought, Inc.
-# License: BSD Style.
-
-"""This module generates the class hierarchy for any given Python
-modules. This can be used (among other things) to generate the
-traitified VTK classes in the correct order.
-
-"""
-
-import __builtin__
-
-
-class TreeNode(object):
- """Represents a node in the class tree.
-
- Stores information on the sub and super classes of a particular
- class. It also stores the inheritance level of the class inside
- the inheritance tree (essentially how many levels of inheritance
- are there below this class). This inheritance level is computed
- when the `get_level` method is called. The `get_level` method
- works only when the parent information is complete.
-
- """
-
- def __init__(self, klass):
- """Given a class, create a node in the tree.
-
- Parameters
- ----------
- - klass : `class`
-
- The class which is represented as a node in the tree.
-
- """
- self.klass = klass
- self.name = klass.__name__
- self.children = []
- self.parents = []
- # Uninitialized level is set to None
- self.level = None
-
- def add_parent(self, parent):
- """Add a parent node."""
- assert isinstance(parent, TreeNode)
- if parent not in self.parents:
- self.parents.append(parent)
-
- def add_child(self, child):
- """Add a child node. """
- assert isinstance(child, TreeNode)
- if child not in self.children:
- self.children.append(child)
-
- def get_level(self):
- """Returns the inheritance level of the node (an int). If the
- level has not been set, the method computes it. Note however,
- that this computation will fail if the parent information is
- incorrect.
-
- """
- if not self.level:
- if self.parents:
- self.level = max([x.get_level() for x in self.parents]) + 1
- else:
- self.level = 0
- return self.level
-
- def get_ancestors(self):
- """Returns a list of ancestor nodes from which this class has
- descended.
-
- """
- def _get_ancestors(node, ancestors):
- ancestors.extend(node.parents)
- for p in node.parents:
- _get_ancestors(p, ancestors)
- ancestors = []
- _get_ancestors(self, ancestors)
- return ancestors
-
-
-class ClassTree(object):
- """Contains and generates all the class tree information.
-
- On initialization of the instance, nothing is done. The classes
- are obtained using the list of modules (or a single module) that
- is used to initialize the instance. One must then call the
- `create` method to generate the tree structure. The instance of
- the class also can be treated as an iterator which iterates over
- the nodes of the tree.
-
- There are two ways in which the tree hierarchy is stored. A
- dictionary mapping class names to the tree node and a tree
- represented as a list of lists containing the nodes. The tree is
- organized based on a concept of an inheritance level. A class
- that has no parent classes (no base classes) is said to be at
- level zero. If a class inherits successively from 7 classes, it
- is at level 6. An example of inheritance for a vtkFoo class is
- given below:
-
- vtkFoo -> vtkBar -> vtkObject -> vtkObjectBase
-
- Here, vtkObjectBase has an inheritance level of 0 and vtkFoo a
- level of 3. One can traverse the tree by using the level as an
- index and find all the classes at a particular level.
-
- Here is some example usage of this class::
-
- >>> import vtk
- >>> t = ClassTree(vtk)
- >>> t.create()
- >>> print t.get_node('vtkObject').name
- vtkObject
- >>> print t.get_node('vtkObject').parents[0].name
- vtkObjectBase
- >>> print len(t.tree[0])
- 1
- >>> t.tree[0][0].name
- vtkObjectBase
-
- """
-
- def __init__(self, modules):
- """Initialize the instance with the given modules.
-
- Parameters
- ----------
-
- - modules : `sequence` of modules or a module
-
- This is either a single module or a sequence of modules.
- The instance uses these list of modules to generate the
- class tree.
-
- """
- self.nodes = {}
- self.tree = [[]]
- if not hasattr(modules, '__iter__'):
- self.modules = [modules]
- else:
- self.modules = modules
-
- def __iter__(self):
- return iter(self.nodes.values())
-
- def _generate_hierarchy(self, klass):
- """Does the hard work of generating the class hierarchy."""
- node = self.get_node(klass.__name__, create=1)
- for base in klass.__bases__:
- base_node = self.get_node_from_class(base, create=1)
- node.add_parent(base_node)
- base_node.add_child(node)
- self._generate_hierarchy(base)
-
- def get_class(self, name):
- """Given a class name in the given modules returns the class."""
- klass = None
- for m in self.modules:
- if hasattr(m, name):
- return getattr(m, name)
- if hasattr(__builtin__, name):
- klass = getattr(__builtin__, name)
- if not klass:
- try:
- klass = self.nodes[name].klass
- except KeyError:
- raise KeyError, "Cannot find class of name %s"%name
- return klass
-
- def add_node(self, klass):
- """Create a node for the given class."""
- name = klass.__name__
- if not self.nodes.has_key(name):
- node = TreeNode(klass)
- self.nodes[name] = node
- return node
-
- def get_node(self, name, create=0):
- """Get a node of the given name.
-
- Parameters
- ----------
-
- - name : `str`
-
- Name of the node to get.
-
- - create : `boolean`
-
- If True, a new node will be added if no node of the given
- name is available. Defaults to False.
-
- Returns
- -------
-
- - `TreeNode`
-
- """
- if self.nodes.has_key(name):
- return self.nodes[name]
- elif create:
- return self.add_node(self.get_class(name))
-
- def get_node_from_class(self, cls, create=0):
- """Get a node of the given class.
-
- Parameters
- ----------
-
- - cls : `class`
-
- Class of the node to get.
-
- - create : `boolean`
-
- If True, a new node will be added if no node of the given
- name is available. Defaults to False.
-
- Returns
- -------
-
- - `TreeNode`
-
- """
- name = cls.__name__
- if self.nodes.has_key(name):
- return self.nodes[name]
- elif create:
- return self.add_node(cls)
-
- def create(self, class_names=None):
- """This method generates the class tree given an optional list
- of class names.
-
- Parameters
- ----------
-
- - class_names - `list` of `str`
-
- An optional list of names of the classes to generate the
- tree for. Defaults to None where the class list is computed
- from the modules.
-
- """
- if class_names is None:
- class_names = []
- for m in self.modules:
- class_names.extend(dir(m))
-
- # Generate the nodes.
- for name in class_names:
- klass = self.get_class(name)
- if klass and hasattr(klass, '__bases__'):
- self._generate_hierarchy(klass)
-
- # Compute the inheritance level and store the nodes in the tree.
- for node in self:
- d = node.get_level()
- while len(self.tree) <= d:
- self.tree.append([])
- self.tree[d].append(node)
-
- # Sort the nodes alphabetically.
- def _comp(x, y):
- return cmp(x.name, y.name)
- for nodes in self.tree:
- nodes.sort(_comp)
diff --git a/contrib/vtksnl/fix_classes.py b/contrib/vtksnl/fix_classes.py
deleted file mode 100644
index 90b608d..0000000
--- a/contrib/vtksnl/fix_classes.py
+++ /dev/null
@@ -1,51 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-import vtksnl
-
-################################################################################
-# Some fixed classes that solve a few VTK API issues
-
-# This dictionary stores the patched class to vtk class mapping.
-# This would be naturally better stored as an attribute directly on the
-# patched class. VTK, however, doesn't like class attributes.
-description = {}
-
-# http://www.vtk.org/doc/nightly/html/classvtkImagePlaneWidget.html
-# SetUserControlledLookupTable needs to be set before calling
-# SetLookupTable. VTK should do it automatically, so let's fix it
-
-
-# This fix seems to break on VTK versions larger than 5.0.3. It might also
-# be because of an interaction with python 2.6, but I haven't checked that.
-class vtkImagePlaneWidget_fixed(vtksnl.vtkImagePlaneWidget):
- def SetLookupTable(self, lookup_table):
- self.UserControlledLookupTableOn()
- vtksnl.vtkImagePlaneWidget.SetLookupTable(self, lookup_table)
-
-if tuple(vtksnl.vtkVersion().GetVTKVersion().split('.')) < ('5', '0', '4'):
- description[vtkImagePlaneWidget_fixed] = vtksnl.vtkImagePlaneWidget
-else:
- description[id(vtkImagePlaneWidget_fixed)] = vtksnl.vtkImagePlaneWidget
-
-# Set docstring to wrap it correctly
-vtkImagePlaneWidget_fixed.SetLookupTable.__doc__ = vtksnl.vtkImagePlaneWidget.SetLookupTable.__doc__
diff --git a/contrib/vtksnl/hasher.py b/contrib/vtksnl/hasher.py
deleted file mode 100644
index 34909ec..0000000
--- a/contrib/vtksnl/hasher.py
+++ /dev/null
@@ -1,36 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-# This is the user-defined hasher for VTK, that takes into account
-# incoming and outgoing connections
-from core.cache.hasher import Hasher
-
-def vtk_hasher(pipeline, module, chm):
- outgoing_connections = pipeline.graph.edges_from(module.id)
- incoming_connections = pipeline.graph.edges_to(module.id)
- current_hash = Hasher.module_signature(module, chm)
- chashes = [Hasher.connection_signature(pipeline.connections[c_id])
- for (_, c_id) in outgoing_connections]
- chashes += [Hasher.connection_signature(pipeline.connections[c_id])
- for (_, c_id) in incoming_connections]
- compound_hash = Hasher.compound_signature(chashes)
- return Hasher.compound_signature([current_hash, compound_hash])
diff --git a/contrib/vtksnl/init.py b/contrib/vtksnl/init.py
deleted file mode 100644
index 118f102..0000000
--- a/contrib/vtksnl/init.py
+++ /dev/null
@@ -1,1073 +0,0 @@
-###########################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-################################################################################
-# VTK-SNL Package for VisTrails (Sandia National Laboratories)
-################################################################################
-
-from core.bundles import py_import
-import vtksnl
-
-from core.utils import all, any, VistrailsInternalError, InstanceObject
-from core.debug import debug
-from core.modules.basic_modules import Integer, Float, String, File, \
- Variant, Color
-from core.modules.module_registry import get_module_registry
-from core.modules.vistrails_module import new_module, ModuleError
-from base_module import vtkBaseModule
-from class_tree import ClassTree
-from vtk_parser import VTKMethodParser
-import re
-import os.path
-from itertools import izip
-from vtkcell import VTKCell
-import tf_widget
-import offscreen
-import fix_classes
-import inspectors
-from hasher import vtk_hasher
-import sys
-
-################################################################################
-
-# filter some deprecation warnings coming from the fact that vtk calls
-# range() with float parameters
-
-import warnings
-warnings.filterwarnings("ignore",
- message="integer argument expected, got float")
-
-################################################################################
-
-if tuple(vtksnl.vtkVersion().GetVTKVersion().split('.')) < ('5', '0', '4'):
- def get_description_class(klass):
- """Because sometimes we need to patch VTK classes, the klass that
- has the methods is different than the klass we want to
- instantiate. get_description_class makes sure that for patched
- classes we get the correct one."""
- try:
- return fix_classes.description[klass]
- except KeyError:
- return klass
-else:
- # On VTK 5.0.4, we use the id of the class to hash, because it
- # seems that VTK hasn't implemented hash() correctly for their
- # classes.
- def get_description_class(klass):
- """Because sometimes we need to patch VTK classes, the klass that
- has the methods is different than the klass we want to
- instantiate. get_description_class makes sure that for patched
- classes we get the correct one."""
- try:
- return fix_classes.description[id(klass)]
- except KeyError:
- return klass
-
-parser = VTKMethodParser()
-
-typeMapDict = {'int': Integer,
- 'long': Integer,
- 'float': Float,
- 'char*': String,
- 'char *': String,
- 'string': String,
- 'char': String,
- 'const char*': String,
- 'const char *': String}
-typeMapDictValues = [Integer, Float, String]
-
-file_name_pattern = re.compile('.*FileName$')
-set_file_name_pattern = re.compile('Set.*FileName$')
-
-def resolve_overloaded_name(name, ix, signatures):
- # VTK supports static overloading, VisTrails does not. The
- # solution is to check whether the current function has
- # overloads and change the names appropriately.
- if len(signatures) == 1:
- return name
- else:
- return name + '_' + str(ix+1)
-
-def typeMap(name, package=None):
- """ typeMap(name: str) -> Module
- Convert from C/C++ types into VisTrails Module type
-
- """
- if package is None:
- package = identifier
- if type(name) == tuple:
- return [typeMap(x, package) for x in name]
- if name in typeMapDict:
- return typeMapDict[name]
- else:
- registry = get_module_registry()
- if not registry.has_descriptor_with_name(package, name):
- return None
- else:
- return registry.get_descriptor_by_name(package,
- name).module
-
-def get_method_signature(method):
- """ get_method_signature(method: vtkmethod) -> [ret, arg]
- Re-wrap Prabu's method to increase performance
-
- """
- doc = method.__doc__
- tmptmp = doc.split('\n')
- tmp = []
- for l in tmptmp:
- l = l.strip('\n \t')
- if l.startswith('V.') or l.startswith('C++:'):
- tmp.append(l)
- else:
- tmp[-1] = tmp[-1] + l
- tmp.append('')
- sig = []
- pat = re.compile(r'\b')
-
- # Remove all the C++ function signatures and V.<method_name> field
- offset = 2+len(method.__name__)
- for i in xrange(len(tmp)):
- s = tmp[i]
- if s=='': break
- if i%2==0:
- x = s.split('->')
- arg = x[0].strip()[offset:]
- if len(x) == 1: # No return value
- ret = None
- else:
- ret = x[1].strip()
-
- # Remove leading and trailing parens for arguments.
- arg = arg[1:-1]
- if not arg:
- arg = None
- if arg and arg[-1] == ')':
- arg = arg + ','
-
- # Now quote the args and eval them. Easy!
- if ret and ret[:3]!='vtk':
- try:
- ret = eval(pat.sub('\"', ret))
- except:
- continue
- if arg:
- if arg.find('(')!=-1:
- try:
- arg = eval(pat.sub('\"', arg))
- except:
- continue
- else:
- arg = arg.split(', ')
- if len(arg)>1:
- arg = tuple(arg)
- else:
- arg = arg[0]
- if type(arg) == str:
- arg = [arg]
-
- sig.append(([ret], arg))
- return sig
-
-def prune_signatures(module, name, signatures, output=False):
- """prune_signatures tries to remove redundant signatures to reduce
- overloading. It _mutates_ the given parameter.
-
- It does this by performing several operations:
-
- 1) It compares a 'flattened' version of the types
- against the other 'flattened' signatures. If any of them match, we
- keep only the 'flatter' ones.
-
- A 'flattened' signature is one where parameters are not inside a
- tuple.
-
- 2) We explicitly forbid a few signatures based on modules and names
-
- """
- # yeah, this is Omega(n^2) on the number of overloads. Who cares?
-
- def flatten(type_):
- if type_ is None:
- return []
- def convert(entry):
- if type(entry) == tuple:
- return list(entry)
- else:
- assert(type(entry) == str)
- return [entry]
- result = []
- for entry in type_:
- result.extend(convert(entry))
- return result
-
- flattened_entries = [flatten(sig[1]) for
- sig in signatures]
- def hit_count(entry):
- result = 0
- for entry in flattened_entries:
- if entry in flattened_entries:
- result += 1
- return result
- hits = [hit_count(entry) for entry in flattened_entries]
-
- def forbidden(flattened, hit_count, original):
- if (issubclass(get_description_class(module.vtkClass), vtksnl.vtk3DWidget) and
- name == 'PlaceWidget' and
- flattened == []):
- return True
- # We forbid this because addPorts hardcodes this but
- # SetInputArrayToProcess is an exception for the InfoVis
- # package
- if (get_description_class(module.vtkClass) == vtksnl.vtkAlgorithm and
- name!='SetInputArrayToProcess'):
- return True
- return False
-
- # This is messy: a signature is only allowed if there's no
- # explicit disallowing of it. Then, if it's not overloaded,
- # it is also allowed. If it is overloaded and not the flattened
- # version, it is pruned. If these are output ports, there can be
- # no parameters.
-
- def passes(flattened, hit_count, original):
- if forbidden(flattened, hit_count, original):
- return False
- if hit_count == 1:
- return True
- if original[1] is None:
- return True
- if output and len(original[1]) > 0:
- return False
- if hit_count > 1 and len(original[1]) == len(flattened):
- return True
- return False
-
- signatures[:] = [original for (flattened, hit_count, original)
- in izip(flattened_entries,
- hits,
- signatures)
- if passes(flattened, hit_count, original)]
-
- #then we remove the duplicates, if necessary
- unique_signatures = []
- [unique_signatures.append(s) for s in signatures if not unique_signatures.count(s)]
- signatures[:] = unique_signatures
-
-disallowed_classes = set(
- [
- 'vtkCriticalSection',
- 'vtkDataArraySelection',
- 'vtkDebugLeaks',
- 'vtkDirectory',
- 'vtkDynamicLoader',
- 'vtkFunctionParser',
- 'vtkGarbageCollector',
- 'vtkHeap',
- 'vtkInformationKey',
- 'vtkInstantiator',
- 'vtkLogLookupTable', # VTK: use vtkLookupTable.SetScaleToLog10() instead
- 'vtkMath',
- 'vtkModelMetadata',
- 'vtkMultiProcessController',
- 'vtkMutexLock',
- 'vtkOutputWindow',
- 'vtkPriorityQueue',
- 'vtkReferenceCount',
- 'vtkRenderWindowCollection',
- 'vtkRenderWindowInteractor',
- 'vtkTesting',
- 'vtkWindow',
- 'vtksnlVersion',
- 'vtkDiffFilter',
- 'vtkDocumentM3MetaData'
- #'vtkXMLUtilities',
- #'vtkXMLShader',
- #'vtkXMLMaterialReader',
- #'vtkXMLMaterial',
- #'vtkXMLDataElement'
- ])
-
-def is_class_allowed(module):
- if module is None:
- return False
- try:
- name = module.__name__
- return not (name in disallowed_classes)
- except AttributeError:
- return True
-
-def addAlgorithmPorts(module):
- """ addAlgorithmPorts(module: Module) -> None
- If module is a subclass of vtkAlgorithm, this function will add all
- SetInputConnection([id],[port]) and GetOutputPort([id]) as
- SetInputConnection{id}([port]) and GetOutputPort{id}.
-
- """
- if issubclass(get_description_class(module.vtkClass), vtksnl.vtkAlgorithm):
- if get_description_class(module.vtkClass)!=vtksnl.vtkStructuredPointsGeometryFilter:
- # We try to instantiate the class here to get the number of
- # ports and to avoid abstract classes
- try:
- instance = module.vtkClass()
- except TypeError:
- pass
- else:
- registry = get_module_registry()
- des = registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtksnl',
- 'vtkAlgorithmOutput')
- for i in xrange(0,instance.GetNumberOfInputPorts()):
- registry.add_input_port(module, 'SetInputConnection%d'%i,
- des.module)
- for i in xrange(0,instance.GetNumberOfOutputPorts()):
- registry.add_output_port(module, 'GetOutputPort%d'%i,
- des.module)
-
-disallowed_set_get_ports = set(['ReferenceCount',
- 'InputConnection',
- 'OutputPort',
- 'Progress',
- 'ProgressText',
- 'InputArrayToProcess',
- ])
-def addSetGetPorts(module, get_set_dict, delayed):
- """ addSetGetPorts(module: Module, get_set_dict: dict) -> None
- Convert all Setxxx methods of module into input ports and all Getxxx
- methods of module into output ports
-
- Keyword arguments:
- module --- Module
- get_set_dict --- the Set/Get method signatures returned by vtk_parser
-
- """
-
- klass = get_description_class(module.vtkClass)
- registry = get_module_registry()
- for name in get_set_dict.iterkeys():
- if name in disallowed_set_get_ports: continue
- getterMethod = getattr(klass, 'Get%s'%name)
- setterMethod = getattr(klass, 'Set%s'%name)
- getterSig = get_method_signature(getterMethod)
- setterSig = get_method_signature(setterMethod)
- if len(getterSig) > 1:
- prune_signatures(module, 'Get%s'%name, getterSig, output=True)
- for order, getter in enumerate(getterSig):
- if getter[1]:
- debug("Can't handle getter %s (%s) of class %s: Needs input to "
- "get output" % (order+1, name, klass))
- continue
- if len(getter[0]) != 1:
- debug("Can't handle getter %s (%s) of class %s: More than a "
- "single output" % (order+1, name, str(klass)))
- continue
- class_ = typeMap(getter[0][0])
- if is_class_allowed(class_):
- registry.add_output_port(module, 'Get'+name, class_, True)
- if len(setterSig) > 1:
- prune_signatures(module, 'Set%s'%name, setterSig)
- for ix, setter in enumerate(setterSig):
- if setter[1]==None: continue
- n = resolve_overloaded_name('Set' + name, ix, setterSig)
- if len(setter[1]) == 1 and is_class_allowed(typeMap(setter[1][0])):
- registry.add_input_port(module, n,
- typeMap(setter[1][0]),
- setter[1][0] in typeMapDict)
- else:
- classes = [typeMap(i) for i in setter[1]]
- if all(is_class_allowed(x) for x in classes):
- registry.add_input_port(module, n, classes, True)
- # Wrap SetFileNames for VisTrails file access
- if file_name_pattern.match(name):
- registry.add_input_port(module, 'Set' + name[:-4],
- (File, 'input file'), False)
- # Wrap SetRenderWindow for exporters
- elif name == 'RenderWindow':
- # cscheid 2008-07-11 This is messy: VTKCell isn't
- # registered yet, so we can't use it as a port
- # However, we can't register VTKCell before these either,
- # because VTKCell requires vtkRenderer. The "right" way would
- # be to add all modules first, then all ports. However, that would
- # be too slow.
- # Workaround: delay the addition of the port by storing
- # the information in a list
- if registry.has_module('edu.utah.sci.vistrails.spreadsheet',
- 'SpreadsheetCell'):
- delayed.add_input_port.append((module, 'SetVTKCell', VTKCell, False))
- # Wrap color methods for VisTrails GUI facilities
- elif name == 'DiffuseColor':
- registry.add_input_port(module, 'SetDiffuseColorWidget',
- (Color, 'color'), True)
- elif name == 'Color':
- registry.add_input_port(module, 'SetColorWidget',
- (Color, 'color'), True)
- elif name == 'AmbientColor':
- registry.add_input_port(module, 'SetAmbientColorWidget',
- (Color, 'color'), True)
- elif name == 'SpecularColor':
- registry.add_input_port(module, 'SetSpecularColorWidget',
- (Color, 'color'), True)
- elif name == 'EdgeColor':
- registry.add_input_port(module, 'SetEdgeColorWidget',
- (Color, 'color'), True)
- elif name == 'Background' :
- registry.add_input_port(module, 'SetBackgroundWidget',
- (Color, 'color'), True)
- elif name == 'Background2' :
- registry.add_input_port(module, 'SetBackground2Widget',
- (Color, 'color'), True)
-
-disallowed_toggle_ports = set(['GlobalWarningDisplay',
- 'Debug',
- ])
-def addTogglePorts(module, toggle_dict):
- """ addTogglePorts(module: Module, toggle_dict: dict) -> None
- Convert all xxxOn/Off methods of module into input ports
-
- Keyword arguments:
- module --- Module
- toggle_dict --- the Toggle method signatures returned by vtk_parser
-
- """
- registry = get_module_registry()
- for name in toggle_dict.iterkeys():
- if name in disallowed_toggle_ports:
- continue
- registry.add_input_port(module, name+'On', [], True)
- registry.add_input_port(module, name+'Off', [], True)
-
-disallowed_state_ports = set(['SetInputArrayToProcess'])
-def addStatePorts(module, state_dict):
- """ addStatePorts(module: Module, state_dict: dict) -> None
- Convert all SetxxxToyyy methods of module into input ports
-
- Keyword arguments:
- module --- Module
- state_dict --- the State method signatures returned by vtk_parser
-
- """
- klass = get_description_class(module.vtkClass)
- registry = get_module_registry()
- for name in state_dict.iterkeys():
- for mode in state_dict[name]:
- # Creates the port Set foo to bar
- field = 'Set'+name+'To'+mode[0]
- if field in disallowed_state_ports:
- continue
- if not registry.has_input_port(module, field):
- registry.add_input_port(module, field, [], True)
-
- # Now create the port Set foo with parameter
- if hasattr(klass, 'Set%s'%name):
- setterMethod = getattr(klass, 'Set%s'%name)
- setterSig = get_method_signature(setterMethod)
- # if the signature looks like an enum, we'll skip it, it shouldn't
- # be necessary
- if len(setterSig) > 1:
- prune_signatures(module, 'Set%s'%name, setterSig)
- for ix, setter in enumerate(setterSig):
- n = resolve_overloaded_name('Set' + name, ix, setterSig)
- tm = typeMap(setter[1][0])
- if len(setter[1]) == 1 and is_class_allowed(tm):
- registry.add_input_port(module, n, tm,
- setter[1][0] in typeMapDict)
- else:
- classes = [typeMap(i) for i in setter[1]]
- if all(is_class_allowed(x) for x in classes):
- registry.add_input_port(module, n, classes, True)
-
-disallowed_other_ports = set(
- [
- 'BreakOnError',
- 'DeepCopy',
- 'FastDelete',
- 'HasObserver',
- 'HasExecutive',
- 'INPUT_ARRAYS_TO_PROCESS',
- 'INPUT_CONNECTION',
- 'INPUT_IS_OPTIONAL',
- 'INPUT_IS_REPEATABLE',
- 'INPUT_PORT',
- 'INPUT_REQUIRED_DATA_TYPE',
- 'INPUT_REQUIRED_FIELDS',
- 'InvokeEvent',
- 'IsA',
- 'Modified',
- 'NewInstance',
- 'PrintRevisions',
- 'RemoveAllInputs',
- 'RemoveObserver',
- 'RemoveObservers',
- 'SafeDownCast',
-# 'SetInputArrayToProcess',
- 'ShallowCopy',
- 'Update',
- 'UpdateInformation',
- 'UpdateProgress',
- 'UpdateWholeExtent',
- ])
-
-force_not_optional_port = set(
- ['ApplyViewTheme',
- ])
-
-
-def addOtherPorts(module, other_list):
- """ addOtherPorts(module: Module, other_list: list) -> None
- Convert all other ports such as Insert/Add.... into input/output
-
- Keyword arguments:
- module --- Module
- other_dict --- any other method signatures that is not
- Algorithm/SetGet/Toggle/State type
-
- """
- klass = get_description_class(module.vtkClass)
- registry = get_module_registry()
- for name in other_list:
- if name[:3] in ['Add','Set'] or name[:6]=='Insert':
- if name in disallowed_other_ports:
- continue
- method = getattr(klass, name)
- signatures = get_method_signature(method)
- if len(signatures) > 1:
- prune_signatures(module, name, signatures)
- for (ix, sig) in enumerate(signatures):
- ([result], params) = sig
- types = []
- if params:
- for p in params:
- t = typeMap(p)
- if not t:
- types = None
- break
- else: types.append(t)
- else:
- types = [[]]
- if types:
- if not all(is_class_allowed(x) for x in types):
- continue
- n = resolve_overloaded_name(name, ix, signatures)
- if len(types)<=1:
- registry.add_input_port(module, n, types[0],
- types[0] in typeMapDictValues)
- else:
- registry.add_input_port(module, n, types, True)
- else:
- if name in disallowed_other_ports:
- continue
- method = getattr(klass, name)
- signatures = get_method_signature(method)
- if len(signatures) > 1:
- prune_signatures(module, name, signatures)
- for (ix, sig) in enumerate(signatures):
- ([result], params) = sig
- types = []
- if params:
- types = [typeMap(p) for p in params]
- else:
- types = []
- if not all(is_class_allowed(x) for x in types):
- continue
- if types==[] or (result==None):
- n = resolve_overloaded_name(name, ix, signatures)
- registry.add_input_port(module, n, types,
- not (n in force_not_optional_port))
-
-disallowed_get_ports = set([
- 'GetClassName',
- 'GetErrorCode',
- 'GetNumberOfInputPorts',
- 'GetNumberOfOutputPorts',
- 'GetOutputPortInformation',
- 'GetTotalNumberOfInputConnections',
- ])
-
-def addGetPorts(module, get_list):
- klass = get_description_class(module.vtkClass)
- registry = get_module_registry()
- for name in get_list:
- if name in disallowed_get_ports:
- continue
- method = getattr(klass, name)
- signatures = get_method_signature(method)
- if len(signatures) > 1:
- prune_signatures(module, name, signatures, output=True)
- for ix, getter in enumerate(signatures):
- if getter[1] or len(getter[0]) > 1:
- continue
- class_ = typeMap(getter[0][0])
- if is_class_allowed(class_):
- if len(signatures) > 1:
- n = name + "_" + str(ix+1)
- else:
- n = name
- registry.add_output_port(module, n, class_, True)
-
-def addPorts(module, delayed):
- """ addPorts(module: VTK module inherited from Module,
- delayed: object with add_input_port slot
- ) -> None
-
- Search all metamethods of module and add appropriate ports
-
- ports that cannot be added immediately should be appended to
- the delayed object that is passed. see the SetRenderWindow cases.
-
- """
- klass = get_description_class(module.vtkClass)
- registry = get_module_registry()
- registry.add_output_port(module, 'self', module)
- parser.parse(klass)
- addAlgorithmPorts(module)
- addGetPorts(module, parser.get_get_methods())
- addSetGetPorts(module, parser.get_get_set_methods(), delayed)
- addTogglePorts(module, parser.get_toggle_methods())
- addStatePorts(module, parser.get_state_methods())
- addOtherPorts(module, parser.get_other_methods())
- # CVS version of VTK doesn't support AddInputConnect(vtkAlgorithmOutput)
- if klass==vtksnl.vtkAlgorithm:
- registry.add_input_port(module, 'AddInputConnection',
- typeMap('vtkAlgorithmOutput'))
- # vtkWriters have a custom File port
- elif klass==vtksnl.vtkWriter:
- registry.add_output_port(module, 'file',
- typeMap('File','edu.utah.sci.vistrails.basic'))
- elif klass==vtksnl.vtkImageWriter:
- registry.add_output_port(module, 'file',
- typeMap('File','edu.utah.sci.vistrails.basic'))
- elif klass==vtksnl.vtkVolumeProperty:
- registry.add_input_port(module, 'SetTransferFunction',
- typeMap('TransferFunction'))
- elif klass==vtksnl.vtkDataSet:
- registry.add_input_port(module, 'SetPointData', typeMap('vtkPointData'))
- registry.add_input_port(module, 'SetCallData', typeMap('vtkCellData'))
- elif klass==vtksnl.vtkCell:
- registry.add_input_port(module, 'SetPointIds', typeMap('vtkIdList'))
-
-def setAllPorts(descriptor, delayed):
- """ setAllPorts(descriptor: ModuleDescriptor) -> None
- Traverse descriptor and all of its children/grand-children to add all ports
-
- """
- addPorts(descriptor.module, delayed)
- for child in descriptor.children:
- setAllPorts(child, delayed)
-
-def class_dict(base_module, node):
- """class_dict(base_module, node) -> dict
- Returns the class dictionary for the module represented by node and
- with base class base_module"""
-
- class_dict_ = {}
- def update_dict(name, callable_):
- if class_dict_.has_key(name):
- class_dict_[name] = callable_(class_dict_[name])
- elif hasattr(base_module, name):
- class_dict_[name] = callable_(getattr(base_module, name))
- else:
- class_dict_[name] = callable_(None)
-
- def guarded_SimpleScalarTree_wrap_compute(old_compute):
- # This builds the scalar tree and makes it cacheable
-
- def compute(self):
- self.is_cacheable = lambda *args, **kwargs: True
- old_compute(self)
- self.vtkInstance.BuildTree()
- return compute
-
- def guarded_SetFileName_wrap_compute(old_compute):
- # This checks for the presence of file in VTK readers
- def compute(self):
-
- # Skips the check if it's a vtkImageReader or vtkPLOT3DReader, because
- # it has other ways of specifying files, like SetFilePrefix for
- # multiple files
- if any(issubclass(self.vtkClass, x)
- for x in
- [vtksnl.vtkBYUReader,
- vtksnl.vtkImageReader,
- vtksnl.vtkPLOT3DReader,
- vtksnl.vtkDICOMImageReader,
- vtksnl.vtkTIFFReader]):
- old_compute(self)
- return
- if self.hasInputFromPort('SetFileName'):
- name = self.getInputFromPort('SetFileName')
- elif self.hasInputFromPort('SetFile'):
- name = self.getInputFromPort('SetFile').name
- else:
- raise ModuleError(self, 'Missing filename')
- if not os.path.isfile(name):
- raise ModuleError(self, 'File does not exist')
- old_compute(self)
- return compute
-
- def compute_SetDiffuseColorWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetDiffuseColorWidget(self, color):
- self.vtkInstance.SetDiffuseColor(color.tuple)
- return call_SetDiffuseColorWidget
-
- def compute_SetAmbientColorWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetAmbientColorWidget(self, color):
- self.vtkInstance.SetAmbientColor(color.tuple)
- return call_SetAmbientColorWidget
-
- def compute_SetSpecularColorWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetSpecularColorWidget(self, color):
- self.vtkInstance.SetSpecularColor(color.tuple)
- return call_SetSpecularColorWidget
-
- def compute_SetColorWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetColorWidget(self, color):
- self.vtkInstance.SetColor(color.tuple)
- return call_SetColorWidget
-
- def compute_SetEdgeColorWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetEdgeColorWidget(self, color):
- self.vtkInstance.SetEdgeColor(color.tuple)
- return call_SetEdgeColorWidget
-
- def compute_SetBackgroundWidget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetBackgroundWidget(self, color):
- self.vtkInstance.SetBackground(color.tuple)
- return call_SetBackgroundWidget
-
- def compute_SetBackground2Widget(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetBackground2Widget(self, color):
- self.vtkInstance.SetBackground2(color.tuple)
- return call_SetBackground2Widget
-
- def compute_SetVTKCell(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetRenderWindow(self, cellObj):
- if cellObj.cellWidget:
- self.vtkInstance.SetRenderWindow(cellObj.cellWidget.mRenWin)
- return call_SetRenderWindow
-
- def compute_SetTransferFunction(old_compute):
- # This sets the transfer function
- if old_compute != None:
- return old_compute
- def call_SetTransferFunction(self, tf):
- tf.set_on_vtk_volume_property(self.vtkInstance)
- return call_SetTransferFunction
-
- def compute_SetPointData(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetPointData(self, pd):
- self.vtkInstance.GetPointData().ShallowCopy(pd)
- return call_SetPointData
-
- def compute_SetCellData(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetCellData(self, cd):
- self.vtkInstance.GetCellData().ShallowCopy(cd)
- return call_SetCellData
-
- def compute_SetPointIds(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetPointIds(self, point_ids):
- self.vtkInstance.GetPointIds().SetNumberOfIds(point_ids.GetNumberOfIds())
- for i in xrange(point_ids.GetNumberOfIds()):
- self.vtkInstance.GetPointIds().SetId(i, point_ids.GetId(i))
- return call_SetPointIds
-
- def guarded_Writer_wrap_compute(old_compute):
- # The behavior for vtkWriter subclasses is to call Write()
- # If the user sets a name, we will create a file with that name
- # If not, we will create a temporary file from the file pool
- def compute(self):
- old_compute(self)
- fn = self.vtkInstance.GetFileName()
- if not fn:
- o = self.interpreter.filePool.create_file(suffix='.vtk')
- self.vtkInstance.SetFileName(o.name)
- else:
- o = File()
- o.name = fn
- self.vtkInstance.Write()
- self.setResult('file', o)
- return compute
-
- for var in dir(node.klass):
- # Everyone that has a Set.*FileName should have a Set.*File port too
- if set_file_name_pattern.match(var):
- def get_compute_SetFile(method_name):
- def compute_SetFile(old_compute):
- if old_compute != None:
- return old_compute
- def call_SetFile(self, file_obj):
- getattr(self.vtkInstance, method_name)(file_obj.name)
- return call_SetFile
- return compute_SetFile
- update_dict('_special_input_function_' + var[:-4],
- get_compute_SetFile(var))
-
- if hasattr(node.klass, 'SetFileName'):
- # ... BUT we only want to check existence of filenames on
- # readers. VTK is nice enough to be consistent with names, but
- # this is brittle..
- if node.klass.__name__.endswith('Reader'):
- if not node.klass.__name__.endswith('TiffReader'):
- update_dict('compute', guarded_SetFileName_wrap_compute)
- if hasattr(node.klass, 'SetRenderWindow'):
- update_dict('_special_input_function_SetVTKCell',
- compute_SetVTKCell)
- #color gui wrapping
- if hasattr(node.klass, 'SetDiffuseColor'):
- update_dict('_special_input_function_SetDiffuseColorWidget',
- compute_SetDiffuseColorWidget)
- if hasattr(node.klass, 'SetAmbientColor'):
- update_dict('_special_input_function_SetAmbientColorWidget',
- compute_SetAmbientColorWidget)
- if hasattr(node.klass, 'SetSpecularColor'):
- update_dict('_special_input_function_SetSpecularColorWidget',
- compute_SetSpecularColorWidget)
- if hasattr(node.klass, 'SetEdgeColor'):
- update_dict('_special_input_function_SetEdgeColorWidget',
- compute_SetEdgeColorWidget)
- if hasattr(node.klass, 'SetColor'):
- update_dict('_special_input_function_SetColorWidget',
- compute_SetColorWidget)
- if (issubclass(node.klass, vtksnl.vtkRenderer) and
- hasattr(node.klass, 'SetBackground')):
- update_dict('_special_input_function_SetBackgroundWidget',
- compute_SetBackgroundWidget)
- if (issubclass(node.klass, vtksnl.vtkRenderer) and
- hasattr(node.klass, 'SetBackground2')):
- update_dict('_special_input_function_SetBackground2Widget',
- compute_SetBackground2Widget)
- if issubclass(node.klass, vtksnl.vtkWriter):
- update_dict('compute', guarded_Writer_wrap_compute)
-
- if issubclass(node.klass, vtksnl.vtkScalarTree):
- update_dict('compute', guarded_SimpleScalarTree_wrap_compute)
-
- if issubclass(node.klass, vtksnl.vtkVolumeProperty):
- update_dict('_special_input_function_SetTransferFunction',
- compute_SetTransferFunction)
- if issubclass(node.klass, vtksnl.vtkDataSet):
- update_dict('_special_input_function_SetPointData',
- compute_SetPointData)
- update_dict('_special_input_function_SetCellData',
- compute_SetCellData)
- if issubclass(node.klass, vtksnl.vtkCell):
- update_dict('_special_input_function_SetPointIds',
- compute_SetPointIds)
- return class_dict_
-
-disallowed_modules = set([
-# 'vtkGeoAlignedImageCache',
-# 'vtkGeoTerrainCache',
-# 'vtkMimeTypeStrategy',
-# 'vtkMPIGroup',
- 'vtkPlotWriter', # Segfaults when being destroyed (when created without a reference, or when last reference is removed)
- 'vtkRenderedLandscapeRepresentation' # Segfaults when calling: GetPeakLabelStopWords()
- ])
-def createModule(baseModule, node):
- """ createModule(baseModule: a Module subclass, node: TreeNode) -> None
- Construct a module inherits baseModule with specification from node
-
- """
- if node.name in disallowed_modules: return
- def obsolete_class_list():
- lst = []
- items = ['vtkInteractorStyleTrackball',
- 'vtkStructuredPointsGeometryFilter',
- 'vtkConstrainedPointHandleRepresentation',
- 'vtkTypePromotion']
- def try_to_add_item(item):
- try:
- lst.append(getattr(vtksnl, item))
- except AttributeError:
- pass
- for item in items:
- try_to_add_item(item)
- return lst
-
- obsolete_list = obsolete_class_list()
-
- def is_abstract():
- """is_abstract tries to instantiate the class. If it's
- abstract, this will raise."""
- # Consider obsolete classes abstract
- if node.klass in obsolete_list:
- return True
- try:
- getattr(vtksnl, node.name)()
- except TypeError: # VTK raises type error on abstract classes
- return True
- return False
- module = new_module(baseModule, node.name,
- class_dict(baseModule, node),
- docstring=getattr(vtksnl, node.name).__doc__
- )
-
- # This is sitting on the class
- if hasattr(fix_classes, node.klass.__name__ + '_fixed'):
- module.vtkClass = getattr(fix_classes, node.klass.__name__ + '_fixed')
- else:
- module.vtkClass = node.klass
- registry = get_module_registry()
- registry.add_module(module, abstract=is_abstract(),
- signatureCallable=vtk_hasher)
- for child in node.children:
- if child.name in disallowed_classes:
- continue
- createModule(module, child)
-
-def createAllModules(g):
- """ createAllModules(g: ClassTree) -> None
- Traverse the VTK class tree and add all modules into the module registry
-
- """
- assert len(g.tree[0]) == 1
- base = g.tree[0][0]
- assert base.name == 'vtkObjectBase'
- vtkObjectBase = new_module(vtkBaseModule, 'vtkObjectBase')
- vtkObjectBase.vtkClass = vtksnl.vtkObjectBase
- registry = get_module_registry()
- registry.add_module(vtkObjectBase)
- for child in base.children:
- if child.name in disallowed_classes:
- continue
- createModule(vtkObjectBase, child)
-
-##############################################################################
-# Convenience methods
-
-def extract_vtk_instance(vistrails_obj):
- """extract_vtk_instance(vistrails_obj) -> vtk_object
-
- takes an instance of a VisTrails module that is a subclass
- of the vtkObjectBase module and returns the corresponding
- instance."""
- global identifier
- vtkObjectBase = registry.get_descriptor_by_name(identifier,
- 'vtkObjectBase').module
- assert isinstance(vistrails_obj, vtkObjectBase)
- return vistrails_obj.vtkInstance
-
-def wrap_vtk_instance(vtk_obj):
- """wrap_vtk_instance(vtk_object) -> VisTrails module
-
- takes a vtk instance and returns a corresponding
- wrapped instance of a VisTrails module"""
- global identifier
-
- assert isinstance(vtk_obj, vtksnl.vtkObjectBase)
- m = registry.get_descriptor_by_name(identifier,
- vtk_obj.GetClassName())
- result = m.module()
- result.vtkInstance = vtk_obj
- return result
-
-################################################################################
-
-def initialize():
- """ initialize() -> None
- Package-entry to initialize the package
-
- """
- # Check VTK version
- v = vtksnl.vtkVersion()
- version = [v.GetVTKMajorVersion(),
- v.GetVTKMinorVersion(),
- v.GetVTKBuildVersion()]
- if version < [5, 0, 0]:
- raise Exception("You need to upgrade your VTK install to version \
- > >= 5.0.0")
- inheritanceGraph = ClassTree(vtksnl)
- inheritanceGraph.create()
-
- # Transfer Function constant
- tf_widget.initialize()
-
- delayed = InstanceObject(add_input_port=[])
- # Add VTK modules
- registry = get_module_registry()
- registry.add_module(vtkBaseModule)
- createAllModules(inheritanceGraph)
- setAllPorts(registry.get_descriptor_by_name(identifier,
- 'vtkObjectBase'),
- delayed)
-
- # Register the VTKCell and VTKHandler type if the spreadsheet is up
- if registry.has_module('edu.utah.sci.vistrails.spreadsheet',
- 'SpreadsheetCell'):
- import vtkhandler
- import vtkcell
- import vtkviewcell
- vtkhandler.registerSelf()
- vtkcell.registerSelf()
- vtkviewcell.registerSelf()
-
- # register offscreen rendering module
- offscreen.register_self()
-
- # Now add all "delayed" ports - see comment on addSetGetPorts
- for args in delayed.add_input_port:
-
- registry.add_input_port(*args)
-
- # register Transfer Function adjustment
- # This can't be reordered -- TransferFunction needs to go before
- # vtkVolumeProperty, but vtkScaledTransferFunction needs
- # to go after vtkAlgorithmOutput
-
- getter = registry.get_descriptor_by_name
- registry.add_module(tf_widget.vtkScaledTransferFunction)
- registry.add_input_port(tf_widget.vtkScaledTransferFunction,
- 'Input', getter('edu.utah.sci.vistrails.vtksnl',
- 'vtkAlgorithmOutput').module)
- registry.add_input_port(tf_widget.vtkScaledTransferFunction,
- 'Dataset', getter ('edu.utah.sci.vistrails.vtksnl',
- 'vtkDataObject').module)
- registry.add_input_port(tf_widget.vtkScaledTransferFunction,
- 'Range', [Float, Float])
- registry.add_input_port(tf_widget.vtkScaledTransferFunction,
- 'TransferFunction',
- tf_widget.TransferFunctionConstant)
- registry.add_output_port(tf_widget.vtkScaledTransferFunction,
- 'TransferFunction',
- tf_widget.TransferFunctionConstant)
- inspectors.initialize()
-
-################################################################################
diff --git a/contrib/vtksnl/inspectors.py b/contrib/vtksnl/inspectors.py
deleted file mode 100644
index 9a40acf..0000000
--- a/contrib/vtksnl/inspectors.py
+++ /dev/null
@@ -1,231 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-##############################################################################
-# Data inspectors for VTK
-
-from core.modules.vistrails_module import ModuleError
-from core.utils import VistrailsInternalError
-from core.modules.basic_modules import Module, Float, Integer
-from core.modules.module_registry import get_module_registry
-import vtksnl
-from base_module import vtkBaseModule
-from hasher import vtk_hasher
-
-class vtkBaseInspector(Module):
-
- @classmethod
- def register_self(cls, **kwargs):
- registry = get_module_registry()
- def resolve_type(t):
- if type(t) == tuple:
- return registry.get_descriptor_by_name(*t).module
- elif type(t) == type:
- return t
- else:
- assert False, ("Unknown type " + str(type(t)))
-
- registry.add_module(cls, **kwargs)
- try:
- ips = cls.input_ports
- except AttributeError:
- pass
- else:
- for (port_name, types) in ips:
- registry.add_input_port(cls,
- port_name,
- list(resolve_type(t) for t in types))
-
- try:
- ops = cls.output_ports
- except AttributeError:
- pass
- else:
- for (port_name, types) in ops:
- registry.add_output_port(cls,
- port_name,
- list(resolve_type(t) for t in types))
-
- def auto_set_results(self, vtk_object):
- for function in self.outputPorts.keys():
- if hasattr(vtk_object, function):
- retValues = getattr(vtk_object, function)()
- if issubclass(retValues.__class__, vtksnl.vtkObject):
- className = retValues.GetClassName()
- output = vtkBaseModule.wrapperModule(className, retValues)
- self.setResult(function, output)
- elif type(retValues) in [tuple, list]:
- result = list(retValues)
- for i in xrange(len(result)):
- if issubclass(result[i].__class__, vtksnl.vtkObject):
- className = result[i].GetClassName()
- result[i] = vtkBaseModule.wrapperModule(className,
- result[i])
- self.setResult(function, type(retValues)(result))
- else:
- self.setResult(function, retValues)
-
-class vtkDataSetInspector(vtkBaseInspector):
-
- def compute(self):
- vtk_object = None
- if self.hasInputFromPort("SetInputConnection0"):
- ic = self.getInputFromPort("SetInputConnection0")
- port_object = ic.vtkInstance
- ix = port_object.GetIndex()
- producer = port_object.GetProducer()
- try:
- vtk_object = producer.GetOutput()
- except AttributeError:
- raise ModuleError(self,
- "expected a module that supports GetOutput")
- elif self.hasInputFromPort("SetInput"):
- port_object = self.getInputFromPort("SetInput")
- if hasattr(port_object, "vtkInstance"):
- vtk_object = port_object.vtkInstance
- else:
- raise ModuleError(self, "expected a vtk module")
- if vtk_object:
- self.auto_set_results(vtk_object)
-
- input_ports = [('SetInputConnection0',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkAlgorithmOutput')]),
- ('SetInput',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkDataSet')]),
- ]
- output_ports = [('GetBounds', [Float] * 6),
- ('GetScalarRange', [Float] * 2),
- ('GetLength', [Float]),
- ('GetCenter', [Float] * 3),
- ('GetNumberOfPoints', [Integer]),
- ('GetNumberOfCells', [Integer]),
- ('GetPointData',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkPointData')]),
- ('GetCellData',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkCellData')]),
- ]
-
-class vtkDataSetAttributesInspector(vtkBaseInspector):
-
- def compute(self):
- vtk_object = None
- if self.hasInputFromPort("SetInput"):
- port_object = self.getInputFromPort("SetInput")
- if hasattr(port_object, "vtkInstance"):
- vtk_object = port_object.vtkInstance
- else:
- raise ModuleError(self, "expected a vtk module")
- if vtk_object:
- self.auto_set_results(vtk_object)
-
- input_ports = [('SetInput',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkDataSetAttributes')]),
- ]
- output_ports = [('GetScalars',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
- ('GetVectors',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
- ('GetNormals',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
- ('GetTCoords',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
- ('GetTensors',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
- ('GetGlobalIds',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')]),
- ('GetPedigreeIds',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkAbstractArray')]),
- ]
-
-class vtkDataArrayInspector(vtkBaseInspector):
-
- def compute(self):
- vtk_object = None
- if self.hasInputFromPort("SetInput"):
- port_object = self.getInputFromPort("SetInput")
- if hasattr(port_object, "vtkInstance"):
- vtk_object = port_object.vtkInstance
- else:
- raise ModuleError(self, "expected a vtk module")
- if vtk_object:
- self.auto_set_results(vtk_object)
-
- input_ports = [('SetInput',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkDataArray')])]
- output_ports = [('GetMaxNorm', [Float]),
- ('GetRange', [Float] * 2)]
-
-class vtkPolyDataInspector(vtkDataSetInspector):
-
- def compute(self):
- vtk_object = None
- if self.hasInputFromPort("SetInputConnection0"):
- ic = self.getInputFromPort("SetInputConnection0")
- port_object = ic.vtkInstance
- ix = port_object.GetIndex()
- producer = port_object.GetProducer()
- try:
- vtk_object = producer.GetOutput()
- except AttributeError:
- raise ModuleError(self,
- "expected a module that supports GetOutput")
- elif self.hasInputFromPort("SetInput"):
- port_object = self.getInputFromPort("SetInput")
- if hasattr(port_object, "vtkInstance"):
- vtk_object = port_object.vtkInstance
- else:
- raise ModuleError(self, "expected a vtk module")
- if vtk_object:
- self.auto_set_results(vtk_object)
-
- input_ports = [('SetInputConnection0',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkAlgorithmOutput')]),
- ('SetInput',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkDataSet')]),
- ]
- output_ports = [('GetVerts',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkCellArray')]),
- ('GetLines',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkCellArray')]),
- ('GetPolys',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkCellArray')]),
- ('GetStrips',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkCellArray')]),
- ('GetPoints',
- [('edu.utah.sci.vistrails.vtksnl', 'vtkPoints')]),
- ('GetNumberOfVerts', [Integer]),
- ('GetNumberOfLines', [Integer]),
- ('GetNumberOfPolys', [Integer]),
- ('GetNumberOfStrips', [Integer]),
- ]
-
-def initialize():
- vtkBaseInspector.register_self(abstract=True, signatureCallable=vtk_hasher)
- vtkDataSetInspector.register_self(abstract=False,
- signatureCallable=vtk_hasher)
- vtkDataSetAttributesInspector.register_self(abstract=False,
- signatureCallable=vtk_hasher)
- vtkDataArrayInspector.register_self(abstract=False,
- signatureCallable=vtk_hasher)
- vtkPolyDataInspector.register_self(abstract=False,
- signatureCallable=vtk_hasher)
-
diff --git a/contrib/vtksnl/offscreen.py b/contrib/vtksnl/offscreen.py
deleted file mode 100644
index 508baa3..0000000
--- a/contrib/vtksnl/offscreen.py
+++ /dev/null
@@ -1,62 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-import vtksnl
-from core.modules.module_registry import get_module_registry
-from core.modules.vistrails_module import Module
-from core.modules.basic_modules import File, Integer
-
-class VTKRenderOffscreen(Module):
-
- def compute(self):
- r = self.getInputFromPort("renderer").vtkInstance
- window = vtksnl.vtkRenderWindow()
- w = self.forceGetInputFromPort("width", 512)
- h = self.forceGetInputFromPort("height", 512)
- window.OffScreenRenderingOn()
- window.SetSize(w, h)
- # r.ResetCamera()
- window.AddRenderer(r)
- window.Start()
- window.Render()
- win2image = vtksnl.vtkWindowToImageFilter()
- win2image.SetInput(window)
- win2image.Update()
- writer = vtksnl.vtkPNGWriter()
- writer.SetInput(win2image.GetOutput())
- output = self.interpreter.filePool.create_file(suffix='.png')
- writer.SetFileName(output.name)
- writer.Write()
- window.Finalize()
- self.setResult("image", output)
-
-def register_self():
- registry = get_module_registry()
- r = registry.get_descriptor_by_name(
- 'edu.utah.sci.vistrails.vtksnl',
- 'vtkRenderer').module
- registry.add_module(VTKRenderOffscreen)
- registry.add_input_port(VTKRenderOffscreen, 'renderer', r)
- registry.add_input_port(VTKRenderOffscreen, 'width', Integer)
- registry.add_input_port(VTKRenderOffscreen, 'height', Integer)
- registry.add_output_port(VTKRenderOffscreen, 'image', File)
-
diff --git a/contrib/vtksnl/tf_widget.py b/contrib/vtksnl/tf_widget.py
deleted file mode 100644
index 7ad6838..0000000
--- a/contrib/vtksnl/tf_widget.py
+++ /dev/null
@@ -1,575 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-
-##############################################################################
-# Transfer Function Widget for VTK
-
-from PyQt4 import QtCore, QtGui
-from core.modules.constant_configuration import ConstantWidgetMixin
-from core.modules.basic_modules import new_constant, init_constant, Module
-from core.utils.color import ColorByName
-import vtksnl
-import math
-import pickle
-import copy
-
-################################################################################
-# etc
-
-def clamp(v, mn, mx, eps=0.0):
- mn += eps
- mx -= eps
- if v < mn: return mn
- if v > mx: return mx
- return v
-
-##############################################################################
-# Transfer Function object
-
-class TransferFunction(object):
-
- def __init__(self):
- self._min_range = 0.0
- self._max_range = 1.0
- self._pts = []
-
- def set_range(self, mn, mx):
- self._min_range = mn
- self._max_range = mx
-
- def set_on_vtk_volume_property(self, vtk_volume_property):
- # Builds the opacity and color functions
- of = vtksnl.vtkPiecewiseFunction()
- cf = vtksnl.vtkColorTransferFunction()
- vp = vtk_volume_property
- for pt in self._pts:
- (scalar, opacity, color) = pt
- # Map scalar to tf range
- s = self._min_range + (self._max_range - self._min_range) * scalar
- of.AddPoint(s, opacity)
- cf.AddRGBPoint(s, color[0], color[1], color[2])
- vp.SetScalarOpacity(of)
- vp.SetColor(cf)
-
- def add_point(self, scalar, opacity, color):
- self._pts.append((scalar, opacity, color))
- self._pts.sort()
-
- def get_value(self, scalar):
- """get_value(scalar): returns the opacity and color
- linearly interpolated at the value. Useful for
- adding knots."""
- ix = 0
- while ix < len(self._pts) and self._pts[ix][0] > scalar:
- ix += 1
- if ix == 0:
- return (self._pts[0][1], self._pts[0][2])
- elif ix == len(self._pts):
- return (self._pts[-1][1], self._pts[-1][2])
- else:
- u = ((self._pts[ix][0] - scalar) /
- (self._pts[ix][0] - self._pts[ix-1][0]))
- do = self._pts[ix][1] - self._pts[ix-1][1]
- dr = self._pts[ix][2][0] - self._pts[ix-1][2][0]
- dg = self._pts[ix][2][1] - self._pts[ix-1][2][1]
- db = self._pts[ix][2][2] - self._pts[ix-1][2][2]
- return (self._pts[ix-1][1] + u * do,
- (self._pts[ix-1][2][0] + u * dr,
- self._pts[ix-1][2][1] + u * dg,
- self._pts[ix-1][2][2] + u * db))
-
- def __copy__(self):
- result = TransferFunction()
- result._min_range = self._min_range
- result._max_range = self._max_range
- result._pts = copy.copy(self._pts)
- return result
-
- def __eq__(self, other):
- if type(other) != type(self):
- return False
- if self._min_range != other._min_range:
- return False
- if self._max_range != other._max_range:
- return False
- for my_pt, other_pt in zip(self._pts, other._pts):
- if my_pt != other_pt:
- return False
- return True
-
- def __ne__(self, other):
- return not self.__eq__(other)
-
-##############################################################################
-# Graphics Items
-
-class TransferFunctionPoint(QtGui.QGraphicsEllipseItem):
-
- selection_pens = { True: QtGui.QPen(QtGui.QBrush(
- QtGui.QColor(*(ColorByName.get_int('goldenrod_medium')))),0.012),
- False: QtGui.QPen() }
-
- def __init__(self, scalar, opacity, color, parent=None):
- QtGui.QGraphicsEllipseItem.__init__(self, parent)
- self._scalar = scalar
- self._opacity = opacity
- self._color = QtGui.QColor(color[0]*255,
- color[1]*255,
- color[2]*255)
- self.setPen(QtGui.QPen(QtGui.QColor(0,0,0)))
- self.setFlag(QtGui.QGraphicsItem.ItemIsMovable)
- self.setFlag(QtGui.QGraphicsItem.ItemIsSelectable)
- self.setFlag(QtGui.QGraphicsItem.ItemIsFocusable)
- self.setZValue(2.0)
-
- self._sx = 1.0
- self._sy = 1.0
- self._left_line = None
- self._right_line = None
- self._point = QtCore.QPointF(scalar, opacity)
- self.refresh()
-
- self.setToolTip("Double-click to change color\n"
- "Right-click to remove point\n"
- "Scalar: %.5f, Opacity: %.5f" % (self._scalar,
- self._opacity))
- # This sets up the linked list of Lines
-
- def keyPressEvent(self, event):
- if event.key() == QtCore.Qt.Key_Backspace or \
- event.key() == QtCore.Qt.Key_Delete:
- self.remove_self()
-
- def refresh(self):
- dx = 0.025 / self._sx
- dy = 0.025 / self._sy
- # this is the setup
- self.setBrush(QtGui.QBrush(self._color))
- self.setRect(-dx,
- -dy,
- 2 * dx, 2 * dy)
- self.setPos(self._scalar,
- self._opacity)
-
- def update_scale(self, sx, sy):
- self._sx = sx
- self._sy = sy
- self.refresh()
-
- def itemChange(self, change, value):
- if change == QtGui.QGraphicsItem.ItemSelectedChange:
- self.setPen(self.selection_pens[value.toBool()])
- if change == QtGui.QGraphicsItem.ItemPositionChange:
- # moves point
- pt = value.toPointF()
- pt.setY(clamp(pt.y(), 0.0, 1.0))
- self._opacity = pt.y()
- self._point.setY(pt.y())
- if not self._left_line:
- pt.setX(0.0)
- elif not self._right_line:
- pt.setX(1.0)
- else:
- assert self._left_line._point_right == self
- assert self._right_line._point_left == self
- pt.setX(clamp(pt.x(),
- self._left_line._point_left._point.x(),
- self._right_line._point_right._point.x(),
- 1e-6))
- self._point.setX(pt.x())
- self._scalar = pt.x()
- if self._left_line:
- self._left_line.refresh()
- if self._right_line:
- self._right_line.refresh()
- if self.scene():
- self.scene()._tf_poly.setup()
- self.setToolTip("Double-click to change color\n"
- "Right-click to remove point\n"
- "Scalar: %.5f, Opacity: %.5f" % (self._scalar,
- self._opacity))
- return QtGui.QGraphicsItem.itemChange(self, change,
- QtCore.QVariant(pt))
- return QtGui.QGraphicsItem.itemChange(self, change, value)
-
- def remove_self(self):
- if not self._left_line or not self._right_line:
- # Ignore, self is a corner node that can't be removed
- return
-
- # Removes the right line and self, re-ties data structure
- self._left_line._point_right = self._right_line._point_right
- self._left_line._point_right._left_line = self._left_line
-
- # be friends with garbage collector
- self._right_line._point_left = None
- self._right_line._point_right = None
- self.scene()._tf_poly.setup()
- self.scene().removeItem(self._right_line)
- self.scene().removeItem(self)
- self._left_line.refresh()
-
- def mouseDoubleClickEvent(self, event):
- new_color = QtGui.QColorDialog.getColor(self._color)
- if not new_color.isValid():
- return
- self._color = new_color
- if self._left_line:
- self._left_line.refresh()
- if self._right_line:
- self._right_line.refresh()
- self.refresh()
- self.scene()._tf_poly.setup()
-
- def mousePressEvent(self, event):
- if event.button() == QtCore.Qt.RightButton:
- event.accept()
- self.remove_self()
- else:
- QtGui.QGraphicsEllipseItem.mousePressEvent(self, event)
-
- def add_self_to_transfer_function(self, tf):
- tf.add_point(self._scalar,
- self._opacity,
- (self._color.redF(),
- self._color.greenF(),
- self._color.blueF()))
-
-class TransferFunctionPolygon(QtGui.QGraphicsPolygonItem):
-
- def __init__(self):
- QtGui.QGraphicsPolygonItem.__init__(self)
-
- def setup(self):
- # This inspects the scene, finds the left-most point, and
- # then builds the polygon traversing the linked list structure
- if not self.scene():
- return
- pt = self.scene().get_leftmost_point()
- first_pt = pt
- self.setZValue(1.25)
- g = QtGui.QLinearGradient()
- g.setStart(0.0, 0.5)
- g.setFinalStop(1.0, 0.5)
- p = QtGui.QPen()
- p.setStyle(QtCore.Qt.NoPen)
- pts = [QtCore.QPointF(pt.x(), 0)]
- self.setPen(p)
-
- while 1:
- c = QtGui.QColor(pt._color)
- c.setAlphaF(pt._opacity)
- g.setColorAt(pt._scalar, c)
- pts.append(pt._point)
- # move cursor fwd
- if pt._right_line:
- pt = pt._right_line._point_right
- else:
- break
- self.setBrush(QtGui.QBrush(g))
- pts.append(QtCore.QPointF(pt.x(), 0))
- self.setPolygon(QtGui.QPolygonF(pts))
-
-class TransferFunctionLine(QtGui.QGraphicsPolygonItem):
-
- def __init__(self, point_left, point_right, parent=None):
- assert point_right._scalar >= point_left._scalar
- QtGui.QGraphicsPolygonItem.__init__(self, parent)
- self._point_left = point_left
- self._point_right = point_right
- self._point_left._right_line = self
- self._point_right._left_line = self
- self.setup(1.0, 1.0)
- self._sx = 1.0
- self._sy = 1.0
-
- def setup(self, sx, sy):
- d = self._point_right._point - self._point_left._point
- d_normal = QtCore.QPointF(d.y(), -d.x())
- l = math.sqrt(d.x() * d.x() + d.y() * d.y())
- if l != 0.0:
- d_normal /= l
- d_normal *= 0.010
- d_normal.setX(d_normal.x() / sx)
- d_normal.setY(d_normal.y() / sy)
- ps = [self._point_left._point + d_normal,
- self._point_right._point + d_normal,
- self._point_right._point - d_normal,
- self._point_left._point - d_normal]
- self.setPolygon(QtGui.QPolygonF(ps))
- self.setZValue(1.5)
- # Gradient for filling
- g = QtGui.QLinearGradient()
- g.setStart(self._point_left._point)
- g.setFinalStop(self._point_right._point)
- g.setColorAt(0.0, self._point_left._color)
- g.setColorAt(1.0, self._point_right._color)
- self.setBrush(QtGui.QBrush(g))
- # Gradient for outlining
- g = QtGui.QLinearGradient()
- g.setStart(self._point_left._point)
- g.setFinalStop(self._point_right._point)
- dark_pl = QtGui.QColor(self._point_left._color.red() * 0.5,
- self._point_left._color.green() * 0.5,
- self._point_left._color.blue() * 0.5)
- dark_pr = QtGui.QColor(self._point_right._color.red() * 0.5,
- self._point_right._color.green() * 0.5,
- self._point_right._color.blue() * 0.5)
- g.setColorAt(0.0, dark_pl)
- g.setColorAt(1.0, dark_pr)
- p = QtGui.QPen()
- p.setBrush(QtGui.QBrush(g))
- self.setPen(p)
-
- def update_scale(self, sx, sy):
- self._sx = sx
- self._sy = sy
- self.refresh()
-
- def refresh(self):
- self.setup(self._sx, self._sy)
-
- def mouseDoubleClickEvent(self, event):
- p = event.scenePos()
- c_left = self._point_left._color
- c_right = self._point_right._color
- u = ((p.x() - self._point_left._point.x()) /
- (self._point_right._point.x() - self._point_left._point.x()))
- new_c = (u * c_right.redF() + (1-u) * c_left.redF(),
- u * c_right.greenF() + (1-u) * c_left.greenF(),
- u * c_right.blueF() + (1-u) * c_left.blueF())
- new_point = TransferFunctionPoint(p.x(), p.y(), new_c)
- new_line = TransferFunctionLine(new_point, self._point_right)
- new_point._left_line = self
- self._point_right = new_point
- self.scene().addItem(new_line)
- self.scene().addItem(new_point)
- new_line.update_scale(self._point_left._sx,
- self._point_left._sy)
- new_point.update_scale(self._point_left._sx,
- self._point_left._sy)
- new_point.refresh()
- self.refresh()
-
- def mousePressEvent(self, event):
- # This needs to be here, otherwise mouseDoubleClickEvent does
- # not get called.
- event.accept()
-
-
-##############################################################################
-# Scene, view, widget
-
-class TransferFunctionScene(QtGui.QGraphicsScene):
-
- def __init__(self, tf, parent=None):
- QtGui.QGraphicsScene.__init__(self, parent)
- self._tf_items = []
- poly = TransferFunctionPolygon()
- poly.setup()
- self._tf_poly = poly
- self.addItem(poly)
- self.create_tf_items(tf)
- #current scale
- self._sx = 1.0
- self._sy = 1.0
- # Add outlines
- line_color = QtGui.QColor(200, 200, 200)
- pen = QtGui.QPen(line_color)
- ps = [QtCore.QPointF(0.0, 0.0),
- QtCore.QPointF(1.0, 0.0),
- QtCore.QPointF(1.0, 1.0),
- QtCore.QPointF(0.0, 1.0)]
- outline = QtGui.QPolygonF(ps)
- self.addPolygon(outline, pen)
-
- for i in xrange(51):
- u = float(i) / 50.0
- self.addLine(QtCore.QLineF(u, 0.0, u, 1.0), pen)
- self.addLine(QtCore.QLineF(0.0, u, 1.0, u), pen)
-
- def reset_transfer_function(self, tf):
- self.create_tf_items(tf)
- self.update_scale(self._sx, self._sy)
- self._tf_poly.setup()
-
- def removeItem(self, item):
- if item in self._tf_items:
- self._tf_items.remove(item)
- QtGui.QGraphicsScene.removeItem(self, item)
-
- def addItem(self, item):
- # Ugly, but hey
- if isinstance(item, TransferFunctionLine) or \
- isinstance(item, TransferFunctionPoint):
- self._tf_items.append(item)
- QtGui.QGraphicsScene.addItem(self, item)
-
- def create_tf_items(self, tf):
- items = copy.copy(self._tf_items)
- for item in items:
- self.removeItem(item)
- self._tf_items = []
- if len(tf._pts) == 0:
- pt_left = TransferFunctionPoint(0.0, 0.0, (0.0, 0.0, 0.0))
- pt_right = TransferFunctionPoint(1.0, 0.0, (0.0, 0.0, 0.0))
- line = TransferFunctionLine(pt_left, pt_right)
-
- self.addItem(pt_left)
- self.addItem(pt_right)
- self.addItem(line)
-
- else:
- pts = [TransferFunctionPoint(*pt)
- for pt in tf._pts]
- lines = [TransferFunctionLine(pt_l, pt_r)
- for (pt_l, pt_r) in zip(pts[:-1], pts[1:])]
- for pt in pts:
- self.addItem(pt)
- for line in lines:
- self.addItem(line)
-
- def add_knot(self, scalar, opacity):
- pass
-
- def update_scale(self, sx, sy):
- for item in self._tf_items:
- item.update_scale(sx, sy)
- self._sx = sx
- self._sy = sy
-
- def get_leftmost_point(self):
- pt = None
-
- for item in self._tf_items:
- if hasattr(item, '_left_line') and not item._left_line:
- pt = item
- break
- assert pt
- return pt
-
- def get_transfer_function(self):
- result = TransferFunction()
- pt = self.get_leftmost_point()
- while 1:
- pt.add_self_to_transfer_function(result)
- if pt._right_line:
- pt = pt._right_line._point_right
- else:
- break
- return result
-
-class TransferFunctionView(QtGui.QGraphicsView):
- def __init__(self, parent=None):
- QtGui.QGraphicsView.__init__(self, parent)
- self.setRenderHint(QtGui.QPainter.Antialiasing)
- self.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
- self.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
-
- def resizeEvent(self, event):
- self.setMatrix(QtGui.QMatrix(event.size().width() / (10.0/9), 0,
- 0, -event.size().height() / (10.0/9), 0, 0))
- self.scene().update_scale(event.size().width()/(2000.0/9), event.size().height()/(2000.0/9))
-
- def focusOutEvent(self, event):
- self.parent().update_parent()
- QtGui.QGraphicsView.focusOutEvent(self, event)
-
-default_tf = TransferFunction()
-default_tf.add_point(0.0, 0.0, (0.0, 0.0, 0.0))
-default_tf.add_point(1.0, 0.0, (0.0, 0.0, 0.0))
-
-class TransferFunctionWidget(QtGui.QWidget, ConstantWidgetMixin):
-
- def __init__(self, param, parent=None):
- QtGui.QWidget.__init__(self, parent)
- ConstantWidgetMixin.__init__(self, param.strValue)
- if not param.strValue:
- self._tf = copy.copy(default_tf)
- else:
- self._tf = pickle.loads(param.strValue.decode('hex'))
- self._scene = TransferFunctionScene(self._tf, self)
- layout = QtGui.QVBoxLayout()
- self.setLayout(layout)
- self._view = TransferFunctionView()
- self._view.setScene(self._scene)
- self._view.setMinimumSize(200,200)
- self._view.show()
- self._view.setSizePolicy(QtGui.QSizePolicy.Expanding,
- QtGui.QSizePolicy.Expanding)
- self._view.setMatrix(QtGui.QMatrix(180, 0, 0, -180, 0, 0))
- self.setMinimumSize(200,200)
- caption = QtGui.QLabel("Double-click on the line to add a point")
- font = QtGui.QFont('Arial', 11)
- font.setItalic(True)
- caption.setFont(font)
- layout.addWidget(self._view)
- layout.addWidget(caption)
-
- def contents(self):
- return pickle.dumps(self._scene.get_transfer_function()).encode('hex')
-
- def setContents(self, strValue, silent=True):
- if not strValue:
- self._tf = copy.copy(default_tf)
- else:
- self._tf = pickle.loads(strValue.decode('hex'))
- self._scene.reset_transfer_function(self._tf)
- if not silent:
- self.update_parent()
-
-##############################################################################
-# Helper module to adjust range
-
-class vtkScaledTransferFunction(Module):
-
- def compute(self):
- tf = self.getInputFromPort('TransferFunction')
- new_tf = copy.copy(tf)
- if self.hasInputFromPort('Input'):
- port = self.getInputFromPort('Input')
- algo = port.vtkInstance.GetProducer()
- output = algo.GetOutput(port.vtkInstance.GetIndex())
- (new_tf._min_range, new_tf._max_range) = output.GetScalarRange()
- elif self.hasInputFromPort('Dataset'):
- algo = self.getInputFromPort('Dataset').vtkInstance
- output = algo
- (new_tf._min_range, new_tf._max_range) = output.GetScalarRange()
- else:
- (new_tf._min_range, new_tf._max_range) = self.getInputFromPort('Range')
-
- self.setResult('TransferFunction', new_tf)
-
-string_conversion = staticmethod(lambda x: pickle.dumps(x).encode('hex'))
-conversion = staticmethod(lambda x: pickle.loads(x.decode('hex')))
-validation = staticmethod(lambda x: isinstance(x, TransferFunction))
-TransferFunctionConstant = new_constant('TransferFunction',
- conversion,
- default_tf,
- validation,
- TransferFunctionWidget)
-TransferFunctionConstant.translate_to_string = string_conversion
-
-##############################################################################
-
-def initialize():
- init_constant(TransferFunctionConstant)
diff --git a/contrib/vtksnl/vtk_parser.py b/contrib/vtksnl/vtk_parser.py
deleted file mode 100644
index 1624f09..0000000
--- a/contrib/vtksnl/vtk_parser.py
+++ /dev/null
@@ -1,514 +0,0 @@
-# Author: Prabhu Ramachandran
-# Copyright (c) 2004, Enthought, Inc.
-# License: BSD Style.
-
-# Modified for VisTrails by the VisTrails team.
-
-"""This module parses the VTK methods, obtains the argument and return
-type information, and organizes them.
-
-"""
-
-import re
-import vtksnl
-import class_tree
-import core.debug
-
-log = core.debug.log
-warning = core.debug.warning
-critical = core.debug.critical
-debug = core.debug.debug
-
-class VTKMethodParser(object):
- """This class provides useful methods for parsing methods of a VTK
- class or instance.
-
- The class allows one to categorize the methods of the VTK class
- and also obtain the method signatures in a form that is easy to
- use. When the `parse` method is called, it in turn calls the
- `_organize_methods` method. This method organizes the VTK methods
- into different instance variables described in the following.
- `self.toggle_meths` contains a dictionary of all the boolean
- methods of the form <Value>On/Off. The dictionary keys are
- strings with the <Value>'s and the value of each item is the
- default value (0/1) of the item (the example below will clarify
- this). `self.state_meths` contains a dictionary which collects
- the Set<Prop>To<Value> type of methods. The key is the <Prop> and
- the value is a list containing the different string <Value>'s and
- their corresponding mapped value. The first value in these is the
- default value of the <Prop>. `self.get_set_meths` will contain a
- dictionary which collects all the methods of the form
- Set/Get<Prop> that are not already specified in
- `self.toggle_meths` or `self.state_meths`. The default value of
- the Get<Prop> is stored. If the value accepted by the method has
- a range (via the methods `Get<Prop>MinValue` and
- `Get<Prop>MaxValue`), then that range is computed and stored.
- `self.get_meths` stores the methods that are of the form
- `Get<Prop>`. `self.other_meths` stores the remaining methods.
- The parsing is quite fast. Parsing every class in the VTK API
- takes a couple of seconds (on a Pentium III @ 450Mhz).
-
- Here is an example::
-
- >>> import vtk
- >>> p = VTKMethodParser()
- >>> p.parse(vtk.vtkProperty)
- >>> print p.get_toggle_methods()
- {'EdgeVisibility': 0, 'BackfaceCulling': 0, 'FrontfaceCulling': 0}
- >>> print p.get_state_methods()['Representation']
- [['Surface', 2], ['Points', 0], ['Surface', 2], ['Wireframe', 1]]
- >>> print p.get_get_set_methods()['Opacity']
- (1.0, (0.0, 1.0))
- >>> print p.get_get_methods()
- ['GetClassName']
- >>> print p.get_other_methods()[:3]
- ['BackfaceRender', 'DeepCopy', 'IsA']
-
-
- The class also provides a method called `get_method_signature`
- that obtains the Python method signature given the VTK method
- object. Here is an example::
-
- >>> import vtk
- >>> p = VTKMethodParser()
- >>> o = vtk.vtkProperty
- >>> print p.get_method_signature(o.GetClassName)
- [(['string'], None)]
- >>> print p.get_method_signature(o.GetColor)[0]
- ([('float', 'float', 'float')], None)
- >>> print p.get_method_signature(o.GetColor)[1]
- ([None], (('float', 'float', 'float'),))
-
- The `get_method_signature` is fairly efficient and obtaining the
- signature for every method in every class in the VTK API takes
- around 6 seconds (on a Pentium III @ 450Mhz).
-
- """
-
- def __init__(self, use_tree=True):
- """Initializes the object.
-
- Parameters
- ----------
-
- - use_tree : `bool`
-
- If True (default), use a ClassTree instance to obtain a
- concrete subclass for an abstract base class. This is used
- only to find the range and default values for some of the
- methods. If False, no ClassTree instance is created.
-
- This is optional because, creating a ClassTree is expensive.
- The parser functionality can be very useful even without the
- use of a ClassTree. For example, if one wants to save the
- state of a VTK object one only needs to know the names of
- the methods and not their default values, ranges etc. In
- that case using a parser should be cheap.
-
- """
- # The ClassTree is needed to find an instantiable child class
- # for an abstract VTK parent class. This instance is used to
- # obtain the state values and the ranges of the arguments
- # accepted by the Get/Set methods that have a
- # Get<Prop>{MaxValue,MinValue} method.
- if use_tree:
- self._tree = class_tree.ClassTree(vtksnl)
- self._tree.create()
- else:
- self._tree = None
- self._state_patn = re.compile('To[A-Z0-9]')
- self._initialize()
-
- #################################################################
- # 'VTKMethodParser' interface.
- #################################################################
-
- def parse(self, obj, no_warn=True):
- """Parse the methods for a given VTK object/class.
-
- Given a VTK class or object, this method parses the methods
- and orgaizes them into useful categories. The categories and
- their usage is documented in the documentation for the class.
-
- Parameters
- ----------
-
- - obj : VTK class or instance
-
- - no_warn : `bool` (default: True)
-
- If True (default), it suppresses any warnings generated by
- the VTK object when parsing the methods. This is safe to
- use.
-
- """
- if not hasattr(obj, '__bases__'):
- klass = obj.__class__
- else:
- klass = obj
-
- methods = self.get_methods(klass)
-
- if no_warn:
- # Save warning setting and shut it off before parsing.
- warn = vtksnl.vtkObject.GetGlobalWarningDisplay()
- if klass.__name__ <> 'vtkObject':
- vtksnl.vtkObject.GlobalWarningDisplayOff()
-
- self._organize_methods(klass, methods)
-
- if no_warn:
- # Reset warning status.
- vtksnl.vtkObject.SetGlobalWarningDisplay(warn)
-
- def get_methods(self, klass):
- """Returns all the relevant methods of the given VTK class."""
- methods = dir(klass)[:]
- if hasattr(klass, '__members__'):
- # Only VTK versions < 4.5 have these.
- for m in klass.__members__:
- methods.remove(m)
-
- return methods
-
- def get_toggle_methods(self):
- """Returns a dictionary of the parsed <Value>On/Off methods
- along with the default value.
-
- """
- return self.toggle_meths
-
- def get_state_methods(self):
- """Returns a dict of the parsed Set<Prop>To<Value>.
-
- The keys are the <Prop> string with a list of the different
- <Value> strings along with their corresponding value (if
- obtainable). The first value is the default value of the
- state.
-
- """
- return self.state_meths
-
- def get_get_set_methods(self):
- """Returns a dict of the parsed Get/Set<Value> methods.
-
- The keys of the dict are the <Value> strings and contain a
- two-tuple containing the default value (or None if it is not
- obtainable for some reason) and a pair of numbers specifying
- an acceptable range of values (or None if not obtainable).
-
- """
- return self.get_set_meths
-
- def get_get_methods(self):
- """Return a list of parsed Get<Value> methods.
-
- All of these methods do NOT have a corresponding Set<Value>.
-
- """
- return self.get_meths
-
- def get_other_methods(self):
- """Return list of all other methods, that are not
- categorizable.
-
- """
- return self.other_meths
-
- def get_method_signature(self, method):
- """Returns information on the Python method signature given
- the VTK method.
-
- The doc string of the given method object to get the method
- signature. The method returns a list of tuples, each of which
- contains 2 items, the first is a list representing the return
- value the second represents the arguments to be passed to the
- function. If the method supports different return values and
- arguments, this function returns all of their signatures.
-
- Parameters
- ----------
-
- - method : `method`
-
- A VTK method object.
-
- """
- doc = method.__doc__
- doc = doc[:doc.find('\n\n')]
- sig = doc.split('\n')
- sig = [x.strip() for x in sig]
-
- # Remove all the C++ function signatures.
- for i in sig[:]:
- if i[:4] == 'C++:':
- sig.remove(i)
-
- # Remove the V.<method_name>
- sig = [x.replace('V.' + method.__name__, '') for x in sig]
-
- pat = re.compile(r'\b')
-
- # Split into [return_value, arguments] after processing them.
- tmp = list(sig)
- sig = []
- for i in tmp:
- # Split to get return values.
- x = i.split('->')
- # Strip each part.
- x = [y.strip() for y in x]
-
- if len(x) == 1: # No return value
- x = [None, x[0]]
- else:
- x.reverse()
-
- ret, arg = x
-
- # Remove leading and trailing parens for arguments.
- arg = arg[1:-1]
- if not arg:
- arg = None
- if arg and arg[-1] == ')':
- arg = arg + ','
-
- # Now quote the args and eval them. Easy!
- if ret:
- ret = eval(pat.sub('\"', ret))
- if arg:
- arg = eval(pat.sub('\"', arg))
- if type(arg) == type('str'):
- arg = [arg]
-
- sig.append(([ret], arg))
-
- return sig
-
- def get_tree(self):
- """Return the ClassTree instance used by this class."""
- return self._tree
-
- #################################################################
- # Non-public interface.
- #################################################################
-
- def _initialize(self):
- """Initializes the method categories."""
- # Collects the <Value>On/Off methods.
- self.toggle_meths = {}
- # Collects the Set<Prop>To<Value> methods.
- self.state_meths = {}
- # Collects the Set/Get<Value> pairs.
- self.get_set_meths = {}
- # Collects the Get<Value> methods.
- self.get_meths = []
- # Collects all the remaining methods.
- self.other_meths = []
-
- def _organize_methods(self, klass, methods):
- """Organizes the given methods of a VTK class into different
- categories.
-
- Parameters
- ----------
-
- - klass : A VTK class
-
- - methods : `list` of `str`
-
- A list of the methods to be categorized.
-
- """
- self._initialize()
- meths = methods[:]
- meths = self._find_toggle_methods(klass, meths)
- meths = self._find_state_methods(klass, meths)
- meths = self._find_get_set_methods(klass, meths)
- meths = self._find_get_methods(klass, meths)
- self.other_meths = [x for x in meths if '__' not in x]
-
- def _remove_method(self, meths, method):
- try:
- meths.remove(method)
- except ValueError:
- pass
-
- def _find_toggle_methods(self, klass, methods):
- """Find/store methods of the form <Value>{On,Off} in the given
- `methods`. Returns the remaining list of methods.
-
- """
- meths = methods[:]
- tm = self.toggle_meths
- for method in meths[:]:
- if method[-2:] == 'On':
- key = method[:-2]
- if (key + 'Off') in meths and ('Get' + key) in meths:
- tm[key] = None
- meths.remove(method)
- meths.remove(key + 'Off')
- self._remove_method(meths, 'Set' + key)
- self._remove_method(meths, 'Get' + key)
- # get defaults
- if tm:
- obj = self._get_instance(klass)
- if obj:
- for key in tm:
- try:
- tm[key] = getattr(obj, 'Get%s'%key)()
- except TypeError, e:
- log("Type error during parsing: class %s will not expose method %s " % (klass.__name__, key))
- except AttributeError, e:
- log("Attribute error during parsing: class %s will not expose method %s " % (klass.__name__, key))
- return meths
-
- def _find_state_methods(self, klass, methods):
- """Find/store methods of the form Set<Prop>To<Value> in the
- given `methods`. Returns the remaining list of methods. The
- method also computes the mapped value of the different
- <Values>.
-
- """
- # These ignored ones are really not state methods.
- ignore = ['SetUpdateExtentToWholeExtent']
- meths = methods[:]
- sm = self.state_meths
- for method in meths[:]:
- if method not in ignore and method[:3] == 'Set':
- # Methods of form Set<Prop>To<Value>
- match = self._state_patn.search(method)
- # Second cond. ensures that this is not an accident.
- if match and (('Get'+method[3:]) not in meths):
- key = method[3:match.start()] # The <Prop> part.
- if (('Get' + key) in methods):
- val = method[match.start()+2:] # <Value> part.
- meths.remove(method)
- if sm.has_key(key):
- sm[key].append([val, None])
- else:
- sm[key] = [[val, None]]
- meths.remove('Get'+ key)
- self._remove_method(meths, 'Set'+ key)
- if ('Get' + key + 'MaxValue') in meths:
- meths.remove('Get' + key + 'MaxValue')
- meths.remove('Get' + key + 'MinValue')
- try:
- meths.remove('Get' + key + 'AsString')
- except ValueError:
- pass
-
- # Find the values for each of the states, i.e. find that
- # vtkProperty.SetRepresentationToWireframe() corresponds to
- # vtkProperty.SetRepresentation(1).
- if sm:
- obj = self._get_instance(klass)
- if obj:
- for key, values in sm.items():
- default = getattr(obj, 'Get%s'%key)()
- for x in values[:]:
- try:
- getattr(obj, 'Set%sTo%s'%(key, x[0]))()
- except:
- continue
- val = getattr(obj, 'Get%s'%key)()
- x[1] = val
- if val == default:
- values.insert(0, [x[0], val])
- return meths
-
- def _find_get_set_methods(self, klass, methods):
- """Find/store methods of the form {Get,Set}Prop in the given
- `methods` and returns the remaining list of methods.
-
- Note that it makes sense to call this *after*
- `_find_state_methods` is called in order to avoid incorrect
- duplication. This method also computes the default value and
- the ranges of the arguments (when possible) by using the
- Get<Prop>{MaxValue,MinValue} methods.
-
- """
- meths = methods[:]
- gsm = self.get_set_meths
-
- for method in meths[:]:
- # Methods of the Set/Get form.
- if method in ['Get', 'Set']:
- # This occurs with the vtkInformation class.
- continue
- elif (method[:3] == 'Set') and ('Get' + method[3:]) in methods:
- key = method[3:]
- meths.remove('Set' + key)
- meths.remove('Get' + key)
- if ('Get' + key + 'MaxValue') in meths:
- meths.remove('Get' + key + 'MaxValue')
- meths.remove('Get' + key + 'MinValue')
- gsm[key] = 1
- else:
- gsm[key] = None
-
- # Find the default and range of the values.
- if gsm:
- obj = self._get_instance(klass)
- if obj:
- klass_name = klass.__name__
- for key, value in gsm.items():
- if klass_name == 'vtkPolyData':
- # Evil hack, this class segfaults!
- default = None
- else:
- try:
- default = getattr(obj, 'Get%s'%key)()
- except TypeError:
- default = None
- if value:
- low = getattr(obj, 'Get%sMinValue'%key)()
- high = getattr(obj, 'Get%sMaxValue'%key)()
- gsm[key] = (default, (low, high))
- else:
- gsm[key] = (default, None)
- else:
- # We still might have methods that have a default range.
- for key, value in gsm.items():
- if value == 1:
- gsm[key] = None
-
- return meths
-
- def _find_get_methods(self, klass, methods):
- """Find/store methods of the form Get<Value> in the given
- `methods` and returns the remaining list of methods.
-
- """
- meths = methods[:]
- gm = self.get_meths
- for method in meths[:]:
- if method == 'Get':
- # Occurs with vtkInformation
- continue
- elif method[:3] == 'Get':
- gm.append(method)
- meths.remove(method)
- return meths
-
- def _get_instance(self, klass):
- """Given a VTK class, `klass`, returns an instance of the
- class.
-
- If the class is abstract, it uses the class tree to return an
- instantiable subclass. This is necessary to get the values of
- the 'state' methods and the ranges for the Get/Set methods.
-
- """
- obj = None
- try:
- obj = klass()
- except TypeError:
- if self._tree:
- t = self._tree
- n = t.get_node(klass.__name__)
- for c in n.children:
- obj = self._get_instance(t.get_class(c.name))
- if obj:
- break
- return obj
-
diff --git a/contrib/vtksnl/vtkcell.py b/contrib/vtksnl/vtkcell.py
deleted file mode 100644
index fa61481..0000000
--- a/contrib/vtksnl/vtkcell.py
+++ /dev/null
@@ -1,1094 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-################################################################################
-# File QVTKWidget.py
-# File for displaying a vtkRenderWindow in a Qt's QWidget ported from
-# VTK/GUISupport/QVTK. Combine altogether to a single class: QVTKWidget
-################################################################################
-import vtksnl
-from PyQt4 import QtCore, QtGui
-import sip
-from core import system
-from core.modules.module_registry import get_module_registry
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
-import vtkcell_rc
-import gc
-from gui.qt import qt_super
-import core.db.action
-from core.vistrail.action import Action
-from core.vistrail.port import Port
-from core.vistrail import module
-from core.vistrail import connection
-from core.vistrail.module_function import ModuleFunction
-from core.vistrail.module_param import ModuleParam
-from core.vistrail.location import Location
-from core.modules.vistrails_module import ModuleError
-import copy
-
-################################################################################
-
-class VTKCell(SpreadsheetCell):
- """
- VTKCell is a VisTrails Module that can display vtkRenderWindow inside a cell
-
- """
-
- def __init__(self):
- SpreadsheetCell.__init__(self)
- self.cellWidget = None
-
- def compute(self):
- """ compute() -> None
- Dispatch the vtkRenderer to the actual rendering widget
- """
- renderers = self.forceGetInputListFromPort('AddRenderer')
- renderViews = self.forceGetInputListFromPort('SetRenderView')
- if len(renderViews)>1:
- raise ModuleError(self, 'There can only be one vtkRenderView '
- 'per cell')
- if len(renderViews)==1 and len(renderers)>0:
- raise ModuleError(self, 'Cannot set both vtkRenderView '
- 'and vtkRenderer to a cell')
- renderView = self.forceGetInputFromPort('SetRenderView')
- iHandlers = self.forceGetInputListFromPort('InteractionHandler')
- iStyle = self.forceGetInputFromPort('InteractorStyle')
- picker = self.forceGetInputFromPort('AddPicker')
- self.cellWidget = self.displayAndWait(QVTKWidget, (renderers, renderView, iHandlers, iStyle, picker))
-
-AsciiToKeySymTable = ( None, None, None, None, None, None, None,
- None, None,
- "Tab", None, None, None, None, None, None,
- None, None, None, None, None, None,
- None, None, None, None, None, None,
- None, None, None, None,
- "space", "exclam", "quotedbl", "numbersign",
- "dollar", "percent", "ampersand", "quoteright",
- "parenleft", "parenright", "asterisk", "plus",
- "comma", "minus", "period", "slash",
- "0", "1", "2", "3", "4", "5", "6", "7",
- "8", "9", "colon", "semicolon", "less", "equal",
- "greater", "question",
- "at", "A", "B", "C", "D", "E", "F", "G",
- "H", "I", "J", "K", "L", "M", "N", "O",
- "P", "Q", "R", "S", "T", "U", "V", "W",
- "X", "Y", "Z", "bracketleft",
- "backslash", "bracketright", "asciicircum",
- "underscore",
- "quoteleft", "a", "b", "c", "d", "e", "f", "g",
- "h", "i", "j", "k", "l", "m", "n", "o",
- "p", "q", "r", "s", "t", "u", "v", "w",
- "x", "y", "z", "braceleft", "bar", "braceright",
- "asciitilde", "Delete",
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None)
-
-class QVTKWidget(QCellWidget):
- """
- QVTKWidget is the actual rendering widget that can display
- vtkRenderer inside a Qt QWidget
-
- """
- def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
- """ QVTKWidget(parent: QWidget, f: WindowFlags) -> QVTKWidget
- Initialize QVTKWidget with a toolbar with its own device
- context
-
- """
- QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
-
- self.interacting = None
- self.mRenWin = None
- self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
- self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
- self.setMouseTracking(True)
- self.setFocusPolicy(QtCore.Qt.StrongFocus)
- self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
- QtGui.QSizePolicy.Expanding))
- self.toolBarType = QVTKWidgetToolBar
- self.iHandlers = []
- self.setAnimationEnabled(True)
- self.renderer_maps = {}
-
- def removeObserversFromInteractorStyle(self):
- """ removeObserversFromInteractorStyle() -> None
- Remove all python binding from interactor style observers for
- safely freeing the cell
-
- """
- iren = self.mRenWin.GetInteractor()
- if iren:
- style = iren.GetInteractorStyle()
- style.RemoveObservers("InteractionEvent")
- style.RemoveObservers("EndPickEvent")
- style.RemoveObservers("CharEvent")
- style.RemoveObservers("MouseWheelForwardEvent")
- style.RemoveObservers("MouseWheelBackwardEvent")
-
- def addObserversToInteractorStyle(self):
- """ addObserversToInteractorStyle() -> None
- Assign observer to the current interactor style
-
- """
- iren = self.mRenWin.GetInteractor()
- if iren:
- style = iren.GetInteractorStyle()
- style.AddObserver("InteractionEvent", self.interactionEvent)
- style.AddObserver("EndPickEvent", self.interactionEvent)
- style.AddObserver("CharEvent", self.charEvent)
- style.AddObserver("MouseWheelForwardEvent", self.interactionEvent)
- style.AddObserver("MouseWheelBackwardEvent", self.interactionEvent)
-
- def deleteLater(self):
- """ deleteLater() -> None
- Make sure to free render window resource when
- deallocating. Overriding PyQt deleteLater to free up
- resources
-
- """
- self.renderer_maps = {}
- for ren in self.getRendererList():
- self.mRenWin.RemoveRenderer(ren)
-
- self.removeObserversFromInteractorStyle()
-
- self.updateContents(([], None, [], None, None))
-
- self.SetRenderWindow(None)
-
- QCellWidget.deleteLater(self)
-
- def updateContents(self, inputPorts):
- """ updateContents(inputPorts: tuple)
- Updates the cell contents with new vtkRenderer
-
- """
- renWin = self.GetRenderWindow()
- for iHandler in self.iHandlers:
- if iHandler.observer:
- iHandler.observer.vtkInstance.SetInteractor(None)
- iHandler.clear()
-
- # Remove old renderers first
- oldRenderers = self.getRendererList()
- for renderer in oldRenderers:
- renWin.RemoveRenderer(renderer)
- renderer.SetRenderWindow(None)
- del oldRenderers
-
- (renderers, renderView, self.iHandlers, iStyle, picker) = inputPorts
- if renderView:
- renderView.vtkInstance.SetupRenderWindow(renWin)
- renderers = [renderView.vtkInstance.GetRenderer()]
- self.renderer_maps = {}
- for renderer in renderers:
- if renderView==None:
- vtkInstance = renderer.vtkInstance
- renWin.AddRenderer(vtkInstance)
- self.renderer_maps[vtkInstance] = renderer.moduleInfo['moduleId']
- else:
- vtkInstance = renderer
- if hasattr(vtkInstance, 'IsActiveCameraCreated'):
- if not vtkInstance.IsActiveCameraCreated():
- vtkInstance.ResetCamera()
- else:
- vtkInstance.ResetCameraClippingRange()
-
- iren = renWin.GetInteractor()
- if picker:
- iren.SetPicker(picker.vtkInstance)
-
- # Update interactor style
- self.removeObserversFromInteractorStyle()
- if renderView==None:
- if iStyle==None:
- iStyleInstance = vtksnl.vtkInteractorStyleTrackballCamera()
- else:
- iStyleInstance = iStyle.vtkInstance
- iren.SetInteractorStyle(iStyleInstance)
- self.addObserversToInteractorStyle()
-
- for iHandler in self.iHandlers:
- if iHandler.observer:
- iHandler.observer.vtkInstance.SetInteractor(iren)
- renWin.Render()
-
- # Capture window into history for playback
- # Call this at the end to capture the image after rendering
- QCellWidget.updateContents(self, inputPorts)
-
- def GetRenderWindow(self):
- """ GetRenderWindow() -> vtkRenderWindow
- Return the associated vtkRenderWindow
-
- """
- if not self.mRenWin:
- win = vtksnl.vtkRenderWindow()
- win.DoubleBufferOn()
- self.SetRenderWindow(win)
- del win
-
- return self.mRenWin
-
- def SetRenderWindow(self,w):
- """ SetRenderWindow(w: vtkRenderWindow)
- Set a new render window to QVTKWidget and initialize the
- interactor as well
-
- """
- if w == self.mRenWin:
- return
-
- if self.mRenWin:
- if system.systemType!='Linux':
- self.mRenWin.SetInteractor(None)
- if self.mRenWin.GetMapped():
- self.mRenWin.Finalize()
-
- self.mRenWin = w
-
- if self.mRenWin:
- self.mRenWin.Register(None)
- if self.mRenWin.GetMapped():
- self.mRenWin.Finalize()
- if system.systemType=='Linux':
- try:
- vp = '_%s_void_p' % (hex(int(QtGui.QX11Info.display()))[2:])
- except TypeError:
- #This was change for PyQt4.2
- if isinstance(QtGui.QX11Info.display(),QtGui.Display):
- display = sip.unwrapinstance(QtGui.QX11Info.display())
- vp = '_%s_void_p' % (hex(display)[2:])
- self.mRenWin.SetDisplayId(vp)
- self.resizeWindow(1,1)
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- if self.isVisible():
- self.mRenWin.Start()
-
- if not self.mRenWin.GetInteractor():
- iren = vtksnl.vtkRenderWindowInteractor()
- if system.systemType=='Darwin':
- iren.InstallMessageProcOff()
- iren.SetRenderWindow(self.mRenWin)
- iren.Initialize()
- if system.systemType=='Linux':
- system.XDestroyWindow(self.mRenWin.GetGenericDisplayId(),
- self.mRenWin.GetGenericWindowId())
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- self.resizeWindow(self.width(), self.height())
- self.mRenWin.SetPosition(self.x(), self.y())
-
- def GetInteractor(self):
- """ GetInteractor() -> vtkInteractor
- Return the vtkInteractor control this QVTKWidget
- """
- return self.GetRenderWindow().GetInteractor()
-
- def event(self, e):
- """ event(e: QEvent) -> depends on event type
- Process window and interaction events
-
- """
- if e.type()==QtCore.QEvent.ParentAboutToChange:
- if self.mRenWin:
- if self.mRenWin.GetMapped():
- self.mRenWin.Finalize()
- else:
- if e.type()==QtCore.QEvent.ParentChange:
- if self.mRenWin:
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- if self.isVisible():
- self.mRenWin.Start()
-
- if QtCore.QObject.event(self,e):
- return 1
-
- if e.type() == QtCore.QEvent.KeyPress:
- self.keyPressEvent(e)
- if e.isAccepted():
- return e.isAccepted()
-
- return qt_super(QVTKWidget, self).event(e)
-
- # return QtGui.QWidget.event(self,e)
- # Was this right? Wasn't this supposed to be QCellWidget.event()?
-
- def resizeWindow(self, width, height):
- """ resizeWindow(width: int, height: int) -> None
- Work around vtk bugs for resizing window
-
- """
- ########################################################
- # VTK - BUGGGGGGGGG - GRRRRRRRRR
- # This is a 'bug' in vtkWin32OpenGLRenderWindow(.cxx)
- # If a render window is mapped to screen, the actual
- # window size is the client area of the window in Win32.
- # However, this real window size is only updated through
- # vtkWin32OpenGLRenderWindow::GetSize(). So this has to
- # be called here to get the cell size correctly. This
- # invalidates the condition in the next SetSize().
- # We can use self.mRenWin.SetSize(0,0) here but it will
- # cause flickering and decrease performance!
- # SetPosition(curX,curY) also works here but slower.
- self.mRenWin.GetSize()
-
- self.mRenWin.SetSize(width, height)
- if self.mRenWin.GetInteractor():
- self.mRenWin.GetInteractor().SetSize(width, height)
-
- def resizeEvent(self, e):
- """ resizeEvent(e: QEvent) -> None
- Re-adjust the vtkRenderWindow size then QVTKWidget resized
-
- """
- qt_super(QVTKWidget, self).resizeEvent(e)
- if not self.mRenWin:
- return
-
- self.resizeWindow(self.width(), self.height())
- self.mRenWin.Render()
-
- def moveEvent(self,e):
- """ moveEvent(e: QEvent) -> None
- Echo the move event into vtkRenderWindow
-
- """
- qt_super(QVTKWidget, self).moveEvent(e)
- if not self.mRenWin:
- return
-
- self.mRenWin.SetPosition(self.x(),self.y())
-
- def paintEvent(self, e):
- """ paintEvent(e: QPaintEvent) -> None
- Paint the QVTKWidget with vtkRenderWindow
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- if hasattr(self.mRenWin, 'UpdateGLRegion'):
- self.mRenWin.UpdateGLRegion()
- self.mRenWin.Render()
-
- def SelectActiveRenderer(self,iren):
- """ SelectActiveRenderer(iren: vtkRenderWindowIteractor) -> None
- Only make the vtkRenderer below the mouse cursor active
-
- """
- epos = iren.GetEventPosition()
- rens = iren.GetRenderWindow().GetRenderers()
- rens.InitTraversal()
- for i in xrange(rens.GetNumberOfItems()):
- ren = rens.GetNextItem()
- ren.SetInteractive(ren.IsInViewport(epos[0], epos[1]))
-
- def mousePressEvent(self,e):
- """ mousePressEvent(e: QMouseEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- isDoubleClick = e.type()==QtCore.QEvent.MouseButtonDblClick
- iren.SetEventInformationFlipY(e.x(),e.y(),
- ctrl,
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),
- isDoubleClick,
- None)
- invoke = {QtCore.Qt.LeftButton:"LeftButtonPressEvent",
- QtCore.Qt.MidButton:"MiddleButtonPressEvent",
- QtCore.Qt.RightButton:"RightButtonPressEvent"}
-
- self.SelectActiveRenderer(iren)
-
- if ctrl:
- e.ignore()
- return
-
- self.interacting = self.getActiveRenderer(iren)
-
- if e.button() in invoke:
- iren.InvokeEvent(invoke[e.button()])
-
- def mouseMoveEvent(self,e):
- """ mouseMoveEvent(e: QMouseEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0), 0, None)
-
- iren.InvokeEvent("MouseMoveEvent")
-
- def enterEvent(self,e):
- """ enterEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.InvokeEvent("EnterEvent")
-
- def leaveEvent(self,e):
- """ leaveEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.InvokeEvent("LeaveEvent")
-
- def mouseReleaseEvent(self,e):
- """ mouseReleaseEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),0,None)
-
- invoke = {QtCore.Qt.LeftButton:"LeftButtonReleaseEvent",
- QtCore.Qt.MidButton:"MiddleButtonReleaseEvent",
- QtCore.Qt.RightButton:"RightButtonReleaseEvent"}
-
- self.interacting = None
-
- if e.button() in invoke:
- iren.InvokeEvent(invoke[e.button()])
-
- def keyPressEvent(self,e):
- """ keyPressEvent(e: QKeyEvent) -> None
- Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ascii_key = None
- if e.text().length()>0:
- ascii_key = e.text().toLatin1()[0]
- else:
- ascii_key = chr(0)
-
- keysym = self.ascii_to_key_sym(ord(ascii_key))
-
- if not keysym:
- keysym = self.qt_key_to_key_sym(e.key())
-
- # Ignore 'q' or 'e' or Ctrl-anykey
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
- if (keysym in ['q', 'e'] or ctrl):
- e.ignore()
- return
-
- iren.SetKeyEventInformation(ctrl,shift,ascii_key, e.count(), keysym)
-
- iren.InvokeEvent("KeyPressEvent")
-
- if ascii_key:
- iren.InvokeEvent("CharEvent")
-
-
- def keyReleaseEvent(self,e):
- """ keyReleaseEvent(e: QKeyEvent) -> None
- Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ascii_key = None
- if e.text().length()>0:
- ascii_key = e.text().toLatin1()[0]
- else:
- ascii_key = chr(0)
-
- keysym = self.ascii_to_key_sym(ord(ascii_key))
-
- if not keysym:
- keysym = self.qt_key_to_key_sym(e.key())
-
- # Ignore 'q' or 'e' or Ctrl-anykey
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
- if (keysym in ['q','e'] or ctrl):
- e.ignore()
- return
-
- iren.SetKeyEventInformation(ctrl, shift, ascii_key, e.count(), keysym)
-
- iren.InvokeEvent("KeyReleaseEvent")
-
- def wheelEvent(self,e):
- """ wheelEvent(e: QWheelEvent) -> None
- Zoom in/out while scrolling the mouse
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),0,None)
-
- self.SelectActiveRenderer(iren)
-
- if e.delta()>0:
- iren.InvokeEvent("MouseWheelForwardEvent")
- else:
- iren.InvokeEvent("MouseWheelBackwardEvent")
-
- def focusInEvent(self,e):
- """ focusInEvent(e: QFocusEvent) -> None
- Ignore focus event
-
- """
- pass
-
- def focusOutEvent(self,e):
- """ focusOutEvent(e: QFocusEvent) -> None
- Ignore focus event
-
- """
- pass
-
- def contextMenuEvent(self,e):
- """ contextMenuEvent(e: QContextMenuEvent) -> None
- Make sure to get the right mouse position for the context menu
- event, i.e. also the right click
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ctrl = int(e.modifiers()&QtCore.Qt.ControlModifier)
- shift = int(e.modifiers()&QtCore.Qt.ShiftModifier)
- iren.SetEventInformationFlipY(e.x(),e.y(),ctrl,shift,chr(0),0,None)
- iren.InvokeEvent("ContextMenuEvent")
-
- def ascii_to_key_sym(self,i):
- """ ascii_to_key_sym(i: int) -> str
- Convert ASCII code into key name
-
- """
- global AsciiToKeySymTable
- return AsciiToKeySymTable[i]
-
- def qt_key_to_key_sym(self,i):
- """ qt_key_to_key_sym(i: QtCore.Qt.Keycode) -> str
- Convert Qt key code into key name
-
- """
- handler = {QtCore.Qt.Key_Backspace:"BackSpace",
- QtCore.Qt.Key_Tab:"Tab",
- QtCore.Qt.Key_Backtab:"Tab",
- QtCore.Qt.Key_Return:"Return",
- QtCore.Qt.Key_Enter:"Return",
- QtCore.Qt.Key_Shift:"Shift_L",
- QtCore.Qt.Key_Control:"Control_L",
- QtCore.Qt.Key_Alt:"Alt_L",
- QtCore.Qt.Key_Pause:"Pause",
- QtCore.Qt.Key_CapsLock:"Caps_Lock",
- QtCore.Qt.Key_Escape:"Escape",
- QtCore.Qt.Key_Space:"space",
- QtCore.Qt.Key_End:"End",
- QtCore.Qt.Key_Home:"Home",
- QtCore.Qt.Key_Left:"Left",
- QtCore.Qt.Key_Up:"Up",
- QtCore.Qt.Key_Right:"Right",
- QtCore.Qt.Key_Down:"Down",
- QtCore.Qt.Key_SysReq:"Snapshot",
- QtCore.Qt.Key_Insert:"Insert",
- QtCore.Qt.Key_Delete:"Delete",
- QtCore.Qt.Key_Help:"Help",
- QtCore.Qt.Key_0:"0",
- QtCore.Qt.Key_1:"1",
- QtCore.Qt.Key_2:"2",
- QtCore.Qt.Key_3:"3",
- QtCore.Qt.Key_4:"4",
- QtCore.Qt.Key_5:"5",
- QtCore.Qt.Key_6:"6",
- QtCore.Qt.Key_7:"7",
- QtCore.Qt.Key_8:"8",
- QtCore.Qt.Key_9:"9",
- QtCore.Qt.Key_A:"a",
- QtCore.Qt.Key_B:"b",
- QtCore.Qt.Key_C:"c",
- QtCore.Qt.Key_D:"d",
- QtCore.Qt.Key_E:"e",
- QtCore.Qt.Key_F:"f",
- QtCore.Qt.Key_G:"g",
- QtCore.Qt.Key_H:"h",
- QtCore.Qt.Key_I:"i",
- QtCore.Qt.Key_J:"h",
- QtCore.Qt.Key_K:"k",
- QtCore.Qt.Key_L:"l",
- QtCore.Qt.Key_M:"m",
- QtCore.Qt.Key_N:"n",
- QtCore.Qt.Key_O:"o",
- QtCore.Qt.Key_P:"p",
- QtCore.Qt.Key_Q:"q",
- QtCore.Qt.Key_R:"r",
- QtCore.Qt.Key_S:"s",
- QtCore.Qt.Key_T:"t",
- QtCore.Qt.Key_U:"u",
- QtCore.Qt.Key_V:"v",
- QtCore.Qt.Key_W:"w",
- QtCore.Qt.Key_X:"x",
- QtCore.Qt.Key_Y:"y",
- QtCore.Qt.Key_Z:"z",
- QtCore.Qt.Key_Asterisk:"asterisk",
- QtCore.Qt.Key_Plus:"plus",
- QtCore.Qt.Key_Minus:"minus",
- QtCore.Qt.Key_Period:"period",
- QtCore.Qt.Key_Slash:"slash",
- QtCore.Qt.Key_F1:"F1",
- QtCore.Qt.Key_F2:"F2",
- QtCore.Qt.Key_F3:"F3",
- QtCore.Qt.Key_F4:"F4",
- QtCore.Qt.Key_F5:"F5",
- QtCore.Qt.Key_F6:"F6",
- QtCore.Qt.Key_F7:"F7",
- QtCore.Qt.Key_F8:"F8",
- QtCore.Qt.Key_F9:"F9",
- QtCore.Qt.Key_F10:"F10",
- QtCore.Qt.Key_F11:"F11",
- QtCore.Qt.Key_F12:"F12",
- QtCore.Qt.Key_F13:"F13",
- QtCore.Qt.Key_F14:"F14",
- QtCore.Qt.Key_F15:"F15",
- QtCore.Qt.Key_F16:"F16",
- QtCore.Qt.Key_F17:"F17",
- QtCore.Qt.Key_F18:"F18",
- QtCore.Qt.Key_F19:"F19",
- QtCore.Qt.Key_F20:"F20",
- QtCore.Qt.Key_F21:"F21",
- QtCore.Qt.Key_F22:"F22",
- QtCore.Qt.Key_F23:"F23",
- QtCore.Qt.Key_F24:"F24",
- QtCore.Qt.Key_NumLock:"Num_Lock",
- QtCore.Qt.Key_ScrollLock:"Scroll_Lock"}
- if i in handler:
- return handler[i]
- else:
- return "None"
-
- def getRendererList(self):
- """ getRendererList() -> list
- Return a list of vtkRenderer running in this QVTKWidget
- """
- result = []
- renWin = self.GetRenderWindow()
- renderers = renWin.GetRenderers()
- renderers.InitTraversal()
- for i in xrange(renderers.GetNumberOfItems()):
- result.append(renderers.GetNextItem())
- return result
-
- def getActiveRenderer(self, iren):
- """ getActiveRenderer(iren: vtkRenderWindowwInteractor) -> vtkRenderer
- Return the active vtkRenderer under mouse
-
- """
- epos = list(iren.GetEventPosition())
- if epos[1]<0:
- epos[1] = -epos[1]
- rens = iren.GetRenderWindow().GetRenderers()
- rens.InitTraversal()
- for i in xrange(rens.GetNumberOfItems()):
- ren = rens.GetNextItem()
- if ren.IsInViewport(epos[0], epos[1]):
- return ren
- return None
-
- def findSheetTabWidget(self):
- """ findSheetTabWidget() -> QTabWidget
- Find and return the sheet tab widget
-
- """
- p = self.parent()
- while p:
- if hasattr(p, 'isSheetTabWidget'):
- if p.isSheetTabWidget()==True:
- return p
- p = p.parent()
- return None
-
- def getRenderersInCellList(self, sheet, cells):
- """ isRendererIn(sheet: spreadsheet.StandardWidgetSheet,
- cells: [(int,int)]) -> bool
- Get the list of renderers in side a list of (row, column)
- cells.
-
- """
- rens = []
- for (row, col) in cells:
- cell = sheet.getCell(row, col)
- if hasattr(cell, 'getRendererList'):
- rens += cell.getRendererList()
- return rens
-
- def getSelectedCellWidgets(self):
- sheet = self.findSheetTabWidget()
- if sheet:
- iren = self.mRenWin.GetInteractor()
- ren = self.interacting
- if not ren: ren = self.getActiveRenderer(iren)
- if ren:
- cells = sheet.getSelectedLocations()
- if (ren in self.getRenderersInCellList(sheet, cells)):
- return [sheet.getCell(row, col)
- for (row, col) in cells
- if hasattr(sheet.getCell(row, col),
- 'getRendererList')]
- return []
-
- def interactionEvent(self, istyle, name):
- """ interactionEvent(istyle: vtkInteractorStyle, name: str) -> None
- Make sure interactions sync across selected renderers
-
- """
- if name=='MouseWheelForwardEvent':
- istyle.OnMouseWheelForward()
- if name=='MouseWheelBackwardEvent':
- istyle.OnMouseWheelBackward()
- ren = self.interacting
- if not ren:
- ren = self.getActiveRenderer(istyle.GetInteractor())
- if ren:
- cam = ren.GetActiveCamera()
- cpos = cam.GetPosition()
- cfol = cam.GetFocalPoint()
- cup = cam.GetViewUp()
- for cell in self.getSelectedCellWidgets():
- if cell!=self and hasattr(cell, 'getRendererList'):
- rens = cell.getRendererList()
- for r in rens:
- if r!=ren:
- dcam = r.GetActiveCamera()
- dcam.SetPosition(cpos)
- dcam.SetFocalPoint(cfol)
- dcam.SetViewUp(cup)
- r.ResetCameraClippingRange()
- cell.update()
-
- def charEvent(self, istyle, name):
- """ charEvent(istyle: vtkInteractorStyle, name: str) -> None
- Make sure key presses also sync across selected renderers
-
- """
- iren = istyle.GetInteractor()
- ren = self.interacting
- if not ren: ren = self.getActiveRenderer(iren)
- if ren:
- keyCode = iren.GetKeyCode()
- if keyCode in ['w','W','s','S','r','R','p','P']:
- for cell in self.getSelectedCellWidgets():
- if hasattr(cell, 'GetInteractor'):
- selectedIren = cell.GetInteractor()
- selectedIren.SetKeyCode(keyCode)
- selectedIren.GetInteractorStyle().OnChar()
- selectedIren.Render()
- istyle.OnChar()
-
- def saveToPNG(self, filename):
- """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
-
- Save the current widget contents to an image file. If
- str==None, then it returns the vtkUnsignedCharArray containing
- the PNG image. Otherwise, the filename is returned.
-
- """
- w2i = vtksnl.vtkWindowToImageFilter()
- w2i.ReadFrontBufferOff()
- w2i.SetInput(self.mRenWin)
- # Render twice to get a clean image on the back buffer
- self.mRenWin.Render()
- self.mRenWin.Render()
- w2i.Update()
- writer = vtksnl.vtkPNGWriter()
- writer.SetInputConnection(w2i.GetOutputPort())
- if filename!=None:
- writer.SetFileName(filename)
- else:
- writer.WriteToMemoryOn()
- writer.Write()
- if filename:
- return filename
- else:
- return writer.GetResult()
-
- def captureWindow(self):
- """ captureWindow() -> None
- Capture the window contents to file
-
- """
- fn = QtGui.QFileDialog.getSaveFileName(None,
- "Save file as...",
- "screenshot.png",
- "Images (*.png)")
- if fn.isNull():
- return
- self.saveToPNG(str(fn))
-
- def grabWindowPixmap(self):
- """ grabWindowImage() -> QPixmap
- Widget special grabbing function
-
- """
- uchar = self.saveToPNG(None)
-
- ba = QtCore.QByteArray()
- buf = QtCore.QBuffer(ba)
- buf.open(QtCore.QIODevice.WriteOnly)
- for i in xrange(uchar.GetNumberOfTuples()):
- c = uchar.GetValue(i)
- buf.putChar(chr(c))
- buf.close()
-
- pixmap = QtGui.QPixmap()
- pixmap.loadFromData(ba, 'PNG')
- return pixmap
-
- def dumpToFile(self, filename):
- """dumpToFile() -> None
- Dumps itself as an image to a file, calling saveToPNG
- """
- self.saveToPNG(filename)
-
-class QVTKWidgetCapture(QtGui.QAction):
- """
- QVTKWidgetCapture is the action to capture the vtk rendering
- window to an image
-
- """
- def __init__(self, parent=None):
- """ QVTKWidgetCapture(parent: QWidget) -> QVTKWidgetCapture
- Setup the image, status tip, etc. of the action
-
- """
- QtGui.QAction.__init__(self,
- QtGui.QIcon(":/images/camera.png"),
- "&Capture image to file",
- parent)
- self.setStatusTip("Capture the rendered image to a file")
-
- def triggeredSlot(self, checked=False):
- """ toggledSlot(checked: boolean) -> None
- Execute the action when the button is clicked
-
- """
- cellWidget = self.toolBar.getSnappedWidget()
- cellWidget.captureWindow()
-
-class QVTKWidgetSaveCamera(QtGui.QAction):
- """
- QVTKWidgetSaveCamera is the action to capture the current camera
- of the vtk renderers and save it back to the pipeline
-
- """
- def __init__(self, parent=None):
- """ QVTKWidgetSaveCamera(parent: QWidget) -> QVTKWidgetSaveCamera
- Setup the image, status tip, etc. of the action
-
- """
- QtGui.QAction.__init__(self,
- "Save &Camera",
- parent)
- self.setStatusTip("Save current camera views to the pipeline")
-
- def setCamera(self, controller):
- ops = []
- pipeline = controller.current_pipeline
- cellWidget = self.toolBar.getSnappedWidget()
- renderers = cellWidget.getRendererList()
- for ren in renderers:
- cam = ren.GetActiveCamera()
- cpos = cam.GetPosition()
- cfol = cam.GetFocalPoint()
- cup = cam.GetViewUp()
- rendererId = cellWidget.renderer_maps[ren]
- # Looking for SetActiveCamera()
- camera = None
- renderer = pipeline.modules[rendererId]
- for c in pipeline.connections.values():
- if c.destination.moduleId==rendererId:
- if c.destination.name=='SetActiveCamera':
- camera = pipeline.modules[c.source.moduleId]
- break
-
- if not camera:
- # Create camera
- vtk_package = 'edu.utah.sci.vistrails.vtksnl'
- camera = controller.create_module(vtk_package, 'vtkCamera', '',
- 0.0, 0.0)
- ops.append(('add', camera))
-
- # Connect camera to renderer
- camera_conn = controller.create_connection(camera, 'self',
- renderer,
- 'SetActiveCamera')
- ops.append(('add', camera_conn))
- # update functions
- def convert_to_str(arglist):
- new_arglist = []
- for arg in arglist:
- new_arglist.append(str(arg))
- return new_arglist
- functions = [('SetPosition', convert_to_str(cpos)),
- ('SetFocalPoint', convert_to_str(cfol)),
- ('SetViewUp', convert_to_str(cup))]
- ops.extend(controller.update_functions_ops(camera, functions))
-
- action = core.db.action.create_action(ops)
- controller.add_new_action(action)
- controller.perform_action(action)
- controller.select_latest_version()
-
- def triggeredSlot(self, checked=False):
- """ toggledSlot(checked: boolean) -> None
- Execute the action when the button is clicked
-
- """
- visApp = QtCore.QCoreApplication.instance()
- if hasattr(visApp, 'builderWindow'):
- builderWindow = visApp.builderWindow
- if builderWindow:
- info = self.toolBar.sheet.getCellPipelineInfo(
- self.toolBar.row, self.toolBar.col)
- if info:
- info = info[0]
- viewManager = builderWindow.viewManager
- view = viewManager.ensureVistrail(info['locator'])
- if view:
- controller = view.controller
- controller.change_selected_version(info['version'])
- self.setCamera(controller)
-
-
-class QVTKWidgetToolBar(QCellToolBar):
- """
- QVTKWidgetToolBar derives from QCellToolBar to give the VTKCell
- a customizable toolbar
-
- """
- def createToolBar(self):
- """ createToolBar() -> None
- This will get call initiallly to add customizable widgets
-
- """
- self.appendAction(QVTKWidgetCapture(self))
- self.addAnimationButtons()
- self.appendAction(QVTKWidgetSaveCamera(self))
-
-def registerSelf():
- """ registerSelf() -> None
- Registry module with the registry
- """
- identifier = 'edu.utah.sci.vistrails.vtksnl'
- registry = get_module_registry()
- registry.add_module(VTKCell)
- registry.add_input_port(VTKCell, "Location", CellLocation)
- import core.debug
- for (port,module) in [("AddRenderer",'vtkRenderer'),
- ("SetRenderView",'vtkRenderView'),
- ("InteractionHandler",'vtkInteractionHandler'),
- ("InteractorStyle", 'vtkInteractorStyle'),
- ("AddPicker",'vtkAbstractPicker')]:
- try:
- registry.add_input_port(VTKCell, port,'(%s:%s)'%(identifier,module))
-
- except Exception, e:
- core.debug.warning(str(e))
-
- registry.add_output_port(VTKCell, "self", VTKCell)
diff --git a/contrib/vtksnl/vtkcell_rc.py b/contrib/vtksnl/vtkcell_rc.py
deleted file mode 100644
index 8aa8cbf..0000000
--- a/contrib/vtksnl/vtkcell_rc.py
+++ /dev/null
@@ -1,793 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-# Resource object code
-#
-# Created: Fri Sep 22 09:09:40 2006
-# by: The Resource Compiler for PyQt (Qt v4.1.3)
-#
-# WARNING! All changes made in this file will be lost!
-
-from PyQt4 import QtCore
-
-qt_resource_data = "\
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-"
-
-qt_resource_name = "\
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-"
-
-qt_resource_struct = "\
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-"
-
-def qInitResources():
- QtCore.qRegisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
-
-def qCleanupResources():
- QtCore.qUnregisterResourceData(0x01, qt_resource_struct, qt_resource_name, qt_resource_data)
-
-qInitResources()
diff --git a/contrib/vtksnl/vtkhandler.py b/contrib/vtksnl/vtkhandler.py
deleted file mode 100644
index 36b344c..0000000
--- a/contrib/vtksnl/vtkhandler.py
+++ /dev/null
@@ -1,291 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-"""Modules for handling vtkRenderWindowInteractor events"""
-from PyQt4 import QtCore, QtGui
-from core.modules.basic_modules import String
-from core.modules.vistrails_module import Module, NotCacheable
-from core.modules.module_registry import get_module_registry
-from core.modules.module_configure import StandardModuleConfigurationWidget
-from core.modules.python_source_configure import PythonEditor
-from core.vistrail.module_function import ModuleFunction, ModuleParam
-import urllib
-
-################################################################################
-class vtkInteractionHandler(NotCacheable, Module):
- """
- vtkInteractionHandler allow users to insert callback code for interacting
- with the vtkRenderWindowInteractor InteractionEvent
-
- """
-
- # Since vtkCommand is not wrapped in Python, we need to hardcoded all events
- # string from vtkCommand.h
- vtkEvents = [
- 'AnyEvent',
- 'DeleteEvent',
- 'StartEvent',
- 'EndEvent',
- 'RenderEvent',
- 'ProgressEvent',
- 'PickEvent',
- 'StartPickEvent',
- 'EndPickEvent',
- 'AbortCheckEvent',
- 'ExitEvent',
- 'LeftButtonPressEvent',
- 'LeftButtonReleaseEvent',
- 'MiddleButtonPressEvent',
- 'MiddleButtonReleaseEvent',
- 'RightButtonPressEvent',
- 'RightButtonReleaseEvent',
- 'EnterEvent',
- 'LeaveEvent',
- 'KeyPressEvent',
- 'KeyReleaseEvent',
- 'CharEvent',
- 'ExposeEvent',
- 'ConfigureEvent',
- 'TimerEvent',
- 'MouseMoveEvent',
- 'MouseWheelForwardEvent',
- 'MouseWheelBackwardEvent',
- 'ResetCameraEvent',
- 'ResetCameraClippingRangeEvent',
- 'ModifiedEvent',
- 'WindowLevelEvent',
- 'StartWindowLevelEvent',
- 'EndWindowLevelEvent',
- 'ResetWindowLevelEvent',
- 'SetOutputEvent',
- 'ErrorEvent',
- 'WarningEvent',
- 'StartInteractionEvent',
- 'InteractionEvent',
- 'EndInteractionEvent',
- 'EnableEvent',
- 'DisableEvent',
- 'CreateTimerEvent',
- 'DestroyTimerEvent',
- 'PlacePointEvent',
- 'PlaceWidgetEvent',
- 'CursorChangedEvent',
- 'ExecuteInformationEvent',
- 'RenderWindowMessageEvent',
- 'WrongTagEvent',
- 'StartAnimationCueEvent',
- 'AnimationCueTickEvent',
- 'EndAnimationCueEvent',
- 'VolumeMapperRenderEndEvent',
- 'VolumeMapperRenderProgressEvent',
- 'VolumeMapperRenderStartEvent',
- 'VolumeMapperComputeGradientsEndEvent',
- 'VolumeMapperComputeGradientsProgressEvent',
- 'VolumeMapperComputeGradientsStartEvent',
- 'WidgetModifiedEvent',
- 'WidgetValueChangedEvent',
- 'WidgetActivateEvent',
- 'ConnectionCreatedEvent',
- 'ConnectionClosedEvent',
- 'DomainModifiedEvent',
- 'PropertyModifiedEvent',
- 'UpdateEvent',
- 'RegisterEvent',
- 'UnRegisterEvent',
- 'UpdateInformationEvent']
-
- def __init__(self):
- Module.__init__(self)
- self.observer = None
- self.handler = None
- self.shareddata = None
-
- def compute(self):
- """ compute() -> None
- Actually compute nothing
- """
- self.observer = self.forceGetInputFromPort('Observer')
- self.handler = self.forceGetInputFromPort('Handler', '')
- self.shareddata = self.forceGetInputListFromPort('SharedData')
- if len(self.shareddata)==1:
- self.shareddata = self.shareddata[0]
- if self.observer:
- source = urllib.unquote(self.handler)
- observer = self.observer.vtkInstance
- for e in vtkInteractionHandler.vtkEvents:
- f = e[0].lower() + e[1:]
- f = f.replace('Event', 'Handler')
- source += ('\nif locals().has_key("%s"):\n' % f +
- '\tobserver.AddObserver("%s", ' % e +
- 'self.eventHandler)\n')
- exec(source)
- if hasattr(self.observer.vtkInstance, 'PlaceWidget'):
- self.observer.vtkInstance.PlaceWidget()
-
- def eventHandler(self, obj, event):
- """ eventHandler(obj: vtkObject, event: str) -> None
- A proxy for all vtk events to direct to the correct calls
-
- """
- if self.handler!='':
- source = urllib.unquote(self.handler)
- f = event[0].lower() + event[1:]
- f = f.replace('Event', 'Handler')
- myGlobals = globals()
- myGlobals.update({'self':self})
- exec(source + ('\nif locals().has_key("%s"):\n' % f)+
- ('\t%s(obj, self.shareddata)' % f)) in myGlobals, locals()
-
- def clear(self):
- """ clear() -> None
- Remove event handler so the object can be freed correctly
-
- """
- # Remove all observers
- if self.observer:
- for e in vtkInteractionHandler.vtkEvents:
- self.observer.vtkInstance.RemoveObservers(e)
- Module.clear(self)
-
- def repaintCells(self):
- """ repaintCells() -> None
- Redraw all cells on the current sheet
-
- """
- from packages.spreadsheet.spreadsheet_controller \
- import spreadsheetController
- from packages.spreadsheet.spreadsheet_event \
- import RepaintCurrentSheetEvent
- spreadsheetController.postEventToSpreadsheet(RepaintCurrentSheetEvent())
-
-class HandlerConfigurationWidget(StandardModuleConfigurationWidget):
- """
- HandlerConfigurationWidget is simialr to PythonSource
- configuration widget except that it doesn't allow add/remove
- ports. In this configuration widget, the user will enter their
- python code to handle a specifc event
-
- """
- def __init__(self, module, controller, parent=None):
- """ HandlerConfigurationWidget(module: Module,
- controller: VistrailController,
- parent: QWidget)
- -> HandlerConfigurationWidget
- Setup the dialog to have a single python source editor and 2
- buttons
-
- """
- StandardModuleConfigurationWidget.__init__(self, module,
- controller, parent)
- self.setWindowTitle('Handler Python Script Editor')
- self.setLayout(QtGui.QVBoxLayout())
- self.layout().setMargin(0)
- self.layout().setSpacing(0)
- self.createEditor()
- self.createButtonLayout()
-
- def findHandlerFunction(self):
- """ findHandlerFunction() -> int
- Return the function id associated with input port 'source'
-
- """
- fid = -1
- for i in xrange(self.module.getNumFunctions()):
- if self.module.functions[i].name=='Handler':
- fid = i
- break
- return fid
-
- def createEditor(self):
- """ createEditor() -> None
- Add a python editor into the widget layout
-
- """
- self.codeEditor = PythonEditor(self)
- fid = self.findHandlerFunction()
- if fid!=-1:
- f = self.module.functions[fid]
- self.codeEditor.setPlainText(urllib.unquote(f.params[0].strValue))
- self.codeEditor.document().setModified(False)
- self.layout().addWidget(self.codeEditor, 1)
-
- def createButtonLayout(self):
- """ createButtonLayout() -> None
- Construct Ok & Cancel button
-
- """
- self.buttonLayout = QtGui.QHBoxLayout()
- self.buttonLayout.setMargin(5)
- self.okButton = QtGui.QPushButton('&OK', self)
- self.okButton.setAutoDefault(False)
- self.okButton.setFixedWidth(100)
- self.buttonLayout.addWidget(self.okButton)
- self.cancelButton = QtGui.QPushButton('&Cancel', self)
- self.cancelButton.setAutoDefault(False)
- self.cancelButton.setShortcut('Esc')
- self.cancelButton.setFixedWidth(100)
- self.buttonLayout.addWidget(self.cancelButton)
- self.layout().addLayout(self.buttonLayout)
- self.connect(self.okButton, QtCore.SIGNAL('clicked(bool)'), self.okTriggered)
- self.connect(self.cancelButton, QtCore.SIGNAL('clicked(bool)'), self.close)
-
- def sizeHint(self):
- """ sizeHint() -> QSize
- Return the recommendation size of this widget
-
- """
- return QtCore.QSize(512, 512)
-
- def updateController(self, controller):
- """ updateController() -> None
- Based on the input of the python editor, update the vistrail
- controller appropriately
-
- """
- if self.codeEditor.document().isModified():
- code = urllib.quote(str(self.codeEditor.toPlainText()))
- functions = [('Handler', [code])]
- self.controller.update_functions(self.module, functions)
-
- def okTriggered(self, checked = False):
- """ okTriggered(checked: bool) -> None
- Update vistrail controller (if neccesssary) then close the widget
-
- """
- self.updateController(self.controller)
- self.emit(QtCore.SIGNAL('doneConfigure()'))
- self.close()
-
-
-def registerSelf():
- """ registerSelf() -> None
- Registry module with the registry
- """
- registry = get_module_registry()
- vIO = registry.get_descriptor_by_name(
- 'edu.utah.sci.vistrails.vtksnl',
- 'vtkInteractorObserver').module
- registry.add_module(vtkInteractionHandler, configureWidgetType=HandlerConfigurationWidget)
- registry.add_input_port(vtkInteractionHandler, 'Observer', vIO)
- registry.add_input_port(vtkInteractionHandler, 'Handler', String, True)
- registry.add_input_port(vtkInteractionHandler, 'SharedData', Module)
- registry.add_output_port(vtkInteractionHandler, 'self',
- vtkInteractionHandler)
diff --git a/contrib/vtksnl/vtkviewcell.py b/contrib/vtksnl/vtkviewcell.py
deleted file mode 100644
index 1611d95..0000000
--- a/contrib/vtksnl/vtkviewcell.py
+++ /dev/null
@@ -1,1032 +0,0 @@
-############################################################################
-##
-## Copyright (C) 2006-2010 University of Utah. All rights reserved.
-##
-## This file is part of VisTrails.
-##
-## This file may be used under the terms of the GNU General Public
-## License version 2.0 as published by the Free Software Foundation
-## and appearing in the file LICENSE.GPL included in the packaging of
-## this file. Please review the following to ensure GNU General Public
-## Licensing requirements will be met:
-## http://www.opensource.org/licenses/gpl-license.php
-##
-## If you are unsure which license is appropriate for your use (for
-## instance, you are interested in developing a commercial derivative
-## of VisTrails), please contact us at contact at vistrails.org.
-##
-## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
-## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-##
-############################################################################
-################################################################################
-# File QVTKViewWidget.py
-# File for displaying a vtkRenderWindow in a Qt's QWidget ported from
-# VTK/GUISupport/QVTK. Combine altogether to a single class: QVTKViewWidget
-################################################################################
-import vtksnl
-from PyQt4 import QtCore, QtGui
-import sip
-from core import system
-from core.modules.module_registry import get_module_registry
-from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
-from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
-import vtkcell_rc
-import gc
-from gui.qt import qt_super
-import core.db.action
-from core.vistrail.action import Action
-from core.vistrail.port import Port
-from core.vistrail import module
-from core.vistrail import connection
-from core.vistrail.module_function import ModuleFunction
-from core.vistrail.module_param import ModuleParam
-from core.vistrail.location import Location
-from core.modules.vistrails_module import ModuleError
-import copy
-
-################################################################################
-
-class VTKViewCell(SpreadsheetCell):
- """
- VTKViewCell is a VisTrails Module that can display vtkRenderWindow inside a cell
-
- """
-
- def __init__(self):
- SpreadsheetCell.__init__(self)
- self.cellWidget = None
-
- def compute(self):
- """ compute() -> None
- Dispatch the vtkRenderer to the actual rendering widget
- """
- renderView = self.forceGetInputFromPort('SetRenderView')
- if renderView==None:
- raise ModuleError(self, 'A vtkRenderView input is required.')
- self.cellWidget = self.displayAndWait(QVTKViewWidget, (renderView,))
-
-AsciiToKeySymTable = ( None, None, None, None, None, None, None,
- None, None,
- "Tab", None, None, None, None, None, None,
- None, None, None, None, None, None,
- None, None, None, None, None, None,
- None, None, None, None,
- "space", "exclam", "quotedbl", "numbersign",
- "dollar", "percent", "ampersand", "quoteright",
- "parenleft", "parenright", "asterisk", "plus",
- "comma", "minus", "period", "slash",
- "0", "1", "2", "3", "4", "5", "6", "7",
- "8", "9", "colon", "semicolon", "less", "equal",
- "greater", "question",
- "at", "A", "B", "C", "D", "E", "F", "G",
- "H", "I", "J", "K", "L", "M", "N", "O",
- "P", "Q", "R", "S", "T", "U", "V", "W",
- "X", "Y", "Z", "bracketleft",
- "backslash", "bracketright", "asciicircum",
- "underscore",
- "quoteleft", "a", "b", "c", "d", "e", "f", "g",
- "h", "i", "j", "k", "l", "m", "n", "o",
- "p", "q", "r", "s", "t", "u", "v", "w",
- "x", "y", "z", "braceleft", "bar", "braceright",
- "asciitilde", "Delete",
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None,
- None, None, None, None, None, None, None, None)
-
-class QVTKViewWidget(QCellWidget):
- """
- QVTKViewWidget is the actual rendering widget that can display
- vtkRenderer inside a Qt QWidget
-
- """
- def __init__(self, parent=None, f=QtCore.Qt.WindowFlags()):
- """ QVTKViewWidget(parent: QWidget, f: WindowFlags) -> QVTKViewWidget
- Initialize QVTKViewWidget with a toolbar with its own device
- context
-
- """
- QCellWidget.__init__(self, parent, f | QtCore.Qt.MSWindowsOwnDC)
-
- self.interacting = None
- self.mRenWin = None
- self.setAttribute(QtCore.Qt.WA_OpaquePaintEvent)
- self.setAttribute(QtCore.Qt.WA_PaintOnScreen)
- self.setMouseTracking(True)
- self.setFocusPolicy(QtCore.Qt.StrongFocus)
- self.setSizePolicy(QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
- QtGui.QSizePolicy.Expanding))
- self.toolBarType = QVTKViewWidgetToolBar
- self.setAnimationEnabled(True)
-
- def removeObserversFromInteractorStyle(self):
- """ removeObserversFromInteractorStyle() -> None
- Remove all python binding from interactor style observers for
- safely freeing the cell
-
- """
- iren = self.mRenWin.GetInteractor()
- if iren:
- style = iren.GetInteractorStyle()
- style.RemoveObservers("InteractionEvent")
- style.RemoveObservers("EndPickEvent")
- style.RemoveObservers("CharEvent")
- style.RemoveObservers("MouseWheelForwardEvent")
- style.RemoveObservers("MouseWheelBackwardEvent")
-
- def addObserversToInteractorStyle(self):
- """ addObserversToInteractorStyle() -> None
- Assign observer to the current interactor style
-
- """
- iren = self.mRenWin.GetInteractor()
- if iren:
- style = iren.GetInteractorStyle()
- style.AddObserver("InteractionEvent", self.interactionEvent)
- style.AddObserver("EndPickEvent", self.interactionEvent)
- style.AddObserver("CharEvent", self.charEvent)
- style.AddObserver("MouseWheelForwardEvent", self.interactionEvent)
- style.AddObserver("MouseWheelBackwardEvent", self.interactionEvent)
-
- def deleteLater(self):
- """ deleteLater() -> None
- Make sure to free render window resource when
- deallocating. Overriding PyQt deleteLater to free up
- resources
-
- """
- self.renderer_maps = {}
- for ren in self.getRendererList():
- self.mRenWin.RemoveRenderer(ren)
- self.removeObserversFromInteractorStyle()
- self.SetRenderWindow(None)
- QCellWidget.deleteLater(self)
-
- def updateContents(self, inputPorts):
- """ updateContents(inputPorts: tuple)
- Updates the cell contents with new vtkRenderer
-
- """
- (renderView, ) = inputPorts
- renWin = renderView.vtkInstance.GetRenderWindow()
- renWin.DoubleBufferOn()
- self.SetRenderWindow(renWin)
- renderView.vtkInstance.ResetCamera()
- self.addObserversToInteractorStyle()
-
-# renWin = self.GetRenderWindow()
-# renderers = [renderView.vtkInstance.GetRenderer()]
-# iren = renWin.GetInteractor()
- # Update interactor style
-# self.removeObserversFromInteractorStyle()
-# if renderView==None:
-# if iStyle==None:
-# iStyleInstance = vtk.vtkInteractorStyleTrackballCamera()
-# else:
-# iStyleInstance = iStyle.vtkInstance
-# iren.SetInteractorStyle(iStyleInstance)
-# self.addObserversToInteractorStyle()
- # Capture window into history for playback
- # Call this at the end to capture the image after rendering
- QCellWidget.updateContents(self, inputPorts)
-
- def GetRenderWindow(self):
- """ GetRenderWindow() -> vtkRenderWindow
- Return the associated vtkRenderWindow
-
- """
- if not self.mRenWin:
- win = vtksnl.vtkRenderWindow()
- win.DoubleBufferOn()
- self.SetRenderWindow(win)
- del win
-
- return self.mRenWin
-
- def SetRenderWindow(self,w):
- """ SetRenderWindow(w: vtkRenderWindow)
- Set a new render window to QVTKViewWidget and initialize the
- interactor as well
-
- """
- if w == self.mRenWin:
- return
-
- if self.mRenWin:
- if self.mRenWin.GetMapped():
- self.mRenWin.Finalize()
-
- self.mRenWin = w
-
- if self.mRenWin:
- self.mRenWin.Register(None)
- if system.systemType=='Linux':
- try:
- vp = '_%s_void_p' % (hex(int(QtGui.QX11Info.display()))[2:])
- except TypeError:
- #This was change for PyQt4.2
- if isinstance(QtGui.QX11Info.display(),QtGui.Display):
- display = sip.unwrapinstance(QtGui.QX11Info.display())
- vp = '_%s_void_p' % (hex(display)[2:])
- self.mRenWin.SetDisplayId(vp)
- if not self.mRenWin.GetMapped():
- self.mRenWin.GetInteractor().Initialize()
- system.XDestroyWindow(self.mRenWin.GetGenericDisplayId(),
- self.mRenWin.GetGenericWindowId())
- self.mRenWin.Finalize()
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- else:
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- if self.isVisible():
- self.mRenWin.Start()
-
- def GetInteractor(self):
- """ GetInteractor() -> vtkInteractor
- Return the vtkInteractor control this QVTKViewWidget
- """
- return self.GetRenderWindow().GetInteractor()
-
- def event(self, e):
- """ event(e: QEvent) -> depends on event type
- Process window and interaction events
-
- """
- if e.type()==QtCore.QEvent.ParentAboutToChange:
- if self.mRenWin:
- if self.mRenWin.GetMapped():
- self.mRenWin.Finalize()
- else:
- if e.type()==QtCore.QEvent.ParentChange:
- if self.mRenWin:
- self.mRenWin.SetWindowInfo(str(int(self.winId())))
- if self.isVisible():
- self.mRenWin.Start()
-
- if QtCore.QObject.event(self,e):
- return 1
-
- if e.type() == QtCore.QEvent.KeyPress:
- self.keyPressEvent(e)
- if e.isAccepted():
- return e.isAccepted()
-
- return qt_super(QVTKViewWidget, self).event(e)
-
- # return QtGui.QWidget.event(self,e)
- # Was this right? Wasn't this supposed to be QCellWidget.event()?
-
- def resizeWindow(self, width, height):
- """ resizeWindow(width: int, height: int) -> None
- Work around vtk bugs for resizing window
-
- """
- ########################################################
- # VTK - BUGGGGGGGGG - GRRRRRRRRR
- # This is a 'bug' in vtkWin32OpenGLRenderWindow(.cxx)
- # If a render window is mapped to screen, the actual
- # window size is the client area of the window in Win32.
- # However, this real window size is only updated through
- # vtkWin32OpenGLRenderWindow::GetSize(). So this has to
- # be called here to get the cell size correctly. This
- # invalidates the condition in the next SetSize().
- # We can use self.mRenWin.SetSize(0,0) here but it will
- # cause flickering and decrease performance!
- # SetPosition(curX,curY) also works here but slower.
- self.mRenWin.GetSize()
-
- self.mRenWin.SetSize(width, height)
- if self.mRenWin.GetInteractor():
- self.mRenWin.GetInteractor().SetSize(width, height)
-
- def resizeEvent(self, e):
- """ resizeEvent(e: QEvent) -> None
- Re-adjust the vtkRenderWindow size then QVTKViewWidget resized
-
- """
- qt_super(QVTKViewWidget, self).resizeEvent(e)
- if not self.mRenWin:
- return
-
- self.resizeWindow(self.width(), self.height())
- self.mRenWin.Render()
-
- def moveEvent(self,e):
- """ moveEvent(e: QEvent) -> None
- Echo the move event into vtkRenderWindow
-
- """
- qt_super(QVTKViewWidget, self).moveEvent(e)
- if not self.mRenWin:
- return
-
- self.mRenWin.SetPosition(self.x(),self.y())
-
- def paintEvent(self, e):
- """ paintEvent(e: QPaintEvent) -> None
- Paint the QVTKViewWidget with vtkRenderWindow
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- if hasattr(self.mRenWin, 'UpdateGLRegion'):
- self.mRenWin.UpdateGLRegion()
- self.mRenWin.Render()
-
- def SelectActiveRenderer(self,iren):
- """ SelectActiveRenderer(iren: vtkRenderWindowIteractor) -> None
- Only make the vtkRenderer below the mouse cursor active
-
- """
- epos = iren.GetEventPosition()
- rens = iren.GetRenderWindow().GetRenderers()
- rens.InitTraversal()
- for i in xrange(rens.GetNumberOfItems()):
- ren = rens.GetNextItem()
- ren.SetInteractive(ren.IsInViewport(epos[0], epos[1]))
-
- def mousePressEvent(self,e):
- """ mousePressEvent(e: QMouseEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- isDoubleClick = e.type()==QtCore.QEvent.MouseButtonDblClick
- iren.SetEventInformationFlipY(e.x(),e.y(),
- ctrl,
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),
- isDoubleClick,
- None)
- invoke = {QtCore.Qt.LeftButton:"LeftButtonPressEvent",
- QtCore.Qt.MidButton:"MiddleButtonPressEvent",
- QtCore.Qt.RightButton:"RightButtonPressEvent"}
-
- self.SelectActiveRenderer(iren)
-
- if ctrl:
- e.ignore()
- return
-
- self.interacting = self.getActiveRenderer(iren)
-
- if e.button() in invoke:
- iren.InvokeEvent(invoke[e.button()])
-
- def mouseMoveEvent(self,e):
- """ mouseMoveEvent(e: QMouseEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0), 0, None)
-
- iren.InvokeEvent("MouseMoveEvent")
-
- def enterEvent(self,e):
- """ enterEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.InvokeEvent("EnterEvent")
-
- def leaveEvent(self,e):
- """ leaveEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.InvokeEvent("LeaveEvent")
-
- def mouseReleaseEvent(self,e):
- """ mouseReleaseEvent(e: QEvent) -> None
- Echo mouse event to vtkRenderWindowwInteractor
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),0,None)
-
- invoke = {QtCore.Qt.LeftButton:"LeftButtonReleaseEvent",
- QtCore.Qt.MidButton:"MiddleButtonReleaseEvent",
- QtCore.Qt.RightButton:"RightButtonReleaseEvent"}
-
- self.interacting = None
-
- if e.button() in invoke:
- iren.InvokeEvent(invoke[e.button()])
-
- def keyPressEvent(self,e):
- """ keyPressEvent(e: QKeyEvent) -> None
- Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ascii_key = None
- if e.text().length()>0:
- ascii_key = e.text().toLatin1()[0]
- else:
- ascii_key = chr(0)
-
- keysym = self.ascii_to_key_sym(ord(ascii_key))
-
- if not keysym:
- keysym = self.qt_key_to_key_sym(e.key())
-
- # Ignore 'q' or 'e' or Ctrl-anykey
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
- if (keysym in ['q', 'e'] or ctrl):
- e.ignore()
- return
-
- iren.SetKeyEventInformation(ctrl,shift,ascii_key, e.count(), keysym)
-
- iren.InvokeEvent("KeyPressEvent")
-
- if ascii_key:
- iren.InvokeEvent("CharEvent")
-
-
- def keyReleaseEvent(self,e):
- """ keyReleaseEvent(e: QKeyEvent) -> None
- Disallow 'quit' key in vtkRenderWindowwInteractor and sync the others
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ascii_key = None
- if e.text().length()>0:
- ascii_key = e.text().toLatin1()[0]
- else:
- ascii_key = chr(0)
-
- keysym = self.ascii_to_key_sym(ord(ascii_key))
-
- if not keysym:
- keysym = self.qt_key_to_key_sym(e.key())
-
- # Ignore 'q' or 'e' or Ctrl-anykey
- ctrl = (e.modifiers()&QtCore.Qt.ControlModifier)
- shift = (e.modifiers()&QtCore.Qt.ShiftModifier)
- if (keysym in ['q','e'] or ctrl):
- e.ignore()
- return
-
- iren.SetKeyEventInformation(ctrl, shift, ascii_key, e.count(), keysym)
-
- iren.InvokeEvent("KeyReleaseEvent")
-
- def wheelEvent(self,e):
- """ wheelEvent(e: QWheelEvent) -> None
- Zoom in/out while scrolling the mouse
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- iren.SetEventInformationFlipY(e.x(),e.y(),
- (e.modifiers()&QtCore.Qt.ControlModifier),
- (e.modifiers()&QtCore.Qt.ShiftModifier),
- chr(0),0,None)
-
- self.SelectActiveRenderer(iren)
-
- if e.delta()>0:
- iren.InvokeEvent("MouseWheelForwardEvent")
- else:
- iren.InvokeEvent("MouseWheelBackwardEvent")
-
- def focusInEvent(self,e):
- """ focusInEvent(e: QFocusEvent) -> None
- Ignore focus event
-
- """
- pass
-
- def focusOutEvent(self,e):
- """ focusOutEvent(e: QFocusEvent) -> None
- Ignore focus event
-
- """
- pass
-
- def contextMenuEvent(self,e):
- """ contextMenuEvent(e: QContextMenuEvent) -> None
- Make sure to get the right mouse position for the context menu
- event, i.e. also the right click
-
- """
- iren = None
- if self.mRenWin:
- iren = self.mRenWin.GetInteractor()
-
- if (not iren) or (not iren.GetEnabled()):
- return
-
- ctrl = int(e.modifiers()&QtCore.Qt.ControlModifier)
- shift = int(e.modifiers()&QtCore.Qt.ShiftModifier)
- iren.SetEventInformationFlipY(e.x(),e.y(),ctrl,shift,chr(0),0,None)
- iren.InvokeEvent("ContextMenuEvent")
-
- def ascii_to_key_sym(self,i):
- """ ascii_to_key_sym(i: int) -> str
- Convert ASCII code into key name
-
- """
- global AsciiToKeySymTable
- return AsciiToKeySymTable[i]
-
- def qt_key_to_key_sym(self,i):
- """ qt_key_to_key_sym(i: QtCore.Qt.Keycode) -> str
- Convert Qt key code into key name
-
- """
- handler = {QtCore.Qt.Key_Backspace:"BackSpace",
- QtCore.Qt.Key_Tab:"Tab",
- QtCore.Qt.Key_Backtab:"Tab",
- QtCore.Qt.Key_Return:"Return",
- QtCore.Qt.Key_Enter:"Return",
- QtCore.Qt.Key_Shift:"Shift_L",
- QtCore.Qt.Key_Control:"Control_L",
- QtCore.Qt.Key_Alt:"Alt_L",
- QtCore.Qt.Key_Pause:"Pause",
- QtCore.Qt.Key_CapsLock:"Caps_Lock",
- QtCore.Qt.Key_Escape:"Escape",
- QtCore.Qt.Key_Space:"space",
- QtCore.Qt.Key_End:"End",
- QtCore.Qt.Key_Home:"Home",
- QtCore.Qt.Key_Left:"Left",
- QtCore.Qt.Key_Up:"Up",
- QtCore.Qt.Key_Right:"Right",
- QtCore.Qt.Key_Down:"Down",
- QtCore.Qt.Key_SysReq:"Snapshot",
- QtCore.Qt.Key_Insert:"Insert",
- QtCore.Qt.Key_Delete:"Delete",
- QtCore.Qt.Key_Help:"Help",
- QtCore.Qt.Key_0:"0",
- QtCore.Qt.Key_1:"1",
- QtCore.Qt.Key_2:"2",
- QtCore.Qt.Key_3:"3",
- QtCore.Qt.Key_4:"4",
- QtCore.Qt.Key_5:"5",
- QtCore.Qt.Key_6:"6",
- QtCore.Qt.Key_7:"7",
- QtCore.Qt.Key_8:"8",
- QtCore.Qt.Key_9:"9",
- QtCore.Qt.Key_A:"a",
- QtCore.Qt.Key_B:"b",
- QtCore.Qt.Key_C:"c",
- QtCore.Qt.Key_D:"d",
- QtCore.Qt.Key_E:"e",
- QtCore.Qt.Key_F:"f",
- QtCore.Qt.Key_G:"g",
- QtCore.Qt.Key_H:"h",
- QtCore.Qt.Key_I:"i",
- QtCore.Qt.Key_J:"h",
- QtCore.Qt.Key_K:"k",
- QtCore.Qt.Key_L:"l",
- QtCore.Qt.Key_M:"m",
- QtCore.Qt.Key_N:"n",
- QtCore.Qt.Key_O:"o",
- QtCore.Qt.Key_P:"p",
- QtCore.Qt.Key_Q:"q",
- QtCore.Qt.Key_R:"r",
- QtCore.Qt.Key_S:"s",
- QtCore.Qt.Key_T:"t",
- QtCore.Qt.Key_U:"u",
- QtCore.Qt.Key_V:"v",
- QtCore.Qt.Key_W:"w",
- QtCore.Qt.Key_X:"x",
- QtCore.Qt.Key_Y:"y",
- QtCore.Qt.Key_Z:"z",
- QtCore.Qt.Key_Asterisk:"asterisk",
- QtCore.Qt.Key_Plus:"plus",
- QtCore.Qt.Key_Minus:"minus",
- QtCore.Qt.Key_Period:"period",
- QtCore.Qt.Key_Slash:"slash",
- QtCore.Qt.Key_F1:"F1",
- QtCore.Qt.Key_F2:"F2",
- QtCore.Qt.Key_F3:"F3",
- QtCore.Qt.Key_F4:"F4",
- QtCore.Qt.Key_F5:"F5",
- QtCore.Qt.Key_F6:"F6",
- QtCore.Qt.Key_F7:"F7",
- QtCore.Qt.Key_F8:"F8",
- QtCore.Qt.Key_F9:"F9",
- QtCore.Qt.Key_F10:"F10",
- QtCore.Qt.Key_F11:"F11",
- QtCore.Qt.Key_F12:"F12",
- QtCore.Qt.Key_F13:"F13",
- QtCore.Qt.Key_F14:"F14",
- QtCore.Qt.Key_F15:"F15",
- QtCore.Qt.Key_F16:"F16",
- QtCore.Qt.Key_F17:"F17",
- QtCore.Qt.Key_F18:"F18",
- QtCore.Qt.Key_F19:"F19",
- QtCore.Qt.Key_F20:"F20",
- QtCore.Qt.Key_F21:"F21",
- QtCore.Qt.Key_F22:"F22",
- QtCore.Qt.Key_F23:"F23",
- QtCore.Qt.Key_F24:"F24",
- QtCore.Qt.Key_NumLock:"Num_Lock",
- QtCore.Qt.Key_ScrollLock:"Scroll_Lock"}
- if i in handler:
- return handler[i]
- else:
- return "None"
-
- def getRendererList(self):
- """ getRendererList() -> list
- Return a list of vtkRenderer running in this QVTKViewWidget
- """
- result = []
- renWin = self.GetRenderWindow()
- renderers = renWin.GetRenderers()
- renderers.InitTraversal()
- for i in xrange(renderers.GetNumberOfItems()):
- result.append(renderers.GetNextItem())
- return result
-
- def getActiveRenderer(self, iren):
- """ getActiveRenderer(iren: vtkRenderWindowwInteractor) -> vtkRenderer
- Return the active vtkRenderer under mouse
-
- """
- epos = list(iren.GetEventPosition())
- if epos[1]<0:
- epos[1] = -epos[1]
- rens = iren.GetRenderWindow().GetRenderers()
- rens.InitTraversal()
- for i in xrange(rens.GetNumberOfItems()):
- ren = rens.GetNextItem()
- if ren.IsInViewport(epos[0], epos[1]):
- return ren
- return None
-
- def findSheetTabWidget(self):
- """ findSheetTabWidget() -> QTabWidget
- Find and return the sheet tab widget
-
- """
- p = self.parent()
- while p:
- if hasattr(p, 'isSheetTabWidget'):
- if p.isSheetTabWidget()==True:
- return p
- p = p.parent()
- return None
-
- def getRenderersInCellList(self, sheet, cells):
- """ isRendererIn(sheet: spreadsheet.StandardWidgetSheet,
- cells: [(int,int)]) -> bool
- Get the list of renderers in side a list of (row, column)
- cells.
-
- """
- rens = []
- for (row, col) in cells:
- cell = sheet.getCell(row, col)
- if hasattr(cell, 'getRendererList'):
- rens += cell.getRendererList()
- return rens
-
- def getSelectedCellWidgets(self):
- sheet = self.findSheetTabWidget()
- if sheet:
- iren = self.mRenWin.GetInteractor()
- ren = self.interacting
- if not ren: ren = self.getActiveRenderer(iren)
- if ren:
- cells = sheet.getSelectedLocations()
- if (ren in self.getRenderersInCellList(sheet, cells)):
- return [sheet.getCell(row, col)
- for (row, col) in cells
- if hasattr(sheet.getCell(row, col),
- 'getRendererList')]
- return []
-
- def interactionEvent(self, istyle, name):
- """ interactionEvent(istyle: vtkInteractorStyle, name: str) -> None
- Make sure interactions sync across selected renderers
-
- """
- if name=='MouseWheelForwardEvent':
- istyle.OnMouseWheelForward()
- if name=='MouseWheelBackwardEvent':
- istyle.OnMouseWheelBackward()
- ren = self.interacting
- if not ren:
- ren = self.getActiveRenderer(istyle.GetInteractor())
- if ren:
- cam = ren.GetActiveCamera()
- cpos = cam.GetPosition()
- cfol = cam.GetFocalPoint()
- cup = cam.GetViewUp()
- for cell in self.getSelectedCellWidgets():
- if cell!=self and hasattr(cell, 'getRendererList'):
- rens = cell.getRendererList()
- for r in rens:
- if r!=ren:
- dcam = r.GetActiveCamera()
- dcam.SetPosition(cpos)
- dcam.SetFocalPoint(cfol)
- dcam.SetViewUp(cup)
- r.ResetCameraClippingRange()
- cell.update()
-
- def charEvent(self, istyle, name):
- """ charEvent(istyle: vtkInteractorStyle, name: str) -> None
- Make sure key presses also sync across selected renderers
-
- """
- iren = istyle.GetInteractor()
- ren = self.interacting
- if not ren: ren = self.getActiveRenderer(iren)
- if ren:
- keyCode = iren.GetKeyCode()
- if keyCode in ['w','W','s','S','r','R','p','P']:
- for cell in self.getSelectedCellWidgets():
- if hasattr(cell, 'GetInteractor'):
- selectedIren = cell.GetInteractor()
- selectedIren.SetKeyCode(keyCode)
- selectedIren.GetInteractorStyle().OnChar()
- selectedIren.Render()
- istyle.OnChar()
-
- def saveToPNG(self, filename):
- """ saveToPNG(filename: str) -> filename or vtkUnsignedCharArray
-
- Save the current widget contents to an image file. If
- str==None, then it returns the vtkUnsignedCharArray containing
- the PNG image. Otherwise, the filename is returned.
-
- """
- w2i = vtksnl.vtkWindowToImageFilter()
- w2i.ReadFrontBufferOff()
- w2i.SetInput(self.mRenWin)
- # Render twice to get a clean image on the back buffer
- self.mRenWin.Render()
- self.mRenWin.Render()
- w2i.Update()
- writer = vtksnl.vtkPNGWriter()
- writer.SetInputConnection(w2i.GetOutputPort())
- if filename!=None:
- writer.SetFileName(filename)
- else:
- writer.WriteToMemoryOn()
- writer.Write()
- if filename:
- return filename
- else:
- return writer.GetResult()
-
- def captureWindow(self):
- """ captureWindow() -> None
- Capture the window contents to file
-
- """
- fn = QtGui.QFileDialog.getSaveFileName(None,
- "Save file as...",
- "screenshot.png",
- "Images (*.png)")
- if fn.isNull():
- return
- self.saveToPNG(str(fn))
-
- def grabWindowPixmap(self):
- """ grabWindowImage() -> QPixmap
- Widget special grabbing function
-
- """
- uchar = self.saveToPNG(None)
-
- ba = QtCore.QByteArray()
- buf = QtCore.QBuffer(ba)
- buf.open(QtCore.QIODevice.WriteOnly)
- for i in xrange(uchar.GetNumberOfTuples()):
- c = uchar.GetValue(i)
- buf.putChar(chr(c))
- buf.close()
-
- pixmap = QtGui.QPixmap()
- pixmap.loadFromData(ba, 'PNG')
- return pixmap
-
- def dumpToFile(self, filename):
- """dumpToFile() -> None
- Dumps itself as an image to a file, calling saveToPNG
- """
- self.saveToPNG(filename)
-
-class QVTKViewWidgetCapture(QtGui.QAction):
- """
- QVTKViewWidgetCapture is the action to capture the vtk rendering
- window to an image
-
- """
- def __init__(self, parent=None):
- """ QVTKViewWidgetCapture(parent: QWidget) -> QVTKViewWidgetCapture
- Setup the image, status tip, etc. of the action
-
- """
- QtGui.QAction.__init__(self,
- QtGui.QIcon(":/images/camera.png"),
- "&Capture image to file",
- parent)
- self.setStatusTip("Capture the rendered image to a file")
-
- def triggeredSlot(self, checked=False):
- """ toggledSlot(checked: boolean) -> None
- Execute the action when the button is clicked
-
- """
- cellWidget = self.toolBar.getSnappedWidget()
- cellWidget.captureWindow()
-
-class QVTKViewWidgetSaveCamera(QtGui.QAction):
- """
- QVTKViewWidgetSaveCamera is the action to capture the current camera
- of the vtk renderers and save it back to the pipeline
-
- """
- def __init__(self, parent=None):
- """ QVTKViewWidgetSaveCamera(parent: QWidget) -> QVTKViewWidgetSaveCamera
- Setup the image, status tip, etc. of the action
-
- """
- QtGui.QAction.__init__(self,
- "Save &Camera",
- parent)
- self.setStatusTip("Save current camera views to the pipeline")
-
- def setCamera(self, controller):
- ops = []
- pipeline = controller.current_pipeline
- cellWidget = self.toolBar.getSnappedWidget()
- renderers = cellWidget.getRendererList()
- for ren in renderers:
- cam = ren.GetActiveCamera()
- cpos = cam.GetPosition()
- cfol = cam.GetFocalPoint()
- cup = cam.GetViewUp()
- rendererId = cellWidget.renderer_maps[ren]
- # Looking for SetActiveCamera()
- camera = None
- renderer = pipeline.modules[rendererId]
- for c in pipeline.connections.values():
- if c.destination.moduleId==rendererId:
- if c.destination.name=='SetActiveCamera':
- camera = pipeline.modules[c.source.moduleId]
- break
-
- if not camera:
- # Create camera
- vtk_package = 'edu.utah.sci.vistrails.vtksnl'
- camera = controller.create_module(vtk_package, 'vtkCamera', '',
- 0.0, 0.0)
- ops.append(('add', camera))
-
- # Connect camera to renderer
- camera_conn = controller.create_connection(camera, 'self',
- renderer,
- 'SetActiveCamera')
- ops.append(('add', camera_conn))
- # update functions
- def convert_to_str(arglist):
- new_arglist = []
- for arg in arglist:
- new_arglist.append(str(arg))
- return new_arglist
- functions = [('SetPosition', convert_to_str(cpos)),
- ('SetFocalPoint', convert_to_str(cfol)),
- ('SetViewUp', convert_to_str(cup))]
- ops.extend(controller.update_functions_ops(camera, functions))
-
- action = core.db.action.create_action(ops)
- controller.add_new_action(action)
- controller.perform_action(action)
- controller.select_latest_version()
-
- def triggeredSlot(self, checked=False):
- """ toggledSlot(checked: boolean) -> None
- Execute the action when the button is clicked
-
- """
- visApp = QtCore.QCoreApplication.instance()
- if hasattr(visApp, 'builderWindow'):
- builderWindow = visApp.builderWindow
- if builderWindow:
- info = self.toolBar.sheet.getCellPipelineInfo(
- self.toolBar.row, self.toolBar.col)
- if info:
- info = info[0]
- viewManager = builderWindow.viewManager
- view = viewManager.ensureVistrail(info['locator'])
- if view:
- controller = view.controller
- controller.change_selected_version(info['version'])
- self.setCamera(controller)
-
-
-class QVTKViewWidgetToolBar(QCellToolBar):
- """
- QVTKViewWidgetToolBar derives from QCellToolBar to give the VTKViewCell
- a customizable toolbar
-
- """
- def createToolBar(self):
- """ createToolBar() -> None
- This will get call initiallly to add customizable widgets
-
- """
- self.appendAction(QVTKViewWidgetCapture(self))
- self.addAnimationButtons()
- self.appendAction(QVTKViewWidgetSaveCamera(self))
-
-def registerSelf():
- """ registerSelf() -> None
- Registry module with the registry
- """
- identifier = 'edu.utah.sci.vistrails.vtksnl'
- registry = get_module_registry()
- registry.add_module(VTKViewCell)
- registry.add_input_port(VTKViewCell, "Location", CellLocation)
- import core.debug
- for (port,module) in [("SetRenderView",'vtkRenderView')]:
- try:
- registry.add_input_port(VTKViewCell, port,'(%s:%s)'%(identifier,module))
-
- except Exception, e:
- core.debug.warning(str(e))
-
- registry.add_output_port(VTKViewCell, "self", VTKViewCell)
diff --git a/data/1n25.pdb b/data/1n25.pdb
deleted file mode 100644
index c7b0213..0000000
--- a/data/1n25.pdb
+++ /dev/null
@@ -1,6334 +0,0 @@
-HEADER VIRUS/VIRAL PROTEIN 21-OCT-02 1N25
-TITLE CRYSTAL STRUCTURE OF THE SV40 LARGE T ANTIGEN HELICASE
-TITLE 2 DOMAIN
-COMPND MOL_ID: 1;
-COMPND 2 MOLECULE: LARGE T ANTIGEN;
-COMPND 3 CHAIN: A, B;
-COMPND 4 FRAGMENT: HELICASE DOMAIN;
-COMPND 5 ENGINEERED: YES
-SOURCE MOL_ID: 1;
-SOURCE 2 ORGANISM_SCIENTIFIC: SIMIAN VIRUS 40;
-SOURCE 3 ORGANISM_COMMON: VIRUS;
-SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
-SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA;
-SOURCE 6 EXPRESSION_SYSTEM_STRAIN: XA90;
-SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
-SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-2TK
-KEYWDS HELICASE DOMAIN
-EXPDTA X-RAY DIFFRACTION
-AUTHOR D.LI,R.ZHAO,W.LILYESTROM,D.GAI,R.ZHANG,J.A.DECAPRIO,
-AUTHOR 2 E.FANNING,A.JOCHIMIAK,G.SZAKONYI,X.S.CHEN
-REVDAT 1 03-JUN-03 1N25 0
-JRNL AUTH D.LI,R.ZHAO,W.LILYESTROM,D.GAI,R.ZHANG,
-JRNL AUTH 2 J.A.DECAPRIO,E.FANNING,A.JOCHIMIAK,G.SZAKONYI,
-JRNL AUTH 3 X.S.CHEN
-JRNL TITL STRUCTURE OF THE REPLICATIVE HELICASE OF THE
-JRNL TITL 2 ONCOPROTEIN SV40 LARGE TUMOUR ANTIGEN
-JRNL REF NATURE V. 423 512 2003
-JRNL REFN ASTM NATUAS UK ISSN 0028-0836
-REMARK 1
-REMARK 2
-REMARK 2 RESOLUTION. 2.80 ANGSTROMS.
-REMARK 3
-REMARK 3 REFINEMENT.
-REMARK 3 PROGRAM : CNS
-REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
-REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
-REMARK 3 : READ,RICE,SIMONSON,WARREN
-REMARK 3
-REMARK 3 REFINEMENT TARGET : ENGH & HUBER
-REMARK 3
-REMARK 3 DATA USED IN REFINEMENT.
-REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80
-REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00
-REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
-REMARK 3 OUTLIER CUTOFF HIGH (RMS(ABS(F))) : NULL
-REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.3
-REMARK 3 NUMBER OF REFLECTIONS : 26688
-REMARK 3
-REMARK 3 FIT TO DATA USED IN REFINEMENT.
-REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
-REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
-REMARK 3 R VALUE (WORKING SET) : 0.243
-REMARK 3 FREE R VALUE : 0.276
-REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
-REMARK 3 FREE R VALUE TEST SET COUNT : 1333
-REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
-REMARK 3
-REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
-REMARK 3 TOTAL NUMBER OF BINS USED : 26
-REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80
-REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.84
-REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
-REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 921
-REMARK 3 BIN R VALUE (WORKING SET) : 0.3670
-REMARK 3 BIN FREE R VALUE : 0.3920
-REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00
-REMARK 3 BIN FREE R VALUE TEST SET COUNT : 49
-REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
-REMARK 3
-REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
-REMARK 3 PROTEIN ATOMS : 5806
-REMARK 3 NUCLEIC ACID ATOMS : 0
-REMARK 3 HETEROGEN ATOMS : 0
-REMARK 3 SOLVENT ATOMS : 0
-REMARK 3
-REMARK 3 B VALUES.
-REMARK 3 FROM WILSON PLOT (A**2) : NULL
-REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.79
-REMARK 3 OVERALL ANISOTROPIC B VALUE.
-REMARK 3 B11 (A**2) : 13.86600
-REMARK 3 B22 (A**2) : 13.86600
-REMARK 3 B33 (A**2) : -27.73200
-REMARK 3 B12 (A**2) : 3.91200
-REMARK 3 B13 (A**2) : 0.00000
-REMARK 3 B23 (A**2) : 0.00000
-REMARK 3
-REMARK 3 ESTIMATED COORDINATE ERROR.
-REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40
-REMARK 3 ESD FROM SIGMAA (A) : 0.57
-REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
-REMARK 3
-REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
-REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.47
-REMARK 3 ESD FROM C-V SIGMAA (A) : 0.62
-REMARK 3
-REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
-REMARK 3 BOND LENGTHS (A) : 0.009
-REMARK 3 BOND ANGLES (DEGREES) : 1.37
-REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.54
-REMARK 3 IMPROPER ANGLES (DEGREES) : 0.80
-REMARK 3
-REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC
-REMARK 3
-REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
-REMARK 3 MAIN-CHAIN BOND (A**2) : 2.953 ; NULL
-REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.570 ; NULL
-REMARK 3 SIDE-CHAIN BOND (A**2) : 4.926 ; NULL
-REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.546 ; NULL
-REMARK 3
-REMARK 3 BULK SOLVENT MODELING.
-REMARK 3 METHOD USED : ANISOTROPIC
-REMARK 3 KSOL : 0.33
-REMARK 3 BSOL : 30.79
-REMARK 3
-REMARK 3 NCS MODEL : NULL
-REMARK 3
-REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
-REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
-REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
-REMARK 3
-REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
-REMARK 3 PARAMETER FILE 2 : ION.PARAM
-REMARK 3 PARAMETER FILE 3 : NULL
-REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
-REMARK 3 TOPOLOGY FILE 2 : ION.TOP
-REMARK 3 TOPOLOGY FILE 3 : NULL
-REMARK 3
-REMARK 3 OTHER REFINEMENT REMARKS: NULL
-REMARK 4
-REMARK 4 1N25 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
-REMARK 100
-REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-2002.
-REMARK 100 THE RCSB ID CODE IS RCSB017424.
-REMARK 200
-REMARK 200 EXPERIMENTAL DETAILS
-REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
-REMARK 200 DATE OF DATA COLLECTION : 20-JUN-2001
-REMARK 200 TEMPERATURE (KELVIN) : 100.0
-REMARK 200 PH : 7.60
-REMARK 200 NUMBER OF CRYSTALS USED : 1
-REMARK 200
-REMARK 200 SYNCHROTRON (Y/N) : Y
-REMARK 200 RADIATION SOURCE : APS
-REMARK 200 BEAMLINE : 19ID
-REMARK 200 X-RAY GENERATOR MODEL : NULL
-REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
-REMARK 200 WAVELENGTH OR RANGE (A) : 1.074385
-REMARK 200 MONOCHROMATOR : SI 220
-REMARK 200 OPTICS : UNDULATOR A
-REMARK 200
-REMARK 200 DETECTOR TYPE : CCD
-REMARK 200 DETECTOR MANUFACTURER : SBC2 3K X 3K CCD BUILT BY ANL
-REMARK 200 -ECT 210MM X 210MM ACTIVE AREA
-REMARK 200 1.8 SEC READOUT
-REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
-REMARK 200 DATA SCALING SOFTWARE : TRUNCATE
-REMARK 200
-REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27610
-REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800
-REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
-REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
-REMARK 200
-REMARK 200 OVERALL.
-REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4
-REMARK 200 DATA REDUNDANCY : 6.200
-REMARK 200 R MERGE (I) : 0.12500
-REMARK 200 R SYM (I) : NULL
-REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000
-REMARK 200
-REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
-REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80
-REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90
-REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2
-REMARK 200 DATA REDUNDANCY IN SHELL : 5.40
-REMARK 200 R MERGE FOR SHELL (I) : 0.54400
-REMARK 200 R SYM FOR SHELL (I) : 0.54400
-REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900
-REMARK 200
-REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
-REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
-REMARK 200 SOFTWARE USED: SOLVE
-REMARK 200 STARTING MODEL: NULL
-REMARK 200
-REMARK 200 REMARK: NULL
-REMARK 280
-REMARK 280 CRYSTAL
-REMARK 280 SOLVENT CONTENT, VS (%): 64.0
-REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40
-REMARK 280
-REMARK 280 CRYSTALLIZATION CONDITIONS: GLYCEROL, DTT, HEPES, NACL, ETOH,
-REMARK 280 EDTA, PH 7.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
-REMARK 290
-REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
-REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1
-REMARK 290
-REMARK 290 SYMOP SYMMETRY
-REMARK 290 NNNMMM OPERATOR
-REMARK 290 1555 X,Y,Z
-REMARK 290 2555 -Y,X-Y,Z
-REMARK 290 3555 -X+Y,-X,Z
-REMARK 290 4555 Y,X,-Z
-REMARK 290 5555 X-Y,-Y,-Z
-REMARK 290 6555 -X,-X+Y,-Z
-REMARK 290
-REMARK 290 WHERE NNN -> OPERATOR NUMBER
-REMARK 290 MMM -> TRANSLATION VECTOR
-REMARK 290
-REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
-REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
-REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
-REMARK 290 RELATED MOLECULES.
-REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
-REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
-REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
-REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
-REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
-REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
-REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
-REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
-REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
-REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
-REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
-REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
-REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000
-REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
-REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
-REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000
-REMARK 290
-REMARK 290 REMARK: NULL
-REMARK 300
-REMARK 300 BIOMOLECULE: 1
-REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
-REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR
-REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
-REMARK 350
-REMARK 350 GENERATING THE BIOMOLECULE
-REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
-REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
-REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
-REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
-REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
-REMARK 350
-REMARK 350 BIOMOLECULE: 1
-REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
-REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
-REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
-REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
-REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 120.32100
-REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000
-REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
-REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 60.16050
-REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 104.20104
-REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
-REMARK 465
-REMARK 465 MISSING RESIDUES
-REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
-REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
-REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
-REMARK 465
-REMARK 465 M RES C SSSEQI
-REMARK 465 GLU A 260
-REMARK 465 GLU A 261
-REMARK 465 ALA A 262
-REMARK 465 GLU A 263
-REMARK 465 GLU A 264
-REMARK 465 THR A 265
-REMARK 465 GLU B 260
-REMARK 465 GLU B 261
-REMARK 465 ALA B 262
-REMARK 465 GLU B 263
-REMARK 465 GLU B 264
-REMARK 465 THR B 265
-REMARK 500
-REMARK 500 GEOMETRY AND STEREOCHEMISTRY
-REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
-REMARK 500
-REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
-REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
-REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
-REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
-REMARK 500
-REMARK 500 STANDARD TABLE:
-REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3)
-REMARK 500
-REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
-REMARK 500
-REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
-REMARK 500 MET A 360 SD MET A 360 CE 0.096
-REMARK 500 MET A 401 SD MET A 401 CE -0.092
-REMARK 500 MET A 528 SD MET A 528 CE -0.069
-REMARK 500 MET A 578 SD MET A 578 CE -0.195
-REMARK 500 MET A 615 CG MET A 615 SD 0.074
-REMARK 500 MET A 615 SD MET A 615 CE -0.109
-REMARK 500 MET B 360 SD MET B 360 CE -0.073
-REMARK 500 MET B 388 SD MET B 388 CE -0.170
-REMARK 500 MET B 412 SD MET B 412 CE -0.057
-REMARK 500 CYS B 443 CB CYS B 443 SG -0.061
-REMARK 500 MET B 528 SD MET B 528 CE -0.095
-REMARK 500 MET B 578 SD MET B 578 CE -0.190
-REMARK 500 MET B 615 SD MET B 615 CE -0.104
-REMARK 500
-REMARK 500 GEOMETRY AND STEREOCHEMISTRY
-REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
-REMARK 500
-REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
-REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
-REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
-REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
-REMARK 500
-REMARK 500 STANDARD TABLE:
-REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
-REMARK 500
-REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
-REMARK 500
-REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
-REMARK 500 GLY A 480 N - CA - C ANGL. DEV. = 16.4 DEGREES
-REMARK 500 GLY A 503 N - CA - C ANGL. DEV. = 8.3 DEGREES
-REMARK 500 THR A 518 N - CA - C ANGL. DEV. = -8.8 DEGREES
-REMARK 500 ILE A 520 N - CA - C ANGL. DEV. = -8.3 DEGREES
-REMARK 500 MET A 528 CB - CG - SD ANGL. DEV. = -8.6 DEGREES
-REMARK 500 ILE A 623 N - CA - C ANGL. DEV. = 9.4 DEGREES
-REMARK 500 THR B 356 N - CA - C ANGL. DEV. = -9.0 DEGREES
-REMARK 500 ALA B 389 N - CA - C ANGL. DEV. = -9.1 DEGREES
-REMARK 500 GLY B 444 N - CA - C ANGL. DEV. = -9.9 DEGREES
-REMARK 500 ASN B 451 N - CA - C ANGL. DEV. =-10.2 DEGREES
-REMARK 500 ARG B 517 N - CA - C ANGL. DEV. = 9.2 DEGREES
-REMARK 500 THR B 518 N - CA - C ANGL. DEV. =-11.1 DEGREES
-REMARK 500 ILE B 520 N - CA - C ANGL. DEV. = -9.5 DEGREES
-REMARK 500 VAL B 526 N - CA - C ANGL. DEV. = -8.9 DEGREES
-REMARK 500 ASN B 529 N - CA - C ANGL. DEV. = 9.5 DEGREES
-REMARK 500 VAL B 625 N - CA - C ANGL. DEV. = 9.3 DEGREES
-DBREF 1N25 A 260 627 GB 335056 AAB59924 260 627
-DBREF 1N25 B 260 627 GB 335056 AAB59924 260 627
-SEQRES 1 A 368 GLU GLU ALA GLU GLU THR LYS GLN VAL SER TRP LYS LEU
-SEQRES 2 A 368 VAL THR GLU TYR ALA MET GLU THR LYS CYS ASP ASP VAL
-SEQRES 3 A 368 LEU LEU LEU LEU GLY MET TYR LEU GLU PHE GLN TYR SER
-SEQRES 4 A 368 PHE GLU MET CYS LEU LYS CYS ILE LYS LYS GLU GLN PRO
-SEQRES 5 A 368 SER HIS TYR LYS TYR HIS GLU LYS HIS TYR ALA ASN ALA
-SEQRES 6 A 368 ALA ILE PHE ALA ASP SER LYS ASN GLN LYS THR ILE CYS
-SEQRES 7 A 368 GLN GLN ALA VAL ASP THR VAL LEU ALA LYS LYS ARG VAL
-SEQRES 8 A 368 ASP SER LEU GLN LEU THR ARG GLU GLN MET LEU THR ASN
-SEQRES 9 A 368 ARG PHE ASN ASP LEU LEU ASP ARG MET ASP ILE MET PHE
-SEQRES 10 A 368 GLY SER THR GLY SER ALA ASP ILE GLU GLU TRP MET ALA
-SEQRES 11 A 368 GLY VAL ALA TRP LEU HIS CYS LEU LEU PRO LYS MET ASP
-SEQRES 12 A 368 SER VAL VAL TYR ASP PHE LEU LYS CYS MET VAL TYR ASN
-SEQRES 13 A 368 ILE PRO LYS LYS ARG TYR TRP LEU PHE LYS GLY PRO ILE
-SEQRES 14 A 368 ASP SER GLY LYS THR THR LEU ALA ALA ALA LEU LEU GLU
-SEQRES 15 A 368 LEU CYS GLY GLY LYS ALA LEU ASN VAL ASN LEU PRO LEU
-SEQRES 16 A 368 ASP ARG LEU ASN PHE GLU LEU GLY VAL ALA ILE ASP GLN
-SEQRES 17 A 368 PHE LEU VAL VAL PHE GLU ASP VAL LYS GLY THR GLY GLY
-SEQRES 18 A 368 GLU SER ARG ASP LEU PRO SER GLY GLN GLY ILE ASN ASN
-SEQRES 19 A 368 LEU ASP ASN LEU ARG ASP TYR LEU ASP GLY SER VAL LYS
-SEQRES 20 A 368 VAL ASN LEU GLU LYS LYS HIS LEU ASN LYS ARG THR GLN
-SEQRES 21 A 368 ILE PHE PRO PRO GLY ILE VAL THR MET ASN GLU TYR SER
-SEQRES 22 A 368 VAL PRO LYS THR LEU GLN ALA ARG PHE VAL LYS GLN ILE
-SEQRES 23 A 368 ASP PHE ARG PRO LYS ASP TYR LEU LYS HIS CYS LEU GLU
-SEQRES 24 A 368 ARG SER GLU PHE LEU LEU GLU LYS ARG ILE ILE GLN SER
-SEQRES 25 A 368 GLY ILE ALA LEU LEU LEU MET LEU ILE TRP TYR ARG PRO
-SEQRES 26 A 368 VAL ALA GLU PHE ALA GLN SER ILE GLN SER ARG ILE VAL
-SEQRES 27 A 368 GLU TRP LYS GLU ARG LEU ASP LYS GLU PHE SER LEU SER
-SEQRES 28 A 368 VAL TYR GLN LYS MET LYS PHE ASN VAL ALA MET GLY ILE
-SEQRES 29 A 368 GLY VAL LEU ASP
-SEQRES 1 B 368 GLU GLU ALA GLU GLU THR LYS GLN VAL SER TRP LYS LEU
-SEQRES 2 B 368 VAL THR GLU TYR ALA MET GLU THR LYS CYS ASP ASP VAL
-SEQRES 3 B 368 LEU LEU LEU LEU GLY MET TYR LEU GLU PHE GLN TYR SER
-SEQRES 4 B 368 PHE GLU MET CYS LEU LYS CYS ILE LYS LYS GLU GLN PRO
-SEQRES 5 B 368 SER HIS TYR LYS TYR HIS GLU LYS HIS TYR ALA ASN ALA
-SEQRES 6 B 368 ALA ILE PHE ALA ASP SER LYS ASN GLN LYS THR ILE CYS
-SEQRES 7 B 368 GLN GLN ALA VAL ASP THR VAL LEU ALA LYS LYS ARG VAL
-SEQRES 8 B 368 ASP SER LEU GLN LEU THR ARG GLU GLN MET LEU THR ASN
-SEQRES 9 B 368 ARG PHE ASN ASP LEU LEU ASP ARG MET ASP ILE MET PHE
-SEQRES 10 B 368 GLY SER THR GLY SER ALA ASP ILE GLU GLU TRP MET ALA
-SEQRES 11 B 368 GLY VAL ALA TRP LEU HIS CYS LEU LEU PRO LYS MET ASP
-SEQRES 12 B 368 SER VAL VAL TYR ASP PHE LEU LYS CYS MET VAL TYR ASN
-SEQRES 13 B 368 ILE PRO LYS LYS ARG TYR TRP LEU PHE LYS GLY PRO ILE
-SEQRES 14 B 368 ASP SER GLY LYS THR THR LEU ALA ALA ALA LEU LEU GLU
-SEQRES 15 B 368 LEU CYS GLY GLY LYS ALA LEU ASN VAL ASN LEU PRO LEU
-SEQRES 16 B 368 ASP ARG LEU ASN PHE GLU LEU GLY VAL ALA ILE ASP GLN
-SEQRES 17 B 368 PHE LEU VAL VAL PHE GLU ASP VAL LYS GLY THR GLY GLY
-SEQRES 18 B 368 GLU SER ARG ASP LEU PRO SER GLY GLN GLY ILE ASN ASN
-SEQRES 19 B 368 LEU ASP ASN LEU ARG ASP TYR LEU ASP GLY SER VAL LYS
-SEQRES 20 B 368 VAL ASN LEU GLU LYS LYS HIS LEU ASN LYS ARG THR GLN
-SEQRES 21 B 368 ILE PHE PRO PRO GLY ILE VAL THR MET ASN GLU TYR SER
-SEQRES 22 B 368 VAL PRO LYS THR LEU GLN ALA ARG PHE VAL LYS GLN ILE
-SEQRES 23 B 368 ASP PHE ARG PRO LYS ASP TYR LEU LYS HIS CYS LEU GLU
-SEQRES 24 B 368 ARG SER GLU PHE LEU LEU GLU LYS ARG ILE ILE GLN SER
-SEQRES 25 B 368 GLY ILE ALA LEU LEU LEU MET LEU ILE TRP TYR ARG PRO
-SEQRES 26 B 368 VAL ALA GLU PHE ALA GLN SER ILE GLN SER ARG ILE VAL
-SEQRES 27 B 368 GLU TRP LYS GLU ARG LEU ASP LYS GLU PHE SER LEU SER
-SEQRES 28 B 368 VAL TYR GLN LYS MET LYS PHE ASN VAL ALA MET GLY ILE
-SEQRES 29 B 368 GLY VAL LEU ASP
-HET ZN A 700 1
-HET ZN B 700 1
-HETNAM ZN ZINC ION
-FORMUL 3 ZN 2(ZN1 2+)
-HELIX 1 1 SER A 269 LYS A 281 1 13
-HELIX 2 2 ASP A 284 LEU A 293 1 10
-HELIX 3 3 GLU A 294 TYR A 297 5 4
-HELIX 4 4 CYS A 302 LYS A 307 1 6
-HELIX 5 5 GLN A 310 LYS A 315 1 6
-HELIX 6 6 TYR A 316 ALA A 328 1 13
-HELIX 7 7 ASN A 332 LEU A 355 1 24
-HELIX 8 8 THR A 356 PHE A 376 1 21
-HELIX 9 9 ASP A 383 HIS A 395 1 13
-HELIX 10 10 LYS A 400 ASN A 415 1 16
-HELIX 11 11 GLY A 431 GLY A 444 1 14
-HELIX 12 12 ARG A 456 GLY A 462 1 7
-HELIX 13 13 VAL A 463 ILE A 465 5 3
-HELIX 14 14 GLN A 489 ASP A 495 1 7
-HELIX 15 15 LEU A 497 GLY A 503 1 7
-HELIX 16 16 PRO A 534 ALA A 539 1 6
-HELIX 17 17 LYS A 550 ARG A 559 1 10
-HELIX 18 18 GLU A 561 LYS A 566 1 6
-HELIX 19 19 SER A 571 ARG A 583 1 13
-HELIX 20 20 PRO A 584 PHE A 588 5 5
-HELIX 21 21 ALA A 589 LYS A 605 1 17
-HELIX 22 22 SER A 608 MET A 621 1 14
-HELIX 23 23 SER B 269 GLU B 279 1 11
-HELIX 24 24 ASP B 284 LEU B 293 1 10
-HELIX 25 25 GLU B 294 TYR B 297 5 4
-HELIX 26 26 CYS B 302 LYS B 307 1 6
-HELIX 27 27 GLN B 310 LYS B 315 1 6
-HELIX 28 28 TYR B 316 ALA B 328 1 13
-HELIX 29 29 ASN B 332 LEU B 355 1 24
-HELIX 30 30 THR B 356 PHE B 376 1 21
-HELIX 31 31 ASP B 383 LEU B 398 1 16
-HELIX 32 32 LYS B 400 ASN B 415 1 16
-HELIX 33 33 GLY B 431 GLY B 444 1 14
-HELIX 34 34 ARG B 456 GLY B 462 1 7
-HELIX 35 35 VAL B 463 ILE B 465 5 3
-HELIX 36 36 GLN B 489 ASP B 495 1 7
-HELIX 37 37 LEU B 497 ASP B 502 1 6
-HELIX 38 38 PRO B 534 ALA B 539 1 6
-HELIX 39 39 LYS B 550 SER B 560 1 11
-HELIX 40 40 GLU B 561 LYS B 566 1 6
-HELIX 41 41 SER B 571 ARG B 583 1 13
-HELIX 42 42 PRO B 584 PHE B 588 5 5
-HELIX 43 43 ALA B 589 PHE B 607 1 19
-HELIX 44 44 SER B 608 GLY B 622 1 15
-SHEET 1 A 5 GLY A 445 LEU A 448 0
-SHEET 2 A 5 LEU A 469 VAL A 475 1 O VAL A 471 N LEU A 448
-SHEET 3 A 5 GLY A 524 MET A 528 1 O ILE A 525 N PHE A 472
-SHEET 4 A 5 TYR A 421 LYS A 425 1 N PHE A 424 O MET A 528
-SHEET 5 A 5 LYS A 543 ASP A 546 1 O ILE A 545 N LEU A 423
-SHEET 1 B 2 VAL A 507 LYS A 511 0
-SHEET 2 B 2 LEU A 514 GLN A 519 -1 O GLN A 519 N VAL A 507
-SHEET 1 C 5 LYS B 446 LEU B 448 0
-SHEET 2 C 5 VAL B 470 VAL B 475 1 O VAL B 471 N LEU B 448
-SHEET 3 C 5 GLY B 524 MET B 528 1 O THR B 527 N PHE B 472
-SHEET 4 C 5 TYR B 421 LYS B 425 1 N PHE B 424 O VAL B 526
-SHEET 5 C 5 LYS B 543 ASP B 546 1 O ILE B 545 N LEU B 423
-SHEET 1 D 2 VAL B 507 LYS B 511 0
-SHEET 2 D 2 LEU B 514 GLN B 519 -1 O GLN B 519 N VAL B 507
-CRYST1 120.321 120.321 132.202 90.00 90.00 120.00 P 3 2 1 12
-ORIGX1 1.000000 0.000000 0.000000 0.00000
-ORIGX2 0.000000 1.000000 0.000000 0.00000
-ORIGX3 0.000000 0.000000 1.000000 0.00000
-SCALE1 0.008311 0.004798 0.000000 0.00000
-SCALE2 0.000000 0.009596 0.000000 0.00000
-SCALE3 0.000000 0.000000 0.007564 0.00000
-ATOM 1 N LYS A 266 44.458 43.722 -0.913 1.00 78.76 N
-ATOM 2 CA LYS A 266 45.695 44.058 -1.666 1.00 79.67 C
-ATOM 3 C LYS A 266 46.880 44.311 -0.754 1.00 83.17 C
-ATOM 4 O LYS A 266 47.722 43.438 -0.543 1.00 81.29 O
-ATOM 5 CB LYS A 266 45.465 45.286 -2.545 1.00 78.46 C
-ATOM 6 CG LYS A 266 45.019 44.931 -3.946 1.00 78.06 C
-ATOM 7 CD LYS A 266 46.037 44.013 -4.599 1.00 76.42 C
-ATOM 8 CE LYS A 266 45.609 43.599 -5.987 1.00 75.78 C
-ATOM 9 NZ LYS A 266 46.626 42.697 -6.594 1.00 77.33 N
-ATOM 10 N GLN A 267 46.954 45.520 -0.220 1.00 83.76 N
-ATOM 11 CA GLN A 267 48.046 45.864 0.670 1.00 82.59 C
-ATOM 12 C GLN A 267 47.527 46.868 1.687 1.00 77.07 C
-ATOM 13 O GLN A 267 47.300 48.035 1.367 1.00 70.67 O
-ATOM 14 CB GLN A 267 49.216 46.436 -0.142 1.00 92.78 C
-ATOM 15 CG GLN A 267 50.558 46.410 0.584 1.00112.09 C
-ATOM 16 CD GLN A 267 50.893 45.038 1.149 1.00120.64 C
-ATOM 17 OE1 GLN A 267 51.357 44.925 2.285 1.00123.65 O
-ATOM 18 NE2 GLN A 267 50.667 43.990 0.355 1.00123.10 N
-ATOM 19 N VAL A 268 47.311 46.392 2.908 1.00 65.08 N
-ATOM 20 CA VAL A 268 46.806 47.239 3.975 1.00 54.25 C
-ATOM 21 C VAL A 268 47.773 48.372 4.244 1.00 49.67 C
-ATOM 22 O VAL A 268 48.984 48.188 4.225 1.00 45.61 O
-ATOM 23 CB VAL A 268 46.609 46.441 5.283 1.00 51.93 C
-ATOM 24 CG1 VAL A 268 45.932 47.311 6.332 1.00 50.50 C
-ATOM 25 CG2 VAL A 268 45.783 45.197 5.007 1.00 53.61 C
-ATOM 26 N SER A 269 47.222 49.550 4.491 1.00 42.47 N
-ATOM 27 CA SER A 269 48.028 50.724 4.785 1.00 38.57 C
-ATOM 28 C SER A 269 48.313 50.842 6.279 1.00 37.02 C
-ATOM 29 O SER A 269 47.508 51.403 7.011 1.00 37.31 O
-ATOM 30 CB SER A 269 47.308 51.988 4.316 1.00 36.94 C
-ATOM 31 OG SER A 269 47.925 53.135 4.865 1.00 35.77 O
-ATOM 32 N TRP A 270 49.453 50.322 6.729 1.00 34.84 N
-ATOM 33 CA TRP A 270 49.826 50.394 8.142 1.00 34.47 C
-ATOM 34 C TRP A 270 49.854 51.843 8.626 1.00 36.89 C
-ATOM 35 O TRP A 270 49.569 52.133 9.787 1.00 35.43 O
-ATOM 36 CB TRP A 270 51.213 49.789 8.364 1.00 30.01 C
-ATOM 37 CG TRP A 270 51.305 48.330 8.150 1.00 25.31 C
-ATOM 38 CD1 TRP A 270 50.766 47.631 7.132 1.00 22.40 C
-ATOM 39 CD2 TRP A 270 52.034 47.385 8.948 1.00 24.93 C
-ATOM 40 NE1 TRP A 270 51.106 46.301 7.231 1.00 23.28 N
-ATOM 41 CE2 TRP A 270 51.884 46.123 8.343 1.00 22.30 C
-ATOM 42 CE3 TRP A 270 52.800 47.485 10.122 1.00 24.62 C
-ATOM 43 CZ2 TRP A 270 52.466 44.966 8.859 1.00 21.50 C
-ATOM 44 CZ3 TRP A 270 53.386 46.324 10.642 1.00 22.83 C
-ATOM 45 CH2 TRP A 270 53.210 45.084 10.008 1.00 21.47 C
-ATOM 46 N LYS A 271 50.199 52.749 7.717 1.00 40.89 N
-ATOM 47 CA LYS A 271 50.301 54.165 8.038 1.00 42.20 C
-ATOM 48 C LYS A 271 48.975 54.744 8.497 1.00 42.18 C
-ATOM 49 O LYS A 271 48.900 55.424 9.517 1.00 39.54 O
-ATOM 50 CB LYS A 271 50.813 54.932 6.821 1.00 45.61 C
-ATOM 51 CG LYS A 271 51.162 56.372 7.116 1.00 52.18 C
-ATOM 52 CD LYS A 271 51.635 57.082 5.873 1.00 55.28 C
-ATOM 53 CE LYS A 271 52.058 58.502 6.200 1.00 56.96 C
-ATOM 54 NZ LYS A 271 52.538 59.205 4.983 1.00 58.32 N
-ATOM 55 N LEU A 272 47.927 54.474 7.734 1.00 41.75 N
-ATOM 56 CA LEU A 272 46.607 54.968 8.079 1.00 41.77 C
-ATOM 57 C LEU A 272 46.188 54.484 9.455 1.00 40.55 C
-ATOM 58 O LEU A 272 45.714 55.266 10.274 1.00 41.22 O
-ATOM 59 CB LEU A 272 45.573 54.511 7.056 1.00 45.58 C
-ATOM 60 CG LEU A 272 45.159 55.560 6.032 1.00 49.61 C
-ATOM 61 CD1 LEU A 272 44.056 54.975 5.176 1.00 53.46 C
-ATOM 62 CD2 LEU A 272 44.671 56.826 6.739 1.00 51.91 C
-ATOM 63 N VAL A 273 46.350 53.191 9.709 1.00 38.10 N
-ATOM 64 CA VAL A 273 45.985 52.642 11.006 1.00 35.48 C
-ATOM 65 C VAL A 273 46.730 53.378 12.126 1.00 35.01 C
-ATOM 66 O VAL A 273 46.175 53.638 13.201 1.00 33.73 O
-ATOM 67 CB VAL A 273 46.292 51.135 11.061 1.00 32.73 C
-ATOM 68 CG1 VAL A 273 46.020 50.599 12.452 1.00 27.49 C
-ATOM 69 CG2 VAL A 273 45.438 50.410 10.025 1.00 30.52 C
-ATOM 70 N THR A 274 47.986 53.726 11.862 1.00 35.07 N
-ATOM 71 CA THR A 274 48.785 54.440 12.840 1.00 37.62 C
-ATOM 72 C THR A 274 48.232 55.844 13.028 1.00 43.27 C
-ATOM 73 O THR A 274 48.231 56.374 14.141 1.00 39.74 O
-ATOM 74 CB THR A 274 50.252 54.544 12.407 1.00 34.96 C
-ATOM 75 OG1 THR A 274 50.851 53.245 12.441 1.00 35.24 O
-ATOM 76 CG2 THR A 274 51.017 55.469 13.339 1.00 33.38 C
-ATOM 77 N GLU A 275 47.766 56.445 11.936 1.00 49.90 N
-ATOM 78 CA GLU A 275 47.214 57.792 11.990 1.00 52.53 C
-ATOM 79 C GLU A 275 45.987 57.804 12.883 1.00 48.41 C
-ATOM 80 O GLU A 275 45.806 58.698 13.707 1.00 43.54 O
-ATOM 81 CB GLU A 275 46.840 58.272 10.591 1.00 65.86 C
-ATOM 82 CG GLU A 275 46.164 59.624 10.593 1.00 93.06 C
-ATOM 83 CD GLU A 275 45.756 60.068 9.215 1.00104.71 C
-ATOM 84 OE1 GLU A 275 45.841 59.243 8.279 1.00108.70 O
-ATOM 85 OE2 GLU A 275 45.343 61.238 9.074 1.00109.07 O
-ATOM 86 N TYR A 276 45.140 56.801 12.715 1.00 40.92 N
-ATOM 87 CA TYR A 276 43.940 56.691 13.525 1.00 33.40 C
-ATOM 88 C TYR A 276 44.363 56.535 14.988 1.00 30.54 C
-ATOM 89 O TYR A 276 43.845 57.220 15.869 1.00 27.65 O
-ATOM 90 CB TYR A 276 43.114 55.490 13.068 1.00 33.41 C
-ATOM 91 CG TYR A 276 41.929 55.197 13.950 1.00 36.52 C
-ATOM 92 CD1 TYR A 276 40.893 56.122 14.096 1.00 37.24 C
-ATOM 93 CD2 TYR A 276 41.856 53.999 14.671 1.00 37.54 C
-ATOM 94 CE1 TYR A 276 39.816 55.863 14.939 1.00 37.19 C
-ATOM 95 CE2 TYR A 276 40.790 53.732 15.512 1.00 37.31 C
-ATOM 96 CZ TYR A 276 39.772 54.665 15.645 1.00 37.89 C
-ATOM 97 OH TYR A 276 38.714 54.392 16.492 1.00 40.18 O
-ATOM 98 N ALA A 277 45.318 55.644 15.240 1.00 28.42 N
-ATOM 99 CA ALA A 277 45.806 55.429 16.597 1.00 27.30 C
-ATOM 100 C ALA A 277 46.291 56.743 17.236 1.00 27.20 C
-ATOM 101 O ALA A 277 45.897 57.082 18.354 1.00 26.98 O
-ATOM 102 CB ALA A 277 46.938 54.382 16.588 1.00 23.86 C
-ATOM 103 N MET A 278 47.149 57.476 16.533 1.00 30.99 N
-ATOM 104 CA MET A 278 47.666 58.740 17.049 1.00 35.54 C
-ATOM 105 C MET A 278 46.589 59.808 17.213 1.00 39.94 C
-ATOM 106 O MET A 278 46.722 60.694 18.057 1.00 39.37 O
-ATOM 107 CB MET A 278 48.772 59.262 16.141 1.00 35.32 C
-ATOM 108 CG MET A 278 50.084 58.515 16.318 1.00 37.07 C
-ATOM 109 SD MET A 278 51.308 59.375 17.330 1.00 36.64 S
-ATOM 110 CE MET A 278 50.257 60.467 18.334 1.00 34.84 C
-ATOM 111 N GLU A 279 45.527 59.718 16.410 1.00 45.14 N
-ATOM 112 CA GLU A 279 44.408 60.666 16.458 1.00 47.29 C
-ATOM 113 C GLU A 279 43.443 60.328 17.617 1.00 48.11 C
-ATOM 114 O GLU A 279 42.838 61.207 18.241 1.00 41.82 O
-ATOM 115 CB GLU A 279 43.661 60.641 15.114 1.00 54.04 C
-ATOM 116 CG GLU A 279 43.583 61.989 14.410 1.00 69.60 C
-ATOM 117 CD GLU A 279 43.865 61.889 12.919 1.00 77.60 C
-ATOM 118 OE1 GLU A 279 43.135 61.158 12.214 1.00 80.48 O
-ATOM 119 OE2 GLU A 279 44.821 62.543 12.446 1.00 80.21 O
-ATOM 120 N THR A 280 43.313 59.037 17.900 1.00 48.69 N
-ATOM 121 CA THR A 280 42.449 58.548 18.963 1.00 44.94 C
-ATOM 122 C THR A 280 43.267 58.525 20.257 1.00 44.45 C
-ATOM 123 O THR A 280 42.723 58.373 21.356 1.00 42.62 O
-ATOM 124 CB THR A 280 41.969 57.116 18.625 1.00 47.20 C
-ATOM 125 OG1 THR A 280 41.123 57.162 17.473 1.00 52.10 O
-ATOM 126 CG2 THR A 280 41.207 56.501 19.782 1.00 54.38 C
-ATOM 127 N LYS A 281 44.581 58.675 20.110 1.00 47.63 N
-ATOM 128 CA LYS A 281 45.490 58.656 21.249 1.00 49.19 C
-ATOM 129 C LYS A 281 45.463 57.267 21.876 1.00 48.67 C
-ATOM 130 O LYS A 281 45.724 57.099 23.068 1.00 54.24 O
-ATOM 131 CB LYS A 281 45.060 59.701 22.279 1.00 49.36 C
-ATOM 132 CG LYS A 281 45.353 61.144 21.890 1.00 47.49 C
-ATOM 133 CD LYS A 281 44.762 62.105 22.922 1.00 46.90 C
-ATOM 134 CE LYS A 281 45.391 63.496 22.846 1.00 46.08 C
-ATOM 135 NZ LYS A 281 46.778 63.540 23.393 1.00 44.64 N
-ATOM 136 N CYS A 282 45.168 56.268 21.055 1.00 48.98 N
-ATOM 137 CA CYS A 282 45.064 54.905 21.533 1.00 49.25 C
-ATOM 138 C CYS A 282 46.374 54.167 21.774 1.00 49.91 C
-ATOM 139 O CYS A 282 47.074 53.804 20.835 1.00 51.42 O
-ATOM 140 CB CYS A 282 44.213 54.101 20.573 1.00 46.97 C
-ATOM 141 SG CYS A 282 43.966 52.455 21.201 1.00 40.88 S
-ATOM 142 N ASP A 283 46.681 53.920 23.043 1.00 47.36 N
-ATOM 143 CA ASP A 283 47.907 53.225 23.421 1.00 44.65 C
-ATOM 144 C ASP A 283 47.664 51.759 23.774 1.00 43.93 C
-ATOM 145 O ASP A 283 48.568 51.074 24.255 1.00 39.51 O
-ATOM 146 CB ASP A 283 48.576 53.937 24.606 1.00 44.58 C
-ATOM 147 CG ASP A 283 47.640 54.114 25.787 1.00 46.75 C
-ATOM 148 OD1 ASP A 283 47.110 53.103 26.297 1.00 48.30 O
-ATOM 149 OD2 ASP A 283 47.430 55.269 26.211 1.00 49.39 O
-ATOM 150 N ASP A 284 46.444 51.281 23.538 1.00 40.95 N
-ATOM 151 CA ASP A 284 46.081 49.888 23.825 1.00 40.00 C
-ATOM 152 C ASP A 284 45.963 49.101 22.515 1.00 38.39 C
-ATOM 153 O ASP A 284 45.175 49.464 21.636 1.00 36.59 O
-ATOM 154 CB ASP A 284 44.746 49.840 24.571 1.00 45.90 C
-ATOM 155 CG ASP A 284 44.389 48.442 25.049 1.00 54.16 C
-ATOM 156 OD1 ASP A 284 44.402 47.491 24.236 1.00 57.69 O
-ATOM 157 OD2 ASP A 284 44.084 48.298 26.248 1.00 58.14 O
-ATOM 158 N VAL A 285 46.726 48.020 22.380 1.00 34.05 N
-ATOM 159 CA VAL A 285 46.675 47.250 21.146 1.00 29.65 C
-ATOM 160 C VAL A 285 45.341 46.555 20.888 1.00 29.63 C
-ATOM 161 O VAL A 285 44.776 46.674 19.802 1.00 29.84 O
-ATOM 162 CB VAL A 285 47.777 46.201 21.084 1.00 27.34 C
-ATOM 163 CG1 VAL A 285 47.800 45.592 19.702 1.00 27.94 C
-ATOM 164 CG2 VAL A 285 49.116 46.834 21.384 1.00 28.25 C
-ATOM 165 N LEU A 286 44.832 45.819 21.869 1.00 30.50 N
-ATOM 166 CA LEU A 286 43.556 45.141 21.678 1.00 31.23 C
-ATOM 167 C LEU A 286 42.409 46.133 21.489 1.00 31.47 C
-ATOM 168 O LEU A 286 41.468 45.877 20.743 1.00 33.17 O
-ATOM 169 CB LEU A 286 43.261 44.206 22.853 1.00 29.32 C
-ATOM 170 CG LEU A 286 43.987 42.858 22.807 1.00 27.27 C
-ATOM 171 CD1 LEU A 286 43.789 42.142 24.118 1.00 27.98 C
-ATOM 172 CD2 LEU A 286 43.466 42.005 21.657 1.00 26.33 C
-ATOM 173 N LEU A 287 42.492 47.277 22.151 1.00 32.01 N
-ATOM 174 CA LEU A 287 41.447 48.279 22.018 1.00 30.98 C
-ATOM 175 C LEU A 287 41.486 48.882 20.623 1.00 29.38 C
-ATOM 176 O LEU A 287 40.457 49.173 20.043 1.00 28.73 O
-ATOM 177 CB LEU A 287 41.618 49.379 23.065 1.00 31.75 C
-ATOM 178 CG LEU A 287 40.501 50.417 23.035 1.00 31.98 C
-ATOM 179 CD1 LEU A 287 39.167 49.733 23.319 1.00 33.54 C
-ATOM 180 CD2 LEU A 287 40.776 51.500 24.054 1.00 32.79 C
-ATOM 181 N LEU A 288 42.681 49.062 20.078 1.00 26.92 N
-ATOM 182 CA LEU A 288 42.805 49.619 18.738 1.00 25.93 C
-ATOM 183 C LEU A 288 42.277 48.635 17.712 1.00 27.61 C
-ATOM 184 O LEU A 288 41.464 48.988 16.856 1.00 27.45 O
-ATOM 185 CB LEU A 288 44.261 49.937 18.411 1.00 23.92 C
-ATOM 186 CG LEU A 288 44.527 50.272 16.936 1.00 21.52 C
-ATOM 187 CD1 LEU A 288 43.758 51.499 16.492 1.00 20.19 C
-ATOM 188 CD2 LEU A 288 46.007 50.510 16.770 1.00 23.14 C
-ATOM 189 N LEU A 289 42.751 47.396 17.804 1.00 29.02 N
-ATOM 190 CA LEU A 289 42.341 46.342 16.886 1.00 29.78 C
-ATOM 191 C LEU A 289 40.827 46.264 16.785 1.00 30.56 C
-ATOM 192 O LEU A 289 40.258 46.381 15.697 1.00 29.97 O
-ATOM 193 CB LEU A 289 42.877 44.995 17.365 1.00 30.20 C
-ATOM 194 CG LEU A 289 42.445 43.786 16.539 1.00 32.47 C
-ATOM 195 CD1 LEU A 289 43.221 43.753 15.238 1.00 33.31 C
-ATOM 196 CD2 LEU A 289 42.692 42.516 17.333 1.00 32.60 C
-ATOM 197 N GLY A 290 40.186 46.061 17.935 1.00 31.54 N
-ATOM 198 CA GLY A 290 38.748 45.949 17.977 1.00 31.64 C
-ATOM 199 C GLY A 290 38.024 47.142 17.390 1.00 33.25 C
-ATOM 200 O GLY A 290 36.953 47.002 16.804 1.00 33.35 O
-ATOM 201 N MET A 291 38.590 48.331 17.534 1.00 33.56 N
-ATOM 202 CA MET A 291 37.919 49.510 17.007 1.00 32.79 C
-ATOM 203 C MET A 291 38.125 49.676 15.515 1.00 32.18 C
-ATOM 204 O MET A 291 37.185 49.993 14.782 1.00 29.93 O
-ATOM 205 CB MET A 291 38.371 50.764 17.755 1.00 34.17 C
-ATOM 206 CG MET A 291 37.883 50.791 19.186 1.00 40.00 C
-ATOM 207 SD MET A 291 38.213 52.345 20.021 1.00 47.45 S
-ATOM 208 CE MET A 291 36.613 53.084 19.764 1.00 46.12 C
-ATOM 209 N TYR A 292 39.339 49.440 15.045 1.00 31.64 N
-ATOM 210 CA TYR A 292 39.569 49.597 13.625 1.00 30.61 C
-ATOM 211 C TYR A 292 38.693 48.640 12.840 1.00 30.33 C
-ATOM 212 O TYR A 292 38.165 49.004 11.791 1.00 32.95 O
-ATOM 213 CB TYR A 292 41.029 49.350 13.271 1.00 30.70 C
-ATOM 214 CG TYR A 292 41.460 50.144 12.075 1.00 31.55 C
-ATOM 215 CD1 TYR A 292 41.531 51.535 12.137 1.00 30.37 C
-ATOM 216 CD2 TYR A 292 41.764 49.512 10.867 1.00 31.91 C
-ATOM 217 CE1 TYR A 292 41.898 52.283 11.017 1.00 31.27 C
-ATOM 218 CE2 TYR A 292 42.128 50.245 9.742 1.00 31.93 C
-ATOM 219 CZ TYR A 292 42.194 51.626 9.825 1.00 31.36 C
-ATOM 220 OH TYR A 292 42.574 52.346 8.725 1.00 31.38 O
-ATOM 221 N LEU A 293 38.533 47.422 13.356 1.00 31.72 N
-ATOM 222 CA LEU A 293 37.725 46.398 12.703 1.00 32.56 C
-ATOM 223 C LEU A 293 36.244 46.754 12.582 1.00 33.99 C
-ATOM 224 O LEU A 293 35.511 46.123 11.816 1.00 34.48 O
-ATOM 225 CB LEU A 293 37.873 45.066 13.437 1.00 30.72 C
-ATOM 226 CG LEU A 293 39.182 44.300 13.219 1.00 28.22 C
-ATOM 227 CD1 LEU A 293 39.293 43.225 14.283 1.00 26.90 C
-ATOM 228 CD2 LEU A 293 39.235 43.705 11.807 1.00 25.91 C
-ATOM 229 N GLU A 294 35.791 47.751 13.331 1.00 36.51 N
-ATOM 230 CA GLU A 294 34.396 48.146 13.226 1.00 37.48 C
-ATOM 231 C GLU A 294 34.181 48.882 11.909 1.00 36.98 C
-ATOM 232 O GLU A 294 33.093 48.838 11.337 1.00 37.79 O
-ATOM 233 CB GLU A 294 33.999 49.053 14.382 1.00 38.80 C
-ATOM 234 CG GLU A 294 34.133 48.398 15.726 1.00 42.71 C
-ATOM 235 CD GLU A 294 33.342 49.111 16.798 1.00 44.92 C
-ATOM 236 OE1 GLU A 294 33.487 50.349 16.935 1.00 46.13 O
-ATOM 237 OE2 GLU A 294 32.575 48.425 17.509 1.00 47.02 O
-ATOM 238 N PHE A 295 35.235 49.547 11.437 1.00 36.80 N
-ATOM 239 CA PHE A 295 35.203 50.308 10.192 1.00 36.65 C
-ATOM 240 C PHE A 295 35.100 49.447 8.920 1.00 38.06 C
-ATOM 241 O PHE A 295 34.784 49.962 7.852 1.00 41.09 O
-ATOM 242 CB PHE A 295 36.458 51.190 10.064 1.00 34.45 C
-ATOM 243 CG PHE A 295 36.716 52.103 11.237 1.00 28.80 C
-ATOM 244 CD1 PHE A 295 35.676 52.604 12.006 1.00 26.98 C
-ATOM 245 CD2 PHE A 295 38.013 52.517 11.527 1.00 27.49 C
-ATOM 246 CE1 PHE A 295 35.934 53.511 13.046 1.00 25.92 C
-ATOM 247 CE2 PHE A 295 38.267 53.424 12.567 1.00 25.37 C
-ATOM 248 CZ PHE A 295 37.233 53.916 13.318 1.00 22.99 C
-ATOM 249 N GLN A 296 35.372 48.151 9.026 1.00 41.46 N
-ATOM 250 CA GLN A 296 35.325 47.246 7.872 1.00 43.34 C
-ATOM 251 C GLN A 296 33.955 47.119 7.193 1.00 45.29 C
-ATOM 252 O GLN A 296 33.822 46.470 6.148 1.00 46.84 O
-ATOM 253 CB GLN A 296 35.752 45.847 8.290 1.00 40.41 C
-ATOM 254 CG GLN A 296 34.576 44.965 8.702 1.00 35.59 C
-ATOM 255 CD GLN A 296 35.033 43.677 9.319 1.00 35.21 C
-ATOM 256 OE1 GLN A 296 35.316 43.621 10.511 1.00 35.54 O
-ATOM 257 NE2 GLN A 296 35.132 42.632 8.508 1.00 36.66 N
-ATOM 258 N TYR A 297 32.931 47.699 7.799 1.00 49.42 N
-ATOM 259 CA TYR A 297 31.597 47.622 7.230 1.00 54.13 C
-ATOM 260 C TYR A 297 31.305 48.903 6.475 1.00 57.45 C
-ATOM 261 O TYR A 297 31.844 49.957 6.808 1.00 57.90 O
-ATOM 262 CB TYR A 297 30.584 47.432 8.342 1.00 55.85 C
-ATOM 263 CG TYR A 297 30.882 46.234 9.196 1.00 56.79 C
-ATOM 264 CD1 TYR A 297 30.788 44.943 8.678 1.00 56.08 C
-ATOM 265 CD2 TYR A 297 31.254 46.387 10.528 1.00 56.58 C
-ATOM 266 CE1 TYR A 297 31.051 43.838 9.474 1.00 55.80 C
-ATOM 267 CE2 TYR A 297 31.521 45.290 11.329 1.00 55.64 C
-ATOM 268 CZ TYR A 297 31.418 44.022 10.802 1.00 55.36 C
-ATOM 269 OH TYR A 297 31.668 42.942 11.614 1.00 56.00 O
-ATOM 270 N SER A 298 30.459 48.819 5.456 1.00 60.51 N
-ATOM 271 CA SER A 298 30.141 50.008 4.684 1.00 60.31 C
-ATOM 272 C SER A 298 29.560 51.029 5.643 1.00 62.98 C
-ATOM 273 O SER A 298 28.634 50.732 6.412 1.00 53.59 O
-ATOM 274 CB SER A 298 29.128 49.707 3.575 1.00 60.41 C
-ATOM 275 OG SER A 298 27.801 49.832 4.051 1.00 68.55 O
-ATOM 276 N PHE A 299 30.135 52.226 5.605 1.00 70.43 N
-ATOM 277 CA PHE A 299 29.692 53.320 6.447 1.00 75.17 C
-ATOM 278 C PHE A 299 28.403 53.835 5.820 1.00 76.91 C
-ATOM 279 O PHE A 299 27.603 54.516 6.464 1.00 78.45 O
-ATOM 280 CB PHE A 299 30.774 54.402 6.479 1.00 80.94 C
-ATOM 281 CG PHE A 299 30.373 55.689 5.831 1.00 93.15 C
-ATOM 282 CD1 PHE A 299 29.946 56.762 6.603 1.00 98.29 C
-ATOM 283 CD2 PHE A 299 30.407 55.827 4.449 1.00 98.25 C
-ATOM 284 CE1 PHE A 299 29.558 57.960 6.007 1.00100.97 C
-ATOM 285 CE2 PHE A 299 30.021 57.020 3.838 1.00100.52 C
-ATOM 286 CZ PHE A 299 29.595 58.090 4.617 1.00101.11 C
-ATOM 287 N GLU A 300 28.209 53.477 4.554 1.00 85.28 N
-ATOM 288 CA GLU A 300 27.027 53.877 3.804 1.00 93.02 C
-ATOM 289 C GLU A 300 25.768 53.306 4.451 1.00 98.29 C
-ATOM 290 O GLU A 300 24.737 53.182 3.796 1.00100.57 O
-ATOM 291 CB GLU A 300 27.095 53.364 2.362 1.00 96.63 C
-ATOM 292 CG GLU A 300 28.484 53.174 1.782 1.00 99.09 C
-ATOM 293 CD GLU A 300 28.436 52.797 0.309 1.00100.18 C
-ATOM 294 OE1 GLU A 300 27.623 51.919 -0.059 1.00100.10 O
-ATOM 295 OE2 GLU A 300 29.213 53.376 -0.481 1.00100.08 O
-ATOM 296 N MET A 301 25.850 52.945 5.726 1.00105.50 N
-ATOM 297 CA MET A 301 24.699 52.380 6.418 1.00104.07 C
-ATOM 298 C MET A 301 24.951 52.309 7.925 1.00 96.31 C
-ATOM 299 O MET A 301 24.012 52.192 8.712 1.00 97.43 O
-ATOM 300 CB MET A 301 24.406 50.977 5.861 1.00109.33 C
-ATOM 301 CG MET A 301 22.926 50.599 5.789 1.00122.12 C
-ATOM 302 SD MET A 301 22.079 51.080 4.247 1.00128.75 S
-ATOM 303 CE MET A 301 21.741 49.459 3.509 1.00130.64 C
-ATOM 304 N CYS A 302 26.224 52.382 8.314 1.00 84.94 N
-ATOM 305 CA CYS A 302 26.635 52.322 9.725 1.00 81.73 C
-ATOM 306 C CYS A 302 25.698 53.097 10.649 1.00 82.88 C
-ATOM 307 O CYS A 302 25.638 54.327 10.591 1.00 85.64 O
-ATOM 308 CB CYS A 302 28.080 52.850 9.881 1.00 75.87 C
-ATOM 309 SG CYS A 302 28.610 53.402 11.543 1.00 58.95 S
-ATOM 310 N LEU A 303 24.964 52.372 11.493 1.00 79.96 N
-ATOM 311 CA LEU A 303 24.052 53.006 12.437 1.00 74.47 C
-ATOM 312 C LEU A 303 24.825 53.665 13.568 1.00 72.34 C
-ATOM 313 O LEU A 303 24.363 54.649 14.147 1.00 61.98 O
-ATOM 314 CB LEU A 303 23.064 51.989 13.020 1.00 76.93 C
-ATOM 315 CG LEU A 303 21.716 51.852 12.303 1.00 83.85 C
-ATOM 316 CD1 LEU A 303 20.805 50.926 13.092 1.00 88.23 C
-ATOM 317 CD2 LEU A 303 21.064 53.227 12.161 1.00 88.93 C
-ATOM 318 N LYS A 304 26.003 53.117 13.873 1.00 65.87 N
-ATOM 319 CA LYS A 304 26.866 53.647 14.927 1.00 62.29 C
-ATOM 320 C LYS A 304 27.254 55.074 14.585 1.00 59.80 C
-ATOM 321 O LYS A 304 27.462 55.909 15.464 1.00 57.26 O
-ATOM 322 CB LYS A 304 28.125 52.788 15.063 1.00 68.05 C
-ATOM 323 CG LYS A 304 27.831 51.352 15.445 1.00 80.77 C
-ATOM 324 CD LYS A 304 29.060 50.586 15.904 1.00 85.84 C
-ATOM 325 CE LYS A 304 28.649 49.195 16.371 1.00 88.26 C
-ATOM 326 NZ LYS A 304 29.799 48.349 16.773 1.00 89.31 N
-ATOM 327 N CYS A 305 27.335 55.334 13.287 1.00 59.51 N
-ATOM 328 CA CYS A 305 27.683 56.640 12.746 1.00 57.56 C
-ATOM 329 C CYS A 305 26.429 57.495 12.663 1.00 56.90 C
-ATOM 330 O CYS A 305 26.410 58.621 13.151 1.00 62.03 O
-ATOM 331 CB CYS A 305 28.263 56.473 11.347 1.00 52.85 C
-ATOM 332 SG CYS A 305 29.564 55.208 11.239 1.00 52.95 S
-ATOM 333 N ILE A 306 25.388 56.951 12.032 1.00 60.49 N
-ATOM 334 CA ILE A 306 24.121 57.664 11.888 1.00 70.12 C
-ATOM 335 C ILE A 306 23.653 58.114 13.265 1.00 73.00 C
-ATOM 336 O ILE A 306 23.259 59.269 13.455 1.00 74.36 O
-ATOM 337 CB ILE A 306 23.011 56.773 11.251 1.00 68.00 C
-ATOM 338 CG1 ILE A 306 23.422 56.330 9.846 1.00 65.88 C
-ATOM 339 CG2 ILE A 306 21.705 57.557 11.166 1.00 67.57 C
-ATOM 340 CD1 ILE A 306 22.407 55.432 9.170 1.00 62.53 C
-ATOM 341 N LYS A 307 23.704 57.199 14.229 1.00 76.09 N
-ATOM 342 CA LYS A 307 23.287 57.526 15.583 1.00 72.32 C
-ATOM 343 C LYS A 307 24.365 58.239 16.403 1.00 67.09 C
-ATOM 344 O LYS A 307 24.117 58.620 17.542 1.00 60.11 O
-ATOM 345 CB LYS A 307 22.801 56.269 16.313 1.00 76.95 C
-ATOM 346 CG LYS A 307 21.450 55.771 15.811 1.00 92.17 C
-ATOM 347 CD LYS A 307 20.821 54.741 16.741 1.00100.72 C
-ATOM 348 CE LYS A 307 19.438 54.327 16.236 1.00104.46 C
-ATOM 349 NZ LYS A 307 18.753 53.346 17.129 1.00105.22 N
-ATOM 350 N LYS A 308 25.550 58.427 15.823 1.00 59.56 N
-ATOM 351 CA LYS A 308 26.651 59.119 16.501 1.00 58.92 C
-ATOM 352 C LYS A 308 26.902 58.586 17.923 1.00 64.36 C
-ATOM 353 O LYS A 308 26.993 59.360 18.881 1.00 61.71 O
-ATOM 354 CB LYS A 308 26.348 60.624 16.561 1.00 55.07 C
-ATOM 355 CG LYS A 308 26.189 61.303 15.201 1.00 52.50 C
-ATOM 356 CD LYS A 308 27.542 61.670 14.586 1.00 51.89 C
-ATOM 357 CE LYS A 308 27.411 62.323 13.198 1.00 50.22 C
-ATOM 358 NZ LYS A 308 28.708 62.882 12.700 1.00 49.81 N
-ATOM 359 N GLU A 309 27.036 57.265 18.039 1.00 71.33 N
-ATOM 360 CA GLU A 309 27.241 56.577 19.316 1.00 72.64 C
-ATOM 361 C GLU A 309 28.564 56.869 20.017 1.00 67.99 C
-ATOM 362 O GLU A 309 28.587 57.165 21.214 1.00 61.21 O
-ATOM 363 CB GLU A 309 27.126 55.066 19.110 1.00 84.01 C
-ATOM 364 CG GLU A 309 25.987 54.641 18.201 1.00109.26 C
-ATOM 365 CD GLU A 309 25.892 53.134 18.065 1.00120.47 C
-ATOM 366 OE1 GLU A 309 26.947 52.495 17.862 1.00124.79 O
-ATOM 367 OE2 GLU A 309 24.768 52.591 18.154 1.00124.00 O
-ATOM 368 N GLN A 310 29.663 56.759 19.272 1.00 60.61 N
-ATOM 369 CA GLN A 310 31.002 56.992 19.813 1.00 53.51 C
-ATOM 370 C GLN A 310 31.822 57.844 18.856 1.00 50.70 C
-ATOM 371 O GLN A 310 32.034 57.471 17.700 1.00 50.89 O
-ATOM 372 CB GLN A 310 31.723 55.663 20.030 1.00 53.87 C
-ATOM 373 CG GLN A 310 31.165 54.801 21.149 1.00 54.31 C
-ATOM 374 CD GLN A 310 31.465 55.355 22.526 1.00 52.49 C
-ATOM 375 OE1 GLN A 310 32.597 55.734 22.820 1.00 52.36 O
-ATOM 376 NE2 GLN A 310 30.453 55.388 23.384 1.00 53.03 N
-ATOM 377 N PRO A 311 32.310 58.997 19.335 1.00 45.68 N
-ATOM 378 CA PRO A 311 33.110 59.911 18.513 1.00 46.38 C
-ATOM 379 C PRO A 311 34.350 59.235 17.944 1.00 47.63 C
-ATOM 380 O PRO A 311 34.780 59.549 16.832 1.00 45.34 O
-ATOM 381 CB PRO A 311 33.450 61.040 19.481 1.00 44.83 C
-ATOM 382 CG PRO A 311 32.301 61.010 20.452 1.00 44.16 C
-ATOM 383 CD PRO A 311 32.122 59.540 20.689 1.00 45.84 C
-ATOM 384 N SER A 312 34.921 58.309 18.713 1.00 48.85 N
-ATOM 385 CA SER A 312 36.114 57.572 18.285 1.00 48.81 C
-ATOM 386 C SER A 312 35.786 56.714 17.057 1.00 47.29 C
-ATOM 387 O SER A 312 36.670 56.198 16.372 1.00 44.34 O
-ATOM 388 CB SER A 312 36.612 56.676 19.422 1.00 51.14 C
-ATOM 389 OG SER A 312 35.594 55.780 19.841 1.00 59.07 O
-ATOM 390 N HIS A 313 34.498 56.580 16.783 1.00 45.05 N
-ATOM 391 CA HIS A 313 34.056 55.793 15.655 1.00 43.34 C
-ATOM 392 C HIS A 313 33.432 56.636 14.544 1.00 43.10 C
-ATOM 393 O HIS A 313 33.909 56.636 13.402 1.00 42.21 O
-ATOM 394 CB HIS A 313 33.041 54.757 16.127 1.00 42.86 C
-ATOM 395 CG HIS A 313 32.443 53.951 15.016 1.00 43.56 C
-ATOM 396 ND1 HIS A 313 33.117 52.920 14.396 1.00 43.88 N
-ATOM 397 CD2 HIS A 313 31.235 54.029 14.406 1.00 43.46 C
-ATOM 398 CE1 HIS A 313 32.349 52.396 13.454 1.00 43.76 C
-ATOM 399 NE2 HIS A 313 31.203 53.055 13.445 1.00 43.67 N
-ATOM 400 N TYR A 314 32.374 57.364 14.881 1.00 43.28 N
-ATOM 401 CA TYR A 314 31.668 58.153 13.884 1.00 44.30 C
-ATOM 402 C TYR A 314 32.403 59.332 13.240 1.00 45.53 C
-ATOM 403 O TYR A 314 31.806 60.065 12.455 1.00 44.80 O
-ATOM 404 CB TYR A 314 30.324 58.614 14.455 1.00 43.58 C
-ATOM 405 CG TYR A 314 30.396 59.740 15.462 1.00 44.86 C
-ATOM 406 CD1 TYR A 314 30.866 61.003 15.096 1.00 44.37 C
-ATOM 407 CD2 TYR A 314 29.939 59.562 16.767 1.00 45.29 C
-ATOM 408 CE1 TYR A 314 30.876 62.056 15.997 1.00 45.24 C
-ATOM 409 CE2 TYR A 314 29.947 60.615 17.682 1.00 45.95 C
-ATOM 410 CZ TYR A 314 30.416 61.857 17.286 1.00 45.59 C
-ATOM 411 OH TYR A 314 30.419 62.905 18.174 1.00 45.85 O
-ATOM 412 N LYS A 315 33.682 59.517 13.566 1.00 46.71 N
-ATOM 413 CA LYS A 315 34.472 60.606 12.989 1.00 47.03 C
-ATOM 414 C LYS A 315 35.580 60.032 12.116 1.00 46.55 C
-ATOM 415 O LYS A 315 36.360 60.777 11.526 1.00 46.18 O
-ATOM 416 CB LYS A 315 35.120 61.464 14.081 1.00 48.16 C
-ATOM 417 CG LYS A 315 34.153 62.153 15.023 1.00 53.01 C
-ATOM 418 CD LYS A 315 34.889 62.929 16.130 1.00 55.42 C
-ATOM 419 CE LYS A 315 35.460 64.261 15.647 1.00 56.95 C
-ATOM 420 NZ LYS A 315 36.411 64.130 14.503 1.00 58.49 N
-ATOM 421 N TYR A 316 35.658 58.708 12.036 1.00 45.41 N
-ATOM 422 CA TYR A 316 36.703 58.088 11.242 1.00 43.87 C
-ATOM 423 C TYR A 316 36.234 56.940 10.369 1.00 43.53 C
-ATOM 424 O TYR A 316 36.970 56.498 9.482 1.00 42.95 O
-ATOM 425 CB TYR A 316 37.830 57.597 12.156 1.00 44.35 C
-ATOM 426 CG TYR A 316 38.382 58.654 13.092 1.00 46.19 C
-ATOM 427 CD1 TYR A 316 37.716 58.989 14.274 1.00 47.17 C
-ATOM 428 CD2 TYR A 316 39.559 59.337 12.784 1.00 46.48 C
-ATOM 429 CE1 TYR A 316 38.215 59.986 15.130 1.00 46.53 C
-ATOM 430 CE2 TYR A 316 40.064 60.330 13.623 1.00 46.53 C
-ATOM 431 CZ TYR A 316 39.389 60.652 14.793 1.00 47.19 C
-ATOM 432 OH TYR A 316 39.876 61.647 15.614 1.00 48.47 O
-ATOM 433 N HIS A 317 35.019 56.451 10.604 1.00 42.74 N
-ATOM 434 CA HIS A 317 34.520 55.329 9.809 1.00 42.88 C
-ATOM 435 C HIS A 317 34.611 55.606 8.312 1.00 48.40 C
-ATOM 436 O HIS A 317 35.125 54.784 7.551 1.00 44.88 O
-ATOM 437 CB HIS A 317 33.074 54.977 10.181 1.00 38.29 C
-ATOM 438 CG HIS A 317 32.600 53.685 9.579 1.00 35.44 C
-ATOM 439 ND1 HIS A 317 31.340 53.174 9.798 1.00 34.68 N
-ATOM 440 CD2 HIS A 317 33.235 52.783 8.794 1.00 34.44 C
-ATOM 441 CE1 HIS A 317 31.219 52.010 9.180 1.00 34.29 C
-ATOM 442 NE2 HIS A 317 32.358 51.752 8.563 1.00 34.04 N
-ATOM 443 N GLU A 318 34.115 56.768 7.903 1.00 57.52 N
-ATOM 444 CA GLU A 318 34.138 57.173 6.503 1.00 64.21 C
-ATOM 445 C GLU A 318 35.550 57.019 5.942 1.00 62.43 C
-ATOM 446 O GLU A 318 35.825 56.147 5.119 1.00 61.63 O
-ATOM 447 CB GLU A 318 33.703 58.636 6.381 1.00 77.63 C
-ATOM 448 CG GLU A 318 32.624 58.916 5.339 1.00100.73 C
-ATOM 449 CD GLU A 318 33.055 58.603 3.918 1.00110.50 C
-ATOM 450 OE1 GLU A 318 32.296 58.938 2.982 1.00113.70 O
-ATOM 451 OE2 GLU A 318 34.146 58.025 3.736 1.00114.14 O
-ATOM 452 N LYS A 319 36.447 57.871 6.417 1.00 58.22 N
-ATOM 453 CA LYS A 319 37.830 57.876 5.973 1.00 52.13 C
-ATOM 454 C LYS A 319 38.534 56.524 5.992 1.00 49.19 C
-ATOM 455 O LYS A 319 39.405 56.259 5.161 1.00 49.24 O
-ATOM 456 CB LYS A 319 38.628 58.869 6.818 1.00 48.75 C
-ATOM 457 CG LYS A 319 40.097 58.916 6.477 1.00 46.93 C
-ATOM 458 CD LYS A 319 40.779 60.000 7.269 1.00 47.21 C
-ATOM 459 CE LYS A 319 42.255 60.120 6.913 1.00 47.29 C
-ATOM 460 NZ LYS A 319 42.854 61.352 7.538 1.00 48.50 N
-ATOM 461 N HIS A 320 38.155 55.660 6.922 1.00 45.92 N
-ATOM 462 CA HIS A 320 38.827 54.376 7.026 1.00 45.26 C
-ATOM 463 C HIS A 320 38.138 53.140 6.465 1.00 46.44 C
-ATOM 464 O HIS A 320 38.730 52.057 6.482 1.00 45.28 O
-ATOM 465 CB HIS A 320 39.231 54.145 8.488 1.00 41.42 C
-ATOM 466 CG HIS A 320 40.308 55.076 8.960 1.00 37.00 C
-ATOM 467 ND1 HIS A 320 41.643 54.876 8.675 1.00 34.20 N
-ATOM 468 CD2 HIS A 320 40.243 56.242 9.645 1.00 35.15 C
-ATOM 469 CE1 HIS A 320 42.352 55.878 9.164 1.00 32.77 C
-ATOM 470 NE2 HIS A 320 41.526 56.722 9.758 1.00 31.78 N
-ATOM 471 N TYR A 321 36.911 53.280 5.966 1.00 47.30 N
-ATOM 472 CA TYR A 321 36.218 52.120 5.411 1.00 48.38 C
-ATOM 473 C TYR A 321 37.184 51.351 4.506 1.00 48.38 C
-ATOM 474 O TYR A 321 37.630 50.254 4.842 1.00 46.70 O
-ATOM 475 CB TYR A 321 34.991 52.537 4.594 1.00 51.57 C
-ATOM 476 CG TYR A 321 34.400 51.387 3.813 1.00 55.99 C
-ATOM 477 CD1 TYR A 321 33.702 50.371 4.460 1.00 59.02 C
-ATOM 478 CD2 TYR A 321 34.613 51.266 2.441 1.00 58.52 C
-ATOM 479 CE1 TYR A 321 33.227 49.252 3.761 1.00 60.96 C
-ATOM 480 CE2 TYR A 321 34.145 50.153 1.728 1.00 61.16 C
-ATOM 481 CZ TYR A 321 33.456 49.145 2.397 1.00 61.32 C
-ATOM 482 OH TYR A 321 33.009 48.029 1.712 1.00 60.75 O
-ATOM 483 N ALA A 322 37.508 51.954 3.366 1.00 47.79 N
-ATOM 484 CA ALA A 322 38.410 51.370 2.380 1.00 46.61 C
-ATOM 485 C ALA A 322 39.545 50.558 2.990 1.00 45.04 C
-ATOM 486 O ALA A 322 39.636 49.346 2.787 1.00 46.87 O
-ATOM 487 CB ALA A 322 38.994 52.474 1.503 1.00 46.20 C
-ATOM 488 N ASN A 323 40.410 51.234 3.738 1.00 42.98 N
-ATOM 489 CA ASN A 323 41.559 50.586 4.353 1.00 41.24 C
-ATOM 490 C ASN A 323 41.213 49.568 5.435 1.00 40.49 C
-ATOM 491 O ASN A 323 41.909 48.564 5.589 1.00 41.21 O
-ATOM 492 CB ASN A 323 42.495 51.633 4.927 1.00 39.68 C
-ATOM 493 CG ASN A 323 43.783 51.039 5.405 1.00 38.56 C
-ATOM 494 OD1 ASN A 323 44.498 50.398 4.636 1.00 38.32 O
-ATOM 495 ND2 ASN A 323 44.097 51.243 6.683 1.00 39.64 N
-ATOM 496 N ALA A 324 40.146 49.826 6.187 1.00 37.41 N
-ATOM 497 CA ALA A 324 39.724 48.907 7.236 1.00 34.71 C
-ATOM 498 C ALA A 324 39.162 47.641 6.596 1.00 33.63 C
-ATOM 499 O ALA A 324 39.267 46.543 7.143 1.00 34.06 O
-ATOM 500 CB ALA A 324 38.673 49.566 8.107 1.00 30.16 C
-ATOM 501 N ALA A 325 38.554 47.809 5.430 1.00 34.53 N
-ATOM 502 CA ALA A 325 37.987 46.692 4.697 1.00 36.08 C
-ATOM 503 C ALA A 325 39.129 45.790 4.241 1.00 38.91 C
-ATOM 504 O ALA A 325 38.994 44.566 4.216 1.00 42.96 O
-ATOM 505 CB ALA A 325 37.207 47.205 3.511 1.00 34.45 C
-ATOM 506 N ILE A 326 40.255 46.399 3.879 1.00 40.72 N
-ATOM 507 CA ILE A 326 41.429 45.644 3.457 1.00 41.75 C
-ATOM 508 C ILE A 326 42.094 45.062 4.713 1.00 41.19 C
-ATOM 509 O ILE A 326 42.686 43.981 4.679 1.00 42.06 O
-ATOM 510 CB ILE A 326 42.454 46.556 2.729 1.00 42.84 C
-ATOM 511 CG1 ILE A 326 41.782 47.277 1.557 1.00 41.51 C
-ATOM 512 CG2 ILE A 326 43.642 45.729 2.246 1.00 41.67 C
-ATOM 513 CD1 ILE A 326 42.688 48.245 0.842 1.00 40.40 C
-ATOM 514 N PHE A 327 41.976 45.795 5.816 1.00 40.10 N
-ATOM 515 CA PHE A 327 42.547 45.399 7.099 1.00 39.71 C
-ATOM 516 C PHE A 327 41.958 44.094 7.586 1.00 40.75 C
-ATOM 517 O PHE A 327 42.683 43.187 7.968 1.00 43.11 O
-ATOM 518 CB PHE A 327 42.272 46.472 8.155 1.00 36.64 C
-ATOM 519 CG PHE A 327 42.877 46.171 9.500 1.00 30.03 C
-ATOM 520 CD1 PHE A 327 44.242 46.336 9.715 1.00 28.79 C
-ATOM 521 CD2 PHE A 327 42.083 45.726 10.552 1.00 27.98 C
-ATOM 522 CE1 PHE A 327 44.805 46.066 10.950 1.00 26.48 C
-ATOM 523 CE2 PHE A 327 42.641 45.451 11.795 1.00 26.00 C
-ATOM 524 CZ PHE A 327 43.999 45.622 11.994 1.00 26.17 C
-ATOM 525 N ALA A 328 40.636 44.006 7.578 1.00 42.18 N
-ATOM 526 CA ALA A 328 39.960 42.811 8.050 1.00 44.94 C
-ATOM 527 C ALA A 328 40.358 41.549 7.282 1.00 48.29 C
-ATOM 528 O ALA A 328 40.020 40.430 7.690 1.00 46.06 O
-ATOM 529 CB ALA A 328 38.456 43.016 7.985 1.00 45.34 C
-ATOM 530 N ASP A 329 41.078 41.721 6.177 1.00 50.33 N
-ATOM 531 CA ASP A 329 41.506 40.578 5.377 1.00 51.25 C
-ATOM 532 C ASP A 329 43.013 40.358 5.433 1.00 49.93 C
-ATOM 533 O ASP A 329 43.569 39.564 4.678 1.00 45.64 O
-ATOM 534 CB ASP A 329 41.045 40.748 3.926 1.00 59.61 C
-ATOM 535 CG ASP A 329 39.785 39.946 3.615 1.00 72.08 C
-ATOM 536 OD1 ASP A 329 39.877 38.697 3.544 1.00 77.68 O
-ATOM 537 OD2 ASP A 329 38.705 40.562 3.450 1.00 77.97 O
-ATOM 538 N SER A 330 43.666 41.064 6.345 1.00 47.77 N
-ATOM 539 CA SER A 330 45.107 40.946 6.528 1.00 44.94 C
-ATOM 540 C SER A 330 45.404 39.716 7.387 1.00 43.21 C
-ATOM 541 O SER A 330 44.584 39.323 8.220 1.00 40.84 O
-ATOM 542 CB SER A 330 45.642 42.211 7.213 1.00 45.37 C
-ATOM 543 OG SER A 330 46.993 42.062 7.615 1.00 50.61 O
-ATOM 544 N LYS A 331 46.568 39.108 7.185 1.00 41.02 N
-ATOM 545 CA LYS A 331 46.937 37.930 7.968 1.00 40.17 C
-ATOM 546 C LYS A 331 47.723 38.244 9.247 1.00 42.07 C
-ATOM 547 O LYS A 331 48.207 37.341 9.921 1.00 38.53 O
-ATOM 548 CB LYS A 331 47.732 36.951 7.109 1.00 40.02 C
-ATOM 549 CG LYS A 331 46.881 36.142 6.168 1.00 43.49 C
-ATOM 550 CD LYS A 331 47.739 35.208 5.343 1.00 45.95 C
-ATOM 551 CE LYS A 331 46.885 34.262 4.506 1.00 46.76 C
-ATOM 552 NZ LYS A 331 47.689 33.086 4.048 1.00 47.56 N
-ATOM 553 N ASN A 332 47.862 39.518 9.583 1.00 43.52 N
-ATOM 554 CA ASN A 332 48.569 39.872 10.805 1.00 43.47 C
-ATOM 555 C ASN A 332 48.178 41.266 11.270 1.00 41.12 C
-ATOM 556 O ASN A 332 48.985 42.202 11.311 1.00 34.12 O
-ATOM 557 CB ASN A 332 50.088 39.741 10.620 1.00 54.19 C
-ATOM 558 CG ASN A 332 50.629 40.618 9.516 1.00 68.01 C
-ATOM 559 OD1 ASN A 332 49.877 41.168 8.713 1.00 76.57 O
-ATOM 560 ND2 ASN A 332 51.949 40.744 9.463 1.00 76.04 N
-ATOM 561 N GLN A 333 46.909 41.378 11.640 1.00 37.13 N
-ATOM 562 CA GLN A 333 46.363 42.631 12.101 1.00 33.91 C
-ATOM 563 C GLN A 333 47.002 43.088 13.410 1.00 33.58 C
-ATOM 564 O GLN A 333 47.311 44.264 13.570 1.00 32.33 O
-ATOM 565 CB GLN A 333 44.846 42.509 12.250 1.00 34.87 C
-ATOM 566 CG GLN A 333 44.284 41.192 11.761 1.00 39.93 C
-ATOM 567 CD GLN A 333 42.791 41.242 11.500 1.00 41.95 C
-ATOM 568 OE1 GLN A 333 42.345 41.857 10.536 1.00 42.03 O
-ATOM 569 NE2 GLN A 333 42.010 40.594 12.362 1.00 43.19 N
-ATOM 570 N LYS A 334 47.228 42.171 14.340 1.00 33.54 N
-ATOM 571 CA LYS A 334 47.828 42.563 15.611 1.00 33.56 C
-ATOM 572 C LYS A 334 49.231 43.169 15.474 1.00 34.00 C
-ATOM 573 O LYS A 334 49.596 44.083 16.217 1.00 29.56 O
-ATOM 574 CB LYS A 334 47.861 41.375 16.577 1.00 37.38 C
-ATOM 575 CG LYS A 334 48.520 41.705 17.901 1.00 46.32 C
-ATOM 576 CD LYS A 334 47.933 40.908 19.047 1.00 50.87 C
-ATOM 577 CE LYS A 334 48.485 41.407 20.375 1.00 53.82 C
-ATOM 578 NZ LYS A 334 47.702 40.919 21.543 1.00 54.15 N
-ATOM 579 N THR A 335 50.016 42.666 14.529 1.00 34.10 N
-ATOM 580 CA THR A 335 51.365 43.180 14.315 1.00 31.59 C
-ATOM 581 C THR A 335 51.245 44.617 13.833 1.00 29.52 C
-ATOM 582 O THR A 335 52.041 45.465 14.191 1.00 28.13 O
-ATOM 583 CB THR A 335 52.118 42.364 13.245 1.00 36.79 C
-ATOM 584 OG1 THR A 335 52.143 40.974 13.610 1.00 45.65 O
-ATOM 585 CG2 THR A 335 53.535 42.866 13.111 1.00 42.57 C
-ATOM 586 N ILE A 336 50.242 44.885 13.009 1.00 27.64 N
-ATOM 587 CA ILE A 336 50.024 46.227 12.494 1.00 26.82 C
-ATOM 588 C ILE A 336 49.666 47.150 13.660 1.00 28.06 C
-ATOM 589 O ILE A 336 50.250 48.220 13.830 1.00 27.95 O
-ATOM 590 CB ILE A 336 48.873 46.238 11.442 1.00 26.63 C
-ATOM 591 CG1 ILE A 336 49.273 45.404 10.214 1.00 24.66 C
-ATOM 592 CG2 ILE A 336 48.531 47.664 11.040 1.00 23.93 C
-ATOM 593 CD1 ILE A 336 48.174 45.293 9.163 1.00 22.99 C
-ATOM 594 N CYS A 337 48.714 46.724 14.478 1.00 30.43 N
-ATOM 595 CA CYS A 337 48.298 47.528 15.619 1.00 32.29 C
-ATOM 596 C CYS A 337 49.440 47.751 16.597 1.00 33.23 C
-ATOM 597 O CYS A 337 49.527 48.795 17.228 1.00 31.18 O
-ATOM 598 CB CYS A 337 47.117 46.863 16.323 1.00 33.35 C
-ATOM 599 SG CYS A 337 45.599 46.894 15.317 1.00 39.71 S
-ATOM 600 N GLN A 338 50.318 46.769 16.722 1.00 35.00 N
-ATOM 601 CA GLN A 338 51.451 46.902 17.619 1.00 36.01 C
-ATOM 602 C GLN A 338 52.274 48.118 17.236 1.00 34.74 C
-ATOM 603 O GLN A 338 52.705 48.881 18.103 1.00 34.53 O
-ATOM 604 CB GLN A 338 52.344 45.664 17.561 1.00 41.23 C
-ATOM 605 CG GLN A 338 52.077 44.651 18.648 1.00 51.41 C
-ATOM 606 CD GLN A 338 52.005 45.291 20.012 1.00 55.66 C
-ATOM 607 OE1 GLN A 338 52.589 46.355 20.245 1.00 56.13 O
-ATOM 608 NE2 GLN A 338 51.295 44.643 20.931 1.00 56.98 N
-ATOM 609 N GLN A 339 52.490 48.300 15.938 1.00 32.27 N
-ATOM 610 CA GLN A 339 53.269 49.426 15.475 1.00 31.10 C
-ATOM 611 C GLN A 339 52.498 50.729 15.636 1.00 30.96 C
-ATOM 612 O GLN A 339 53.090 51.771 15.917 1.00 32.90 O
-ATOM 613 CB GLN A 339 53.674 49.242 14.016 1.00 31.15 C
-ATOM 614 CG GLN A 339 54.781 50.217 13.576 1.00 32.06 C
-ATOM 615 CD GLN A 339 55.455 49.797 12.286 1.00 32.50 C
-ATOM 616 OE1 GLN A 339 55.110 50.280 11.212 1.00 31.82 O
-ATOM 617 NE2 GLN A 339 56.416 48.880 12.389 1.00 31.42 N
-ATOM 618 N ALA A 340 51.182 50.679 15.457 1.00 31.54 N
-ATOM 619 CA ALA A 340 50.365 51.876 15.616 1.00 31.34 C
-ATOM 620 C ALA A 340 50.524 52.369 17.051 1.00 31.80 C
-ATOM 621 O ALA A 340 50.727 53.567 17.304 1.00 33.84 O
-ATOM 622 CB ALA A 340 48.900 51.559 15.337 1.00 32.52 C
-ATOM 623 N VAL A 341 50.445 51.421 17.981 1.00 29.88 N
-ATOM 624 CA VAL A 341 50.555 51.702 19.406 1.00 28.77 C
-ATOM 625 C VAL A 341 51.956 52.149 19.799 1.00 32.27 C
-ATOM 626 O VAL A 341 52.129 53.163 20.476 1.00 28.35 O
-ATOM 627 CB VAL A 341 50.152 50.450 20.213 1.00 25.53 C
-ATOM 628 CG1 VAL A 341 50.529 50.588 21.690 1.00 22.64 C
-ATOM 629 CG2 VAL A 341 48.665 50.242 20.075 1.00 22.06 C
-ATOM 630 N ASP A 342 52.959 51.394 19.370 1.00 36.29 N
-ATOM 631 CA ASP A 342 54.328 51.744 19.694 1.00 39.02 C
-ATOM 632 C ASP A 342 54.586 53.180 19.248 1.00 36.87 C
-ATOM 633 O ASP A 342 55.376 53.901 19.856 1.00 35.16 O
-ATOM 634 CB ASP A 342 55.304 50.792 19.003 1.00 49.20 C
-ATOM 635 CG ASP A 342 55.270 49.396 19.592 1.00 63.23 C
-ATOM 636 OD1 ASP A 342 55.057 49.278 20.818 1.00 70.17 O
-ATOM 637 OD2 ASP A 342 55.471 48.417 18.838 1.00 70.02 O
-ATOM 638 N THR A 343 53.908 53.596 18.186 1.00 32.36 N
-ATOM 639 CA THR A 343 54.071 54.943 17.679 1.00 27.32 C
-ATOM 640 C THR A 343 53.436 55.933 18.641 1.00 27.11 C
-ATOM 641 O THR A 343 53.964 57.024 18.870 1.00 26.54 O
-ATOM 642 CB THR A 343 53.410 55.118 16.309 1.00 23.74 C
-ATOM 643 OG1 THR A 343 54.093 54.316 15.338 1.00 20.28 O
-ATOM 644 CG2 THR A 343 53.480 56.577 15.886 1.00 23.32 C
-ATOM 645 N VAL A 344 52.290 55.560 19.195 1.00 26.83 N
-ATOM 646 CA VAL A 344 51.615 56.439 20.128 1.00 27.04 C
-ATOM 647 C VAL A 344 52.476 56.612 21.374 1.00 26.22 C
-ATOM 648 O VAL A 344 52.557 57.703 21.940 1.00 27.14 O
-ATOM 649 CB VAL A 344 50.229 55.876 20.509 1.00 28.17 C
-ATOM 650 CG1 VAL A 344 49.637 56.666 21.661 1.00 27.35 C
-ATOM 651 CG2 VAL A 344 49.316 55.934 19.309 1.00 28.15 C
-ATOM 652 N LEU A 345 53.125 55.533 21.790 1.00 25.57 N
-ATOM 653 CA LEU A 345 53.983 55.564 22.966 1.00 25.44 C
-ATOM 654 C LEU A 345 55.298 56.280 22.672 1.00 26.26 C
-ATOM 655 O LEU A 345 55.933 56.829 23.576 1.00 26.98 O
-ATOM 656 CB LEU A 345 54.272 54.137 23.432 1.00 23.39 C
-ATOM 657 CG LEU A 345 53.065 53.293 23.829 1.00 20.96 C
-ATOM 658 CD1 LEU A 345 53.516 51.860 23.877 1.00 19.55 C
-ATOM 659 CD2 LEU A 345 52.490 53.731 25.160 1.00 15.63 C
-ATOM 660 N ALA A 346 55.709 56.263 21.408 1.00 27.40 N
-ATOM 661 CA ALA A 346 56.947 56.913 21.004 1.00 28.96 C
-ATOM 662 C ALA A 346 56.774 58.419 21.120 1.00 32.80 C
-ATOM 663 O ALA A 346 57.720 59.141 21.439 1.00 31.41 O
-ATOM 664 CB ALA A 346 57.298 56.532 19.577 1.00 28.77 C
-ATOM 665 N LYS A 347 55.554 58.884 20.862 1.00 35.50 N
-ATOM 666 CA LYS A 347 55.228 60.306 20.940 1.00 36.16 C
-ATOM 667 C LYS A 347 55.104 60.715 22.402 1.00 35.65 C
-ATOM 668 O LYS A 347 55.637 61.745 22.815 1.00 30.50 O
-ATOM 669 CB LYS A 347 53.913 60.583 20.207 1.00 40.88 C
-ATOM 670 CG LYS A 347 53.530 62.050 20.132 1.00 52.30 C
-ATOM 671 CD LYS A 347 54.613 62.851 19.432 1.00 58.83 C
-ATOM 672 CE LYS A 347 54.266 64.333 19.340 1.00 60.27 C
-ATOM 673 NZ LYS A 347 55.388 65.100 18.716 1.00 60.69 N
-ATOM 674 N LYS A 348 54.414 59.889 23.184 1.00 36.12 N
-ATOM 675 CA LYS A 348 54.230 60.173 24.602 1.00 35.77 C
-ATOM 676 C LYS A 348 55.578 60.177 25.283 1.00 37.11 C
-ATOM 677 O LYS A 348 55.728 60.714 26.382 1.00 32.49 O
-ATOM 678 CB LYS A 348 53.291 59.142 25.255 1.00 37.01 C
-ATOM 679 CG LYS A 348 51.838 59.582 25.207 1.00 44.58 C
-ATOM 680 CD LYS A 348 50.819 58.488 25.496 1.00 48.05 C
-ATOM 681 CE LYS A 348 49.404 59.074 25.332 1.00 50.25 C
-ATOM 682 NZ LYS A 348 48.303 58.065 25.335 1.00 50.48 N
-ATOM 683 N ARG A 349 56.564 59.587 24.613 1.00 38.80 N
-ATOM 684 CA ARG A 349 57.914 59.519 25.153 1.00 38.71 C
-ATOM 685 C ARG A 349 58.713 60.760 24.783 1.00 36.32 C
-ATOM 686 O ARG A 349 59.547 61.235 25.553 1.00 32.87 O
-ATOM 687 CB ARG A 349 58.628 58.270 24.632 1.00 45.89 C
-ATOM 688 CG ARG A 349 60.081 58.169 25.048 1.00 59.74 C
-ATOM 689 CD ARG A 349 60.266 58.645 26.473 1.00 67.52 C
-ATOM 690 NE ARG A 349 61.278 57.875 27.179 1.00 71.26 N
-ATOM 691 CZ ARG A 349 61.215 56.557 27.351 1.00 72.35 C
-ATOM 692 NH1 ARG A 349 60.187 55.869 26.860 1.00 71.04 N
-ATOM 693 NH2 ARG A 349 62.171 55.928 28.028 1.00 72.24 N
-ATOM 694 N VAL A 350 58.463 61.275 23.590 1.00 33.56 N
-ATOM 695 CA VAL A 350 59.160 62.451 23.130 1.00 31.43 C
-ATOM 696 C VAL A 350 58.694 63.630 23.944 1.00 33.24 C
-ATOM 697 O VAL A 350 59.504 64.332 24.545 1.00 31.87 O
-ATOM 698 CB VAL A 350 58.883 62.719 21.631 1.00 30.19 C
-ATOM 699 CG1 VAL A 350 59.149 64.194 21.290 1.00 27.51 C
-ATOM 700 CG2 VAL A 350 59.759 61.790 20.774 1.00 28.93 C
-ATOM 701 N ASP A 351 57.385 63.842 23.976 1.00 37.24 N
-ATOM 702 CA ASP A 351 56.833 64.965 24.718 1.00 39.20 C
-ATOM 703 C ASP A 351 57.235 64.902 26.176 1.00 38.93 C
-ATOM 704 O ASP A 351 57.328 65.923 26.859 1.00 34.74 O
-ATOM 705 CB ASP A 351 55.321 64.999 24.559 1.00 46.34 C
-ATOM 706 CG ASP A 351 54.908 65.206 23.119 1.00 57.86 C
-ATOM 707 OD1 ASP A 351 55.516 66.070 22.443 1.00 63.07 O
-ATOM 708 OD2 ASP A 351 53.977 64.511 22.662 1.00 63.84 O
-ATOM 709 N SER A 352 57.510 63.691 26.634 1.00 40.46 N
-ATOM 710 CA SER A 352 57.940 63.463 28.004 1.00 41.25 C
-ATOM 711 C SER A 352 59.253 64.201 28.290 1.00 42.21 C
-ATOM 712 O SER A 352 59.509 64.614 29.419 1.00 40.42 O
-ATOM 713 CB SER A 352 58.123 61.962 28.239 1.00 42.96 C
-ATOM 714 OG SER A 352 58.586 61.686 29.543 1.00 50.07 O
-ATOM 715 N LEU A 353 60.074 64.382 27.261 1.00 43.11 N
-ATOM 716 CA LEU A 353 61.354 65.061 27.425 1.00 42.72 C
-ATOM 717 C LEU A 353 61.441 66.428 26.744 1.00 41.93 C
-ATOM 718 O LEU A 353 62.174 67.306 27.204 1.00 40.44 O
-ATOM 719 CB LEU A 353 62.470 64.168 26.895 1.00 47.94 C
-ATOM 720 CG LEU A 353 62.261 62.688 27.214 1.00 56.76 C
-ATOM 721 CD1 LEU A 353 63.273 61.861 26.454 1.00 60.24 C
-ATOM 722 CD2 LEU A 353 62.371 62.455 28.712 1.00 60.96 C
-ATOM 723 N GLN A 354 60.694 66.613 25.659 1.00 39.45 N
-ATOM 724 CA GLN A 354 60.740 67.867 24.926 1.00 37.20 C
-ATOM 725 C GLN A 354 59.755 68.935 25.356 1.00 37.18 C
-ATOM 726 O GLN A 354 60.040 70.126 25.217 1.00 38.81 O
-ATOM 727 CB GLN A 354 60.563 67.608 23.434 1.00 36.51 C
-ATOM 728 CG GLN A 354 61.468 66.518 22.903 1.00 38.29 C
-ATOM 729 CD GLN A 354 61.682 66.610 21.413 1.00 40.11 C
-ATOM 730 OE1 GLN A 354 60.786 66.996 20.652 1.00 39.79 O
-ATOM 731 NE2 GLN A 354 62.879 66.242 20.980 1.00 41.38 N
-ATOM 732 N LEU A 355 58.601 68.540 25.878 1.00 37.19 N
-ATOM 733 CA LEU A 355 57.614 69.539 26.291 1.00 38.60 C
-ATOM 734 C LEU A 355 57.882 70.190 27.641 1.00 38.12 C
-ATOM 735 O LEU A 355 58.442 69.569 28.540 1.00 37.71 O
-ATOM 736 CB LEU A 355 56.205 68.937 26.292 1.00 39.14 C
-ATOM 737 CG LEU A 355 55.630 68.616 24.910 1.00 40.92 C
-ATOM 738 CD1 LEU A 355 54.140 68.362 25.035 1.00 39.66 C
-ATOM 739 CD2 LEU A 355 55.880 69.781 23.952 1.00 41.33 C
-ATOM 740 N THR A 356 57.491 71.455 27.768 1.00 37.87 N
-ATOM 741 CA THR A 356 57.657 72.188 29.023 1.00 36.78 C
-ATOM 742 C THR A 356 56.460 71.846 29.924 1.00 35.25 C
-ATOM 743 O THR A 356 55.434 71.359 29.450 1.00 34.70 O
-ATOM 744 CB THR A 356 57.696 73.713 28.780 1.00 37.33 C
-ATOM 745 OG1 THR A 356 56.424 74.154 28.280 1.00 37.69 O
-ATOM 746 CG2 THR A 356 58.784 74.058 27.771 1.00 36.36 C
-ATOM 747 N ARG A 357 56.577 72.096 31.217 1.00 32.91 N
-ATOM 748 CA ARG A 357 55.475 71.757 32.096 1.00 33.17 C
-ATOM 749 C ARG A 357 54.184 72.477 31.723 1.00 36.84 C
-ATOM 750 O ARG A 357 53.119 71.856 31.697 1.00 35.12 O
-ATOM 751 CB ARG A 357 55.863 71.998 33.564 1.00 28.89 C
-ATOM 752 CG ARG A 357 56.906 71.001 34.055 1.00 22.61 C
-ATOM 753 CD ARG A 357 57.315 71.218 35.486 1.00 20.66 C
-ATOM 754 NE ARG A 357 56.241 70.843 36.393 1.00 23.55 N
-ATOM 755 CZ ARG A 357 55.851 69.592 36.610 1.00 22.45 C
-ATOM 756 NH1 ARG A 357 56.466 68.599 35.982 1.00 21.93 N
-ATOM 757 NH2 ARG A 357 54.838 69.335 37.436 1.00 20.72 N
-ATOM 758 N GLU A 358 54.263 73.768 31.402 1.00 42.01 N
-ATOM 759 CA GLU A 358 53.048 74.483 31.019 1.00 45.54 C
-ATOM 760 C GLU A 358 52.400 73.833 29.784 1.00 44.88 C
-ATOM 761 O GLU A 358 51.166 73.785 29.675 1.00 40.96 O
-ATOM 762 CB GLU A 358 53.318 75.968 30.750 1.00 52.44 C
-ATOM 763 CG GLU A 358 52.025 76.788 30.787 1.00 67.91 C
-ATOM 764 CD GLU A 358 52.247 78.288 30.713 1.00 74.83 C
-ATOM 765 OE1 GLU A 358 53.139 78.793 31.433 1.00 77.60 O
-ATOM 766 OE2 GLU A 358 51.518 78.965 29.949 1.00 76.31 O
-ATOM 767 N GLN A 359 53.220 73.332 28.860 1.00 43.80 N
-ATOM 768 CA GLN A 359 52.681 72.671 27.678 1.00 40.66 C
-ATOM 769 C GLN A 359 52.059 71.364 28.132 1.00 37.70 C
-ATOM 770 O GLN A 359 50.992 70.987 27.651 1.00 39.76 O
-ATOM 771 CB GLN A 359 53.768 72.381 26.663 1.00 40.42 C
-ATOM 772 CG GLN A 359 54.542 73.593 26.262 1.00 44.30 C
-ATOM 773 CD GLN A 359 55.505 73.303 25.137 1.00 46.12 C
-ATOM 774 OE1 GLN A 359 55.128 73.313 23.962 1.00 46.15 O
-ATOM 775 NE2 GLN A 359 56.758 73.026 25.489 1.00 46.18 N
-ATOM 776 N MET A 360 52.719 70.675 29.061 1.00 32.83 N
-ATOM 777 CA MET A 360 52.168 69.425 29.564 1.00 30.76 C
-ATOM 778 C MET A 360 50.781 69.748 30.092 1.00 32.62 C
-ATOM 779 O MET A 360 49.797 69.063 29.754 1.00 33.06 O
-ATOM 780 CB MET A 360 53.017 68.842 30.699 1.00 28.13 C
-ATOM 781 CG MET A 360 54.296 68.141 30.258 1.00 25.98 C
-ATOM 782 SD MET A 360 55.359 67.650 31.647 1.00 23.38 S
-ATOM 783 CE MET A 360 54.730 65.895 31.940 1.00 19.00 C
-ATOM 784 N LEU A 361 50.696 70.806 30.900 1.00 30.29 N
-ATOM 785 CA LEU A 361 49.412 71.204 31.466 1.00 29.00 C
-ATOM 786 C LEU A 361 48.361 71.562 30.396 1.00 29.14 C
-ATOM 787 O LEU A 361 47.187 71.160 30.489 1.00 23.55 O
-ATOM 788 CB LEU A 361 49.595 72.391 32.424 1.00 31.42 C
-ATOM 789 CG LEU A 361 48.945 72.325 33.821 1.00 32.27 C
-ATOM 790 CD1 LEU A 361 48.349 73.685 34.145 1.00 32.53 C
-ATOM 791 CD2 LEU A 361 47.842 71.260 33.869 1.00 33.31 C
-ATOM 792 N THR A 362 48.776 72.315 29.382 1.00 30.51 N
-ATOM 793 CA THR A 362 47.842 72.708 28.337 1.00 32.94 C
-ATOM 794 C THR A 362 47.289 71.499 27.593 1.00 33.24 C
-ATOM 795 O THR A 362 46.113 71.486 27.213 1.00 34.26 O
-ATOM 796 CB THR A 362 48.489 73.639 27.318 1.00 34.32 C
-ATOM 797 OG1 THR A 362 48.964 74.813 27.983 1.00 38.78 O
-ATOM 798 CG2 THR A 362 47.481 74.031 26.248 1.00 37.61 C
-ATOM 799 N ASN A 363 48.126 70.486 27.374 1.00 33.71 N
-ATOM 800 CA ASN A 363 47.663 69.293 26.667 1.00 33.44 C
-ATOM 801 C ASN A 363 46.593 68.627 27.501 1.00 32.85 C
-ATOM 802 O ASN A 363 45.569 68.183 26.988 1.00 31.77 O
-ATOM 803 CB ASN A 363 48.809 68.320 26.406 1.00 32.84 C
-ATOM 804 CG ASN A 363 49.726 68.795 25.298 1.00 31.77 C
-ATOM 805 OD1 ASN A 363 49.296 69.515 24.399 1.00 31.32 O
-ATOM 806 ND2 ASN A 363 50.990 68.379 25.345 1.00 30.72 N
-ATOM 807 N ARG A 364 46.837 68.576 28.801 1.00 30.84 N
-ATOM 808 CA ARG A 364 45.870 68.004 29.715 1.00 28.85 C
-ATOM 809 C ARG A 364 44.575 68.778 29.527 1.00 28.57 C
-ATOM 810 O ARG A 364 43.503 68.210 29.288 1.00 26.00 O
-ATOM 811 CB ARG A 364 46.356 68.174 31.147 1.00 30.12 C
-ATOM 812 CG ARG A 364 45.358 67.713 32.171 1.00 33.03 C
-ATOM 813 CD ARG A 364 44.991 66.296 31.907 1.00 32.73 C
-ATOM 814 NE ARG A 364 44.083 65.794 32.915 1.00 36.81 N
-ATOM 815 CZ ARG A 364 43.685 64.529 32.974 1.00 38.28 C
-ATOM 816 NH1 ARG A 364 44.126 63.655 32.074 1.00 37.70 N
-ATOM 817 NH2 ARG A 364 42.850 64.133 33.929 1.00 37.61 N
-ATOM 818 N PHE A 365 44.693 70.094 29.628 1.00 28.29 N
-ATOM 819 CA PHE A 365 43.544 70.960 29.473 1.00 28.45 C
-ATOM 820 C PHE A 365 42.799 70.661 28.183 1.00 29.15 C
-ATOM 821 O PHE A 365 41.594 70.400 28.217 1.00 28.82 O
-ATOM 822 CB PHE A 365 43.988 72.430 29.544 1.00 27.14 C
-ATOM 823 CG PHE A 365 44.078 72.960 30.950 1.00 26.64 C
-ATOM 824 CD1 PHE A 365 44.041 72.093 32.042 1.00 28.20 C
-ATOM 825 CD2 PHE A 365 44.161 74.316 31.190 1.00 24.47 C
-ATOM 826 CE1 PHE A 365 44.080 72.583 33.332 1.00 26.00 C
-ATOM 827 CE2 PHE A 365 44.199 74.803 32.476 1.00 24.52 C
-ATOM 828 CZ PHE A 365 44.158 73.941 33.545 1.00 25.17 C
-ATOM 829 N ASN A 366 43.514 70.676 27.059 1.00 32.81 N
-ATOM 830 CA ASN A 366 42.899 70.403 25.764 1.00 35.64 C
-ATOM 831 C ASN A 366 42.162 69.071 25.761 1.00 38.78 C
-ATOM 832 O ASN A 366 41.112 68.931 25.128 1.00 36.88 O
-ATOM 833 CB ASN A 366 43.949 70.418 24.654 1.00 35.50 C
-ATOM 834 CG ASN A 366 44.186 71.807 24.097 1.00 36.88 C
-ATOM 835 OD1 ASN A 366 43.276 72.426 23.546 1.00 39.37 O
-ATOM 836 ND2 ASN A 366 45.409 72.306 24.236 1.00 37.94 N
-ATOM 837 N ASP A 367 42.698 68.091 26.480 1.00 43.70 N
-ATOM 838 CA ASP A 367 42.048 66.785 26.537 1.00 45.66 C
-ATOM 839 C ASP A 367 40.773 66.840 27.364 1.00 43.94 C
-ATOM 840 O ASP A 367 39.787 66.187 27.031 1.00 40.92 O
-ATOM 841 CB ASP A 367 43.008 65.719 27.085 1.00 53.86 C
-ATOM 842 CG ASP A 367 43.937 65.144 26.004 1.00 65.29 C
-ATOM 843 OD1 ASP A 367 43.424 64.577 25.009 1.00 70.52 O
-ATOM 844 OD2 ASP A 367 45.177 65.252 26.153 1.00 69.72 O
-ATOM 845 N LEU A 368 40.779 67.628 28.434 1.00 40.34 N
-ATOM 846 CA LEU A 368 39.576 67.751 29.260 1.00 35.78 C
-ATOM 847 C LEU A 368 38.484 68.524 28.517 1.00 33.38 C
-ATOM 848 O LEU A 368 37.294 68.310 28.741 1.00 29.00 O
-ATOM 849 CB LEU A 368 39.891 68.434 30.597 1.00 37.93 C
-ATOM 850 CG LEU A 368 40.489 67.547 31.700 1.00 40.32 C
-ATOM 851 CD1 LEU A 368 40.691 68.375 32.967 1.00 40.91 C
-ATOM 852 CD2 LEU A 368 39.556 66.368 31.981 1.00 39.89 C
-ATOM 853 N LEU A 369 38.891 69.423 27.634 1.00 31.08 N
-ATOM 854 CA LEU A 369 37.929 70.171 26.857 1.00 30.91 C
-ATOM 855 C LEU A 369 37.300 69.257 25.795 1.00 32.37 C
-ATOM 856 O LEU A 369 36.121 69.389 25.477 1.00 33.46 O
-ATOM 857 CB LEU A 369 38.590 71.384 26.197 1.00 29.40 C
-ATOM 858 CG LEU A 369 38.867 72.563 27.134 1.00 31.37 C
-ATOM 859 CD1 LEU A 369 39.461 73.704 26.326 1.00 31.37 C
-ATOM 860 CD2 LEU A 369 37.571 73.013 27.835 1.00 32.44 C
-ATOM 861 N ASP A 370 38.073 68.334 25.233 1.00 36.20 N
-ATOM 862 CA ASP A 370 37.494 67.433 24.244 1.00 38.67 C
-ATOM 863 C ASP A 370 36.401 66.628 24.952 1.00 39.79 C
-ATOM 864 O ASP A 370 35.316 66.429 24.399 1.00 40.84 O
-ATOM 865 CB ASP A 370 38.565 66.510 23.642 1.00 39.28 C
-ATOM 866 CG ASP A 370 39.552 67.258 22.744 1.00 42.17 C
-ATOM 867 OD1 ASP A 370 39.114 68.092 21.920 1.00 41.41 O
-ATOM 868 OD2 ASP A 370 40.774 67.006 22.849 1.00 45.37 O
-ATOM 869 N ARG A 371 36.689 66.187 26.180 1.00 41.08 N
-ATOM 870 CA ARG A 371 35.729 65.435 27.008 1.00 40.34 C
-ATOM 871 C ARG A 371 34.476 66.267 27.298 1.00 38.57 C
-ATOM 872 O ARG A 371 33.366 65.741 27.367 1.00 37.33 O
-ATOM 873 CB ARG A 371 36.344 65.065 28.361 1.00 41.98 C
-ATOM 874 CG ARG A 371 37.035 63.722 28.447 1.00 44.98 C
-ATOM 875 CD ARG A 371 37.508 63.429 29.884 1.00 46.97 C
-ATOM 876 NE ARG A 371 36.403 63.276 30.840 1.00 48.95 N
-ATOM 877 CZ ARG A 371 36.548 63.150 32.164 1.00 49.50 C
-ATOM 878 NH1 ARG A 371 37.756 63.159 32.719 1.00 47.15 N
-ATOM 879 NH2 ARG A 371 35.476 63.007 32.939 1.00 49.47 N
-ATOM 880 N MET A 372 34.679 67.566 27.511 1.00 36.37 N
-ATOM 881 CA MET A 372 33.594 68.494 27.804 1.00 34.00 C
-ATOM 882 C MET A 372 32.778 68.789 26.554 1.00 34.72 C
-ATOM 883 O MET A 372 31.557 68.929 26.628 1.00 36.19 O
-ATOM 884 CB MET A 372 34.157 69.798 28.386 1.00 29.98 C
-ATOM 885 CG MET A 372 34.636 69.700 29.871 1.00 20.18 C
-ATOM 886 SD MET A 372 35.665 71.068 30.366 1.00 12.54 S
-ATOM 887 CE MET A 372 34.530 72.463 30.198 1.00 15.35 C
-ATOM 888 N ASP A 373 33.449 68.874 25.408 1.00 37.32 N
-ATOM 889 CA ASP A 373 32.762 69.144 24.153 1.00 40.83 C
-ATOM 890 C ASP A 373 31.695 68.083 23.899 1.00 42.07 C
-ATOM 891 O ASP A 373 30.606 68.381 23.419 1.00 45.01 O
-ATOM 892 CB ASP A 373 33.744 69.148 22.978 1.00 42.78 C
-ATOM 893 CG ASP A 373 34.610 70.386 22.941 1.00 45.33 C
-ATOM 894 OD1 ASP A 373 34.069 71.498 23.088 1.00 46.16 O
-ATOM 895 OD2 ASP A 373 35.836 70.249 22.749 1.00 47.15 O
-ATOM 896 N ILE A 374 32.020 66.838 24.218 1.00 41.14 N
-ATOM 897 CA ILE A 374 31.094 65.744 24.019 1.00 39.38 C
-ATOM 898 C ILE A 374 30.059 65.675 25.136 1.00 38.74 C
-ATOM 899 O ILE A 374 28.876 65.538 24.857 1.00 40.82 O
-ATOM 900 CB ILE A 374 31.839 64.405 23.939 1.00 39.05 C
-ATOM 901 CG1 ILE A 374 32.777 64.417 22.739 1.00 37.37 C
-ATOM 902 CG2 ILE A 374 30.846 63.254 23.817 1.00 37.23 C
-ATOM 903 CD1 ILE A 374 33.633 63.180 22.647 1.00 37.48 C
-ATOM 904 N MET A 375 30.493 65.762 26.392 1.00 37.82 N
-ATOM 905 CA MET A 375 29.563 65.713 27.527 1.00 38.23 C
-ATOM 906 C MET A 375 28.381 66.659 27.330 1.00 39.47 C
-ATOM 907 O MET A 375 27.218 66.268 27.469 1.00 41.00 O
-ATOM 908 CB MET A 375 30.248 66.138 28.827 1.00 36.41 C
-ATOM 909 CG MET A 375 31.314 65.215 29.369 1.00 33.48 C
-ATOM 910 SD MET A 375 32.068 66.016 30.795 1.00 27.97 S
-ATOM 911 CE MET A 375 30.738 65.997 31.926 1.00 27.90 C
-ATOM 912 N PHE A 376 28.692 67.912 27.014 1.00 40.75 N
-ATOM 913 CA PHE A 376 27.672 68.936 26.845 1.00 41.94 C
-ATOM 914 C PHE A 376 27.313 69.231 25.392 1.00 43.72 C
-ATOM 915 O PHE A 376 26.780 70.297 25.084 1.00 43.82 O
-ATOM 916 CB PHE A 376 28.141 70.216 27.529 1.00 37.45 C
-ATOM 917 CG PHE A 376 28.648 69.999 28.933 1.00 32.70 C
-ATOM 918 CD1 PHE A 376 27.791 69.560 29.936 1.00 28.61 C
-ATOM 919 CD2 PHE A 376 29.990 70.242 29.251 1.00 32.55 C
-ATOM 920 CE1 PHE A 376 28.257 69.369 31.233 1.00 31.08 C
-ATOM 921 CE2 PHE A 376 30.471 70.053 30.553 1.00 30.28 C
-ATOM 922 CZ PHE A 376 29.605 69.619 31.542 1.00 31.31 C
-ATOM 923 N GLY A 377 27.586 68.280 24.505 1.00 46.34 N
-ATOM 924 CA GLY A 377 27.290 68.484 23.099 1.00 51.35 C
-ATOM 925 C GLY A 377 25.952 67.920 22.664 1.00 54.81 C
-ATOM 926 O GLY A 377 25.177 67.439 23.497 1.00 56.74 O
-ATOM 927 N SER A 378 25.691 67.988 21.356 1.00 56.90 N
-ATOM 928 CA SER A 378 24.454 67.492 20.744 1.00 55.98 C
-ATOM 929 C SER A 378 24.187 66.034 21.093 1.00 59.12 C
-ATOM 930 O SER A 378 23.072 65.669 21.480 1.00 51.38 O
-ATOM 931 CB SER A 378 24.530 67.636 19.224 1.00 54.17 C
-ATOM 932 OG SER A 378 25.638 66.924 18.707 1.00 57.58 O
-ATOM 933 N THR A 379 25.215 65.204 20.932 1.00 63.57 N
-ATOM 934 CA THR A 379 25.115 63.784 21.253 1.00 66.44 C
-ATOM 935 C THR A 379 25.948 63.539 22.509 1.00 63.46 C
-ATOM 936 O THR A 379 27.086 63.073 22.433 1.00 60.51 O
-ATOM 937 CB THR A 379 25.654 62.900 20.106 1.00 78.47 C
-ATOM 938 OG1 THR A 379 27.083 63.003 20.045 1.00 96.49 O
-ATOM 939 CG2 THR A 379 25.064 63.346 18.773 1.00 96.67 C
-ATOM 940 N GLY A 380 25.373 63.885 23.657 1.00 57.83 N
-ATOM 941 CA GLY A 380 26.046 63.720 24.931 1.00 49.07 C
-ATOM 942 C GLY A 380 24.974 63.730 25.995 1.00 47.41 C
-ATOM 943 O GLY A 380 23.859 64.169 25.727 1.00 46.60 O
-ATOM 944 N SER A 381 25.294 63.266 27.199 1.00 45.98 N
-ATOM 945 CA SER A 381 24.311 63.213 28.281 1.00 46.50 C
-ATOM 946 C SER A 381 24.410 64.350 29.291 1.00 46.30 C
-ATOM 947 O SER A 381 23.394 64.852 29.760 1.00 47.53 O
-ATOM 948 CB SER A 381 24.456 61.907 29.036 1.00 48.06 C
-ATOM 949 OG SER A 381 25.741 61.865 29.627 1.00 54.19 O
-ATOM 950 N ALA A 382 25.635 64.744 29.627 1.00 43.09 N
-ATOM 951 CA ALA A 382 25.893 65.800 30.610 1.00 39.82 C
-ATOM 952 C ALA A 382 24.880 66.949 30.687 1.00 37.80 C
-ATOM 953 O ALA A 382 24.413 67.458 29.665 1.00 34.41 O
-ATOM 954 CB ALA A 382 27.301 66.361 30.400 1.00 39.86 C
-ATOM 955 N ASP A 383 24.551 67.339 31.918 1.00 34.30 N
-ATOM 956 CA ASP A 383 23.608 68.434 32.190 1.00 33.80 C
-ATOM 957 C ASP A 383 24.416 69.611 32.745 1.00 34.31 C
-ATOM 958 O ASP A 383 24.625 69.711 33.950 1.00 34.34 O
-ATOM 959 CB ASP A 383 22.583 67.996 33.235 1.00 35.29 C
-ATOM 960 CG ASP A 383 21.481 69.019 33.444 1.00 38.33 C
-ATOM 961 OD1 ASP A 383 21.735 70.227 33.247 1.00 39.88 O
-ATOM 962 OD2 ASP A 383 20.355 68.615 33.822 1.00 40.92 O
-ATOM 963 N ILE A 384 24.852 70.514 31.873 1.00 33.99 N
-ATOM 964 CA ILE A 384 25.687 71.631 32.301 1.00 33.03 C
-ATOM 965 C ILE A 384 25.199 72.436 33.511 1.00 33.49 C
-ATOM 966 O ILE A 384 26.000 72.978 34.273 1.00 31.18 O
-ATOM 967 CB ILE A 384 25.980 72.567 31.107 1.00 33.99 C
-ATOM 968 CG1 ILE A 384 27.301 73.291 31.352 1.00 36.82 C
-ATOM 969 CG2 ILE A 384 24.853 73.549 30.899 1.00 35.47 C
-ATOM 970 CD1 ILE A 384 27.800 74.028 30.136 1.00 39.49 C
-ATOM 971 N GLU A 385 23.892 72.506 33.701 1.00 33.61 N
-ATOM 972 CA GLU A 385 23.347 73.243 34.831 1.00 32.72 C
-ATOM 973 C GLU A 385 23.749 72.556 36.136 1.00 32.78 C
-ATOM 974 O GLU A 385 23.995 73.209 37.148 1.00 31.37 O
-ATOM 975 CB GLU A 385 21.823 73.313 34.706 1.00 34.14 C
-ATOM 976 CG GLU A 385 21.135 74.086 35.810 1.00 38.54 C
-ATOM 977 CD GLU A 385 19.641 73.795 35.893 1.00 40.19 C
-ATOM 978 OE1 GLU A 385 19.259 72.607 36.008 1.00 40.79 O
-ATOM 979 OE2 GLU A 385 18.846 74.755 35.854 1.00 42.23 O
-ATOM 980 N GLU A 386 23.812 71.231 36.107 1.00 33.82 N
-ATOM 981 CA GLU A 386 24.191 70.462 37.287 1.00 36.75 C
-ATOM 982 C GLU A 386 25.692 70.571 37.533 1.00 36.75 C
-ATOM 983 O GLU A 386 26.167 70.412 38.665 1.00 37.20 O
-ATOM 984 CB GLU A 386 23.788 68.995 37.124 1.00 40.88 C
-ATOM 985 CG GLU A 386 22.332 68.714 37.492 1.00 48.69 C
-ATOM 986 CD GLU A 386 21.922 67.277 37.212 1.00 51.43 C
-ATOM 987 OE1 GLU A 386 22.798 66.489 36.795 1.00 52.06 O
-ATOM 988 OE2 GLU A 386 20.729 66.937 37.407 1.00 51.42 O
-ATOM 989 N TRP A 387 26.442 70.856 36.473 1.00 33.05 N
-ATOM 990 CA TRP A 387 27.879 71.019 36.598 1.00 28.82 C
-ATOM 991 C TRP A 387 28.292 72.418 37.080 1.00 25.70 C
-ATOM 992 O TRP A 387 29.373 72.584 37.639 1.00 24.22 O
-ATOM 993 CB TRP A 387 28.556 70.683 35.279 1.00 28.62 C
-ATOM 994 CG TRP A 387 28.604 69.218 35.047 1.00 29.42 C
-ATOM 995 CD1 TRP A 387 27.621 68.436 34.529 1.00 29.34 C
-ATOM 996 CD2 TRP A 387 29.676 68.338 35.396 1.00 30.22 C
-ATOM 997 NE1 TRP A 387 28.010 67.118 34.536 1.00 30.68 N
-ATOM 998 CE2 TRP A 387 29.269 67.030 35.064 1.00 29.27 C
-ATOM 999 CE3 TRP A 387 30.943 68.534 35.967 1.00 30.28 C
-ATOM 1000 CZ2 TRP A 387 30.080 65.916 35.274 1.00 29.25 C
-ATOM 1001 CZ3 TRP A 387 31.757 67.423 36.180 1.00 31.11 C
-ATOM 1002 CH2 TRP A 387 31.318 66.130 35.835 1.00 30.29 C
-ATOM 1003 N MET A 388 27.451 73.427 36.869 1.00 23.71 N
-ATOM 1004 CA MET A 388 27.788 74.761 37.357 1.00 22.54 C
-ATOM 1005 C MET A 388 27.388 74.762 38.822 1.00 21.87 C
-ATOM 1006 O MET A 388 27.943 75.507 39.632 1.00 22.54 O
-ATOM 1007 CB MET A 388 27.043 75.864 36.579 1.00 21.87 C
-ATOM 1008 CG MET A 388 27.724 76.283 35.264 1.00 18.17 C
-ATOM 1009 SD MET A 388 29.400 76.960 35.445 1.00 15.07 S
-ATOM 1010 CE MET A 388 29.023 78.572 36.115 1.00 10.75 C
-ATOM 1011 N ALA A 389 26.428 73.905 39.156 1.00 21.92 N
-ATOM 1012 CA ALA A 389 25.975 73.769 40.535 1.00 24.23 C
-ATOM 1013 C ALA A 389 27.145 73.162 41.291 1.00 25.26 C
-ATOM 1014 O ALA A 389 27.347 73.460 42.474 1.00 24.11 O
-ATOM 1015 CB ALA A 389 24.768 72.845 40.622 1.00 24.33 C
-ATOM 1016 N GLY A 390 27.902 72.306 40.594 1.00 26.35 N
-ATOM 1017 CA GLY A 390 29.071 71.674 41.189 1.00 27.18 C
-ATOM 1018 C GLY A 390 30.133 72.720 41.503 1.00 26.50 C
-ATOM 1019 O GLY A 390 30.788 72.690 42.548 1.00 27.23 O
-ATOM 1020 N VAL A 391 30.300 73.653 40.576 1.00 24.66 N
-ATOM 1021 CA VAL A 391 31.242 74.737 40.750 1.00 23.66 C
-ATOM 1022 C VAL A 391 30.780 75.597 41.932 1.00 22.94 C
-ATOM 1023 O VAL A 391 31.571 75.961 42.811 1.00 23.44 O
-ATOM 1024 CB VAL A 391 31.310 75.591 39.475 1.00 24.96 C
-ATOM 1025 CG1 VAL A 391 32.140 76.859 39.713 1.00 24.27 C
-ATOM 1026 CG2 VAL A 391 31.907 74.747 38.346 1.00 25.40 C
-ATOM 1027 N ALA A 392 29.491 75.904 41.968 1.00 20.41 N
-ATOM 1028 CA ALA A 392 28.974 76.702 43.055 1.00 20.38 C
-ATOM 1029 C ALA A 392 29.279 76.026 44.400 1.00 22.12 C
-ATOM 1030 O ALA A 392 29.744 76.670 45.344 1.00 21.02 O
-ATOM 1031 CB ALA A 392 27.496 76.887 42.885 1.00 19.94 C
-ATOM 1032 N TRP A 393 29.018 74.732 44.502 1.00 23.53 N
-ATOM 1033 CA TRP A 393 29.293 74.026 45.747 1.00 24.55 C
-ATOM 1034 C TRP A 393 30.792 74.042 46.073 1.00 23.78 C
-ATOM 1035 O TRP A 393 31.181 74.210 47.228 1.00 23.31 O
-ATOM 1036 CB TRP A 393 28.813 72.574 45.660 1.00 28.91 C
-ATOM 1037 CG TRP A 393 28.879 71.868 46.976 1.00 33.67 C
-ATOM 1038 CD1 TRP A 393 27.903 71.818 47.940 1.00 34.59 C
-ATOM 1039 CD2 TRP A 393 30.013 71.180 47.521 1.00 35.26 C
-ATOM 1040 NE1 TRP A 393 28.366 71.147 49.045 1.00 35.58 N
-ATOM 1041 CE2 TRP A 393 29.657 70.745 48.815 1.00 35.44 C
-ATOM 1042 CE3 TRP A 393 31.299 70.892 47.036 1.00 35.79 C
-ATOM 1043 CZ2 TRP A 393 30.540 70.035 49.634 1.00 34.69 C
-ATOM 1044 CZ3 TRP A 393 32.172 70.188 47.850 1.00 35.80 C
-ATOM 1045 CH2 TRP A 393 31.788 69.767 49.135 1.00 35.79 C
-ATOM 1046 N LEU A 394 31.627 73.859 45.054 1.00 24.39 N
-ATOM 1047 CA LEU A 394 33.076 73.868 45.239 1.00 24.37 C
-ATOM 1048 C LEU A 394 33.639 75.226 45.636 1.00 25.03 C
-ATOM 1049 O LEU A 394 34.606 75.319 46.402 1.00 28.71 O
-ATOM 1050 CB LEU A 394 33.773 73.415 43.963 1.00 20.59 C
-ATOM 1051 CG LEU A 394 33.890 71.904 43.802 1.00 19.69 C
-ATOM 1052 CD1 LEU A 394 34.407 71.592 42.416 1.00 17.43 C
-ATOM 1053 CD2 LEU A 394 34.812 71.327 44.893 1.00 18.82 C
-ATOM 1054 N HIS A 395 33.036 76.284 45.115 1.00 26.75 N
-ATOM 1055 CA HIS A 395 33.511 77.623 45.407 1.00 29.15 C
-ATOM 1056 C HIS A 395 33.044 78.083 46.785 1.00 30.98 C
-ATOM 1057 O HIS A 395 33.215 79.250 47.151 1.00 32.79 O
-ATOM 1058 CB HIS A 395 33.035 78.575 44.308 1.00 27.42 C
-ATOM 1059 CG HIS A 395 33.895 79.785 44.146 1.00 24.44 C
-ATOM 1060 ND1 HIS A 395 33.844 80.855 45.014 1.00 22.69 N
-ATOM 1061 CD2 HIS A 395 34.842 80.091 43.227 1.00 22.76 C
-ATOM 1062 CE1 HIS A 395 34.724 81.769 44.632 1.00 21.51 C
-ATOM 1063 NE2 HIS A 395 35.339 81.330 43.553 1.00 18.73 N
-ATOM 1064 N CYS A 396 32.461 77.151 47.539 1.00 30.22 N
-ATOM 1065 CA CYS A 396 31.965 77.421 48.885 1.00 29.88 C
-ATOM 1066 C CYS A 396 32.704 76.538 49.873 1.00 28.74 C
-ATOM 1067 O CYS A 396 32.553 76.681 51.092 1.00 26.71 O
-ATOM 1068 CB CYS A 396 30.457 77.130 48.991 1.00 33.03 C
-ATOM 1069 SG CYS A 396 29.304 78.382 48.316 1.00 39.21 S
-ATOM 1070 N LEU A 397 33.492 75.614 49.335 1.00 26.81 N
-ATOM 1071 CA LEU A 397 34.262 74.678 50.147 1.00 25.36 C
-ATOM 1072 C LEU A 397 35.486 75.336 50.759 1.00 25.37 C
-ATOM 1073 O LEU A 397 35.896 75.007 51.874 1.00 25.16 O
-ATOM 1074 CB LEU A 397 34.724 73.508 49.298 1.00 25.97 C
-ATOM 1075 CG LEU A 397 35.596 72.464 49.991 1.00 25.95 C
-ATOM 1076 CD1 LEU A 397 34.789 71.700 51.035 1.00 24.31 C
-ATOM 1077 CD2 LEU A 397 36.136 71.525 48.925 1.00 26.09 C
-ATOM 1078 N LEU A 398 36.070 76.269 50.015 1.00 26.55 N
-ATOM 1079 CA LEU A 398 37.250 76.978 50.466 1.00 25.79 C
-ATOM 1080 C LEU A 398 37.134 78.425 50.031 1.00 24.05 C
-ATOM 1081 O LEU A 398 36.518 78.731 49.010 1.00 28.55 O
-ATOM 1082 CB LEU A 398 38.490 76.336 49.843 1.00 27.44 C
-ATOM 1083 CG LEU A 398 39.627 75.852 50.739 1.00 28.16 C
-ATOM 1084 CD1 LEU A 398 39.109 75.065 51.944 1.00 26.09 C
-ATOM 1085 CD2 LEU A 398 40.537 74.990 49.876 1.00 27.14 C
-ATOM 1086 N PRO A 399 37.722 79.340 50.805 1.00 24.93 N
-ATOM 1087 CA PRO A 399 37.691 80.776 50.503 1.00 25.13 C
-ATOM 1088 C PRO A 399 38.546 81.085 49.281 1.00 26.38 C
-ATOM 1089 O PRO A 399 39.628 80.518 49.122 1.00 29.12 O
-ATOM 1090 CB PRO A 399 38.285 81.410 51.747 1.00 19.95 C
-ATOM 1091 CG PRO A 399 38.081 80.390 52.812 1.00 19.79 C
-ATOM 1092 CD PRO A 399 38.356 79.094 52.106 1.00 22.16 C
-ATOM 1093 N LYS A 400 38.061 81.979 48.423 1.00 29.66 N
-ATOM 1094 CA LYS A 400 38.794 82.364 47.218 1.00 31.32 C
-ATOM 1095 C LYS A 400 39.242 81.103 46.474 1.00 30.51 C
-ATOM 1096 O LYS A 400 40.323 81.063 45.868 1.00 28.23 O
-ATOM 1097 CB LYS A 400 40.003 83.238 47.601 1.00 32.72 C
-ATOM 1098 CG LYS A 400 39.611 84.545 48.278 1.00 33.65 C
-ATOM 1099 CD LYS A 400 40.797 85.335 48.829 1.00 36.43 C
-ATOM 1100 CE LYS A 400 41.431 86.286 47.796 1.00 40.96 C
-ATOM 1101 NZ LYS A 400 42.457 85.684 46.853 1.00 39.75 N
-ATOM 1102 N MET A 401 38.384 80.082 46.528 1.00 26.98 N
-ATOM 1103 CA MET A 401 38.655 78.801 45.897 1.00 23.45 C
-ATOM 1104 C MET A 401 39.235 78.913 44.498 1.00 22.44 C
-ATOM 1105 O MET A 401 40.199 78.219 44.180 1.00 22.39 O
-ATOM 1106 CB MET A 401 37.388 77.936 45.873 1.00 19.42 C
-ATOM 1107 CG MET A 401 37.571 76.528 45.279 1.00 13.83 C
-ATOM 1108 SD MET A 401 39.000 75.607 45.926 1.00 7.98 S
-ATOM 1109 CE MET A 401 38.323 74.598 47.113 1.00 15.86 C
-ATOM 1110 N ASP A 402 38.697 79.802 43.670 1.00 22.47 N
-ATOM 1111 CA ASP A 402 39.211 79.904 42.308 1.00 25.43 C
-ATOM 1112 C ASP A 402 40.633 80.448 42.246 1.00 27.83 C
-ATOM 1113 O ASP A 402 41.372 80.180 41.294 1.00 29.53 O
-ATOM 1114 CB ASP A 402 38.288 80.746 41.434 1.00 25.72 C
-ATOM 1115 CG ASP A 402 38.433 82.201 41.689 1.00 28.47 C
-ATOM 1116 OD1 ASP A 402 39.048 82.899 40.859 1.00 28.54 O
-ATOM 1117 OD2 ASP A 402 37.932 82.649 42.732 1.00 33.58 O
-ATOM 1118 N SER A 403 41.034 81.207 43.256 1.00 28.91 N
-ATOM 1119 CA SER A 403 42.394 81.736 43.275 1.00 27.72 C
-ATOM 1120 C SER A 403 43.320 80.602 43.757 1.00 26.37 C
-ATOM 1121 O SER A 403 44.476 80.479 43.340 1.00 22.80 O
-ATOM 1122 CB SER A 403 42.431 82.944 44.206 1.00 28.27 C
-ATOM 1123 OG SER A 403 41.289 83.764 43.965 1.00 36.54 O
-ATOM 1124 N VAL A 404 42.768 79.755 44.621 1.00 25.55 N
-ATOM 1125 CA VAL A 404 43.477 78.614 45.169 1.00 23.86 C
-ATOM 1126 C VAL A 404 43.878 77.632 44.083 1.00 23.23 C
-ATOM 1127 O VAL A 404 44.984 77.102 44.099 1.00 25.89 O
-ATOM 1128 CB VAL A 404 42.605 77.863 46.171 1.00 21.72 C
-ATOM 1129 CG1 VAL A 404 43.295 76.575 46.595 1.00 22.60 C
-ATOM 1130 CG2 VAL A 404 42.334 78.734 47.367 1.00 21.45 C
-ATOM 1131 N VAL A 405 42.973 77.380 43.144 1.00 22.29 N
-ATOM 1132 CA VAL A 405 43.251 76.441 42.062 1.00 22.38 C
-ATOM 1133 C VAL A 405 44.261 77.034 41.092 1.00 23.76 C
-ATOM 1134 O VAL A 405 45.112 76.332 40.553 1.00 21.51 O
-ATOM 1135 CB VAL A 405 41.946 76.052 41.301 1.00 22.89 C
-ATOM 1136 CG1 VAL A 405 42.263 75.112 40.130 1.00 22.08 C
-ATOM 1137 CG2 VAL A 405 40.981 75.376 42.255 1.00 22.59 C
-ATOM 1138 N TYR A 406 44.163 78.332 40.856 1.00 26.32 N
-ATOM 1139 CA TYR A 406 45.110 78.977 39.960 1.00 27.52 C
-ATOM 1140 C TYR A 406 46.474 78.918 40.645 1.00 27.30 C
-ATOM 1141 O TYR A 406 47.481 78.580 40.030 1.00 24.17 O
-ATOM 1142 CB TYR A 406 44.697 80.434 39.710 1.00 32.08 C
-ATOM 1143 CG TYR A 406 45.749 81.281 39.014 1.00 37.39 C
-ATOM 1144 CD1 TYR A 406 46.126 81.033 37.692 1.00 39.09 C
-ATOM 1145 CD2 TYR A 406 46.354 82.346 39.678 1.00 39.31 C
-ATOM 1146 CE1 TYR A 406 47.080 81.833 37.049 1.00 40.05 C
-ATOM 1147 CE2 TYR A 406 47.303 83.148 39.047 1.00 40.71 C
-ATOM 1148 CZ TYR A 406 47.665 82.891 37.737 1.00 40.85 C
-ATOM 1149 OH TYR A 406 48.608 83.699 37.133 1.00 41.94 O
-ATOM 1150 N ASP A 407 46.494 79.262 41.928 1.00 29.09 N
-ATOM 1151 CA ASP A 407 47.730 79.224 42.683 1.00 30.28 C
-ATOM 1152 C ASP A 407 48.316 77.827 42.593 1.00 29.91 C
-ATOM 1153 O ASP A 407 49.464 77.650 42.203 1.00 33.30 O
-ATOM 1154 CB ASP A 407 47.497 79.555 44.152 1.00 31.80 C
-ATOM 1155 CG ASP A 407 47.280 81.032 44.400 1.00 35.59 C
-ATOM 1156 OD1 ASP A 407 47.949 81.857 43.736 1.00 37.55 O
-ATOM 1157 OD2 ASP A 407 46.449 81.360 45.282 1.00 36.88 O
-ATOM 1158 N PHE A 408 47.521 76.828 42.949 1.00 28.68 N
-ATOM 1159 CA PHE A 408 47.997 75.456 42.910 1.00 26.43 C
-ATOM 1160 C PHE A 408 48.599 75.085 41.560 1.00 24.63 C
-ATOM 1161 O PHE A 408 49.652 74.452 41.499 1.00 24.71 O
-ATOM 1162 CB PHE A 408 46.871 74.485 43.233 1.00 22.03 C
-ATOM 1163 CG PHE A 408 47.290 73.057 43.163 1.00 18.93 C
-ATOM 1164 CD1 PHE A 408 48.128 72.522 44.127 1.00 19.10 C
-ATOM 1165 CD2 PHE A 408 46.883 72.256 42.108 1.00 18.55 C
-ATOM 1166 CE1 PHE A 408 48.561 71.194 44.044 1.00 19.69 C
-ATOM 1167 CE2 PHE A 408 47.304 70.933 42.009 1.00 16.92 C
-ATOM 1168 CZ PHE A 408 48.144 70.399 42.977 1.00 17.84 C
-ATOM 1169 N LEU A 409 47.919 75.463 40.485 1.00 23.47 N
-ATOM 1170 CA LEU A 409 48.387 75.181 39.134 1.00 23.84 C
-ATOM 1171 C LEU A 409 49.743 75.818 38.876 1.00 27.83 C
-ATOM 1172 O LEU A 409 50.609 75.202 38.259 1.00 25.49 O
-ATOM 1173 CB LEU A 409 47.374 75.696 38.105 1.00 22.10 C
-ATOM 1174 CG LEU A 409 46.083 74.884 37.939 1.00 20.48 C
-ATOM 1175 CD1 LEU A 409 45.170 75.536 36.935 1.00 19.00 C
-ATOM 1176 CD2 LEU A 409 46.449 73.476 37.477 1.00 22.01 C
-ATOM 1177 N LYS A 410 49.943 77.044 39.352 1.00 32.67 N
-ATOM 1178 CA LYS A 410 51.225 77.713 39.125 1.00 36.19 C
-ATOM 1179 C LYS A 410 52.325 77.015 39.941 1.00 35.15 C
-ATOM 1180 O LYS A 410 53.461 76.838 39.491 1.00 30.89 O
-ATOM 1181 CB LYS A 410 51.136 79.204 39.492 1.00 45.80 C
-ATOM 1182 CG LYS A 410 51.192 79.491 40.974 1.00 63.96 C
-ATOM 1183 CD LYS A 410 51.124 80.976 41.284 1.00 72.23 C
-ATOM 1184 CE LYS A 410 51.182 81.197 42.795 1.00 74.82 C
-ATOM 1185 NZ LYS A 410 51.046 82.626 43.169 1.00 75.46 N
-ATOM 1186 N CYS A 411 51.965 76.609 41.147 1.00 33.44 N
-ATOM 1187 CA CYS A 411 52.896 75.914 42.000 1.00 30.81 C
-ATOM 1188 C CYS A 411 53.337 74.658 41.239 1.00 28.55 C
-ATOM 1189 O CYS A 411 54.526 74.439 41.044 1.00 31.80 O
-ATOM 1190 CB CYS A 411 52.206 75.535 43.306 1.00 31.63 C
-ATOM 1191 SG CYS A 411 53.297 74.894 44.583 1.00 34.99 S
-ATOM 1192 N MET A 412 52.374 73.858 40.787 1.00 26.53 N
-ATOM 1193 CA MET A 412 52.669 72.630 40.066 1.00 25.54 C
-ATOM 1194 C MET A 412 53.445 72.851 38.777 1.00 28.04 C
-ATOM 1195 O MET A 412 54.302 72.041 38.431 1.00 30.26 O
-ATOM 1196 CB MET A 412 51.378 71.853 39.736 1.00 22.95 C
-ATOM 1197 CG MET A 412 50.562 71.321 40.932 1.00 14.77 C
-ATOM 1198 SD MET A 412 51.499 70.312 42.097 1.00 8.66 S
-ATOM 1199 CE MET A 412 52.088 71.568 43.198 1.00 9.18 C
-ATOM 1200 N VAL A 413 53.155 73.919 38.043 1.00 28.31 N
-ATOM 1201 CA VAL A 413 53.890 74.137 36.798 1.00 28.45 C
-ATOM 1202 C VAL A 413 55.263 74.724 37.051 1.00 30.04 C
-ATOM 1203 O VAL A 413 56.230 74.313 36.440 1.00 29.00 O
-ATOM 1204 CB VAL A 413 53.141 75.065 35.806 1.00 30.11 C
-ATOM 1205 CG1 VAL A 413 54.123 75.645 34.817 1.00 31.81 C
-ATOM 1206 CG2 VAL A 413 52.101 74.283 35.028 1.00 33.51 C
-ATOM 1207 N TYR A 414 55.351 75.695 37.944 1.00 31.77 N
-ATOM 1208 CA TYR A 414 56.633 76.318 38.241 1.00 33.12 C
-ATOM 1209 C TYR A 414 57.593 75.284 38.837 1.00 32.86 C
-ATOM 1210 O TYR A 414 58.811 75.390 38.693 1.00 33.01 O
-ATOM 1211 CB TYR A 414 56.430 77.503 39.198 1.00 36.82 C
-ATOM 1212 CG TYR A 414 55.855 78.743 38.538 1.00 41.97 C
-ATOM 1213 CD1 TYR A 414 54.798 78.653 37.626 1.00 44.77 C
-ATOM 1214 CD2 TYR A 414 56.337 80.014 38.857 1.00 44.97 C
-ATOM 1215 CE1 TYR A 414 54.233 79.799 37.047 1.00 45.26 C
-ATOM 1216 CE2 TYR A 414 55.781 81.170 38.285 1.00 46.06 C
-ATOM 1217 CZ TYR A 414 54.731 81.052 37.385 1.00 45.74 C
-ATOM 1218 OH TYR A 414 54.189 82.179 36.816 1.00 44.79 O
-ATOM 1219 N ASN A 415 57.030 74.279 39.495 1.00 32.00 N
-ATOM 1220 CA ASN A 415 57.809 73.216 40.108 1.00 29.74 C
-ATOM 1221 C ASN A 415 59.142 73.681 40.690 1.00 29.63 C
-ATOM 1222 O ASN A 415 60.213 73.315 40.188 1.00 28.55 O
-ATOM 1223 CB ASN A 415 58.059 72.126 39.078 1.00 28.33 C
-ATOM 1224 CG ASN A 415 58.638 70.890 39.693 1.00 28.81 C
-ATOM 1225 OD1 ASN A 415 59.198 70.056 39.005 1.00 31.76 O
-ATOM 1226 ND2 ASN A 415 58.502 70.759 41.002 1.00 28.27 N
-ATOM 1227 N ILE A 416 59.080 74.467 41.761 1.00 30.66 N
-ATOM 1228 CA ILE A 416 60.289 74.993 42.387 1.00 30.53 C
-ATOM 1229 C ILE A 416 60.752 74.229 43.621 1.00 30.34 C
-ATOM 1230 O ILE A 416 59.983 73.983 44.551 1.00 33.98 O
-ATOM 1231 CB ILE A 416 60.114 76.480 42.748 1.00 31.45 C
-ATOM 1232 CG1 ILE A 416 60.084 77.293 41.453 1.00 30.13 C
-ATOM 1233 CG2 ILE A 416 61.228 76.945 43.691 1.00 31.65 C
-ATOM 1234 CD1 ILE A 416 60.291 78.767 41.646 1.00 33.94 C
-ATOM 1235 N PRO A 417 62.038 73.861 43.658 1.00 35.04 N
-ATOM 1236 CA PRO A 417 62.514 73.119 44.829 1.00 35.17 C
-ATOM 1237 C PRO A 417 62.058 73.703 46.160 1.00 35.90 C
-ATOM 1238 O PRO A 417 62.099 74.913 46.364 1.00 37.52 O
-ATOM 1239 CB PRO A 417 64.040 73.107 44.647 1.00 33.79 C
-ATOM 1240 CG PRO A 417 64.301 74.212 43.633 1.00 31.76 C
-ATOM 1241 CD PRO A 417 63.132 74.155 42.720 1.00 31.43 C
-ATOM 1242 N LYS A 418 61.593 72.819 47.041 1.00 38.21 N
-ATOM 1243 CA LYS A 418 61.108 73.170 48.378 1.00 38.73 C
-ATOM 1244 C LYS A 418 59.857 74.035 48.396 1.00 38.62 C
-ATOM 1245 O LYS A 418 59.533 74.648 49.412 1.00 37.36 O
-ATOM 1246 CB LYS A 418 62.208 73.859 49.187 1.00 41.51 C
-ATOM 1247 CG LYS A 418 63.351 72.954 49.607 1.00 47.93 C
-ATOM 1248 CD LYS A 418 64.339 73.708 50.467 1.00 51.98 C
-ATOM 1249 CE LYS A 418 65.456 72.804 50.964 1.00 54.81 C
-ATOM 1250 NZ LYS A 418 66.452 73.568 51.786 1.00 54.53 N
-ATOM 1251 N LYS A 419 59.148 74.086 47.275 1.00 36.54 N
-ATOM 1252 CA LYS A 419 57.915 74.865 47.186 1.00 33.29 C
-ATOM 1253 C LYS A 419 57.012 74.154 46.189 1.00 31.53 C
-ATOM 1254 O LYS A 419 56.345 74.802 45.378 1.00 32.04 O
-ATOM 1255 CB LYS A 419 58.204 76.266 46.662 1.00 33.55 C
-ATOM 1256 CG LYS A 419 59.081 77.130 47.527 1.00 38.19 C
-ATOM 1257 CD LYS A 419 59.224 78.477 46.836 1.00 40.30 C
-ATOM 1258 CE LYS A 419 59.907 79.527 47.684 1.00 40.35 C
-ATOM 1259 NZ LYS A 419 59.945 80.830 46.960 1.00 39.64 N
-ATOM 1260 N ARG A 420 56.990 72.825 46.252 1.00 28.25 N
-ATOM 1261 CA ARG A 420 56.208 72.019 45.309 1.00 26.37 C
-ATOM 1262 C ARG A 420 55.089 71.189 45.924 1.00 24.71 C
-ATOM 1263 O ARG A 420 54.338 70.537 45.199 1.00 24.40 O
-ATOM 1264 CB ARG A 420 57.152 71.075 44.564 1.00 24.03 C
-ATOM 1265 CG ARG A 420 58.577 71.549 44.598 1.00 23.53 C
-ATOM 1266 CD ARG A 420 59.466 70.696 43.753 1.00 25.58 C
-ATOM 1267 NE ARG A 420 59.706 69.375 44.332 1.00 24.94 N
-ATOM 1268 CZ ARG A 420 59.532 68.236 43.673 1.00 23.58 C
-ATOM 1269 NH1 ARG A 420 59.108 68.248 42.414 1.00 23.34 N
-ATOM 1270 NH2 ARG A 420 59.803 67.087 44.266 1.00 23.07 N
-ATOM 1271 N TYR A 421 54.987 71.206 47.250 1.00 21.14 N
-ATOM 1272 CA TYR A 421 53.982 70.420 47.928 1.00 18.44 C
-ATOM 1273 C TYR A 421 53.014 71.155 48.801 1.00 19.01 C
-ATOM 1274 O TYR A 421 53.368 72.094 49.487 1.00 16.63 O
-ATOM 1275 CB TYR A 421 54.650 69.310 48.737 1.00 16.41 C
-ATOM 1276 CG TYR A 421 54.911 68.102 47.887 1.00 17.95 C
-ATOM 1277 CD1 TYR A 421 55.999 68.067 47.005 1.00 17.12 C
-ATOM 1278 CD2 TYR A 421 54.004 67.028 47.877 1.00 16.87 C
-ATOM 1279 CE1 TYR A 421 56.179 66.995 46.123 1.00 18.25 C
-ATOM 1280 CE2 TYR A 421 54.173 65.957 47.007 1.00 17.30 C
-ATOM 1281 CZ TYR A 421 55.259 65.952 46.129 1.00 18.54 C
-ATOM 1282 OH TYR A 421 55.415 64.929 45.235 1.00 17.50 O
-ATOM 1283 N TRP A 422 51.769 70.708 48.748 1.00 20.35 N
-ATOM 1284 CA TRP A 422 50.696 71.263 49.555 1.00 20.18 C
-ATOM 1285 C TRP A 422 50.239 70.126 50.448 1.00 19.44 C
-ATOM 1286 O TRP A 422 50.263 68.961 50.040 1.00 18.75 O
-ATOM 1287 CB TRP A 422 49.526 71.742 48.682 1.00 21.03 C
-ATOM 1288 CG TRP A 422 49.767 73.063 48.042 1.00 24.75 C
-ATOM 1289 CD1 TRP A 422 50.979 73.606 47.721 1.00 25.95 C
-ATOM 1290 CD2 TRP A 422 48.777 73.972 47.534 1.00 25.60 C
-ATOM 1291 NE1 TRP A 422 50.807 74.791 47.039 1.00 25.74 N
-ATOM 1292 CE2 TRP A 422 49.464 75.040 46.911 1.00 25.72 C
-ATOM 1293 CE3 TRP A 422 47.372 73.985 47.546 1.00 24.93 C
-ATOM 1294 CZ2 TRP A 422 48.798 76.108 46.292 1.00 24.30 C
-ATOM 1295 CZ3 TRP A 422 46.706 75.052 46.930 1.00 25.30 C
-ATOM 1296 CH2 TRP A 422 47.425 76.098 46.314 1.00 25.30 C
-ATOM 1297 N LEU A 423 49.821 70.483 51.657 1.00 20.27 N
-ATOM 1298 CA LEU A 423 49.351 69.527 52.636 1.00 21.39 C
-ATOM 1299 C LEU A 423 47.887 69.777 53.025 1.00 22.94 C
-ATOM 1300 O LEU A 423 47.557 70.818 53.593 1.00 22.15 O
-ATOM 1301 CB LEU A 423 50.234 69.610 53.877 1.00 18.43 C
-ATOM 1302 CG LEU A 423 49.764 68.706 55.016 1.00 17.98 C
-ATOM 1303 CD1 LEU A 423 50.112 67.246 54.667 1.00 14.98 C
-ATOM 1304 CD2 LEU A 423 50.419 69.152 56.334 1.00 15.97 C
-ATOM 1305 N PHE A 424 47.009 68.832 52.706 1.00 23.85 N
-ATOM 1306 CA PHE A 424 45.607 68.983 53.069 1.00 24.69 C
-ATOM 1307 C PHE A 424 45.363 68.188 54.355 1.00 25.99 C
-ATOM 1308 O PHE A 424 45.549 66.963 54.405 1.00 22.30 O
-ATOM 1309 CB PHE A 424 44.685 68.459 51.953 1.00 26.39 C
-ATOM 1310 CG PHE A 424 44.737 69.246 50.664 1.00 26.89 C
-ATOM 1311 CD1 PHE A 424 45.673 70.248 50.464 1.00 27.41 C
-ATOM 1312 CD2 PHE A 424 43.831 68.967 49.640 1.00 27.27 C
-ATOM 1313 CE1 PHE A 424 45.705 70.964 49.270 1.00 27.06 C
-ATOM 1314 CE2 PHE A 424 43.856 69.676 48.441 1.00 26.84 C
-ATOM 1315 CZ PHE A 424 44.794 70.677 48.258 1.00 26.43 C
-ATOM 1316 N LYS A 425 44.961 68.890 55.403 1.00 28.57 N
-ATOM 1317 CA LYS A 425 44.699 68.243 56.677 1.00 30.98 C
-ATOM 1318 C LYS A 425 43.215 68.329 57.005 1.00 30.85 C
-ATOM 1319 O LYS A 425 42.548 69.280 56.593 1.00 30.78 O
-ATOM 1320 CB LYS A 425 45.520 68.906 57.794 1.00 35.03 C
-ATOM 1321 CG LYS A 425 46.554 67.990 58.433 1.00 41.31 C
-ATOM 1322 CD LYS A 425 47.161 68.632 59.674 1.00 45.59 C
-ATOM 1323 CE LYS A 425 48.023 67.647 60.457 1.00 46.44 C
-ATOM 1324 NZ LYS A 425 48.570 68.247 61.707 1.00 46.77 N
-ATOM 1325 N GLY A 426 42.693 67.332 57.724 1.00 31.01 N
-ATOM 1326 CA GLY A 426 41.289 67.361 58.099 1.00 32.00 C
-ATOM 1327 C GLY A 426 40.678 66.015 58.446 1.00 35.55 C
-ATOM 1328 O GLY A 426 41.200 64.970 58.044 1.00 33.53 O
-ATOM 1329 N PRO A 427 39.558 66.007 59.191 1.00 37.74 N
-ATOM 1330 CA PRO A 427 38.878 64.770 59.586 1.00 38.27 C
-ATOM 1331 C PRO A 427 38.339 64.163 58.312 1.00 40.30 C
-ATOM 1332 O PRO A 427 38.594 64.692 57.239 1.00 38.21 O
-ATOM 1333 CB PRO A 427 37.748 65.264 60.483 1.00 38.50 C
-ATOM 1334 CG PRO A 427 38.251 66.583 60.996 1.00 42.02 C
-ATOM 1335 CD PRO A 427 38.875 67.178 59.764 1.00 38.73 C
-ATOM 1336 N ILE A 428 37.587 63.073 58.412 1.00 42.97 N
-ATOM 1337 CA ILE A 428 37.008 62.473 57.214 1.00 45.86 C
-ATOM 1338 C ILE A 428 35.765 63.295 56.881 1.00 47.57 C
-ATOM 1339 O ILE A 428 35.160 63.889 57.770 1.00 45.94 O
-ATOM 1340 CB ILE A 428 36.604 61.007 57.438 1.00 49.52 C
-ATOM 1341 CG1 ILE A 428 36.125 60.395 56.122 1.00 55.62 C
-ATOM 1342 CG2 ILE A 428 35.488 60.923 58.455 1.00 55.35 C
-ATOM 1343 CD1 ILE A 428 35.724 58.951 56.248 1.00 59.07 C
-ATOM 1344 N ASP A 429 35.399 63.341 55.604 1.00 49.26 N
-ATOM 1345 CA ASP A 429 34.240 64.108 55.144 1.00 48.28 C
-ATOM 1346 C ASP A 429 34.363 65.595 55.454 1.00 45.57 C
-ATOM 1347 O ASP A 429 33.440 66.222 55.989 1.00 42.03 O
-ATOM 1348 CB ASP A 429 32.944 63.550 55.739 1.00 56.60 C
-ATOM 1349 CG ASP A 429 32.586 62.189 55.170 1.00 69.73 C
-ATOM 1350 OD1 ASP A 429 32.899 61.948 53.986 1.00 76.05 O
-ATOM 1351 OD2 ASP A 429 31.979 61.367 55.892 1.00 76.93 O
-ATOM 1352 N SER A 430 35.516 66.155 55.109 1.00 41.37 N
-ATOM 1353 CA SER A 430 35.779 67.571 55.323 1.00 37.97 C
-ATOM 1354 C SER A 430 36.009 68.248 53.977 1.00 35.90 C
-ATOM 1355 O SER A 430 35.960 69.472 53.873 1.00 37.01 O
-ATOM 1356 CB SER A 430 37.005 67.749 56.219 1.00 38.99 C
-ATOM 1357 OG SER A 430 38.125 67.087 55.666 1.00 40.94 O
-ATOM 1358 N GLY A 431 36.268 67.441 52.951 1.00 33.34 N
-ATOM 1359 CA GLY A 431 36.483 67.974 51.616 1.00 30.32 C
-ATOM 1360 C GLY A 431 37.860 67.838 50.974 1.00 29.91 C
-ATOM 1361 O GLY A 431 37.956 68.001 49.753 1.00 26.81 O
-ATOM 1362 N LYS A 432 38.910 67.543 51.755 1.00 29.41 N
-ATOM 1363 CA LYS A 432 40.267 67.405 51.198 1.00 29.05 C
-ATOM 1364 C LYS A 432 40.411 66.294 50.165 1.00 28.61 C
-ATOM 1365 O LYS A 432 41.154 66.433 49.181 1.00 24.24 O
-ATOM 1366 CB LYS A 432 41.299 67.192 52.310 1.00 30.36 C
-ATOM 1367 CG LYS A 432 40.790 66.406 53.493 1.00 34.91 C
-ATOM 1368 CD LYS A 432 41.904 66.154 54.495 1.00 35.46 C
-ATOM 1369 CE LYS A 432 42.262 64.691 54.538 1.00 36.42 C
-ATOM 1370 NZ LYS A 432 41.189 63.851 55.148 1.00 35.30 N
-ATOM 1371 N THR A 433 39.699 65.196 50.397 1.00 29.25 N
-ATOM 1372 CA THR A 433 39.733 64.068 49.491 1.00 30.62 C
-ATOM 1373 C THR A 433 39.110 64.476 48.165 1.00 31.14 C
-ATOM 1374 O THR A 433 39.674 64.227 47.102 1.00 30.59 O
-ATOM 1375 CB THR A 433 38.969 62.887 50.076 1.00 33.21 C
-ATOM 1376 OG1 THR A 433 39.575 62.507 51.319 1.00 37.31 O
-ATOM 1377 CG2 THR A 433 38.997 61.709 49.120 1.00 37.45 C
-ATOM 1378 N THR A 434 37.956 65.127 48.227 1.00 30.55 N
-ATOM 1379 CA THR A 434 37.268 65.573 47.012 1.00 28.56 C
-ATOM 1380 C THR A 434 38.112 66.567 46.187 1.00 28.35 C
-ATOM 1381 O THR A 434 38.352 66.353 44.994 1.00 24.93 O
-ATOM 1382 CB THR A 434 35.913 66.235 47.350 1.00 29.51 C
-ATOM 1383 OG1 THR A 434 35.244 65.458 48.344 1.00 34.62 O
-ATOM 1384 CG2 THR A 434 35.029 66.286 46.125 1.00 31.28 C
-ATOM 1385 N LEU A 435 38.572 67.646 46.817 1.00 28.59 N
-ATOM 1386 CA LEU A 435 39.358 68.623 46.081 1.00 28.57 C
-ATOM 1387 C LEU A 435 40.631 67.974 45.542 1.00 29.16 C
-ATOM 1388 O LEU A 435 41.025 68.203 44.397 1.00 29.25 O
-ATOM 1389 CB LEU A 435 39.708 69.835 46.962 1.00 27.52 C
-ATOM 1390 CG LEU A 435 40.379 70.983 46.170 1.00 28.42 C
-ATOM 1391 CD1 LEU A 435 39.458 71.426 45.025 1.00 26.90 C
-ATOM 1392 CD2 LEU A 435 40.688 72.152 47.085 1.00 25.70 C
-ATOM 1393 N ALA A 436 41.264 67.149 46.365 1.00 29.72 N
-ATOM 1394 CA ALA A 436 42.495 66.489 45.955 1.00 30.34 C
-ATOM 1395 C ALA A 436 42.294 65.567 44.752 1.00 28.16 C
-ATOM 1396 O ALA A 436 43.224 65.334 43.965 1.00 26.88 O
-ATOM 1397 CB ALA A 436 43.080 65.719 47.125 1.00 32.21 C
-ATOM 1398 N ALA A 437 41.078 65.049 44.615 1.00 24.35 N
-ATOM 1399 CA ALA A 437 40.734 64.162 43.511 1.00 22.91 C
-ATOM 1400 C ALA A 437 40.536 64.974 42.228 1.00 24.56 C
-ATOM 1401 O ALA A 437 41.082 64.658 41.172 1.00 24.07 O
-ATOM 1402 CB ALA A 437 39.471 63.405 43.853 1.00 21.00 C
-ATOM 1403 N ALA A 438 39.743 66.028 42.325 1.00 24.75 N
-ATOM 1404 CA ALA A 438 39.500 66.888 41.181 1.00 24.65 C
-ATOM 1405 C ALA A 438 40.826 67.490 40.738 1.00 23.95 C
-ATOM 1406 O ALA A 438 41.113 67.570 39.548 1.00 23.71 O
-ATOM 1407 CB ALA A 438 38.523 67.997 41.567 1.00 24.36 C
-ATOM 1408 N LEU A 439 41.631 67.927 41.703 1.00 25.94 N
-ATOM 1409 CA LEU A 439 42.933 68.510 41.390 1.00 26.91 C
-ATOM 1410 C LEU A 439 43.793 67.499 40.616 1.00 28.33 C
-ATOM 1411 O LEU A 439 44.438 67.836 39.621 1.00 28.13 O
-ATOM 1412 CB LEU A 439 43.637 68.951 42.677 1.00 22.58 C
-ATOM 1413 CG LEU A 439 43.188 70.286 43.306 1.00 23.24 C
-ATOM 1414 CD1 LEU A 439 44.031 70.562 44.561 1.00 20.97 C
-ATOM 1415 CD2 LEU A 439 43.342 71.452 42.312 1.00 19.53 C
-ATOM 1416 N LEU A 440 43.766 66.250 41.067 1.00 33.02 N
-ATOM 1417 CA LEU A 440 44.522 65.200 40.407 1.00 35.72 C
-ATOM 1418 C LEU A 440 44.072 65.077 38.957 1.00 36.00 C
-ATOM 1419 O LEU A 440 44.883 65.115 38.041 1.00 34.66 O
-ATOM 1420 CB LEU A 440 44.308 63.865 41.112 1.00 36.87 C
-ATOM 1421 CG LEU A 440 45.604 63.094 41.349 1.00 40.35 C
-ATOM 1422 CD1 LEU A 440 45.275 61.700 41.830 1.00 39.22 C
-ATOM 1423 CD2 LEU A 440 46.432 63.046 40.063 1.00 40.57 C
-ATOM 1424 N GLU A 441 42.767 64.934 38.764 1.00 35.88 N
-ATOM 1425 CA GLU A 441 42.201 64.799 37.431 1.00 34.50 C
-ATOM 1426 C GLU A 441 42.362 66.077 36.608 1.00 33.18 C
-ATOM 1427 O GLU A 441 42.394 66.028 35.375 1.00 31.37 O
-ATOM 1428 CB GLU A 441 40.724 64.422 37.527 1.00 35.60 C
-ATOM 1429 CG GLU A 441 40.008 64.360 36.193 1.00 42.03 C
-ATOM 1430 CD GLU A 441 38.557 63.926 36.333 1.00 45.81 C
-ATOM 1431 OE1 GLU A 441 37.726 64.274 35.458 1.00 47.50 O
-ATOM 1432 OE2 GLU A 441 38.248 63.227 37.319 1.00 47.92 O
-ATOM 1433 N LEU A 442 42.471 67.221 37.278 1.00 31.15 N
-ATOM 1434 CA LEU A 442 42.631 68.473 36.551 1.00 29.12 C
-ATOM 1435 C LEU A 442 44.019 68.518 35.957 1.00 30.61 C
-ATOM 1436 O LEU A 442 44.211 69.034 34.863 1.00 30.16 O
-ATOM 1437 CB LEU A 442 42.444 69.680 37.473 1.00 26.28 C
-ATOM 1438 CG LEU A 442 42.524 71.083 36.841 1.00 24.61 C
-ATOM 1439 CD1 LEU A 442 41.331 71.321 35.914 1.00 21.36 C
-ATOM 1440 CD2 LEU A 442 42.525 72.151 37.942 1.00 23.29 C
-ATOM 1441 N CYS A 443 44.981 67.936 36.667 1.00 35.93 N
-ATOM 1442 CA CYS A 443 46.373 67.954 36.227 1.00 39.99 C
-ATOM 1443 C CYS A 443 46.940 66.675 35.659 1.00 41.61 C
-ATOM 1444 O CYS A 443 47.911 66.717 34.904 1.00 44.32 O
-ATOM 1445 CB CYS A 443 47.271 68.385 37.381 1.00 40.22 C
-ATOM 1446 SG CYS A 443 46.777 69.948 38.115 1.00 43.25 S
-ATOM 1447 N GLY A 444 46.342 65.545 36.011 1.00 43.27 N
-ATOM 1448 CA GLY A 444 46.866 64.277 35.544 1.00 44.42 C
-ATOM 1449 C GLY A 444 47.965 63.884 36.516 1.00 44.11 C
-ATOM 1450 O GLY A 444 48.694 64.735 37.020 1.00 47.39 O
-ATOM 1451 N GLY A 445 48.092 62.599 36.795 1.00 42.70 N
-ATOM 1452 CA GLY A 445 49.107 62.170 37.738 1.00 39.56 C
-ATOM 1453 C GLY A 445 48.577 61.042 38.597 1.00 39.53 C
-ATOM 1454 O GLY A 445 47.368 60.835 38.683 1.00 34.21 O
-ATOM 1455 N LYS A 446 49.467 60.306 39.245 1.00 40.27 N
-ATOM 1456 CA LYS A 446 49.014 59.191 40.058 1.00 39.57 C
-ATOM 1457 C LYS A 446 49.036 59.452 41.564 1.00 37.20 C
-ATOM 1458 O LYS A 446 49.789 60.296 42.070 1.00 32.87 O
-ATOM 1459 CB LYS A 446 49.849 57.946 39.736 1.00 46.40 C
-ATOM 1460 CG LYS A 446 49.968 57.632 38.239 1.00 60.03 C
-ATOM 1461 CD LYS A 446 48.628 57.281 37.597 1.00 66.89 C
-ATOM 1462 CE LYS A 446 48.106 55.925 38.070 1.00 71.12 C
-ATOM 1463 NZ LYS A 446 46.724 55.613 37.556 1.00 71.25 N
-ATOM 1464 N ALA A 447 48.175 58.733 42.272 1.00 35.71 N
-ATOM 1465 CA ALA A 447 48.125 58.832 43.719 1.00 34.62 C
-ATOM 1466 C ALA A 447 49.059 57.726 44.172 1.00 34.60 C
-ATOM 1467 O ALA A 447 49.251 56.744 43.446 1.00 36.80 O
-ATOM 1468 CB ALA A 447 46.724 58.570 44.221 1.00 34.78 C
-ATOM 1469 N LEU A 448 49.650 57.876 45.350 1.00 33.19 N
-ATOM 1470 CA LEU A 448 50.563 56.858 45.840 1.00 32.37 C
-ATOM 1471 C LEU A 448 50.241 56.600 47.308 1.00 33.49 C
-ATOM 1472 O LEU A 448 49.623 57.434 47.971 1.00 29.81 O
-ATOM 1473 CB LEU A 448 52.021 57.327 45.668 1.00 31.16 C
-ATOM 1474 CG LEU A 448 52.411 58.000 44.333 1.00 30.55 C
-ATOM 1475 CD1 LEU A 448 53.903 58.239 44.288 1.00 32.88 C
-ATOM 1476 CD2 LEU A 448 52.025 57.141 43.165 1.00 31.48 C
-ATOM 1477 N ASN A 449 50.642 55.440 47.815 1.00 35.09 N
-ATOM 1478 CA ASN A 449 50.383 55.101 49.207 1.00 35.57 C
-ATOM 1479 C ASN A 449 51.662 54.765 49.946 1.00 36.22 C
-ATOM 1480 O ASN A 449 52.248 53.716 49.734 1.00 35.06 O
-ATOM 1481 CB ASN A 449 49.425 53.928 49.300 1.00 38.86 C
-ATOM 1482 CG ASN A 449 49.323 53.403 50.693 1.00 44.90 C
-ATOM 1483 OD1 ASN A 449 50.193 52.669 51.143 1.00 48.69 O
-ATOM 1484 ND2 ASN A 449 48.276 53.800 51.406 1.00 49.22 N
-ATOM 1485 N VAL A 450 52.081 55.667 50.824 1.00 40.03 N
-ATOM 1486 CA VAL A 450 53.311 55.510 51.590 1.00 41.32 C
-ATOM 1487 C VAL A 450 53.086 54.799 52.924 1.00 43.14 C
-ATOM 1488 O VAL A 450 53.962 54.787 53.780 1.00 46.98 O
-ATOM 1489 CB VAL A 450 53.945 56.894 51.844 1.00 40.29 C
-ATOM 1490 CG1 VAL A 450 55.287 56.758 52.495 1.00 43.35 C
-ATOM 1491 CG2 VAL A 450 54.111 57.616 50.551 1.00 41.70 C
-ATOM 1492 N ASN A 451 51.906 54.212 53.103 1.00 49.01 N
-ATOM 1493 CA ASN A 451 51.595 53.496 54.337 1.00 53.05 C
-ATOM 1494 C ASN A 451 51.985 52.044 54.149 1.00 55.55 C
-ATOM 1495 O ASN A 451 51.192 51.131 54.370 1.00 60.01 O
-ATOM 1496 CB ASN A 451 50.110 53.611 54.647 1.00 51.69 C
-ATOM 1497 CG ASN A 451 49.703 55.025 55.000 1.00 50.87 C
-ATOM 1498 OD1 ASN A 451 50.163 55.580 55.996 1.00 48.70 O
-ATOM 1499 ND2 ASN A 451 48.836 55.619 54.183 1.00 49.34 N
-ATOM 1500 N LEU A 452 53.224 51.847 53.721 1.00 58.16 N
-ATOM 1501 CA LEU A 452 53.748 50.517 53.468 1.00 59.46 C
-ATOM 1502 C LEU A 452 55.043 50.256 54.227 1.00 60.46 C
-ATOM 1503 O LEU A 452 55.661 51.180 54.780 1.00 57.07 O
-ATOM 1504 CB LEU A 452 53.991 50.332 51.969 1.00 60.08 C
-ATOM 1505 CG LEU A 452 52.770 50.476 51.059 1.00 61.67 C
-ATOM 1506 CD1 LEU A 452 53.172 50.190 49.620 1.00 62.13 C
-ATOM 1507 CD2 LEU A 452 51.675 49.518 51.512 1.00 62.46 C
-ATOM 1508 N PRO A 453 55.457 48.979 54.285 1.00 59.30 N
-ATOM 1509 CA PRO A 453 56.693 48.617 54.985 1.00 58.73 C
-ATOM 1510 C PRO A 453 57.861 49.248 54.247 1.00 58.83 C
-ATOM 1511 O PRO A 453 57.962 49.132 53.025 1.00 57.49 O
-ATOM 1512 CB PRO A 453 56.691 47.097 54.909 1.00 58.78 C
-ATOM 1513 CG PRO A 453 55.210 46.783 54.935 1.00 58.69 C
-ATOM 1514 CD PRO A 453 54.686 47.775 53.931 1.00 57.45 C
-ATOM 1515 N LEU A 454 58.727 49.920 54.997 1.00 59.85 N
-ATOM 1516 CA LEU A 454 59.882 50.617 54.440 1.00 62.91 C
-ATOM 1517 C LEU A 454 60.562 49.959 53.232 1.00 68.80 C
-ATOM 1518 O LEU A 454 61.347 50.600 52.541 1.00 65.23 O
-ATOM 1519 CB LEU A 454 60.917 50.854 55.546 1.00 61.42 C
-ATOM 1520 CG LEU A 454 61.971 51.917 55.224 1.00 61.53 C
-ATOM 1521 CD1 LEU A 454 61.399 53.318 55.490 1.00 60.23 C
-ATOM 1522 CD2 LEU A 454 63.211 51.671 56.067 1.00 60.79 C
-ATOM 1523 N ASP A 455 60.259 48.690 52.975 1.00 77.64 N
-ATOM 1524 CA ASP A 455 60.858 47.960 51.857 1.00 81.59 C
-ATOM 1525 C ASP A 455 59.929 47.896 50.650 1.00 80.32 C
-ATOM 1526 O ASP A 455 60.384 47.777 49.512 1.00 72.73 O
-ATOM 1527 CB ASP A 455 61.207 46.539 52.290 1.00 97.12 C
-ATOM 1528 CG ASP A 455 61.694 46.476 53.719 1.00119.52 C
-ATOM 1529 OD1 ASP A 455 62.749 47.078 54.021 1.00131.43 O
-ATOM 1530 OD2 ASP A 455 61.012 45.828 54.543 1.00131.16 O
-ATOM 1531 N ARG A 456 58.625 47.958 50.909 1.00 77.80 N
-ATOM 1532 CA ARG A 456 57.620 47.924 49.851 1.00 73.16 C
-ATOM 1533 C ARG A 456 57.471 49.314 49.217 1.00 67.15 C
-ATOM 1534 O ARG A 456 56.876 49.469 48.151 1.00 67.41 O
-ATOM 1535 CB ARG A 456 56.267 47.465 50.417 1.00 78.55 C
-ATOM 1536 CG ARG A 456 56.309 46.146 51.183 1.00 89.39 C
-ATOM 1537 CD ARG A 456 55.161 45.218 50.769 1.00 94.81 C
-ATOM 1538 NE ARG A 456 55.130 43.977 51.549 1.00 97.11 N
-ATOM 1539 CZ ARG A 456 54.503 43.831 52.716 1.00 96.88 C
-ATOM 1540 NH1 ARG A 456 53.841 44.848 53.250 1.00 96.76 N
-ATOM 1541 NH2 ARG A 456 54.536 42.667 53.350 1.00 96.07 N
-ATOM 1542 N LEU A 457 58.031 50.316 49.886 1.00 60.00 N
-ATOM 1543 CA LEU A 457 57.973 51.705 49.437 1.00 55.70 C
-ATOM 1544 C LEU A 457 58.371 51.911 47.960 1.00 57.21 C
-ATOM 1545 O LEU A 457 57.507 52.104 47.104 1.00 57.05 O
-ATOM 1546 CB LEU A 457 58.856 52.563 50.360 1.00 46.96 C
-ATOM 1547 CG LEU A 457 58.436 53.997 50.720 1.00 38.08 C
-ATOM 1548 CD1 LEU A 457 56.939 54.042 50.994 1.00 33.65 C
-ATOM 1549 CD2 LEU A 457 59.221 54.485 51.939 1.00 31.33 C
-ATOM 1550 N ASN A 458 59.671 51.860 47.674 1.00 57.81 N
-ATOM 1551 CA ASN A 458 60.219 52.049 46.324 1.00 59.86 C
-ATOM 1552 C ASN A 458 59.365 51.619 45.119 1.00 63.06 C
-ATOM 1553 O ASN A 458 59.319 52.330 44.108 1.00 57.73 O
-ATOM 1554 CB ASN A 458 61.587 51.366 46.229 1.00 63.26 C
-ATOM 1555 CG ASN A 458 62.650 52.065 47.060 1.00 68.14 C
-ATOM 1556 OD1 ASN A 458 63.027 53.203 46.774 1.00 70.50 O
-ATOM 1557 ND2 ASN A 458 63.141 51.384 48.096 1.00 70.20 N
-ATOM 1558 N PHE A 459 58.721 50.454 45.207 1.00 66.24 N
-ATOM 1559 CA PHE A 459 57.866 49.950 44.119 1.00 67.09 C
-ATOM 1560 C PHE A 459 56.825 51.037 43.843 1.00 63.56 C
-ATOM 1561 O PHE A 459 56.664 51.503 42.714 1.00 61.87 O
-ATOM 1562 CB PHE A 459 57.173 48.652 44.577 1.00 76.64 C
-ATOM 1563 CG PHE A 459 56.452 47.892 43.482 1.00 90.28 C
-ATOM 1564 CD1 PHE A 459 57.129 47.452 42.344 1.00 95.54 C
-ATOM 1565 CD2 PHE A 459 55.109 47.538 43.637 1.00 95.52 C
-ATOM 1566 CE1 PHE A 459 56.476 46.665 41.380 1.00 97.44 C
-ATOM 1567 CE2 PHE A 459 54.451 46.752 42.681 1.00 97.48 C
-ATOM 1568 CZ PHE A 459 55.137 46.314 41.552 1.00 97.53 C
-ATOM 1569 N GLU A 460 56.142 51.438 44.915 1.00 59.04 N
-ATOM 1570 CA GLU A 460 55.105 52.462 44.881 1.00 55.09 C
-ATOM 1571 C GLU A 460 55.678 53.778 44.357 1.00 51.99 C
-ATOM 1572 O GLU A 460 55.151 54.351 43.406 1.00 52.49 O
-ATOM 1573 CB GLU A 460 54.538 52.659 46.294 1.00 55.44 C
-ATOM 1574 CG GLU A 460 53.302 53.547 46.392 1.00 54.52 C
-ATOM 1575 CD GLU A 460 51.999 52.774 46.265 1.00 54.08 C
-ATOM 1576 OE1 GLU A 460 51.831 51.774 47.001 1.00 54.18 O
-ATOM 1577 OE2 GLU A 460 51.139 53.168 45.443 1.00 52.93 O
-ATOM 1578 N LEU A 461 56.763 54.248 44.969 1.00 44.37 N
-ATOM 1579 CA LEU A 461 57.389 55.500 44.553 1.00 37.91 C
-ATOM 1580 C LEU A 461 57.727 55.536 43.062 1.00 36.85 C
-ATOM 1581 O LEU A 461 57.846 56.614 42.471 1.00 32.48 O
-ATOM 1582 CB LEU A 461 58.664 55.754 45.351 1.00 32.89 C
-ATOM 1583 CG LEU A 461 58.590 55.999 46.859 1.00 28.90 C
-ATOM 1584 CD1 LEU A 461 60.001 56.190 47.395 1.00 27.67 C
-ATOM 1585 CD2 LEU A 461 57.743 57.230 47.173 1.00 26.32 C
-ATOM 1586 N GLY A 462 57.882 54.360 42.456 1.00 35.79 N
-ATOM 1587 CA GLY A 462 58.212 54.287 41.040 1.00 37.35 C
-ATOM 1588 C GLY A 462 57.044 54.651 40.152 1.00 39.12 C
-ATOM 1589 O GLY A 462 57.226 55.044 39.003 1.00 38.84 O
-ATOM 1590 N VAL A 463 55.840 54.509 40.696 1.00 41.77 N
-ATOM 1591 CA VAL A 463 54.609 54.828 39.980 1.00 41.45 C
-ATOM 1592 C VAL A 463 54.616 56.255 39.448 1.00 39.76 C
-ATOM 1593 O VAL A 463 54.061 56.537 38.385 1.00 39.83 O
-ATOM 1594 CB VAL A 463 53.384 54.666 40.910 1.00 43.86 C
-ATOM 1595 CG1 VAL A 463 52.119 55.177 40.221 1.00 46.49 C
-ATOM 1596 CG2 VAL A 463 53.230 53.205 41.299 1.00 47.59 C
-ATOM 1597 N ALA A 464 55.253 57.142 40.204 1.00 36.92 N
-ATOM 1598 CA ALA A 464 55.345 58.557 39.872 1.00 35.38 C
-ATOM 1599 C ALA A 464 56.178 58.867 38.628 1.00 35.94 C
-ATOM 1600 O ALA A 464 56.262 60.018 38.198 1.00 37.48 O
-ATOM 1601 CB ALA A 464 55.897 59.300 41.056 1.00 32.61 C
-ATOM 1602 N ILE A 465 56.793 57.845 38.053 1.00 37.14 N
-ATOM 1603 CA ILE A 465 57.616 58.028 36.872 1.00 38.23 C
-ATOM 1604 C ILE A 465 56.850 58.674 35.730 1.00 41.29 C
-ATOM 1605 O ILE A 465 55.728 58.281 35.438 1.00 41.49 O
-ATOM 1606 CB ILE A 465 58.209 56.671 36.427 1.00 36.25 C
-ATOM 1607 CG1 ILE A 465 59.476 56.395 37.241 1.00 33.89 C
-ATOM 1608 CG2 ILE A 465 58.499 56.659 34.927 1.00 33.71 C
-ATOM 1609 CD1 ILE A 465 60.130 55.073 36.931 1.00 34.55 C
-ATOM 1610 N ASP A 466 57.465 59.671 35.094 1.00 45.08 N
-ATOM 1611 CA ASP A 466 56.865 60.382 33.962 1.00 48.18 C
-ATOM 1612 C ASP A 466 55.600 61.171 34.307 1.00 47.91 C
-ATOM 1613 O ASP A 466 54.991 61.770 33.418 1.00 49.70 O
-ATOM 1614 CB ASP A 466 56.548 59.394 32.829 1.00 54.16 C
-ATOM 1615 CG ASP A 466 57.796 58.922 32.087 1.00 62.44 C
-ATOM 1616 OD1 ASP A 466 58.811 58.634 32.754 1.00 65.42 O
-ATOM 1617 OD2 ASP A 466 57.760 58.827 30.837 1.00 65.51 O
-ATOM 1618 N GLN A 467 55.215 61.185 35.584 1.00 45.79 N
-ATOM 1619 CA GLN A 467 54.006 61.884 36.024 1.00 43.12 C
-ATOM 1620 C GLN A 467 54.139 63.399 36.176 1.00 41.81 C
-ATOM 1621 O GLN A 467 55.230 63.921 36.420 1.00 42.34 O
-ATOM 1622 CB GLN A 467 53.515 61.295 37.348 1.00 42.30 C
-ATOM 1623 CG GLN A 467 53.136 59.844 37.261 1.00 40.84 C
-ATOM 1624 CD GLN A 467 52.066 59.593 36.227 1.00 40.24 C
-ATOM 1625 OE1 GLN A 467 51.844 58.461 35.825 1.00 41.83 O
-ATOM 1626 NE2 GLN A 467 51.391 60.651 35.794 1.00 41.54 N
-ATOM 1627 N PHE A 468 53.011 64.096 36.037 1.00 39.15 N
-ATOM 1628 CA PHE A 468 52.978 65.551 36.163 1.00 36.91 C
-ATOM 1629 C PHE A 468 52.978 65.902 37.634 1.00 36.42 C
-ATOM 1630 O PHE A 468 53.745 66.747 38.090 1.00 38.57 O
-ATOM 1631 CB PHE A 468 51.720 66.127 35.528 1.00 34.90 C
-ATOM 1632 CG PHE A 468 51.656 67.627 35.569 1.00 35.97 C
-ATOM 1633 CD1 PHE A 468 52.425 68.396 34.695 1.00 36.53 C
-ATOM 1634 CD2 PHE A 468 50.825 68.278 36.479 1.00 37.27 C
-ATOM 1635 CE1 PHE A 468 52.365 69.797 34.718 1.00 36.31 C
-ATOM 1636 CE2 PHE A 468 50.756 69.680 36.516 1.00 36.90 C
-ATOM 1637 CZ PHE A 468 51.530 70.444 35.629 1.00 36.82 C
-ATOM 1638 N LEU A 469 52.092 65.262 38.381 1.00 34.84 N
-ATOM 1639 CA LEU A 469 52.029 65.510 39.808 1.00 33.60 C
-ATOM 1640 C LEU A 469 51.598 64.240 40.505 1.00 32.91 C
-ATOM 1641 O LEU A 469 51.053 63.319 39.895 1.00 33.15 O
-ATOM 1642 CB LEU A 469 51.059 66.660 40.140 1.00 31.26 C
-ATOM 1643 CG LEU A 469 49.548 66.444 40.041 1.00 26.83 C
-ATOM 1644 CD1 LEU A 469 49.030 65.673 41.233 1.00 27.39 C
-ATOM 1645 CD2 LEU A 469 48.875 67.787 40.004 1.00 27.02 C
-ATOM 1646 N VAL A 470 51.851 64.205 41.801 1.00 31.41 N
-ATOM 1647 CA VAL A 470 51.516 63.057 42.603 1.00 30.26 C
-ATOM 1648 C VAL A 470 50.679 63.476 43.811 1.00 29.10 C
-ATOM 1649 O VAL A 470 50.793 64.604 44.301 1.00 29.60 O
-ATOM 1650 CB VAL A 470 52.821 62.357 43.044 1.00 26.81 C
-ATOM 1651 CG1 VAL A 470 52.548 61.308 44.092 1.00 24.49 C
-ATOM 1652 CG2 VAL A 470 53.476 61.734 41.824 1.00 23.72 C
-ATOM 1653 N VAL A 471 49.805 62.575 44.254 1.00 26.97 N
-ATOM 1654 CA VAL A 471 48.995 62.834 45.429 1.00 26.13 C
-ATOM 1655 C VAL A 471 49.145 61.702 46.438 1.00 25.75 C
-ATOM 1656 O VAL A 471 48.664 60.592 46.211 1.00 25.66 O
-ATOM 1657 CB VAL A 471 47.520 62.954 45.099 1.00 25.15 C
-ATOM 1658 CG1 VAL A 471 46.728 62.939 46.391 1.00 23.20 C
-ATOM 1659 CG2 VAL A 471 47.250 64.247 44.327 1.00 23.35 C
-ATOM 1660 N PHE A 472 49.826 61.991 47.545 1.00 24.20 N
-ATOM 1661 CA PHE A 472 50.028 61.022 48.619 1.00 24.12 C
-ATOM 1662 C PHE A 472 48.729 60.942 49.426 1.00 26.41 C
-ATOM 1663 O PHE A 472 48.539 61.694 50.378 1.00 24.01 O
-ATOM 1664 CB PHE A 472 51.169 61.477 49.528 1.00 23.65 C
-ATOM 1665 CG PHE A 472 52.544 61.343 48.911 1.00 22.85 C
-ATOM 1666 CD1 PHE A 472 53.155 60.099 48.807 1.00 22.02 C
-ATOM 1667 CD2 PHE A 472 53.241 62.465 48.449 1.00 21.24 C
-ATOM 1668 CE1 PHE A 472 54.444 59.974 48.252 1.00 21.27 C
-ATOM 1669 CE2 PHE A 472 54.532 62.343 47.894 1.00 19.87 C
-ATOM 1670 CZ PHE A 472 55.125 61.106 47.798 1.00 19.62 C
-ATOM 1671 N GLU A 473 47.853 60.018 49.036 1.00 31.45 N
-ATOM 1672 CA GLU A 473 46.556 59.829 49.675 1.00 35.63 C
-ATOM 1673 C GLU A 473 46.561 59.340 51.109 1.00 39.67 C
-ATOM 1674 O GLU A 473 47.068 58.266 51.405 1.00 37.76 O
-ATOM 1675 CB GLU A 473 45.701 58.850 48.887 1.00 37.58 C
-ATOM 1676 CG GLU A 473 45.139 59.355 47.603 1.00 43.95 C
-ATOM 1677 CD GLU A 473 44.237 58.314 46.968 1.00 47.85 C
-ATOM 1678 OE1 GLU A 473 44.166 57.189 47.513 1.00 48.92 O
-ATOM 1679 OE2 GLU A 473 43.607 58.611 45.931 1.00 48.93 O
-ATOM 1680 N ASP A 474 45.944 60.124 51.984 1.00 46.13 N
-ATOM 1681 CA ASP A 474 45.810 59.799 53.398 1.00 49.06 C
-ATOM 1682 C ASP A 474 47.011 59.131 54.043 1.00 46.09 C
-ATOM 1683 O ASP A 474 47.059 57.909 54.203 1.00 44.28 O
-ATOM 1684 CB ASP A 474 44.574 58.928 53.611 1.00 60.47 C
-ATOM 1685 CG ASP A 474 44.394 58.533 55.057 1.00 75.79 C
-ATOM 1686 OD1 ASP A 474 44.505 59.421 55.935 1.00 82.76 O
-ATOM 1687 OD2 ASP A 474 44.140 57.336 55.312 1.00 83.07 O
-ATOM 1688 N VAL A 475 47.980 59.952 54.420 1.00 40.05 N
-ATOM 1689 CA VAL A 475 49.174 59.465 55.064 1.00 33.79 C
-ATOM 1690 C VAL A 475 48.797 59.277 56.514 1.00 34.24 C
-ATOM 1691 O VAL A 475 48.030 60.063 57.062 1.00 31.38 O
-ATOM 1692 CB VAL A 475 50.296 60.498 54.946 1.00 30.34 C
-ATOM 1693 CG1 VAL A 475 51.589 59.950 55.559 1.00 28.93 C
-ATOM 1694 CG2 VAL A 475 50.489 60.858 53.475 1.00 28.17 C
-ATOM 1695 N LYS A 476 49.319 58.235 57.139 1.00 35.78 N
-ATOM 1696 CA LYS A 476 49.007 57.992 58.541 1.00 36.45 C
-ATOM 1697 C LYS A 476 50.241 58.127 59.420 1.00 36.10 C
-ATOM 1698 O LYS A 476 51.339 57.743 59.023 1.00 32.93 O
-ATOM 1699 CB LYS A 476 48.366 56.610 58.702 1.00 41.99 C
-ATOM 1700 CG LYS A 476 46.973 56.519 58.087 1.00 51.65 C
-ATOM 1701 CD LYS A 476 46.336 55.161 58.324 1.00 57.32 C
-ATOM 1702 CE LYS A 476 47.140 54.039 57.666 1.00 60.18 C
-ATOM 1703 NZ LYS A 476 46.566 52.682 57.929 1.00 59.98 N
-ATOM 1704 N GLY A 477 50.047 58.693 60.610 1.00 37.04 N
-ATOM 1705 CA GLY A 477 51.147 58.891 61.540 1.00 39.86 C
-ATOM 1706 C GLY A 477 51.077 58.002 62.767 1.00 42.88 C
-ATOM 1707 O GLY A 477 50.322 57.032 62.797 1.00 41.28 O
-ATOM 1708 N THR A 478 51.862 58.332 63.785 1.00 51.32 N
-ATOM 1709 CA THR A 478 51.868 57.536 64.999 1.00 58.31 C
-ATOM 1710 C THR A 478 51.035 58.159 66.110 1.00 61.69 C
-ATOM 1711 O THR A 478 49.811 57.996 66.144 1.00 67.19 O
-ATOM 1712 CB THR A 478 53.299 57.317 65.505 1.00 59.03 C
-ATOM 1713 OG1 THR A 478 54.046 56.610 64.511 1.00 60.57 O
-ATOM 1714 CG2 THR A 478 53.293 56.489 66.784 1.00 62.62 C
-ATOM 1715 N GLY A 479 51.703 58.867 67.012 1.00 64.56 N
-ATOM 1716 CA GLY A 479 51.026 59.507 68.124 1.00 67.85 C
-ATOM 1717 C GLY A 479 49.540 59.241 68.338 1.00 67.85 C
-ATOM 1718 O GLY A 479 49.129 58.156 68.753 1.00 72.71 O
-ATOM 1719 N GLY A 480 48.742 60.261 68.037 1.00 66.17 N
-ATOM 1720 CA GLY A 480 47.296 60.245 68.208 1.00 58.48 C
-ATOM 1721 C GLY A 480 46.328 59.077 68.065 1.00 56.07 C
-ATOM 1722 O GLY A 480 45.471 59.097 67.187 1.00 49.76 O
-ATOM 1723 N GLU A 481 46.409 58.088 68.944 1.00 54.74 N
-ATOM 1724 CA GLU A 481 45.477 56.963 68.890 1.00 54.80 C
-ATOM 1725 C GLU A 481 44.373 57.227 69.922 1.00 53.97 C
-ATOM 1726 O GLU A 481 43.368 56.506 69.974 1.00 49.04 O
-ATOM 1727 CB GLU A 481 46.182 55.642 69.220 1.00 61.10 C
-ATOM 1728 CG GLU A 481 46.777 55.596 70.624 1.00 76.28 C
-ATOM 1729 CD GLU A 481 47.046 54.186 71.119 1.00 82.33 C
-ATOM 1730 OE1 GLU A 481 47.865 53.478 70.491 1.00 84.24 O
-ATOM 1731 OE2 GLU A 481 46.437 53.790 72.141 1.00 83.95 O
-ATOM 1732 N SER A 482 44.574 58.268 70.738 1.00 51.75 N
-ATOM 1733 CA SER A 482 43.618 58.670 71.779 1.00 48.00 C
-ATOM 1734 C SER A 482 42.416 59.372 71.166 1.00 47.38 C
-ATOM 1735 O SER A 482 41.348 59.458 71.773 1.00 45.39 O
-ATOM 1736 CB SER A 482 44.281 59.620 72.762 1.00 46.01 C
-ATOM 1737 OG SER A 482 45.393 59.005 73.358 1.00 52.47 O
-ATOM 1738 N ARG A 483 42.605 59.881 69.956 1.00 48.45 N
-ATOM 1739 CA ARG A 483 41.547 60.567 69.255 1.00 49.36 C
-ATOM 1740 C ARG A 483 40.994 59.660 68.161 1.00 51.97 C
-ATOM 1741 O ARG A 483 40.381 60.126 67.196 1.00 52.34 O
-ATOM 1742 CB ARG A 483 42.084 61.870 68.671 1.00 47.17 C
-ATOM 1743 CG ARG A 483 42.790 62.747 69.693 1.00 46.02 C
-ATOM 1744 CD ARG A 483 44.093 63.238 69.109 1.00 46.36 C
-ATOM 1745 NE ARG A 483 43.864 63.868 67.813 1.00 46.74 N
-ATOM 1746 CZ ARG A 483 44.810 64.094 66.910 1.00 46.12 C
-ATOM 1747 NH1 ARG A 483 46.060 63.736 67.157 1.00 46.83 N
-ATOM 1748 NH2 ARG A 483 44.507 64.687 65.764 1.00 47.46 N
-ATOM 1749 N ASP A 484 41.223 58.359 68.321 1.00 57.25 N
-ATOM 1750 CA ASP A 484 40.725 57.357 67.385 1.00 61.32 C
-ATOM 1751 C ASP A 484 41.302 57.440 65.982 1.00 59.15 C
-ATOM 1752 O ASP A 484 40.569 57.534 64.996 1.00 60.35 O
-ATOM 1753 CB ASP A 484 39.193 57.422 67.321 1.00 70.82 C
-ATOM 1754 CG ASP A 484 38.544 57.235 68.682 1.00 80.85 C
-ATOM 1755 OD1 ASP A 484 38.734 56.159 69.288 1.00 85.18 O
-ATOM 1756 OD2 ASP A 484 37.841 58.161 69.143 1.00 84.62 O
-ATOM 1757 N LEU A 485 42.624 57.412 65.899 1.00 54.38 N
-ATOM 1758 CA LEU A 485 43.311 57.464 64.614 1.00 47.43 C
-ATOM 1759 C LEU A 485 44.378 56.369 64.565 1.00 44.51 C
-ATOM 1760 O LEU A 485 45.301 56.348 65.381 1.00 46.56 O
-ATOM 1761 CB LEU A 485 43.953 58.839 64.419 1.00 41.09 C
-ATOM 1762 CG LEU A 485 42.978 60.014 64.356 1.00 31.95 C
-ATOM 1763 CD1 LEU A 485 43.749 61.307 64.142 1.00 28.14 C
-ATOM 1764 CD2 LEU A 485 41.993 59.784 63.218 1.00 28.85 C
-ATOM 1765 N PRO A 486 44.253 55.442 63.607 1.00 46.51 N
-ATOM 1766 CA PRO A 486 45.163 54.313 63.397 1.00 46.48 C
-ATOM 1767 C PRO A 486 46.618 54.706 63.183 1.00 46.46 C
-ATOM 1768 O PRO A 486 46.918 55.566 62.356 1.00 49.52 O
-ATOM 1769 CB PRO A 486 44.577 53.633 62.165 1.00 47.65 C
-ATOM 1770 CG PRO A 486 43.125 53.934 62.273 1.00 48.15 C
-ATOM 1771 CD PRO A 486 43.132 55.385 62.656 1.00 47.49 C
-ATOM 1772 N SER A 487 47.518 54.062 63.922 1.00 45.52 N
-ATOM 1773 CA SER A 487 48.952 54.323 63.794 1.00 42.96 C
-ATOM 1774 C SER A 487 49.490 53.704 62.510 1.00 42.14 C
-ATOM 1775 O SER A 487 49.234 52.531 62.224 1.00 39.93 O
-ATOM 1776 CB SER A 487 49.710 53.749 64.996 1.00 40.77 C
-ATOM 1777 OG SER A 487 49.359 54.433 66.189 1.00 42.39 O
-ATOM 1778 N GLY A 488 50.227 54.496 61.735 1.00 40.33 N
-ATOM 1779 CA GLY A 488 50.785 54.007 60.484 1.00 40.29 C
-ATOM 1780 C GLY A 488 52.188 54.530 60.332 1.00 40.43 C
-ATOM 1781 O GLY A 488 52.613 55.354 61.142 1.00 42.17 O
-ATOM 1782 N GLN A 489 52.917 54.073 59.319 1.00 41.28 N
-ATOM 1783 CA GLN A 489 54.293 54.542 59.143 1.00 41.70 C
-ATOM 1784 C GLN A 489 54.471 55.519 57.978 1.00 40.95 C
-ATOM 1785 O GLN A 489 55.585 55.966 57.704 1.00 39.93 O
-ATOM 1786 CB GLN A 489 55.262 53.354 58.977 1.00 43.14 C
-ATOM 1787 CG GLN A 489 55.499 52.490 60.237 1.00 43.91 C
-ATOM 1788 CD GLN A 489 56.128 53.247 61.416 1.00 44.91 C
-ATOM 1789 OE1 GLN A 489 57.201 53.852 61.299 1.00 43.41 O
-ATOM 1790 NE2 GLN A 489 55.453 53.203 62.563 1.00 45.44 N
-ATOM 1791 N GLY A 490 53.371 55.851 57.307 1.00 40.36 N
-ATOM 1792 CA GLY A 490 53.417 56.770 56.181 1.00 38.73 C
-ATOM 1793 C GLY A 490 54.117 58.083 56.480 1.00 37.84 C
-ATOM 1794 O GLY A 490 55.038 58.471 55.763 1.00 37.01 O
-ATOM 1795 N ILE A 491 53.678 58.776 57.528 1.00 37.89 N
-ATOM 1796 CA ILE A 491 54.302 60.044 57.898 1.00 40.48 C
-ATOM 1797 C ILE A 491 55.789 59.821 58.060 1.00 42.37 C
-ATOM 1798 O ILE A 491 56.612 60.572 57.533 1.00 43.73 O
-ATOM 1799 CB ILE A 491 53.798 60.579 59.247 1.00 36.60 C
-ATOM 1800 CG1 ILE A 491 52.342 60.996 59.130 1.00 32.93 C
-ATOM 1801 CG2 ILE A 491 54.645 61.776 59.679 1.00 31.50 C
-ATOM 1802 CD1 ILE A 491 52.143 62.144 58.200 1.00 31.28 C
-ATOM 1803 N ASN A 492 56.113 58.774 58.810 1.00 46.99 N
-ATOM 1804 CA ASN A 492 57.488 58.421 59.087 1.00 49.22 C
-ATOM 1805 C ASN A 492 58.288 58.241 57.820 1.00 48.68 C
-ATOM 1806 O ASN A 492 59.442 58.646 57.756 1.00 49.53 O
-ATOM 1807 CB ASN A 492 57.549 57.147 59.903 1.00 52.76 C
-ATOM 1808 CG ASN A 492 58.620 57.203 60.935 1.00 57.16 C
-ATOM 1809 OD1 ASN A 492 58.485 57.914 61.932 1.00 59.59 O
-ATOM 1810 ND2 ASN A 492 59.716 56.480 60.701 1.00 59.18 N
-ATOM 1811 N ASN A 493 57.676 57.629 56.814 1.00 47.70 N
-ATOM 1812 CA ASN A 493 58.354 57.415 55.539 1.00 46.10 C
-ATOM 1813 C ASN A 493 58.580 58.738 54.818 1.00 45.42 C
-ATOM 1814 O ASN A 493 59.672 58.993 54.330 1.00 44.39 O
-ATOM 1815 CB ASN A 493 57.550 56.469 54.637 1.00 44.35 C
-ATOM 1816 CG ASN A 493 57.441 55.071 55.208 1.00 42.14 C
-ATOM 1817 OD1 ASN A 493 58.304 54.641 55.971 1.00 42.16 O
-ATOM 1818 ND2 ASN A 493 56.392 54.349 54.830 1.00 39.23 N
-ATOM 1819 N LEU A 494 57.549 59.575 54.747 1.00 45.56 N
-ATOM 1820 CA LEU A 494 57.686 60.868 54.087 1.00 45.58 C
-ATOM 1821 C LEU A 494 58.887 61.628 54.637 1.00 46.12 C
-ATOM 1822 O LEU A 494 59.647 62.233 53.874 1.00 45.94 O
-ATOM 1823 CB LEU A 494 56.423 61.719 54.270 1.00 45.72 C
-ATOM 1824 CG LEU A 494 55.250 61.490 53.310 1.00 44.50 C
-ATOM 1825 CD1 LEU A 494 54.083 62.371 53.719 1.00 43.23 C
-ATOM 1826 CD2 LEU A 494 55.681 61.798 51.877 1.00 43.55 C
-ATOM 1827 N ASP A 495 59.063 61.598 55.956 1.00 46.69 N
-ATOM 1828 CA ASP A 495 60.186 62.297 56.564 1.00 48.62 C
-ATOM 1829 C ASP A 495 61.506 61.712 56.061 1.00 51.10 C
-ATOM 1830 O ASP A 495 62.560 62.346 56.166 1.00 48.01 O
-ATOM 1831 CB ASP A 495 60.123 62.205 58.084 1.00 50.47 C
-ATOM 1832 CG ASP A 495 60.492 63.517 58.759 1.00 54.31 C
-ATOM 1833 OD1 ASP A 495 61.458 64.165 58.312 1.00 55.61 O
-ATOM 1834 OD2 ASP A 495 59.821 63.901 59.741 1.00 57.91 O
-ATOM 1835 N ASN A 496 61.445 60.502 55.512 1.00 52.10 N
-ATOM 1836 CA ASN A 496 62.632 59.850 54.973 1.00 50.67 C
-ATOM 1837 C ASN A 496 62.658 60.034 53.465 1.00 46.98 C
-ATOM 1838 O ASN A 496 63.410 59.363 52.773 1.00 45.88 O
-ATOM 1839 CB ASN A 496 62.620 58.355 55.280 1.00 58.59 C
-ATOM 1840 CG ASN A 496 62.272 58.061 56.718 1.00 69.59 C
-ATOM 1841 OD1 ASN A 496 62.747 58.733 57.638 1.00 75.17 O
-ATOM 1842 ND2 ASN A 496 61.443 57.044 56.926 1.00 76.13 N
-ATOM 1843 N LEU A 497 61.817 60.926 52.954 1.00 42.93 N
-ATOM 1844 CA LEU A 497 61.765 61.178 51.520 1.00 42.16 C
-ATOM 1845 C LEU A 497 61.956 62.662 51.196 1.00 48.34 C
-ATOM 1846 O LEU A 497 61.498 63.151 50.158 1.00 44.98 O
-ATOM 1847 CB LEU A 497 60.442 60.678 50.945 1.00 34.22 C
-ATOM 1848 CG LEU A 497 60.168 59.174 51.035 1.00 26.79 C
-ATOM 1849 CD1 LEU A 497 58.732 58.897 50.583 1.00 24.13 C
-ATOM 1850 CD2 LEU A 497 61.172 58.406 50.188 1.00 23.58 C
-ATOM 1851 N ARG A 498 62.647 63.369 52.089 1.00 57.36 N
-ATOM 1852 CA ARG A 498 62.928 64.786 51.898 1.00 62.61 C
-ATOM 1853 C ARG A 498 63.463 65.024 50.490 1.00 62.12 C
-ATOM 1854 O ARG A 498 63.126 66.019 49.865 1.00 54.57 O
-ATOM 1855 CB ARG A 498 63.950 65.269 52.927 1.00 74.56 C
-ATOM 1856 CG ARG A 498 65.308 64.623 52.779 1.00 99.94 C
-ATOM 1857 CD ARG A 498 66.380 65.434 53.479 1.00112.42 C
-ATOM 1858 NE ARG A 498 67.722 64.897 53.248 1.00116.52 N
-ATOM 1859 CZ ARG A 498 68.466 65.154 52.173 1.00117.25 C
-ATOM 1860 NH1 ARG A 498 68.009 65.949 51.213 1.00117.33 N
-ATOM 1861 NH2 ARG A 498 69.672 64.612 52.058 1.00116.82 N
-ATOM 1862 N ASP A 499 64.287 64.098 49.999 1.00 59.10 N
-ATOM 1863 CA ASP A 499 64.870 64.181 48.656 1.00 54.82 C
-ATOM 1864 C ASP A 499 63.790 64.255 47.584 1.00 50.55 C
-ATOM 1865 O ASP A 499 63.803 65.126 46.708 1.00 45.50 O
-ATOM 1866 CB ASP A 499 65.733 62.951 48.382 1.00 65.08 C
-ATOM 1867 CG ASP A 499 67.164 63.141 48.805 1.00 81.10 C
-ATOM 1868 OD1 ASP A 499 67.389 63.808 49.835 1.00 89.63 O
-ATOM 1869 OD2 ASP A 499 68.063 62.614 48.112 1.00 88.92 O
-ATOM 1870 N TYR A 500 62.859 63.317 47.653 1.00 42.63 N
-ATOM 1871 CA TYR A 500 61.787 63.274 46.691 1.00 35.02 C
-ATOM 1872 C TYR A 500 60.927 64.530 46.778 1.00 32.25 C
-ATOM 1873 O TYR A 500 60.728 65.222 45.784 1.00 29.31 O
-ATOM 1874 CB TYR A 500 60.921 62.029 46.923 1.00 35.29 C
-ATOM 1875 CG TYR A 500 61.664 60.720 46.749 1.00 38.26 C
-ATOM 1876 CD1 TYR A 500 62.622 60.305 47.678 1.00 39.95 C
-ATOM 1877 CD2 TYR A 500 61.448 59.920 45.625 1.00 39.68 C
-ATOM 1878 CE1 TYR A 500 63.352 59.127 47.484 1.00 40.39 C
-ATOM 1879 CE2 TYR A 500 62.169 58.745 45.420 1.00 40.34 C
-ATOM 1880 CZ TYR A 500 63.122 58.356 46.349 1.00 40.13 C
-ATOM 1881 OH TYR A 500 63.875 57.227 46.117 1.00 39.16 O
-ATOM 1882 N LEU A 501 60.436 64.836 47.970 1.00 30.01 N
-ATOM 1883 CA LEU A 501 59.558 65.983 48.147 1.00 31.18 C
-ATOM 1884 C LEU A 501 60.010 67.339 47.596 1.00 35.38 C
-ATOM 1885 O LEU A 501 59.345 67.905 46.720 1.00 33.81 O
-ATOM 1886 CB LEU A 501 59.185 66.125 49.626 1.00 28.48 C
-ATOM 1887 CG LEU A 501 58.211 65.083 50.188 1.00 26.35 C
-ATOM 1888 CD1 LEU A 501 58.113 65.252 51.691 1.00 25.75 C
-ATOM 1889 CD2 LEU A 501 56.845 65.231 49.534 1.00 23.28 C
-ATOM 1890 N ASP A 502 61.123 67.875 48.088 1.00 42.45 N
-ATOM 1891 CA ASP A 502 61.547 69.181 47.603 1.00 47.26 C
-ATOM 1892 C ASP A 502 62.357 69.171 46.321 1.00 46.26 C
-ATOM 1893 O ASP A 502 62.699 70.223 45.796 1.00 45.47 O
-ATOM 1894 CB ASP A 502 62.295 69.939 48.693 1.00 57.98 C
-ATOM 1895 CG ASP A 502 63.244 69.067 49.445 1.00 71.37 C
-ATOM 1896 OD1 ASP A 502 63.870 68.203 48.800 1.00 78.52 O
-ATOM 1897 OD2 ASP A 502 63.370 69.251 50.672 1.00 78.06 O
-ATOM 1898 N GLY A 503 62.650 67.979 45.823 1.00 45.47 N
-ATOM 1899 CA GLY A 503 63.392 67.832 44.586 1.00 43.33 C
-ATOM 1900 C GLY A 503 64.374 68.907 44.132 1.00 42.02 C
-ATOM 1901 O GLY A 503 64.105 69.641 43.173 1.00 41.29 O
-ATOM 1902 N SER A 504 65.521 68.993 44.803 1.00 40.38 N
-ATOM 1903 CA SER A 504 66.558 69.953 44.425 1.00 39.58 C
-ATOM 1904 C SER A 504 67.484 69.251 43.428 1.00 40.11 C
-ATOM 1905 O SER A 504 68.134 69.883 42.600 1.00 39.58 O
-ATOM 1906 CB SER A 504 67.348 70.397 45.660 1.00 38.19 C
-ATOM 1907 OG SER A 504 66.546 71.186 46.526 1.00 33.86 O
-ATOM 1908 N VAL A 505 67.516 67.926 43.518 1.00 39.44 N
-ATOM 1909 CA VAL A 505 68.333 67.089 42.645 1.00 38.88 C
-ATOM 1910 C VAL A 505 67.493 65.882 42.196 1.00 40.02 C
-ATOM 1911 O VAL A 505 66.513 65.521 42.852 1.00 37.04 O
-ATOM 1912 CB VAL A 505 69.609 66.583 43.389 1.00 40.41 C
-ATOM 1913 CG1 VAL A 505 70.589 65.948 42.399 1.00 41.74 C
-ATOM 1914 CG2 VAL A 505 70.281 67.740 44.118 1.00 41.22 C
-ATOM 1915 N LYS A 506 67.877 65.270 41.076 1.00 40.38 N
-ATOM 1916 CA LYS A 506 67.165 64.109 40.540 1.00 39.28 C
-ATOM 1917 C LYS A 506 67.172 62.880 41.450 1.00 38.39 C
-ATOM 1918 O LYS A 506 67.885 62.827 42.457 1.00 37.68 O
-ATOM 1919 CB LYS A 506 67.718 63.743 39.157 1.00 40.31 C
-ATOM 1920 CG LYS A 506 67.047 64.513 38.026 1.00 42.43 C
-ATOM 1921 CD LYS A 506 67.786 64.376 36.715 1.00 43.43 C
-ATOM 1922 CE LYS A 506 69.015 65.286 36.677 1.00 46.06 C
-ATOM 1923 NZ LYS A 506 70.051 64.953 37.712 1.00 47.04 N
-ATOM 1924 N VAL A 507 66.370 61.887 41.074 1.00 38.97 N
-ATOM 1925 CA VAL A 507 66.222 60.655 41.849 1.00 40.05 C
-ATOM 1926 C VAL A 507 65.988 59.456 40.920 1.00 42.50 C
-ATOM 1927 O VAL A 507 65.560 59.615 39.773 1.00 41.16 O
-ATOM 1928 CB VAL A 507 65.028 60.809 42.854 1.00 37.56 C
-ATOM 1929 CG1 VAL A 507 64.604 59.465 43.401 1.00 36.32 C
-ATOM 1930 CG2 VAL A 507 65.425 61.733 44.008 1.00 34.76 C
-ATOM 1931 N ASN A 508 66.287 58.258 41.411 1.00 48.25 N
-ATOM 1932 CA ASN A 508 66.096 57.037 40.622 1.00 50.66 C
-ATOM 1933 C ASN A 508 64.786 56.333 41.004 1.00 49.60 C
-ATOM 1934 O ASN A 508 64.545 56.012 42.173 1.00 46.68 O
-ATOM 1935 CB ASN A 508 67.278 56.083 40.829 1.00 58.34 C
-ATOM 1936 CG ASN A 508 68.620 56.724 40.500 1.00 68.38 C
-ATOM 1937 OD1 ASN A 508 69.648 56.048 40.467 1.00 74.62 O
-ATOM 1938 ND2 ASN A 508 68.616 58.030 40.264 1.00 73.70 N
-ATOM 1939 N LEU A 509 63.940 56.099 40.008 1.00 49.76 N
-ATOM 1940 CA LEU A 509 62.648 55.459 40.230 1.00 50.49 C
-ATOM 1941 C LEU A 509 62.626 54.055 39.639 1.00 58.34 C
-ATOM 1942 O LEU A 509 63.294 53.797 38.639 1.00 54.20 O
-ATOM 1943 CB LEU A 509 61.547 56.328 39.616 1.00 44.00 C
-ATOM 1944 CG LEU A 509 60.784 57.250 40.576 1.00 40.53 C
-ATOM 1945 CD1 LEU A 509 61.705 57.803 41.649 1.00 36.48 C
-ATOM 1946 CD2 LEU A 509 60.112 58.362 39.776 1.00 37.88 C
-ATOM 1947 N GLU A 510 61.848 53.156 40.244 1.00 74.63 N
-ATOM 1948 CA GLU A 510 61.798 51.769 39.778 1.00 85.59 C
-ATOM 1949 C GLU A 510 60.443 51.230 39.323 1.00 89.60 C
-ATOM 1950 O GLU A 510 59.388 51.784 39.652 1.00 87.02 O
-ATOM 1951 CB GLU A 510 62.336 50.844 40.868 1.00 95.97 C
-ATOM 1952 CG GLU A 510 63.502 51.418 41.640 1.00120.13 C
-ATOM 1953 CD GLU A 510 64.108 50.419 42.601 1.00130.61 C
-ATOM 1954 OE1 GLU A 510 63.354 49.818 43.393 1.00134.64 O
-ATOM 1955 OE2 GLU A 510 65.343 50.240 42.568 1.00134.85 O
-ATOM 1956 N LYS A 511 60.508 50.125 38.575 1.00100.17 N
-ATOM 1957 CA LYS A 511 59.350 49.410 38.029 1.00106.24 C
-ATOM 1958 C LYS A 511 59.866 48.086 37.454 1.00107.46 C
-ATOM 1959 O LYS A 511 61.075 47.862 37.418 1.00113.88 O
-ATOM 1960 CB LYS A 511 58.677 50.236 36.926 1.00111.48 C
-ATOM 1961 CG LYS A 511 57.475 49.560 36.266 1.00119.83 C
-ATOM 1962 CD LYS A 511 56.830 50.478 35.236 1.00123.38 C
-ATOM 1963 CE LYS A 511 55.726 49.777 34.455 1.00123.83 C
-ATOM 1964 NZ LYS A 511 55.093 50.692 33.458 1.00124.02 N
-ATOM 1965 N LYS A 512 58.960 47.216 37.010 1.00114.93 N
-ATOM 1966 CA LYS A 512 59.337 45.917 36.443 1.00119.36 C
-ATOM 1967 C LYS A 512 60.455 45.210 37.204 1.00124.50 C
-ATOM 1968 O LYS A 512 61.200 44.416 36.625 1.00129.08 O
-ATOM 1969 CB LYS A 512 59.760 46.064 34.978 1.00113.46 C
-ATOM 1970 CG LYS A 512 58.603 46.162 34.008 1.00103.38 C
-ATOM 1971 CD LYS A 512 57.711 44.931 34.088 1.00 98.05 C
-ATOM 1972 CE LYS A 512 56.553 45.025 33.102 1.00 96.64 C
-ATOM 1973 NZ LYS A 512 55.562 43.926 33.276 1.00 96.01 N
-ATOM 1974 N HIS A 513 60.567 45.502 38.496 1.00134.30 N
-ATOM 1975 CA HIS A 513 61.585 44.897 39.351 1.00140.56 C
-ATOM 1976 C HIS A 513 63.012 45.218 38.889 1.00137.57 C
-ATOM 1977 O HIS A 513 63.886 44.351 38.899 1.00143.66 O
-ATOM 1978 CB HIS A 513 61.380 43.375 39.416 1.00146.45 C
-ATOM 1979 CG HIS A 513 61.756 42.766 40.734 1.00151.21 C
-ATOM 1980 ND1 HIS A 513 63.030 42.853 41.258 1.00152.84 N
-ATOM 1981 CD2 HIS A 513 61.025 42.073 41.637 1.00152.67 C
-ATOM 1982 CE1 HIS A 513 63.064 42.238 42.429 1.00153.27 C
-ATOM 1983 NE2 HIS A 513 61.859 41.757 42.681 1.00153.36 N
-ATOM 1984 N LEU A 514 63.232 46.470 38.489 1.00130.89 N
-ATOM 1985 CA LEU A 514 64.537 46.961 38.035 1.00126.77 C
-ATOM 1986 C LEU A 514 64.455 48.481 37.846 1.00126.70 C
-ATOM 1987 O LEU A 514 63.378 49.014 37.581 1.00128.13 O
-ATOM 1988 CB LEU A 514 64.956 46.286 36.718 1.00118.24 C
-ATOM 1989 CG LEU A 514 65.558 44.872 36.762 1.00104.96 C
-ATOM 1990 CD1 LEU A 514 65.826 44.400 35.344 1.00 97.34 C
-ATOM 1991 CD2 LEU A 514 66.854 44.860 37.569 1.00 97.63 C
-ATOM 1992 N ASN A 515 65.585 49.174 37.984 1.00123.51 N
-ATOM 1993 CA ASN A 515 65.626 50.636 37.849 1.00119.16 C
-ATOM 1994 C ASN A 515 65.289 51.190 36.458 1.00114.13 C
-ATOM 1995 O ASN A 515 65.841 50.750 35.446 1.00113.33 O
-ATOM 1996 CB ASN A 515 67.003 51.172 38.278 1.00117.39 C
-ATOM 1997 CG ASN A 515 67.146 51.301 39.792 1.00115.54 C
-ATOM 1998 OD1 ASN A 515 66.924 50.343 40.534 1.00115.73 O
-ATOM 1999 ND2 ASN A 515 67.525 52.491 40.252 1.00115.50 N
-ATOM 2000 N LYS A 516 64.373 52.159 36.425 1.00103.46 N
-ATOM 2001 CA LYS A 516 63.964 52.810 35.180 1.00100.63 C
-ATOM 2002 C LYS A 516 64.426 54.272 35.247 1.00 99.40 C
-ATOM 2003 O LYS A 516 65.570 54.554 35.617 1.00 97.71 O
-ATOM 2004 CB LYS A 516 62.435 52.776 34.997 1.00101.97 C
-ATOM 2005 CG LYS A 516 61.733 51.489 35.408 1.00 97.89 C
-ATOM 2006 CD LYS A 516 62.306 50.244 34.732 1.00 95.97 C
-ATOM 2007 CE LYS A 516 62.030 50.186 33.236 1.00 93.83 C
-ATOM 2008 NZ LYS A 516 62.525 48.891 32.674 1.00 93.26 N
-ATOM 2009 N ARG A 517 63.520 55.194 34.919 1.00 89.03 N
-ATOM 2010 CA ARG A 517 63.809 56.626 34.911 1.00 76.68 C
-ATOM 2011 C ARG A 517 64.425 57.264 36.154 1.00 72.12 C
-ATOM 2012 O ARG A 517 64.208 56.825 37.286 1.00 59.09 O
-ATOM 2013 CB ARG A 517 62.546 57.403 34.548 1.00 74.59 C
-ATOM 2014 CG ARG A 517 62.178 57.324 33.083 1.00 80.58 C
-ATOM 2015 CD ARG A 517 61.724 58.688 32.601 1.00 85.08 C
-ATOM 2016 NE ARG A 517 62.715 59.716 32.912 1.00 86.38 N
-ATOM 2017 CZ ARG A 517 62.517 61.020 32.747 1.00 86.90 C
-ATOM 2018 NH1 ARG A 517 61.360 61.468 32.273 1.00 86.20 N
-ATOM 2019 NH2 ARG A 517 63.479 61.876 33.060 1.00 87.30 N
-ATOM 2020 N THR A 518 65.204 58.315 35.904 1.00 64.50 N
-ATOM 2021 CA THR A 518 65.865 59.105 36.939 1.00 62.32 C
-ATOM 2022 C THR A 518 65.354 60.513 36.653 1.00 60.46 C
-ATOM 2023 O THR A 518 65.369 60.954 35.501 1.00 60.26 O
-ATOM 2024 CB THR A 518 67.404 59.095 36.788 1.00 66.62 C
-ATOM 2025 OG1 THR A 518 67.890 57.748 36.846 1.00 74.37 O
-ATOM 2026 CG2 THR A 518 68.051 59.911 37.902 1.00 73.41 C
-ATOM 2027 N GLN A 519 64.911 61.226 37.683 1.00 56.28 N
-ATOM 2028 CA GLN A 519 64.355 62.557 37.458 1.00 52.54 C
-ATOM 2029 C GLN A 519 64.072 63.284 38.755 1.00 50.17 C
-ATOM 2030 O GLN A 519 64.417 62.813 39.840 1.00 48.30 O
-ATOM 2031 CB GLN A 519 63.030 62.419 36.722 1.00 52.33 C
-ATOM 2032 CG GLN A 519 62.001 61.673 37.574 1.00 51.32 C
-ATOM 2033 CD GLN A 519 60.667 61.487 36.888 1.00 51.87 C
-ATOM 2034 OE1 GLN A 519 60.553 60.728 35.927 1.00 51.92 O
-ATOM 2035 NE2 GLN A 519 59.644 62.184 37.378 1.00 50.98 N
-ATOM 2036 N ILE A 520 63.424 64.438 38.620 1.00 44.28 N
-ATOM 2037 CA ILE A 520 63.024 65.229 39.773 1.00 39.05 C
-ATOM 2038 C ILE A 520 61.704 64.596 40.176 1.00 36.48 C
-ATOM 2039 O ILE A 520 60.799 64.504 39.345 1.00 34.52 O
-ATOM 2040 CB ILE A 520 62.776 66.699 39.382 1.00 38.42 C
-ATOM 2041 CG1 ILE A 520 64.091 67.362 38.973 1.00 37.72 C
-ATOM 2042 CG2 ILE A 520 62.161 67.458 40.547 1.00 37.50 C
-ATOM 2043 CD1 ILE A 520 65.095 67.491 40.100 1.00 37.25 C
-ATOM 2044 N PHE A 521 61.590 64.131 41.419 1.00 31.08 N
-ATOM 2045 CA PHE A 521 60.333 63.514 41.833 1.00 29.96 C
-ATOM 2046 C PHE A 521 59.279 64.566 41.526 1.00 29.94 C
-ATOM 2047 O PHE A 521 59.554 65.762 41.625 1.00 31.08 O
-ATOM 2048 CB PHE A 521 60.329 63.167 43.323 1.00 27.52 C
-ATOM 2049 CG PHE A 521 59.216 62.243 43.717 1.00 25.56 C
-ATOM 2050 CD1 PHE A 521 59.156 60.953 43.210 1.00 25.34 C
-ATOM 2051 CD2 PHE A 521 58.222 62.653 44.600 1.00 25.75 C
-ATOM 2052 CE1 PHE A 521 58.106 60.068 43.584 1.00 25.11 C
-ATOM 2053 CE2 PHE A 521 57.172 61.778 44.977 1.00 24.84 C
-ATOM 2054 CZ PHE A 521 57.119 60.491 44.468 1.00 23.47 C
-ATOM 2055 N PRO A 522 58.064 64.148 41.140 1.00 26.85 N
-ATOM 2056 CA PRO A 522 57.076 65.181 40.836 1.00 26.10 C
-ATOM 2057 C PRO A 522 56.546 65.881 42.066 1.00 24.34 C
-ATOM 2058 O PRO A 522 56.656 65.367 43.181 1.00 24.30 O
-ATOM 2059 CB PRO A 522 55.977 64.418 40.089 1.00 25.17 C
-ATOM 2060 CG PRO A 522 56.653 63.151 39.640 1.00 26.78 C
-ATOM 2061 CD PRO A 522 57.547 62.819 40.794 1.00 25.02 C
-ATOM 2062 N PRO A 523 55.997 67.091 41.872 1.00 21.36 N
-ATOM 2063 CA PRO A 523 55.416 67.916 42.938 1.00 21.51 C
-ATOM 2064 C PRO A 523 54.017 67.354 43.220 1.00 21.96 C
-ATOM 2065 O PRO A 523 53.515 66.524 42.441 1.00 20.82 O
-ATOM 2066 CB PRO A 523 55.358 69.295 42.301 1.00 20.72 C
-ATOM 2067 CG PRO A 523 55.081 68.969 40.837 1.00 18.36 C
-ATOM 2068 CD PRO A 523 56.034 67.824 40.590 1.00 19.50 C
-ATOM 2069 N GLY A 524 53.390 67.780 44.316 1.00 21.33 N
-ATOM 2070 CA GLY A 524 52.066 67.262 44.605 1.00 22.84 C
-ATOM 2071 C GLY A 524 51.373 67.638 45.900 1.00 23.58 C
-ATOM 2072 O GLY A 524 51.606 68.697 46.478 1.00 23.73 O
-ATOM 2073 N ILE A 525 50.502 66.749 46.356 1.00 24.15 N
-ATOM 2074 CA ILE A 525 49.736 66.989 47.569 1.00 26.08 C
-ATOM 2075 C ILE A 525 49.805 65.801 48.524 1.00 24.70 C
-ATOM 2076 O ILE A 525 49.888 64.642 48.109 1.00 27.53 O
-ATOM 2077 CB ILE A 525 48.226 67.196 47.250 1.00 28.51 C
-ATOM 2078 CG1 ILE A 525 48.048 68.207 46.123 1.00 31.26 C
-ATOM 2079 CG2 ILE A 525 47.487 67.663 48.490 1.00 32.03 C
-ATOM 2080 CD1 ILE A 525 46.625 68.310 45.620 1.00 30.68 C
-ATOM 2081 N VAL A 526 49.766 66.099 49.809 1.00 21.78 N
-ATOM 2082 CA VAL A 526 49.735 65.065 50.812 1.00 21.78 C
-ATOM 2083 C VAL A 526 48.401 65.303 51.520 1.00 27.72 C
-ATOM 2084 O VAL A 526 48.135 66.404 52.020 1.00 22.81 O
-ATOM 2085 CB VAL A 526 50.908 65.194 51.819 1.00 19.35 C
-ATOM 2086 CG1 VAL A 526 50.679 64.285 53.015 1.00 15.90 C
-ATOM 2087 CG2 VAL A 526 52.205 64.789 51.158 1.00 14.77 C
-ATOM 2088 N THR A 527 47.545 64.286 51.508 1.00 35.58 N
-ATOM 2089 CA THR A 527 46.246 64.350 52.174 1.00 38.56 C
-ATOM 2090 C THR A 527 46.446 63.643 53.519 1.00 37.40 C
-ATOM 2091 O THR A 527 46.868 62.483 53.571 1.00 36.32 O
-ATOM 2092 CB THR A 527 45.170 63.638 51.351 1.00 47.75 C
-ATOM 2093 OG1 THR A 527 44.166 63.121 52.228 1.00 63.01 O
-ATOM 2094 CG2 THR A 527 45.770 62.515 50.554 1.00 62.65 C
-ATOM 2095 N MET A 528 46.139 64.339 54.608 1.00 37.10 N
-ATOM 2096 CA MET A 528 46.370 63.785 55.937 1.00 36.44 C
-ATOM 2097 C MET A 528 45.167 63.883 56.884 1.00 37.86 C
-ATOM 2098 O MET A 528 44.286 64.727 56.701 1.00 42.10 O
-ATOM 2099 CB MET A 528 47.582 64.511 56.514 1.00 32.35 C
-ATOM 2100 CG MET A 528 48.172 63.935 57.758 1.00 23.82 C
-ATOM 2101 SD MET A 528 49.416 65.106 58.228 1.00 13.96 S
-ATOM 2102 CE MET A 528 50.696 64.566 57.210 1.00 15.97 C
-ATOM 2103 N ASN A 529 45.155 63.049 57.920 1.00 41.20 N
-ATOM 2104 CA ASN A 529 44.031 63.024 58.847 1.00 43.96 C
-ATOM 2105 C ASN A 529 44.166 63.719 60.201 1.00 45.12 C
-ATOM 2106 O ASN A 529 43.329 63.508 61.077 1.00 44.03 O
-ATOM 2107 CB ASN A 529 43.607 61.579 59.097 1.00 46.83 C
-ATOM 2108 CG ASN A 529 42.128 61.449 59.434 1.00 48.41 C
-ATOM 2109 OD1 ASN A 529 41.591 62.174 60.278 1.00 48.15 O
-ATOM 2110 ND2 ASN A 529 41.463 60.512 58.771 1.00 50.44 N
-ATOM 2111 N GLU A 530 45.203 64.523 60.390 1.00 45.45 N
-ATOM 2112 CA GLU A 530 45.388 65.255 61.649 1.00 47.15 C
-ATOM 2113 C GLU A 530 46.342 64.645 62.661 1.00 47.08 C
-ATOM 2114 O GLU A 530 46.170 64.814 63.870 1.00 47.20 O
-ATOM 2115 CB GLU A 530 44.044 65.549 62.349 1.00 47.01 C
-ATOM 2116 CG GLU A 530 43.201 66.604 61.645 1.00 53.61 C
-ATOM 2117 CD GLU A 530 42.154 67.237 62.545 1.00 56.97 C
-ATOM 2118 OE1 GLU A 530 41.139 66.567 62.858 1.00 57.40 O
-ATOM 2119 OE2 GLU A 530 42.353 68.412 62.935 1.00 58.52 O
-ATOM 2120 N TYR A 531 47.350 63.933 62.171 1.00 46.85 N
-ATOM 2121 CA TYR A 531 48.348 63.369 63.059 1.00 45.57 C
-ATOM 2122 C TYR A 531 49.344 64.500 63.247 1.00 44.83 C
-ATOM 2123 O TYR A 531 49.431 65.400 62.408 1.00 44.60 O
-ATOM 2124 CB TYR A 531 49.069 62.195 62.409 1.00 46.77 C
-ATOM 2125 CG TYR A 531 48.178 61.058 62.002 1.00 48.77 C
-ATOM 2126 CD1 TYR A 531 47.438 61.116 60.823 1.00 49.31 C
-ATOM 2127 CD2 TYR A 531 48.062 59.920 62.806 1.00 49.59 C
-ATOM 2128 CE1 TYR A 531 46.596 60.062 60.450 1.00 49.74 C
-ATOM 2129 CE2 TYR A 531 47.224 58.862 62.445 1.00 49.46 C
-ATOM 2130 CZ TYR A 531 46.494 58.942 61.266 1.00 49.67 C
-ATOM 2131 OH TYR A 531 45.658 57.908 60.908 1.00 49.67 O
-ATOM 2132 N SER A 532 50.084 64.465 64.348 1.00 43.29 N
-ATOM 2133 CA SER A 532 51.092 65.485 64.608 1.00 41.35 C
-ATOM 2134 C SER A 532 52.144 65.320 63.523 1.00 40.13 C
-ATOM 2135 O SER A 532 52.379 64.202 63.048 1.00 39.40 O
-ATOM 2136 CB SER A 532 51.722 65.261 65.982 1.00 40.32 C
-ATOM 2137 OG SER A 532 52.071 63.897 66.144 1.00 41.16 O
-ATOM 2138 N VAL A 533 52.770 66.424 63.130 1.00 38.95 N
-ATOM 2139 CA VAL A 533 53.790 66.374 62.089 1.00 39.14 C
-ATOM 2140 C VAL A 533 55.148 66.848 62.581 1.00 39.44 C
-ATOM 2141 O VAL A 533 55.250 67.851 63.289 1.00 41.56 O
-ATOM 2142 CB VAL A 533 53.382 67.232 60.881 1.00 37.85 C
-ATOM 2143 CG1 VAL A 533 54.481 67.213 59.835 1.00 35.93 C
-ATOM 2144 CG2 VAL A 533 52.068 66.710 60.297 1.00 34.58 C
-ATOM 2145 N PRO A 534 56.213 66.116 62.228 1.00 41.51 N
-ATOM 2146 CA PRO A 534 57.568 66.492 62.648 1.00 42.78 C
-ATOM 2147 C PRO A 534 57.961 67.789 61.958 1.00 43.86 C
-ATOM 2148 O PRO A 534 57.706 67.947 60.766 1.00 42.90 O
-ATOM 2149 CB PRO A 534 58.415 65.313 62.173 1.00 43.01 C
-ATOM 2150 CG PRO A 534 57.450 64.157 62.215 1.00 43.46 C
-ATOM 2151 CD PRO A 534 56.204 64.773 61.622 1.00 42.88 C
-ATOM 2152 N LYS A 535 58.577 68.711 62.700 1.00 44.01 N
-ATOM 2153 CA LYS A 535 58.991 70.002 62.141 1.00 42.60 C
-ATOM 2154 C LYS A 535 59.841 69.855 60.868 1.00 41.40 C
-ATOM 2155 O LYS A 535 59.851 70.744 60.011 1.00 35.53 O
-ATOM 2156 CB LYS A 535 59.773 70.819 63.177 1.00 46.80 C
-ATOM 2157 CG LYS A 535 61.278 70.588 63.148 1.00 58.71 C
-ATOM 2158 CD LYS A 535 62.039 71.857 62.759 1.00 64.10 C
-ATOM 2159 CE LYS A 535 63.535 71.576 62.572 1.00 66.00 C
-ATOM 2160 NZ LYS A 535 64.341 72.793 62.237 1.00 66.30 N
-ATOM 2161 N THR A 536 60.562 68.746 60.742 1.00 38.83 N
-ATOM 2162 CA THR A 536 61.377 68.547 59.552 1.00 37.41 C
-ATOM 2163 C THR A 536 60.487 68.245 58.339 1.00 38.15 C
-ATOM 2164 O THR A 536 60.824 68.573 57.197 1.00 37.52 O
-ATOM 2165 CB THR A 536 62.401 67.403 59.768 1.00 39.04 C
-ATOM 2166 OG1 THR A 536 61.718 66.175 60.054 1.00 43.35 O
-ATOM 2167 CG2 THR A 536 63.307 67.740 60.939 1.00 42.50 C
-ATOM 2168 N LEU A 537 59.341 67.622 58.593 1.00 40.53 N
-ATOM 2169 CA LEU A 537 58.409 67.283 57.524 1.00 41.01 C
-ATOM 2170 C LEU A 537 57.581 68.505 57.157 1.00 39.31 C
-ATOM 2171 O LEU A 537 57.428 68.856 55.990 1.00 39.46 O
-ATOM 2172 CB LEU A 537 57.482 66.157 57.978 1.00 44.91 C
-ATOM 2173 CG LEU A 537 56.472 65.695 56.927 1.00 49.35 C
-ATOM 2174 CD1 LEU A 537 57.199 65.183 55.698 1.00 50.49 C
-ATOM 2175 CD2 LEU A 537 55.592 64.611 57.517 1.00 51.83 C
-ATOM 2176 N GLN A 538 57.039 69.141 58.182 1.00 36.88 N
-ATOM 2177 CA GLN A 538 56.222 70.328 58.019 1.00 35.62 C
-ATOM 2178 C GLN A 538 56.879 71.296 57.039 1.00 35.85 C
-ATOM 2179 O GLN A 538 56.214 71.893 56.183 1.00 34.43 O
-ATOM 2180 CB GLN A 538 56.043 70.997 59.385 1.00 34.70 C
-ATOM 2181 CG GLN A 538 54.984 72.075 59.439 1.00 33.65 C
-ATOM 2182 CD GLN A 538 53.622 71.580 58.972 1.00 34.08 C
-ATOM 2183 OE1 GLN A 538 53.117 70.553 59.445 1.00 33.95 O
-ATOM 2184 NE2 GLN A 538 53.017 72.315 58.043 1.00 34.77 N
-ATOM 2185 N ALA A 539 58.197 71.421 57.169 1.00 36.25 N
-ATOM 2186 CA ALA A 539 59.004 72.321 56.350 1.00 36.95 C
-ATOM 2187 C ALA A 539 59.006 72.011 54.865 1.00 38.74 C
-ATOM 2188 O ALA A 539 59.353 72.866 54.051 1.00 39.34 O
-ATOM 2189 CB ALA A 539 60.433 72.329 56.863 1.00 34.84 C
-ATOM 2190 N ARG A 540 58.623 70.796 54.501 1.00 42.74 N
-ATOM 2191 CA ARG A 540 58.620 70.426 53.097 1.00 44.73 C
-ATOM 2192 C ARG A 540 57.359 70.922 52.415 1.00 43.40 C
-ATOM 2193 O ARG A 540 57.282 70.963 51.186 1.00 42.87 O
-ATOM 2194 CB ARG A 540 58.755 68.914 52.962 1.00 50.46 C
-ATOM 2195 CG ARG A 540 59.901 68.354 53.790 1.00 58.88 C
-ATOM 2196 CD ARG A 540 61.226 69.004 53.438 1.00 62.11 C
-ATOM 2197 NE ARG A 540 62.248 68.680 54.425 1.00 63.75 N
-ATOM 2198 CZ ARG A 540 63.553 68.841 54.232 1.00 65.44 C
-ATOM 2199 NH1 ARG A 540 64.005 69.325 53.084 1.00 66.14 N
-ATOM 2200 NH2 ARG A 540 64.411 68.505 55.184 1.00 66.03 N
-ATOM 2201 N PHE A 541 56.375 71.318 53.214 1.00 39.87 N
-ATOM 2202 CA PHE A 541 55.136 71.832 52.651 1.00 36.33 C
-ATOM 2203 C PHE A 541 55.140 73.351 52.616 1.00 34.81 C
-ATOM 2204 O PHE A 541 55.252 74.009 53.648 1.00 35.51 O
-ATOM 2205 CB PHE A 541 53.940 71.326 53.447 1.00 33.49 C
-ATOM 2206 CG PHE A 541 53.853 69.837 53.490 1.00 32.84 C
-ATOM 2207 CD1 PHE A 541 54.276 69.135 54.610 1.00 32.20 C
-ATOM 2208 CD2 PHE A 541 53.401 69.129 52.389 1.00 31.04 C
-ATOM 2209 CE1 PHE A 541 54.254 67.747 54.631 1.00 31.47 C
-ATOM 2210 CE2 PHE A 541 53.377 67.755 52.398 1.00 30.76 C
-ATOM 2211 CZ PHE A 541 53.804 67.056 53.520 1.00 31.43 C
-ATOM 2212 N VAL A 542 55.031 73.903 51.415 1.00 34.35 N
-ATOM 2213 CA VAL A 542 55.026 75.342 51.250 1.00 36.52 C
-ATOM 2214 C VAL A 542 53.661 75.932 51.561 1.00 36.17 C
-ATOM 2215 O VAL A 542 53.522 77.138 51.770 1.00 39.69 O
-ATOM 2216 CB VAL A 542 55.423 75.739 49.814 1.00 36.15 C
-ATOM 2217 CG1 VAL A 542 54.362 75.288 48.821 1.00 32.62 C
-ATOM 2218 CG2 VAL A 542 55.645 77.250 49.749 1.00 34.52 C
-ATOM 2219 N LYS A 543 52.653 75.070 51.598 1.00 35.60 N
-ATOM 2220 CA LYS A 543 51.287 75.501 51.862 1.00 34.36 C
-ATOM 2221 C LYS A 543 50.495 74.419 52.594 1.00 33.74 C
-ATOM 2222 O LYS A 543 50.662 73.238 52.335 1.00 33.88 O
-ATOM 2223 CB LYS A 543 50.589 75.849 50.538 1.00 31.85 C
-ATOM 2224 CG LYS A 543 49.143 76.192 50.720 1.00 31.38 C
-ATOM 2225 CD LYS A 543 48.645 77.191 49.700 1.00 30.19 C
-ATOM 2226 CE LYS A 543 47.261 77.724 50.100 1.00 30.75 C
-ATOM 2227 NZ LYS A 543 46.804 78.891 49.274 1.00 32.15 N
-ATOM 2228 N GLN A 544 49.650 74.820 53.530 1.00 31.21 N
-ATOM 2229 CA GLN A 544 48.819 73.859 54.250 1.00 29.21 C
-ATOM 2230 C GLN A 544 47.384 74.350 54.269 1.00 29.28 C
-ATOM 2231 O GLN A 544 47.122 75.523 54.532 1.00 27.66 O
-ATOM 2232 CB GLN A 544 49.295 73.654 55.686 1.00 27.97 C
-ATOM 2233 CG GLN A 544 48.314 72.844 56.520 1.00 29.44 C
-ATOM 2234 CD GLN A 544 48.879 72.413 57.866 1.00 31.20 C
-ATOM 2235 OE1 GLN A 544 48.159 71.885 58.714 1.00 32.47 O
-ATOM 2236 NE2 GLN A 544 50.170 72.634 58.066 1.00 32.33 N
-ATOM 2237 N ILE A 545 46.457 73.450 53.972 1.00 28.83 N
-ATOM 2238 CA ILE A 545 45.047 73.795 53.957 1.00 29.08 C
-ATOM 2239 C ILE A 545 44.301 72.919 54.947 1.00 29.59 C
-ATOM 2240 O ILE A 545 44.323 71.695 54.838 1.00 30.57 O
-ATOM 2241 CB ILE A 545 44.427 73.591 52.556 1.00 29.20 C
-ATOM 2242 CG1 ILE A 545 45.134 74.479 51.528 1.00 28.79 C
-ATOM 2243 CG2 ILE A 545 42.928 73.900 52.603 1.00 29.95 C
-ATOM 2244 CD1 ILE A 545 44.548 74.369 50.133 1.00 28.13 C
-ATOM 2245 N ASP A 546 43.643 73.549 55.914 1.00 31.76 N
-ATOM 2246 CA ASP A 546 42.887 72.811 56.909 1.00 31.89 C
-ATOM 2247 C ASP A 546 41.421 72.727 56.540 1.00 31.01 C
-ATOM 2248 O ASP A 546 40.743 73.744 56.364 1.00 31.17 O
-ATOM 2249 CB ASP A 546 43.048 73.447 58.288 1.00 34.08 C
-ATOM 2250 CG ASP A 546 44.450 73.301 58.818 1.00 37.82 C
-ATOM 2251 OD1 ASP A 546 44.970 72.171 58.747 1.00 40.48 O
-ATOM 2252 OD2 ASP A 546 45.032 74.297 59.301 1.00 39.17 O
-ATOM 2253 N PHE A 547 40.941 71.497 56.408 1.00 30.35 N
-ATOM 2254 CA PHE A 547 39.553 71.275 56.071 1.00 30.61 C
-ATOM 2255 C PHE A 547 38.798 70.885 57.326 1.00 33.73 C
-ATOM 2256 O PHE A 547 39.272 70.082 58.132 1.00 31.81 O
-ATOM 2257 CB PHE A 547 39.414 70.177 55.004 1.00 27.96 C
-ATOM 2258 CG PHE A 547 40.089 70.510 53.707 1.00 28.24 C
-ATOM 2259 CD1 PHE A 547 41.481 70.391 53.574 1.00 27.61 C
-ATOM 2260 CD2 PHE A 547 39.345 70.984 52.627 1.00 26.45 C
-ATOM 2261 CE1 PHE A 547 42.129 70.745 52.381 1.00 26.76 C
-ATOM 2262 CE2 PHE A 547 39.971 71.345 51.424 1.00 25.92 C
-ATOM 2263 CZ PHE A 547 41.363 71.228 51.296 1.00 27.03 C
-ATOM 2264 N ARG A 548 37.634 71.494 57.500 1.00 39.02 N
-ATOM 2265 CA ARG A 548 36.781 71.203 58.633 1.00 42.85 C
-ATOM 2266 C ARG A 548 35.409 70.955 58.037 1.00 42.12 C
-ATOM 2267 O ARG A 548 34.932 71.724 57.194 1.00 40.04 O
-ATOM 2268 CB ARG A 548 36.766 72.383 59.598 1.00 48.70 C
-ATOM 2269 CG ARG A 548 38.156 72.695 60.088 1.00 62.54 C
-ATOM 2270 CD ARG A 548 38.266 74.050 60.735 1.00 69.07 C
-ATOM 2271 NE ARG A 548 39.663 74.473 60.774 1.00 70.85 N
-ATOM 2272 CZ ARG A 548 40.092 75.589 61.349 1.00 72.04 C
-ATOM 2273 NH1 ARG A 548 39.226 76.403 61.944 1.00 72.77 N
-ATOM 2274 NH2 ARG A 548 41.386 75.892 61.323 1.00 71.92 N
-ATOM 2275 N PRO A 549 34.767 69.851 58.435 1.00 41.98 N
-ATOM 2276 CA PRO A 549 33.446 69.578 57.880 1.00 39.73 C
-ATOM 2277 C PRO A 549 32.502 70.708 58.230 1.00 38.80 C
-ATOM 2278 O PRO A 549 32.520 71.214 59.355 1.00 37.73 O
-ATOM 2279 CB PRO A 549 33.062 68.265 58.544 1.00 39.46 C
-ATOM 2280 CG PRO A 549 34.387 67.609 58.766 1.00 42.04 C
-ATOM 2281 CD PRO A 549 35.207 68.746 59.299 1.00 41.06 C
-ATOM 2282 N LYS A 550 31.706 71.122 57.250 1.00 37.00 N
-ATOM 2283 CA LYS A 550 30.742 72.190 57.451 1.00 37.15 C
-ATOM 2284 C LYS A 550 29.329 71.617 57.283 1.00 40.74 C
-ATOM 2285 O LYS A 550 29.078 70.789 56.408 1.00 35.41 O
-ATOM 2286 CB LYS A 550 30.988 73.335 56.460 1.00 36.51 C
-ATOM 2287 CG LYS A 550 32.344 74.020 56.596 1.00 39.58 C
-ATOM 2288 CD LYS A 550 32.471 75.102 55.538 1.00 43.40 C
-ATOM 2289 CE LYS A 550 33.909 75.557 55.295 1.00 43.64 C
-ATOM 2290 NZ LYS A 550 33.949 76.515 54.131 1.00 42.42 N
-ATOM 2291 N ASP A 551 28.413 72.071 58.133 1.00 45.20 N
-ATOM 2292 CA ASP A 551 27.035 71.601 58.132 1.00 45.25 C
-ATOM 2293 C ASP A 551 26.234 71.996 56.911 1.00 41.40 C
-ATOM 2294 O ASP A 551 25.554 71.154 56.318 1.00 37.47 O
-ATOM 2295 CB ASP A 551 26.331 72.095 59.394 1.00 58.06 C
-ATOM 2296 CG ASP A 551 26.979 71.571 60.652 1.00 74.69 C
-ATOM 2297 OD1 ASP A 551 26.724 70.405 61.004 1.00 82.52 O
-ATOM 2298 OD2 ASP A 551 27.761 72.318 61.278 1.00 84.94 O
-ATOM 2299 N TYR A 552 26.307 73.265 56.524 1.00 37.38 N
-ATOM 2300 CA TYR A 552 25.532 73.690 55.378 1.00 34.50 C
-ATOM 2301 C TYR A 552 25.937 72.967 54.107 1.00 34.55 C
-ATOM 2302 O TYR A 552 25.083 72.636 53.278 1.00 36.77 O
-ATOM 2303 CB TYR A 552 25.586 75.221 55.209 1.00 31.15 C
-ATOM 2304 CG TYR A 552 26.960 75.830 55.060 1.00 30.45 C
-ATOM 2305 CD1 TYR A 552 27.587 75.894 53.812 1.00 30.34 C
-ATOM 2306 CD2 TYR A 552 27.634 76.354 56.159 1.00 28.46 C
-ATOM 2307 CE1 TYR A 552 28.847 76.460 53.664 1.00 27.62 C
-ATOM 2308 CE2 TYR A 552 28.898 76.925 56.018 1.00 27.60 C
-ATOM 2309 CZ TYR A 552 29.496 76.971 54.769 1.00 27.63 C
-ATOM 2310 OH TYR A 552 30.762 77.494 54.624 1.00 27.86 O
-ATOM 2311 N LEU A 553 27.226 72.683 53.958 1.00 35.06 N
-ATOM 2312 CA LEU A 553 27.685 71.991 52.765 1.00 34.33 C
-ATOM 2313 C LEU A 553 27.170 70.571 52.707 1.00 34.59 C
-ATOM 2314 O LEU A 553 26.882 70.046 51.632 1.00 33.13 O
-ATOM 2315 CB LEU A 553 29.203 71.983 52.710 1.00 33.94 C
-ATOM 2316 CG LEU A 553 29.776 73.296 52.177 1.00 36.49 C
-ATOM 2317 CD1 LEU A 553 31.301 73.246 52.238 1.00 37.32 C
-ATOM 2318 CD2 LEU A 553 29.296 73.522 50.746 1.00 35.37 C
-ATOM 2319 N LYS A 554 27.055 69.950 53.872 1.00 35.55 N
-ATOM 2320 CA LYS A 554 26.577 68.585 53.936 1.00 36.32 C
-ATOM 2321 C LYS A 554 25.090 68.585 53.642 1.00 35.94 C
-ATOM 2322 O LYS A 554 24.595 67.720 52.910 1.00 37.28 O
-ATOM 2323 CB LYS A 554 26.830 67.994 55.320 1.00 37.70 C
-ATOM 2324 CG LYS A 554 26.506 66.532 55.404 1.00 38.79 C
-ATOM 2325 CD LYS A 554 26.573 66.051 56.831 1.00 40.86 C
-ATOM 2326 CE LYS A 554 26.189 64.594 56.909 1.00 41.01 C
-ATOM 2327 NZ LYS A 554 26.270 64.104 58.306 1.00 42.37 N
-ATOM 2328 N HIS A 555 24.386 69.565 54.212 1.00 35.62 N
-ATOM 2329 CA HIS A 555 22.948 69.695 54.017 1.00 34.24 C
-ATOM 2330 C HIS A 555 22.655 69.993 52.576 1.00 34.32 C
-ATOM 2331 O HIS A 555 21.641 69.563 52.039 1.00 36.59 O
-ATOM 2332 CB HIS A 555 22.374 70.820 54.862 1.00 32.77 C
-ATOM 2333 CG HIS A 555 22.419 70.552 56.329 1.00 30.74 C
-ATOM 2334 ND1 HIS A 555 22.456 69.274 56.846 1.00 29.93 N
-ATOM 2335 CD2 HIS A 555 22.425 71.390 57.389 1.00 30.93 C
-ATOM 2336 CE1 HIS A 555 22.485 69.340 58.166 1.00 30.18 C
-ATOM 2337 NE2 HIS A 555 22.467 70.611 58.519 1.00 31.41 N
-ATOM 2338 N CYS A 556 23.538 70.754 51.952 1.00 31.90 N
-ATOM 2339 CA CYS A 556 23.358 71.083 50.552 1.00 29.58 C
-ATOM 2340 C CYS A 556 23.342 69.795 49.728 1.00 28.95 C
-ATOM 2341 O CYS A 556 22.460 69.583 48.901 1.00 25.97 O
-ATOM 2342 CB CYS A 556 24.492 71.985 50.078 1.00 29.37 C
-ATOM 2343 SG CYS A 556 24.277 72.506 48.411 1.00 30.69 S
-ATOM 2344 N LEU A 557 24.324 68.935 49.963 1.00 29.67 N
-ATOM 2345 CA LEU A 557 24.411 67.679 49.239 1.00 31.39 C
-ATOM 2346 C LEU A 557 23.208 66.789 49.522 1.00 34.51 C
-ATOM 2347 O LEU A 557 22.699 66.112 48.625 1.00 35.26 O
-ATOM 2348 CB LEU A 557 25.690 66.941 49.616 1.00 30.62 C
-ATOM 2349 CG LEU A 557 26.976 67.618 49.159 1.00 30.57 C
-ATOM 2350 CD1 LEU A 557 28.187 66.791 49.591 1.00 30.21 C
-ATOM 2351 CD2 LEU A 557 26.939 67.771 47.652 1.00 30.61 C
-ATOM 2352 N GLU A 558 22.760 66.779 50.772 1.00 38.85 N
-ATOM 2353 CA GLU A 558 21.611 65.969 51.135 1.00 42.60 C
-ATOM 2354 C GLU A 558 20.424 66.368 50.254 1.00 43.14 C
-ATOM 2355 O GLU A 558 19.583 65.540 49.922 1.00 43.39 O
-ATOM 2356 CB GLU A 558 21.278 66.156 52.625 1.00 47.84 C
-ATOM 2357 CG GLU A 558 22.436 65.763 53.554 1.00 56.71 C
-ATOM 2358 CD GLU A 558 22.133 65.948 55.037 1.00 59.05 C
-ATOM 2359 OE1 GLU A 558 21.654 67.034 55.417 1.00 60.31 O
-ATOM 2360 OE2 GLU A 558 22.393 65.012 55.825 1.00 60.18 O
-ATOM 2361 N ARG A 559 20.365 67.633 49.854 1.00 41.80 N
-ATOM 2362 CA ARG A 559 19.272 68.099 49.013 1.00 38.09 C
-ATOM 2363 C ARG A 559 19.685 68.267 47.560 1.00 35.57 C
-ATOM 2364 O ARG A 559 18.923 68.812 46.758 1.00 34.40 O
-ATOM 2365 CB ARG A 559 18.714 69.427 49.531 1.00 40.61 C
-ATOM 2366 CG ARG A 559 17.888 69.321 50.795 1.00 45.05 C
-ATOM 2367 CD ARG A 559 18.752 69.338 52.024 1.00 48.75 C
-ATOM 2368 NE ARG A 559 17.961 69.263 53.246 1.00 50.23 N
-ATOM 2369 CZ ARG A 559 18.465 69.423 54.466 1.00 50.86 C
-ATOM 2370 NH1 ARG A 559 19.756 69.671 54.619 1.00 51.72 N
-ATOM 2371 NH2 ARG A 559 17.683 69.332 55.534 1.00 50.40 N
-ATOM 2372 N SER A 560 20.881 67.791 47.220 1.00 32.92 N
-ATOM 2373 CA SER A 560 21.390 67.904 45.848 1.00 32.60 C
-ATOM 2374 C SER A 560 22.111 66.615 45.397 1.00 35.73 C
-ATOM 2375 O SER A 560 23.168 66.660 44.774 1.00 31.32 O
-ATOM 2376 CB SER A 560 22.350 69.103 45.760 1.00 28.88 C
-ATOM 2377 OG SER A 560 21.747 70.293 46.254 1.00 25.81 O
-ATOM 2378 N GLU A 561 21.511 65.471 45.693 1.00 39.91 N
-ATOM 2379 CA GLU A 561 22.105 64.178 45.383 1.00 41.05 C
-ATOM 2380 C GLU A 561 22.927 64.098 44.108 1.00 38.26 C
-ATOM 2381 O GLU A 561 23.984 63.454 44.090 1.00 34.27 O
-ATOM 2382 CB GLU A 561 21.032 63.080 45.374 1.00 49.62 C
-ATOM 2383 CG GLU A 561 20.325 62.869 46.709 1.00 65.93 C
-ATOM 2384 CD GLU A 561 18.994 63.606 46.797 1.00 74.51 C
-ATOM 2385 OE1 GLU A 561 18.951 64.836 46.547 1.00 75.86 O
-ATOM 2386 OE2 GLU A 561 17.984 62.943 47.123 1.00 77.77 O
-ATOM 2387 N PHE A 562 22.472 64.749 43.044 1.00 33.66 N
-ATOM 2388 CA PHE A 562 23.211 64.663 41.782 1.00 29.77 C
-ATOM 2389 C PHE A 562 24.693 65.026 41.876 1.00 28.57 C
-ATOM 2390 O PHE A 562 25.503 64.514 41.116 1.00 28.67 O
-ATOM 2391 CB PHE A 562 22.525 65.499 40.688 1.00 28.26 C
-ATOM 2392 CG PHE A 562 22.501 66.973 40.966 1.00 30.44 C
-ATOM 2393 CD1 PHE A 562 23.592 67.778 40.647 1.00 30.82 C
-ATOM 2394 CD2 PHE A 562 21.402 67.553 41.582 1.00 30.45 C
-ATOM 2395 CE1 PHE A 562 23.590 69.131 40.937 1.00 29.40 C
-ATOM 2396 CE2 PHE A 562 21.392 68.907 41.878 1.00 31.34 C
-ATOM 2397 CZ PHE A 562 22.494 69.698 41.553 1.00 31.87 C
-ATOM 2398 N LEU A 563 25.064 65.885 42.817 1.00 27.04 N
-ATOM 2399 CA LEU A 563 26.467 66.261 42.933 1.00 26.12 C
-ATOM 2400 C LEU A 563 27.371 65.086 43.286 1.00 26.19 C
-ATOM 2401 O LEU A 563 28.552 65.083 42.934 1.00 23.62 O
-ATOM 2402 CB LEU A 563 26.649 67.388 43.967 1.00 25.49 C
-ATOM 2403 CG LEU A 563 26.089 68.768 43.592 1.00 23.41 C
-ATOM 2404 CD1 LEU A 563 26.451 69.770 44.671 1.00 21.75 C
-ATOM 2405 CD2 LEU A 563 26.648 69.212 42.250 1.00 22.93 C
-ATOM 2406 N LEU A 564 26.811 64.093 43.974 1.00 29.23 N
-ATOM 2407 CA LEU A 564 27.559 62.900 44.397 1.00 31.91 C
-ATOM 2408 C LEU A 564 27.315 61.714 43.491 1.00 35.23 C
-ATOM 2409 O LEU A 564 28.247 61.058 43.050 1.00 32.79 O
-ATOM 2410 CB LEU A 564 27.168 62.494 45.813 1.00 32.34 C
-ATOM 2411 CG LEU A 564 27.562 63.461 46.928 1.00 34.96 C
-ATOM 2412 CD1 LEU A 564 26.772 63.131 48.192 1.00 36.57 C
-ATOM 2413 CD2 LEU A 564 29.066 63.382 47.175 1.00 33.93 C
-ATOM 2414 N GLU A 565 26.045 61.444 43.226 1.00 41.21 N
-ATOM 2415 CA GLU A 565 25.662 60.331 42.379 1.00 43.98 C
-ATOM 2416 C GLU A 565 26.297 60.450 40.998 1.00 42.31 C
-ATOM 2417 O GLU A 565 26.641 59.446 40.368 1.00 40.14 O
-ATOM 2418 CB GLU A 565 24.141 60.277 42.269 1.00 53.77 C
-ATOM 2419 CG GLU A 565 23.438 60.242 43.615 1.00 71.49 C
-ATOM 2420 CD GLU A 565 21.979 59.843 43.497 1.00 79.84 C
-ATOM 2421 OE1 GLU A 565 21.271 60.421 42.645 1.00 82.86 O
-ATOM 2422 OE2 GLU A 565 21.534 58.954 44.255 1.00 82.42 O
-ATOM 2423 N LYS A 566 26.452 61.673 40.515 1.00 36.96 N
-ATOM 2424 CA LYS A 566 27.060 61.842 39.210 1.00 31.68 C
-ATOM 2425 C LYS A 566 28.524 62.220 39.338 1.00 29.95 C
-ATOM 2426 O LYS A 566 29.136 62.631 38.353 1.00 28.56 O
-ATOM 2427 CB LYS A 566 26.323 62.893 38.392 1.00 31.04 C
-ATOM 2428 CG LYS A 566 24.925 62.485 37.981 1.00 30.61 C
-ATOM 2429 CD LYS A 566 24.327 63.544 37.087 1.00 31.63 C
-ATOM 2430 CE LYS A 566 22.877 63.258 36.792 1.00 33.25 C
-ATOM 2431 NZ LYS A 566 22.292 64.337 35.938 1.00 35.34 N
-ATOM 2432 N ARG A 567 29.075 62.081 40.545 1.00 30.03 N
-ATOM 2433 CA ARG A 567 30.488 62.388 40.815 1.00 30.85 C
-ATOM 2434 C ARG A 567 30.932 63.718 40.212 1.00 31.32 C
-ATOM 2435 O ARG A 567 31.908 63.750 39.449 1.00 32.60 O
-ATOM 2436 CB ARG A 567 31.381 61.302 40.226 1.00 32.09 C
-ATOM 2437 CG ARG A 567 30.977 59.883 40.536 1.00 31.59 C
-ATOM 2438 CD ARG A 567 31.911 58.949 39.808 1.00 32.17 C
-ATOM 2439 NE ARG A 567 31.823 57.572 40.279 1.00 33.38 N
-ATOM 2440 CZ ARG A 567 30.715 56.836 40.235 1.00 33.98 C
-ATOM 2441 NH1 ARG A 567 29.593 57.350 39.742 1.00 33.40 N
-ATOM 2442 NH2 ARG A 567 30.732 55.582 40.675 1.00 33.36 N
-ATOM 2443 N ILE A 568 30.245 64.808 40.550 1.00 30.01 N
-ATOM 2444 CA ILE A 568 30.600 66.095 39.971 1.00 27.25 C
-ATOM 2445 C ILE A 568 31.623 66.883 40.763 1.00 26.36 C
-ATOM 2446 O ILE A 568 32.595 67.372 40.194 1.00 27.51 O
-ATOM 2447 CB ILE A 568 29.344 66.954 39.738 1.00 25.59 C
-ATOM 2448 CG1 ILE A 568 28.507 66.327 38.611 1.00 21.14 C
-ATOM 2449 CG2 ILE A 568 29.738 68.401 39.397 1.00 21.19 C
-ATOM 2450 CD1 ILE A 568 27.170 66.997 38.418 1.00 19.81 C
-ATOM 2451 N ILE A 569 31.439 66.996 42.069 1.00 26.08 N
-ATOM 2452 CA ILE A 569 32.394 67.759 42.849 1.00 29.82 C
-ATOM 2453 C ILE A 569 33.780 67.118 43.037 1.00 32.11 C
-ATOM 2454 O ILE A 569 34.634 67.720 43.677 1.00 35.02 O
-ATOM 2455 CB ILE A 569 31.824 68.116 44.223 1.00 26.08 C
-ATOM 2456 CG1 ILE A 569 31.496 66.852 45.007 1.00 23.22 C
-ATOM 2457 CG2 ILE A 569 30.585 68.956 44.053 1.00 23.63 C
-ATOM 2458 CD1 ILE A 569 30.989 67.129 46.425 1.00 20.64 C
-ATOM 2459 N GLN A 570 34.009 65.916 42.495 1.00 34.80 N
-ATOM 2460 CA GLN A 570 35.312 65.250 42.607 1.00 34.89 C
-ATOM 2461 C GLN A 570 35.952 65.255 41.233 1.00 34.81 C
-ATOM 2462 O GLN A 570 37.078 64.777 41.054 1.00 35.33 O
-ATOM 2463 CB GLN A 570 35.179 63.787 43.030 1.00 36.00 C
-ATOM 2464 CG GLN A 570 34.200 63.498 44.139 1.00 41.20 C
-ATOM 2465 CD GLN A 570 32.929 62.864 43.613 1.00 41.01 C
-ATOM 2466 OE1 GLN A 570 31.943 63.550 43.345 1.00 40.67 O
-ATOM 2467 NE2 GLN A 570 32.955 61.549 43.441 1.00 39.97 N
-ATOM 2468 N SER A 571 35.224 65.782 40.255 1.00 32.92 N
-ATOM 2469 CA SER A 571 35.716 65.830 38.888 1.00 32.56 C
-ATOM 2470 C SER A 571 36.658 67.000 38.583 1.00 32.22 C
-ATOM 2471 O SER A 571 36.415 68.146 38.978 1.00 31.40 O
-ATOM 2472 CB SER A 571 34.537 65.879 37.924 1.00 33.26 C
-ATOM 2473 OG SER A 571 34.991 65.967 36.587 1.00 36.86 O
-ATOM 2474 N GLY A 572 37.738 66.706 37.869 1.00 30.49 N
-ATOM 2475 CA GLY A 572 38.665 67.757 37.495 1.00 28.33 C
-ATOM 2476 C GLY A 572 38.000 68.695 36.502 1.00 28.00 C
-ATOM 2477 O GLY A 572 38.429 69.832 36.307 1.00 25.21 O
-ATOM 2478 N ILE A 573 36.944 68.210 35.859 1.00 28.62 N
-ATOM 2479 CA ILE A 573 36.216 69.022 34.894 1.00 30.13 C
-ATOM 2480 C ILE A 573 35.486 70.155 35.610 1.00 28.00 C
-ATOM 2481 O ILE A 573 35.309 71.237 35.057 1.00 28.80 O
-ATOM 2482 CB ILE A 573 35.211 68.168 34.090 1.00 33.39 C
-ATOM 2483 CG1 ILE A 573 35.979 67.300 33.084 1.00 35.88 C
-ATOM 2484 CG2 ILE A 573 34.195 69.065 33.385 1.00 36.61 C
-ATOM 2485 CD1 ILE A 573 35.102 66.433 32.206 1.00 36.77 C
-ATOM 2486 N ALA A 574 35.067 69.907 36.844 1.00 23.30 N
-ATOM 2487 CA ALA A 574 34.382 70.943 37.598 1.00 19.88 C
-ATOM 2488 C ALA A 574 35.379 72.062 37.897 1.00 18.72 C
-ATOM 2489 O ALA A 574 34.998 73.233 37.973 1.00 16.48 O
-ATOM 2490 CB ALA A 574 33.795 70.363 38.894 1.00 15.66 C
-ATOM 2491 N LEU A 575 36.652 71.700 38.063 1.00 18.22 N
-ATOM 2492 CA LEU A 575 37.687 72.697 38.321 1.00 19.37 C
-ATOM 2493 C LEU A 575 38.075 73.440 37.034 1.00 20.92 C
-ATOM 2494 O LEU A 575 38.330 74.646 37.066 1.00 23.19 O
-ATOM 2495 CB LEU A 575 38.944 72.060 38.949 1.00 18.21 C
-ATOM 2496 CG LEU A 575 38.798 71.577 40.395 1.00 16.66 C
-ATOM 2497 CD1 LEU A 575 40.155 71.205 41.000 1.00 12.34 C
-ATOM 2498 CD2 LEU A 575 38.137 72.700 41.189 1.00 15.57 C
-ATOM 2499 N LEU A 576 38.133 72.740 35.905 1.00 23.59 N
-ATOM 2500 CA LEU A 576 38.478 73.434 34.676 1.00 28.14 C
-ATOM 2501 C LEU A 576 37.336 74.396 34.378 1.00 29.60 C
-ATOM 2502 O LEU A 576 37.551 75.524 33.927 1.00 30.40 O
-ATOM 2503 CB LEU A 576 38.666 72.461 33.507 1.00 30.69 C
-ATOM 2504 CG LEU A 576 39.033 73.131 32.167 1.00 33.82 C
-ATOM 2505 CD1 LEU A 576 40.246 74.034 32.349 1.00 35.33 C
-ATOM 2506 CD2 LEU A 576 39.313 72.073 31.111 1.00 35.40 C
-ATOM 2507 N LEU A 577 36.119 73.936 34.654 1.00 30.84 N
-ATOM 2508 CA LEU A 577 34.909 74.722 34.456 1.00 29.82 C
-ATOM 2509 C LEU A 577 34.907 75.991 35.314 1.00 27.81 C
-ATOM 2510 O LEU A 577 34.486 77.046 34.835 1.00 29.09 O
-ATOM 2511 CB LEU A 577 33.688 73.873 34.792 1.00 31.00 C
-ATOM 2512 CG LEU A 577 32.753 73.586 33.626 1.00 32.52 C
-ATOM 2513 CD1 LEU A 577 31.801 72.471 34.030 1.00 33.21 C
-ATOM 2514 CD2 LEU A 577 32.005 74.862 33.229 1.00 32.18 C
-ATOM 2515 N MET A 578 35.363 75.876 36.569 1.00 26.30 N
-ATOM 2516 CA MET A 578 35.444 77.004 37.506 1.00 26.32 C
-ATOM 2517 C MET A 578 36.415 78.051 36.947 1.00 27.55 C
-ATOM 2518 O MET A 578 36.116 79.262 36.898 1.00 31.15 O
-ATOM 2519 CB MET A 578 35.941 76.509 38.871 1.00 21.73 C
-ATOM 2520 CG MET A 578 36.187 77.590 39.945 1.00 13.18 C
-ATOM 2521 SD MET A 578 36.528 76.887 41.602 1.00 5.56 S
-ATOM 2522 CE MET A 578 38.121 76.967 41.546 1.00 9.41 C
-ATOM 2523 N LEU A 579 37.580 77.571 36.518 1.00 27.27 N
-ATOM 2524 CA LEU A 579 38.601 78.434 35.941 1.00 28.18 C
-ATOM 2525 C LEU A 579 38.023 79.249 34.782 1.00 28.12 C
-ATOM 2526 O LEU A 579 38.117 80.462 34.768 1.00 27.81 O
-ATOM 2527 CB LEU A 579 39.774 77.585 35.445 1.00 25.25 C
-ATOM 2528 CG LEU A 579 40.679 76.989 36.509 1.00 18.84 C
-ATOM 2529 CD1 LEU A 579 41.788 76.205 35.838 1.00 15.97 C
-ATOM 2530 CD2 LEU A 579 41.254 78.106 37.350 1.00 16.17 C
-ATOM 2531 N ILE A 580 37.435 78.550 33.815 1.00 27.08 N
-ATOM 2532 CA ILE A 580 36.815 79.149 32.636 1.00 25.62 C
-ATOM 2533 C ILE A 580 35.802 80.209 33.055 1.00 25.66 C
-ATOM 2534 O ILE A 580 35.665 81.244 32.405 1.00 22.40 O
-ATOM 2535 CB ILE A 580 36.042 78.073 31.800 1.00 27.92 C
-ATOM 2536 CG1 ILE A 580 37.020 77.094 31.152 1.00 28.62 C
-ATOM 2537 CG2 ILE A 580 35.184 78.748 30.726 1.00 28.40 C
-ATOM 2538 CD1 ILE A 580 36.353 76.031 30.329 1.00 27.85 C
-ATOM 2539 N TRP A 581 35.097 79.929 34.146 1.00 24.66 N
-ATOM 2540 CA TRP A 581 34.059 80.808 34.663 1.00 24.36 C
-ATOM 2541 C TRP A 581 34.578 81.996 35.454 1.00 24.88 C
-ATOM 2542 O TRP A 581 33.966 83.052 35.452 1.00 27.10 O
-ATOM 2543 CB TRP A 581 33.106 79.988 35.525 1.00 25.19 C
-ATOM 2544 CG TRP A 581 32.006 80.757 36.163 1.00 26.56 C
-ATOM 2545 CD1 TRP A 581 31.887 81.080 37.487 1.00 27.51 C
-ATOM 2546 CD2 TRP A 581 30.833 81.257 35.521 1.00 26.96 C
-ATOM 2547 NE1 TRP A 581 30.704 81.747 37.711 1.00 27.07 N
-ATOM 2548 CE2 TRP A 581 30.038 81.872 36.522 1.00 27.92 C
-ATOM 2549 CE3 TRP A 581 30.373 81.247 34.199 1.00 27.26 C
-ATOM 2550 CZ2 TRP A 581 28.803 82.468 36.238 1.00 27.55 C
-ATOM 2551 CZ3 TRP A 581 29.146 81.836 33.915 1.00 27.58 C
-ATOM 2552 CH2 TRP A 581 28.373 82.441 34.935 1.00 28.50 C
-ATOM 2553 N TYR A 582 35.706 81.831 36.134 1.00 25.46 N
-ATOM 2554 CA TYR A 582 36.254 82.919 36.925 1.00 24.01 C
-ATOM 2555 C TYR A 582 37.443 83.644 36.314 1.00 24.51 C
-ATOM 2556 O TYR A 582 37.492 84.862 36.273 1.00 25.82 O
-ATOM 2557 CB TYR A 582 36.684 82.395 38.294 1.00 20.52 C
-ATOM 2558 CG TYR A 582 35.587 82.312 39.316 1.00 18.62 C
-ATOM 2559 CD1 TYR A 582 34.873 81.128 39.509 1.00 17.95 C
-ATOM 2560 CD2 TYR A 582 35.251 83.428 40.088 1.00 17.36 C
-ATOM 2561 CE1 TYR A 582 33.839 81.052 40.447 1.00 16.47 C
-ATOM 2562 CE2 TYR A 582 34.224 83.370 41.032 1.00 17.82 C
-ATOM 2563 CZ TYR A 582 33.520 82.174 41.202 1.00 18.33 C
-ATOM 2564 OH TYR A 582 32.503 82.103 42.111 1.00 21.41 O
-ATOM 2565 N ARG A 583 38.417 82.873 35.862 1.00 27.33 N
-ATOM 2566 CA ARG A 583 39.670 83.398 35.331 1.00 27.02 C
-ATOM 2567 C ARG A 583 39.660 84.125 34.002 1.00 26.94 C
-ATOM 2568 O ARG A 583 38.897 83.788 33.085 1.00 27.10 O
-ATOM 2569 CB ARG A 583 40.695 82.261 35.283 1.00 26.13 C
-ATOM 2570 CG ARG A 583 40.994 81.753 36.661 1.00 24.98 C
-ATOM 2571 CD ARG A 583 41.722 82.848 37.368 1.00 26.55 C
-ATOM 2572 NE ARG A 583 41.536 82.857 38.809 1.00 27.71 N
-ATOM 2573 CZ ARG A 583 42.183 83.686 39.620 1.00 26.66 C
-ATOM 2574 NH1 ARG A 583 43.055 84.554 39.114 1.00 24.90 N
-ATOM 2575 NH2 ARG A 583 41.944 83.662 40.925 1.00 26.75 N
-ATOM 2576 N PRO A 584 40.528 85.145 33.887 1.00 28.80 N
-ATOM 2577 CA PRO A 584 40.688 85.975 32.687 1.00 29.47 C
-ATOM 2578 C PRO A 584 41.414 85.191 31.604 1.00 31.56 C
-ATOM 2579 O PRO A 584 42.400 84.512 31.874 1.00 31.06 O
-ATOM 2580 CB PRO A 584 41.487 87.175 33.199 1.00 27.82 C
-ATOM 2581 CG PRO A 584 42.270 86.603 34.347 1.00 25.32 C
-ATOM 2582 CD PRO A 584 41.285 85.702 35.022 1.00 26.93 C
-ATOM 2583 N VAL A 585 40.909 85.283 30.383 1.00 35.75 N
-ATOM 2584 CA VAL A 585 41.472 84.566 29.242 1.00 37.23 C
-ATOM 2585 C VAL A 585 42.999 84.584 29.060 1.00 36.27 C
-ATOM 2586 O VAL A 585 43.583 83.570 28.692 1.00 36.08 O
-ATOM 2587 CB VAL A 585 40.817 85.054 27.935 1.00 40.72 C
-ATOM 2588 CG1 VAL A 585 41.412 84.333 26.748 1.00 46.60 C
-ATOM 2589 CG2 VAL A 585 39.322 84.812 27.995 1.00 46.16 C
-ATOM 2590 N ALA A 586 43.651 85.718 29.305 1.00 34.65 N
-ATOM 2591 CA ALA A 586 45.101 85.796 29.123 1.00 32.54 C
-ATOM 2592 C ALA A 586 45.890 85.047 30.190 1.00 34.09 C
-ATOM 2593 O ALA A 586 47.113 84.964 30.125 1.00 34.63 O
-ATOM 2594 CB ALA A 586 45.538 87.236 29.094 1.00 27.83 C
-ATOM 2595 N GLU A 587 45.191 84.498 31.172 1.00 36.49 N
-ATOM 2596 CA GLU A 587 45.858 83.771 32.237 1.00 37.91 C
-ATOM 2597 C GLU A 587 46.138 82.349 31.751 1.00 38.18 C
-ATOM 2598 O GLU A 587 46.884 81.601 32.395 1.00 37.07 O
-ATOM 2599 CB GLU A 587 44.983 83.777 33.500 1.00 41.13 C
-ATOM 2600 CG GLU A 587 45.765 83.883 34.814 1.00 45.48 C
-ATOM 2601 CD GLU A 587 44.921 84.427 35.968 1.00 48.26 C
-ATOM 2602 OE1 GLU A 587 43.830 83.877 36.217 1.00 48.04 O
-ATOM 2603 OE2 GLU A 587 45.349 85.401 36.630 1.00 49.66 O
-ATOM 2604 N PHE A 588 45.535 81.989 30.611 1.00 37.92 N
-ATOM 2605 CA PHE A 588 45.735 80.676 29.986 1.00 36.59 C
-ATOM 2606 C PHE A 588 46.836 80.829 28.936 1.00 36.70 C
-ATOM 2607 O PHE A 588 47.228 81.949 28.602 1.00 39.31 O
-ATOM 2608 CB PHE A 588 44.463 80.178 29.278 1.00 35.11 C
-ATOM 2609 CG PHE A 588 43.308 79.904 30.197 1.00 33.37 C
-ATOM 2610 CD1 PHE A 588 42.505 80.935 30.647 1.00 33.60 C
-ATOM 2611 CD2 PHE A 588 43.028 78.607 30.614 1.00 35.16 C
-ATOM 2612 CE1 PHE A 588 41.439 80.688 31.497 1.00 33.35 C
-ATOM 2613 CE2 PHE A 588 41.962 78.345 31.469 1.00 34.59 C
-ATOM 2614 CZ PHE A 588 41.167 79.391 31.911 1.00 34.17 C
-ATOM 2615 N ALA A 589 47.332 79.712 28.414 1.00 39.83 N
-ATOM 2616 CA ALA A 589 48.378 79.748 27.390 1.00 43.14 C
-ATOM 2617 C ALA A 589 47.780 80.222 26.064 1.00 47.90 C
-ATOM 2618 O ALA A 589 46.649 79.867 25.729 1.00 47.33 O
-ATOM 2619 CB ALA A 589 49.006 78.355 27.221 1.00 41.05 C
-ATOM 2620 N GLN A 590 48.539 81.020 25.316 1.00 53.41 N
-ATOM 2621 CA GLN A 590 48.071 81.540 24.038 1.00 56.42 C
-ATOM 2622 C GLN A 590 47.367 80.463 23.229 1.00 54.51 C
-ATOM 2623 O GLN A 590 46.179 80.561 22.933 1.00 51.00 O
-ATOM 2624 CB GLN A 590 49.241 82.116 23.241 1.00 66.29 C
-ATOM 2625 CG GLN A 590 48.905 82.420 21.796 1.00 84.97 C
-ATOM 2626 CD GLN A 590 49.975 83.245 21.111 1.00 93.82 C
-ATOM 2627 OE1 GLN A 590 51.172 83.003 21.286 1.00 96.71 O
-ATOM 2628 NE2 GLN A 590 49.550 84.222 20.313 1.00 96.36 N
-ATOM 2629 N SER A 591 48.111 79.429 22.881 1.00 48.00 N
-ATOM 2630 CA SER A 591 47.584 78.313 22.120 1.00 41.22 C
-ATOM 2631 C SER A 591 46.155 77.899 22.462 1.00 38.84 C
-ATOM 2632 O SER A 591 45.393 77.583 21.569 1.00 35.43 O
-ATOM 2633 CB SER A 591 48.506 77.104 22.299 1.00 41.77 C
-ATOM 2634 OG SER A 591 47.896 75.917 21.826 1.00 49.39 O
-ATOM 2635 N ILE A 592 45.784 77.902 23.740 1.00 36.38 N
-ATOM 2636 CA ILE A 592 44.446 77.456 24.143 1.00 34.42 C
-ATOM 2637 C ILE A 592 43.332 78.504 24.318 1.00 34.84 C
-ATOM 2638 O ILE A 592 42.131 78.157 24.349 1.00 34.41 O
-ATOM 2639 CB ILE A 592 44.538 76.592 25.439 1.00 36.98 C
-ATOM 2640 CG1 ILE A 592 44.225 75.137 25.092 1.00 40.69 C
-ATOM 2641 CG2 ILE A 592 43.596 77.099 26.513 1.00 39.89 C
-ATOM 2642 CD1 ILE A 592 44.065 74.234 26.298 1.00 43.91 C
-ATOM 2643 N GLN A 593 43.724 79.773 24.420 1.00 34.78 N
-ATOM 2644 CA GLN A 593 42.779 80.874 24.612 1.00 35.22 C
-ATOM 2645 C GLN A 593 41.567 80.919 23.671 1.00 38.22 C
-ATOM 2646 O GLN A 593 40.448 81.185 24.113 1.00 35.60 O
-ATOM 2647 CB GLN A 593 43.546 82.191 24.571 1.00 31.57 C
-ATOM 2648 CG GLN A 593 44.330 82.411 25.849 1.00 31.00 C
-ATOM 2649 CD GLN A 593 45.340 83.529 25.763 1.00 28.03 C
-ATOM 2650 OE1 GLN A 593 45.091 84.558 25.145 1.00 29.68 O
-ATOM 2651 NE2 GLN A 593 46.483 83.340 26.408 1.00 27.12 N
-ATOM 2652 N SER A 594 41.787 80.648 22.387 1.00 44.66 N
-ATOM 2653 CA SER A 594 40.711 80.647 21.394 1.00 48.05 C
-ATOM 2654 C SER A 594 39.621 79.661 21.806 1.00 46.69 C
-ATOM 2655 O SER A 594 38.425 79.912 21.627 1.00 45.12 O
-ATOM 2656 CB SER A 594 41.251 80.242 20.013 1.00 53.17 C
-ATOM 2657 OG SER A 594 42.339 81.059 19.614 1.00 67.56 O
-ATOM 2658 N ARG A 595 40.043 78.532 22.361 1.00 44.53 N
-ATOM 2659 CA ARG A 595 39.100 77.516 22.782 1.00 41.48 C
-ATOM 2660 C ARG A 595 38.449 77.910 24.108 1.00 38.75 C
-ATOM 2661 O ARG A 595 37.300 77.565 24.379 1.00 40.07 O
-ATOM 2662 CB ARG A 595 39.820 76.177 22.901 1.00 40.52 C
-ATOM 2663 CG ARG A 595 38.916 74.972 22.734 1.00 39.90 C
-ATOM 2664 CD ARG A 595 39.714 73.678 22.555 1.00 39.79 C
-ATOM 2665 NE ARG A 595 38.842 72.512 22.702 1.00 40.19 N
-ATOM 2666 CZ ARG A 595 39.256 71.251 22.661 1.00 39.91 C
-ATOM 2667 NH1 ARG A 595 40.542 70.978 22.474 1.00 39.38 N
-ATOM 2668 NH2 ARG A 595 38.383 70.265 22.821 1.00 39.87 N
-ATOM 2669 N ILE A 596 39.174 78.651 24.932 1.00 36.72 N
-ATOM 2670 CA ILE A 596 38.616 79.070 26.207 1.00 35.68 C
-ATOM 2671 C ILE A 596 37.556 80.162 26.029 1.00 34.31 C
-ATOM 2672 O ILE A 596 36.470 80.067 26.591 1.00 35.99 O
-ATOM 2673 CB ILE A 596 39.728 79.563 27.167 1.00 31.62 C
-ATOM 2674 CG1 ILE A 596 40.638 78.387 27.541 1.00 26.32 C
-ATOM 2675 CG2 ILE A 596 39.113 80.167 28.432 1.00 25.66 C
-ATOM 2676 CD1 ILE A 596 39.931 77.246 28.261 1.00 22.06 C
-ATOM 2677 N VAL A 597 37.871 81.194 25.249 1.00 33.55 N
-ATOM 2678 CA VAL A 597 36.923 82.283 25.010 1.00 36.20 C
-ATOM 2679 C VAL A 597 35.633 81.684 24.490 1.00 40.37 C
-ATOM 2680 O VAL A 597 34.534 82.155 24.794 1.00 39.19 O
-ATOM 2681 CB VAL A 597 37.443 83.290 23.940 1.00 31.54 C
-ATOM 2682 CG1 VAL A 597 36.335 84.274 23.569 1.00 24.61 C
-ATOM 2683 CG2 VAL A 597 38.680 84.035 24.467 1.00 26.58 C
-ATOM 2684 N GLU A 598 35.794 80.631 23.699 1.00 45.55 N
-ATOM 2685 CA GLU A 598 34.682 79.915 23.085 1.00 48.25 C
-ATOM 2686 C GLU A 598 33.768 79.297 24.148 1.00 46.04 C
-ATOM 2687 O GLU A 598 32.546 79.287 23.993 1.00 41.56 O
-ATOM 2688 CB GLU A 598 35.255 78.838 22.168 1.00 57.33 C
-ATOM 2689 CG GLU A 598 34.370 78.382 21.041 1.00 73.73 C
-ATOM 2690 CD GLU A 598 35.137 77.507 20.070 1.00 82.03 C
-ATOM 2691 OE1 GLU A 598 36.109 78.006 19.464 1.00 84.79 O
-ATOM 2692 OE2 GLU A 598 34.782 76.320 19.917 1.00 85.58 O
-ATOM 2693 N TRP A 599 34.362 78.785 25.226 1.00 42.85 N
-ATOM 2694 CA TRP A 599 33.579 78.186 26.308 1.00 38.81 C
-ATOM 2695 C TRP A 599 32.967 79.237 27.223 1.00 37.56 C
-ATOM 2696 O TRP A 599 31.867 79.042 27.738 1.00 39.66 O
-ATOM 2697 CB TRP A 599 34.432 77.233 27.148 1.00 35.24 C
-ATOM 2698 CG TRP A 599 34.335 75.809 26.707 1.00 33.45 C
-ATOM 2699 CD1 TRP A 599 35.197 75.139 25.890 1.00 31.98 C
-ATOM 2700 CD2 TRP A 599 33.269 74.895 27.000 1.00 31.36 C
-ATOM 2701 NE1 TRP A 599 34.733 73.867 25.657 1.00 32.33 N
-ATOM 2702 CE2 TRP A 599 33.552 73.691 26.330 1.00 30.39 C
-ATOM 2703 CE3 TRP A 599 32.106 74.980 27.777 1.00 31.68 C
-ATOM 2704 CZ2 TRP A 599 32.709 72.581 26.390 1.00 29.61 C
-ATOM 2705 CZ3 TRP A 599 31.264 73.867 27.838 1.00 32.24 C
-ATOM 2706 CH2 TRP A 599 31.577 72.685 27.152 1.00 30.62 C
-ATOM 2707 N LYS A 600 33.688 80.338 27.437 1.00 39.23 N
-ATOM 2708 CA LYS A 600 33.203 81.432 28.282 1.00 42.83 C
-ATOM 2709 C LYS A 600 31.910 81.962 27.687 1.00 46.95 C
-ATOM 2710 O LYS A 600 30.915 82.152 28.395 1.00 47.83 O
-ATOM 2711 CB LYS A 600 34.226 82.568 28.347 1.00 41.74 C
-ATOM 2712 CG LYS A 600 35.355 82.326 29.308 1.00 39.47 C
-ATOM 2713 CD LYS A 600 36.473 83.331 29.110 1.00 37.46 C
-ATOM 2714 CE LYS A 600 37.545 83.143 30.172 1.00 38.36 C
-ATOM 2715 NZ LYS A 600 36.987 83.344 31.548 1.00 38.25 N
-ATOM 2716 N GLU A 601 31.939 82.210 26.379 1.00 49.49 N
-ATOM 2717 CA GLU A 601 30.770 82.693 25.675 1.00 48.89 C
-ATOM 2718 C GLU A 601 29.634 81.711 25.921 1.00 46.57 C
-ATOM 2719 O GLU A 601 28.566 82.092 26.398 1.00 43.63 O
-ATOM 2720 CB GLU A 601 31.072 82.805 24.182 1.00 53.59 C
-ATOM 2721 CG GLU A 601 31.778 84.100 23.811 1.00 65.00 C
-ATOM 2722 CD GLU A 601 32.285 84.127 22.375 1.00 70.52 C
-ATOM 2723 OE1 GLU A 601 31.541 83.708 21.453 1.00 72.89 O
-ATOM 2724 OE2 GLU A 601 33.433 84.583 22.173 1.00 72.11 O
-ATOM 2725 N ARG A 602 29.876 80.441 25.610 1.00 43.42 N
-ATOM 2726 CA ARG A 602 28.868 79.406 25.807 1.00 40.54 C
-ATOM 2727 C ARG A 602 28.247 79.632 27.184 1.00 38.64 C
-ATOM 2728 O ARG A 602 27.058 79.918 27.306 1.00 41.31 O
-ATOM 2729 CB ARG A 602 29.526 78.015 25.736 1.00 38.20 C
-ATOM 2730 CG ARG A 602 28.588 76.841 25.406 1.00 33.40 C
-ATOM 2731 CD ARG A 602 27.815 76.343 26.610 1.00 32.51 C
-ATOM 2732 NE ARG A 602 26.890 75.262 26.267 1.00 33.65 N
-ATOM 2733 CZ ARG A 602 27.253 74.090 25.752 1.00 32.11 C
-ATOM 2734 NH1 ARG A 602 28.528 73.825 25.505 1.00 32.37 N
-ATOM 2735 NH2 ARG A 602 26.336 73.171 25.499 1.00 32.57 N
-ATOM 2736 N LEU A 603 29.076 79.526 28.215 1.00 39.29 N
-ATOM 2737 CA LEU A 603 28.631 79.704 29.585 1.00 42.77 C
-ATOM 2738 C LEU A 603 27.896 81.008 29.816 1.00 49.18 C
-ATOM 2739 O LEU A 603 26.808 81.013 30.386 1.00 49.13 O
-ATOM 2740 CB LEU A 603 29.821 79.629 30.532 1.00 37.61 C
-ATOM 2741 CG LEU A 603 30.094 78.300 31.235 1.00 31.25 C
-ATOM 2742 CD1 LEU A 603 29.483 77.143 30.472 1.00 26.77 C
-ATOM 2743 CD2 LEU A 603 31.599 78.130 31.385 1.00 26.71 C
-ATOM 2744 N ASP A 604 28.487 82.114 29.382 1.00 56.19 N
-ATOM 2745 CA ASP A 604 27.860 83.414 29.581 1.00 59.09 C
-ATOM 2746 C ASP A 604 26.483 83.500 28.955 1.00 58.67 C
-ATOM 2747 O ASP A 604 25.570 84.103 29.526 1.00 52.52 O
-ATOM 2748 CB ASP A 604 28.755 84.533 29.051 1.00 69.55 C
-ATOM 2749 CG ASP A 604 29.865 84.903 30.029 1.00 85.72 C
-ATOM 2750 OD1 ASP A 604 29.542 85.264 31.187 1.00 95.13 O
-ATOM 2751 OD2 ASP A 604 31.056 84.835 29.645 1.00 94.11 O
-ATOM 2752 N LYS A 605 26.325 82.866 27.801 1.00 57.42 N
-ATOM 2753 CA LYS A 605 25.056 82.863 27.083 1.00 57.77 C
-ATOM 2754 C LYS A 605 23.979 81.994 27.754 1.00 57.98 C
-ATOM 2755 O LYS A 605 22.831 82.000 27.334 1.00 54.85 O
-ATOM 2756 CB LYS A 605 25.306 82.395 25.638 1.00 65.08 C
-ATOM 2757 CG LYS A 605 24.066 82.186 24.782 1.00 79.80 C
-ATOM 2758 CD LYS A 605 24.438 81.656 23.399 1.00 86.48 C
-ATOM 2759 CE LYS A 605 23.212 81.162 22.622 1.00 88.26 C
-ATOM 2760 NZ LYS A 605 22.581 79.939 23.222 1.00 87.98 N
-ATOM 2761 N GLU A 606 24.338 81.275 28.811 1.00 55.10 N
-ATOM 2762 CA GLU A 606 23.391 80.383 29.490 1.00 48.33 C
-ATOM 2763 C GLU A 606 23.189 80.657 30.965 1.00 42.25 C
-ATOM 2764 O GLU A 606 22.206 80.219 31.561 1.00 33.08 O
-ATOM 2765 CB GLU A 606 23.843 78.929 29.382 1.00 54.95 C
-ATOM 2766 CG GLU A 606 23.339 78.161 28.194 1.00 73.48 C
-ATOM 2767 CD GLU A 606 23.512 76.669 28.400 1.00 82.09 C
-ATOM 2768 OE1 GLU A 606 22.845 76.127 29.310 1.00 84.95 O
-ATOM 2769 OE2 GLU A 606 24.320 76.045 27.670 1.00 85.05 O
-ATOM 2770 N PHE A 607 24.141 81.344 31.571 1.00 35.19 N
-ATOM 2771 CA PHE A 607 24.028 81.625 32.985 1.00 29.64 C
-ATOM 2772 C PHE A 607 24.369 83.063 33.272 1.00 27.29 C
-ATOM 2773 O PHE A 607 25.403 83.577 32.837 1.00 28.17 O
-ATOM 2774 CB PHE A 607 24.970 80.726 33.793 1.00 28.55 C
-ATOM 2775 CG PHE A 607 24.757 79.268 33.571 1.00 24.92 C
-ATOM 2776 CD1 PHE A 607 25.456 78.596 32.579 1.00 24.35 C
-ATOM 2777 CD2 PHE A 607 23.835 78.570 34.337 1.00 23.12 C
-ATOM 2778 CE1 PHE A 607 25.228 77.235 32.358 1.00 25.72 C
-ATOM 2779 CE2 PHE A 607 23.604 77.222 34.124 1.00 23.34 C
-ATOM 2780 CZ PHE A 607 24.293 76.552 33.138 1.00 23.51 C
-ATOM 2781 N SER A 608 23.484 83.716 34.004 1.00 25.52 N
-ATOM 2782 CA SER A 608 23.723 85.097 34.376 1.00 24.81 C
-ATOM 2783 C SER A 608 24.430 85.047 35.720 1.00 26.75 C
-ATOM 2784 O SER A 608 24.391 84.042 36.433 1.00 21.04 O
-ATOM 2785 CB SER A 608 22.408 85.874 34.524 1.00 22.92 C
-ATOM 2786 OG SER A 608 21.711 85.460 35.682 1.00 22.36 O
-ATOM 2787 N LEU A 609 25.094 86.134 36.057 1.00 28.31 N
-ATOM 2788 CA LEU A 609 25.760 86.189 37.326 1.00 28.84 C
-ATOM 2789 C LEU A 609 24.780 85.995 38.461 1.00 26.62 C
-ATOM 2790 O LEU A 609 25.089 85.275 39.400 1.00 26.74 O
-ATOM 2791 CB LEU A 609 26.477 87.520 37.502 1.00 37.70 C
-ATOM 2792 CG LEU A 609 27.982 87.385 37.329 1.00 47.31 C
-ATOM 2793 CD1 LEU A 609 28.643 88.732 37.485 1.00 53.39 C
-ATOM 2794 CD2 LEU A 609 28.503 86.403 38.364 1.00 52.23 C
-ATOM 2795 N SER A 610 23.594 86.597 38.389 1.00 23.81 N
-ATOM 2796 CA SER A 610 22.669 86.441 39.511 1.00 22.92 C
-ATOM 2797 C SER A 610 22.212 84.994 39.704 1.00 21.40 C
-ATOM 2798 O SER A 610 21.977 84.562 40.836 1.00 21.25 O
-ATOM 2799 CB SER A 610 21.466 87.395 39.394 1.00 23.10 C
-ATOM 2800 OG SER A 610 20.607 87.042 38.331 1.00 27.62 O
-ATOM 2801 N VAL A 611 22.112 84.239 38.611 1.00 20.11 N
-ATOM 2802 CA VAL A 611 21.703 82.843 38.692 1.00 19.36 C
-ATOM 2803 C VAL A 611 22.791 82.037 39.413 1.00 19.17 C
-ATOM 2804 O VAL A 611 22.500 81.299 40.366 1.00 21.78 O
-ATOM 2805 CB VAL A 611 21.435 82.266 37.271 1.00 17.03 C
-ATOM 2806 CG1 VAL A 611 21.189 80.762 37.306 1.00 10.43 C
-ATOM 2807 CG2 VAL A 611 20.219 82.949 36.685 1.00 13.05 C
-ATOM 2808 N TYR A 612 24.036 82.178 38.964 1.00 18.86 N
-ATOM 2809 CA TYR A 612 25.146 81.471 39.591 1.00 21.47 C
-ATOM 2810 C TYR A 612 25.282 81.926 41.031 1.00 24.38 C
-ATOM 2811 O TYR A 612 25.589 81.127 41.920 1.00 22.30 O
-ATOM 2812 CB TYR A 612 26.458 81.755 38.865 1.00 20.33 C
-ATOM 2813 CG TYR A 612 27.680 81.268 39.610 1.00 16.74 C
-ATOM 2814 CD1 TYR A 612 28.014 79.919 39.630 1.00 16.03 C
-ATOM 2815 CD2 TYR A 612 28.499 82.155 40.291 1.00 16.43 C
-ATOM 2816 CE1 TYR A 612 29.148 79.447 40.315 1.00 16.15 C
-ATOM 2817 CE2 TYR A 612 29.631 81.709 40.986 1.00 18.51 C
-ATOM 2818 CZ TYR A 612 29.957 80.347 40.991 1.00 18.39 C
-ATOM 2819 OH TYR A 612 31.083 79.904 41.662 1.00 13.95 O
-ATOM 2820 N GLN A 613 25.072 83.220 41.248 1.00 25.82 N
-ATOM 2821 CA GLN A 613 25.149 83.791 42.583 1.00 28.59 C
-ATOM 2822 C GLN A 613 24.105 83.187 43.520 1.00 28.92 C
-ATOM 2823 O GLN A 613 24.356 83.029 44.706 1.00 24.28 O
-ATOM 2824 CB GLN A 613 24.952 85.300 42.533 1.00 35.32 C
-ATOM 2825 CG GLN A 613 26.248 86.055 42.541 1.00 48.52 C
-ATOM 2826 CD GLN A 613 27.222 85.443 43.506 1.00 54.26 C
-ATOM 2827 OE1 GLN A 613 26.846 85.070 44.619 1.00 58.23 O
-ATOM 2828 NE2 GLN A 613 28.480 85.328 43.094 1.00 55.22 N
-ATOM 2829 N LYS A 614 22.932 82.860 42.989 1.00 27.33 N
-ATOM 2830 CA LYS A 614 21.881 82.266 43.795 1.00 23.98 C
-ATOM 2831 C LYS A 614 22.275 80.855 44.197 1.00 20.88 C
-ATOM 2832 O LYS A 614 21.999 80.438 45.316 1.00 18.07 O
-ATOM 2833 CB LYS A 614 20.558 82.247 43.027 1.00 28.47 C
-ATOM 2834 CG LYS A 614 19.354 81.813 43.871 1.00 37.11 C
-ATOM 2835 CD LYS A 614 18.047 82.294 43.231 1.00 42.35 C
-ATOM 2836 CE LYS A 614 16.822 81.630 43.847 1.00 43.48 C
-ATOM 2837 NZ LYS A 614 16.781 80.164 43.532 1.00 44.05 N
-ATOM 2838 N MET A 615 22.914 80.119 43.289 1.00 18.29 N
-ATOM 2839 CA MET A 615 23.349 78.764 43.606 1.00 16.56 C
-ATOM 2840 C MET A 615 24.278 78.795 44.843 1.00 16.45 C
-ATOM 2841 O MET A 615 24.102 78.015 45.797 1.00 15.06 O
-ATOM 2842 CB MET A 615 24.077 78.134 42.406 1.00 14.76 C
-ATOM 2843 CG MET A 615 23.249 78.064 41.100 1.00 13.78 C
-ATOM 2844 SD MET A 615 23.998 77.183 39.622 1.00 9.75 S
-ATOM 2845 CE MET A 615 25.642 77.410 39.893 1.00 10.37 C
-ATOM 2846 N LYS A 616 25.247 79.712 44.838 1.00 19.52 N
-ATOM 2847 CA LYS A 616 26.177 79.837 45.957 1.00 21.30 C
-ATOM 2848 C LYS A 616 25.424 80.166 47.232 1.00 22.53 C
-ATOM 2849 O LYS A 616 25.790 79.709 48.313 1.00 23.38 O
-ATOM 2850 CB LYS A 616 27.217 80.923 45.678 1.00 21.04 C
-ATOM 2851 CG LYS A 616 28.231 80.563 44.577 1.00 20.90 C
-ATOM 2852 CD LYS A 616 29.512 81.404 44.706 1.00 20.31 C
-ATOM 2853 CE LYS A 616 30.320 80.990 45.945 1.00 21.79 C
-ATOM 2854 NZ LYS A 616 31.278 82.030 46.418 1.00 19.43 N
-ATOM 2855 N PHE A 617 24.363 80.957 47.097 1.00 24.76 N
-ATOM 2856 CA PHE A 617 23.537 81.348 48.238 1.00 26.40 C
-ATOM 2857 C PHE A 617 22.796 80.127 48.770 1.00 25.96 C
-ATOM 2858 O PHE A 617 22.663 79.931 49.980 1.00 25.12 O
-ATOM 2859 CB PHE A 617 22.519 82.413 47.823 1.00 29.39 C
-ATOM 2860 CG PHE A 617 21.526 82.758 48.900 1.00 34.26 C
-ATOM 2861 CD1 PHE A 617 21.832 83.705 49.871 1.00 33.58 C
-ATOM 2862 CD2 PHE A 617 20.281 82.121 48.948 1.00 36.63 C
-ATOM 2863 CE1 PHE A 617 20.914 84.019 50.879 1.00 35.37 C
-ATOM 2864 CE2 PHE A 617 19.355 82.424 49.950 1.00 36.25 C
-ATOM 2865 CZ PHE A 617 19.671 83.376 50.919 1.00 36.19 C
-ATOM 2866 N ASN A 618 22.306 79.301 47.853 1.00 27.23 N
-ATOM 2867 CA ASN A 618 21.587 78.097 48.245 1.00 27.67 C
-ATOM 2868 C ASN A 618 22.514 77.156 49.023 1.00 27.35 C
-ATOM 2869 O ASN A 618 22.105 76.587 50.029 1.00 28.30 O
-ATOM 2870 CB ASN A 618 20.964 77.405 47.009 1.00 24.46 C
-ATOM 2871 CG ASN A 618 19.785 78.201 46.419 1.00 21.11 C
-ATOM 2872 OD1 ASN A 618 19.173 79.036 47.100 1.00 19.68 O
-ATOM 2873 ND2 ASN A 618 19.466 77.939 45.157 1.00 19.80 N
-ATOM 2874 N VAL A 619 23.757 77.003 48.567 1.00 28.91 N
-ATOM 2875 CA VAL A 619 24.722 76.154 49.274 1.00 30.25 C
-ATOM 2876 C VAL A 619 24.951 76.706 50.678 1.00 30.14 C
-ATOM 2877 O VAL A 619 24.969 75.963 51.652 1.00 32.11 O
-ATOM 2878 CB VAL A 619 26.090 76.117 48.570 1.00 28.56 C
-ATOM 2879 CG1 VAL A 619 27.103 75.463 49.463 1.00 25.83 C
-ATOM 2880 CG2 VAL A 619 25.990 75.352 47.265 1.00 25.43 C
-ATOM 2881 N ALA A 620 25.135 78.017 50.770 1.00 32.43 N
-ATOM 2882 CA ALA A 620 25.347 78.669 52.057 1.00 34.47 C
-ATOM 2883 C ALA A 620 24.223 78.326 53.039 1.00 34.97 C
-ATOM 2884 O ALA A 620 24.475 78.025 54.209 1.00 39.08 O
-ATOM 2885 CB ALA A 620 25.432 80.177 51.866 1.00 32.79 C
-ATOM 2886 N MET A 621 22.983 78.383 52.559 1.00 34.89 N
-ATOM 2887 CA MET A 621 21.817 78.066 53.381 1.00 34.57 C
-ATOM 2888 C MET A 621 21.591 76.547 53.482 1.00 35.45 C
-ATOM 2889 O MET A 621 20.667 76.098 54.159 1.00 34.35 O
-ATOM 2890 CB MET A 621 20.575 78.715 52.773 1.00 33.54 C
-ATOM 2891 CG MET A 621 20.609 80.226 52.751 1.00 29.11 C
-ATOM 2892 SD MET A 621 20.573 80.916 54.408 1.00 28.26 S
-ATOM 2893 CE MET A 621 22.237 81.591 54.585 1.00 27.21 C
-ATOM 2894 N GLY A 622 22.443 75.777 52.799 1.00 35.73 N
-ATOM 2895 CA GLY A 622 22.332 74.327 52.782 1.00 33.53 C
-ATOM 2896 C GLY A 622 20.992 73.815 52.283 1.00 31.98 C
-ATOM 2897 O GLY A 622 20.355 73.045 52.986 1.00 32.22 O
-ATOM 2898 N ILE A 623 20.566 74.197 51.078 1.00 30.07 N
-ATOM 2899 CA ILE A 623 19.267 73.741 50.591 1.00 32.89 C
-ATOM 2900 C ILE A 623 19.139 73.076 49.217 1.00 33.69 C
-ATOM 2901 O ILE A 623 18.151 72.369 48.954 1.00 36.79 O
-ATOM 2902 CB ILE A 623 18.232 74.874 50.621 1.00 30.24 C
-ATOM 2903 CG1 ILE A 623 18.709 76.044 49.759 1.00 29.79 C
-ATOM 2904 CG2 ILE A 623 17.976 75.291 52.059 1.00 27.93 C
-ATOM 2905 CD1 ILE A 623 17.661 77.097 49.506 1.00 27.29 C
-ATOM 2906 N GLY A 624 20.099 73.272 48.331 1.00 34.27 N
-ATOM 2907 CA GLY A 624 19.954 72.640 47.032 1.00 34.32 C
-ATOM 2908 C GLY A 624 20.329 73.669 46.002 1.00 34.23 C
-ATOM 2909 O GLY A 624 19.533 74.527 45.631 1.00 32.29 O
-ATOM 2910 N VAL A 625 21.570 73.585 45.550 1.00 33.64 N
-ATOM 2911 CA VAL A 625 22.085 74.525 44.586 1.00 33.38 C
-ATOM 2912 C VAL A 625 21.007 74.965 43.604 1.00 33.30 C
-ATOM 2913 O VAL A 625 20.843 76.153 43.347 1.00 35.04 O
-ATOM 2914 CB VAL A 625 23.272 73.912 43.816 1.00 32.55 C
-ATOM 2915 CG1 VAL A 625 24.097 75.018 43.168 1.00 29.70 C
-ATOM 2916 CG2 VAL A 625 24.123 73.095 44.756 1.00 30.89 C
-ATOM 2917 N LEU A 626 20.241 74.010 43.094 1.00 34.40 N
-ATOM 2918 CA LEU A 626 19.212 74.312 42.108 1.00 35.68 C
-ATOM 2919 C LEU A 626 17.853 74.797 42.581 1.00 38.46 C
-ATOM 2920 O LEU A 626 16.930 74.916 41.776 1.00 39.06 O
-ATOM 2921 CB LEU A 626 19.007 73.110 41.198 1.00 31.73 C
-ATOM 2922 CG LEU A 626 20.280 72.622 40.524 1.00 28.36 C
-ATOM 2923 CD1 LEU A 626 19.894 71.560 39.502 1.00 25.73 C
-ATOM 2924 CD2 LEU A 626 21.015 73.799 39.877 1.00 24.32 C
-ATOM 2925 N ASP A 627 17.701 75.077 43.867 1.00 44.95 N
-ATOM 2926 CA ASP A 627 16.412 75.576 44.321 1.00 50.87 C
-ATOM 2927 C ASP A 627 16.258 77.032 43.872 1.00 53.87 C
-ATOM 2928 O ASP A 627 17.278 77.659 43.480 1.00 55.14 O
-ATOM 2929 CB ASP A 627 16.288 75.481 45.846 1.00 53.95 C
-ATOM 2930 CG ASP A 627 16.030 74.064 46.321 1.00 57.53 C
-ATOM 2931 OD1 ASP A 627 15.698 73.194 45.483 1.00 57.84 O
-ATOM 2932 OD2 ASP A 627 16.149 73.819 47.537 1.00 59.41 O
-ATOM 2933 OXT ASP A 627 15.113 77.534 43.922 1.00 56.88 O
-TER 2934 ASP A 627
-ATOM 2935 N LYS B 266 59.471 52.275 -0.025 1.00 86.31 N
-ATOM 2936 CA LYS B 266 60.374 51.550 -0.960 1.00 84.38 C
-ATOM 2937 C LYS B 266 61.457 50.774 -0.231 1.00 86.62 C
-ATOM 2938 O LYS B 266 61.270 49.602 0.109 1.00 85.27 O
-ATOM 2939 CB LYS B 266 61.018 52.529 -1.947 1.00 84.51 C
-ATOM 2940 CG LYS B 266 60.035 53.072 -2.968 1.00 80.32 C
-ATOM 2941 CD LYS B 266 59.411 51.944 -3.789 1.00 77.55 C
-ATOM 2942 CE LYS B 266 58.226 52.441 -4.597 1.00 76.34 C
-ATOM 2943 NZ LYS B 266 57.670 51.378 -5.469 1.00 76.10 N
-ATOM 2944 N GLN B 267 62.588 51.426 0.010 1.00 81.43 N
-ATOM 2945 CA GLN B 267 63.691 50.771 0.694 1.00 75.99 C
-ATOM 2946 C GLN B 267 64.351 51.732 1.678 1.00 72.16 C
-ATOM 2947 O GLN B 267 65.257 52.473 1.311 1.00 64.47 O
-ATOM 2948 CB GLN B 267 64.712 50.276 -0.340 1.00 79.72 C
-ATOM 2949 CG GLN B 267 65.760 49.321 0.206 1.00 90.15 C
-ATOM 2950 CD GLN B 267 65.151 48.081 0.831 1.00 94.61 C
-ATOM 2951 OE1 GLN B 267 64.548 47.249 0.147 1.00 95.63 O
-ATOM 2952 NE2 GLN B 267 65.303 47.954 2.144 1.00 96.24 N
-ATOM 2953 N VAL B 268 63.894 51.726 2.927 1.00 62.73 N
-ATOM 2954 CA VAL B 268 64.466 52.610 3.941 1.00 55.47 C
-ATOM 2955 C VAL B 268 65.918 52.276 4.259 1.00 52.02 C
-ATOM 2956 O VAL B 268 66.355 51.130 4.146 1.00 49.07 O
-ATOM 2957 CB VAL B 268 63.686 52.556 5.270 1.00 56.78 C
-ATOM 2958 CG1 VAL B 268 64.198 53.633 6.216 1.00 60.42 C
-ATOM 2959 CG2 VAL B 268 62.211 52.747 5.014 1.00 62.50 C
-ATOM 2960 N SER B 269 66.659 53.294 4.670 1.00 46.97 N
-ATOM 2961 CA SER B 269 68.059 53.128 5.010 1.00 43.00 C
-ATOM 2962 C SER B 269 68.184 52.901 6.505 1.00 41.62 C
-ATOM 2963 O SER B 269 67.874 53.788 7.302 1.00 44.05 O
-ATOM 2964 CB SER B 269 68.854 54.375 4.617 1.00 40.42 C
-ATOM 2965 OG SER B 269 70.214 54.240 4.990 1.00 36.78 O
-ATOM 2966 N TRP B 270 68.620 51.709 6.888 1.00 39.70 N
-ATOM 2967 CA TRP B 270 68.790 51.405 8.296 1.00 40.19 C
-ATOM 2968 C TRP B 270 70.035 52.136 8.797 1.00 42.41 C
-ATOM 2969 O TRP B 270 70.124 52.488 9.974 1.00 43.04 O
-ATOM 2970 CB TRP B 270 68.957 49.897 8.490 1.00 36.44 C
-ATOM 2971 CG TRP B 270 67.717 49.116 8.179 1.00 32.82 C
-ATOM 2972 CD1 TRP B 270 66.843 49.350 7.162 1.00 28.94 C
-ATOM 2973 CD2 TRP B 270 67.199 47.982 8.902 1.00 30.98 C
-ATOM 2974 NE1 TRP B 270 65.811 48.440 7.205 1.00 28.11 N
-ATOM 2975 CE2 TRP B 270 66.002 47.590 8.261 1.00 27.79 C
-ATOM 2976 CE3 TRP B 270 67.631 47.264 10.032 1.00 30.12 C
-ATOM 2977 CZ2 TRP B 270 65.221 46.513 8.706 1.00 27.65 C
-ATOM 2978 CZ3 TRP B 270 66.847 46.181 10.482 1.00 28.47 C
-ATOM 2979 CH2 TRP B 270 65.655 45.823 9.813 1.00 27.48 C
-ATOM 2980 N LYS B 271 70.982 52.387 7.892 1.00 43.15 N
-ATOM 2981 CA LYS B 271 72.232 53.048 8.259 1.00 42.97 C
-ATOM 2982 C LYS B 271 72.052 54.537 8.464 1.00 42.28 C
-ATOM 2983 O LYS B 271 72.806 55.162 9.196 1.00 38.58 O
-ATOM 2984 CB LYS B 271 73.305 52.797 7.193 1.00 46.26 C
-ATOM 2985 CG LYS B 271 74.736 52.865 7.734 1.00 53.06 C
-ATOM 2986 CD LYS B 271 75.782 52.441 6.700 1.00 56.56 C
-ATOM 2987 CE LYS B 271 76.322 53.620 5.908 1.00 57.17 C
-ATOM 2988 NZ LYS B 271 75.253 54.340 5.169 1.00 58.31 N
-ATOM 2989 N LEU B 272 71.049 55.111 7.817 1.00 40.42 N
-ATOM 2990 CA LEU B 272 70.809 56.535 7.970 1.00 39.09 C
-ATOM 2991 C LEU B 272 70.158 56.800 9.318 1.00 37.51 C
-ATOM 2992 O LEU B 272 70.376 57.851 9.926 1.00 36.91 O
-ATOM 2993 CB LEU B 272 69.922 57.073 6.845 1.00 43.62 C
-ATOM 2994 CG LEU B 272 70.535 58.222 6.032 1.00 47.96 C
-ATOM 2995 CD1 LEU B 272 69.438 58.892 5.232 1.00 50.99 C
-ATOM 2996 CD2 LEU B 272 71.204 59.239 6.951 1.00 50.25 C
-ATOM 2997 N VAL B 273 69.355 55.846 9.782 1.00 34.46 N
-ATOM 2998 CA VAL B 273 68.702 55.964 11.081 1.00 31.40 C
-ATOM 2999 C VAL B 273 69.756 55.736 12.167 1.00 30.01 C
-ATOM 3000 O VAL B 273 69.811 56.475 13.148 1.00 28.25 O
-ATOM 3001 CB VAL B 273 67.552 54.936 11.221 1.00 31.07 C
-ATOM 3002 CG1 VAL B 273 66.858 55.084 12.577 1.00 28.72 C
-ATOM 3003 CG2 VAL B 273 66.550 55.145 10.097 1.00 29.08 C
-ATOM 3004 N THR B 274 70.607 54.729 11.974 1.00 29.08 N
-ATOM 3005 CA THR B 274 71.661 54.442 12.941 1.00 31.40 C
-ATOM 3006 C THR B 274 72.573 55.656 13.089 1.00 36.97 C
-ATOM 3007 O THR B 274 73.070 55.932 14.179 1.00 33.62 O
-ATOM 3008 CB THR B 274 72.511 53.205 12.535 1.00 27.12 C
-ATOM 3009 OG1 THR B 274 71.710 52.027 12.634 1.00 26.37 O
-ATOM 3010 CG2 THR B 274 73.697 53.020 13.472 1.00 24.28 C
-ATOM 3011 N GLU B 275 72.795 56.382 11.997 1.00 44.33 N
-ATOM 3012 CA GLU B 275 73.624 57.576 12.063 1.00 48.98 C
-ATOM 3013 C GLU B 275 72.955 58.529 13.043 1.00 47.13 C
-ATOM 3014 O GLU B 275 73.559 58.979 14.019 1.00 44.34 O
-ATOM 3015 CB GLU B 275 73.706 58.256 10.700 1.00 61.55 C
-ATOM 3016 CG GLU B 275 74.772 57.717 9.786 1.00 85.55 C
-ATOM 3017 CD GLU B 275 74.741 58.391 8.433 1.00 95.88 C
-ATOM 3018 OE1 GLU B 275 74.791 59.640 8.384 1.00 99.15 O
-ATOM 3019 OE2 GLU B 275 74.666 57.669 7.418 1.00 99.19 O
-ATOM 3020 N TYR B 276 71.689 58.828 12.779 1.00 41.64 N
-ATOM 3021 CA TYR B 276 70.938 59.731 13.628 1.00 34.97 C
-ATOM 3022 C TYR B 276 71.055 59.329 15.092 1.00 33.20 C
-ATOM 3023 O TYR B 276 71.281 60.164 15.950 1.00 31.08 O
-ATOM 3024 CB TYR B 276 69.468 59.752 13.210 1.00 31.86 C
-ATOM 3025 CG TYR B 276 68.637 60.668 14.067 1.00 29.83 C
-ATOM 3026 CD1 TYR B 276 68.897 62.037 14.107 1.00 30.09 C
-ATOM 3027 CD2 TYR B 276 67.606 60.167 14.864 1.00 30.82 C
-ATOM 3028 CE1 TYR B 276 68.162 62.882 14.915 1.00 29.94 C
-ATOM 3029 CE2 TYR B 276 66.862 61.005 15.677 1.00 30.77 C
-ATOM 3030 CZ TYR B 276 67.148 62.362 15.693 1.00 30.80 C
-ATOM 3031 OH TYR B 276 66.410 63.201 16.486 1.00 34.43 O
-ATOM 3032 N ALA B 277 70.911 58.047 15.381 1.00 34.29 N
-ATOM 3033 CA ALA B 277 71.003 57.600 16.759 1.00 35.87 C
-ATOM 3034 C ALA B 277 72.387 57.866 17.347 1.00 36.14 C
-ATOM 3035 O ALA B 277 72.499 58.424 18.441 1.00 37.64 O
-ATOM 3036 CB ALA B 277 70.664 56.114 16.852 1.00 36.71 C
-ATOM 3037 N MET B 278 73.433 57.471 16.618 1.00 35.83 N
-ATOM 3038 CA MET B 278 74.817 57.642 17.068 1.00 36.61 C
-ATOM 3039 C MET B 278 75.210 59.080 17.347 1.00 40.00 C
-ATOM 3040 O MET B 278 76.012 59.342 18.232 1.00 37.10 O
-ATOM 3041 CB MET B 278 75.797 57.078 16.041 1.00 35.98 C
-ATOM 3042 CG MET B 278 75.964 55.573 16.058 1.00 38.79 C
-ATOM 3043 SD MET B 278 76.782 54.900 17.532 1.00 41.29 S
-ATOM 3044 CE MET B 278 77.491 56.401 18.327 1.00 38.77 C
-ATOM 3045 N GLU B 279 74.644 60.011 16.589 1.00 42.20 N
-ATOM 3046 CA GLU B 279 74.965 61.423 16.749 1.00 42.49 C
-ATOM 3047 C GLU B 279 74.025 62.122 17.720 1.00 41.80 C
-ATOM 3048 O GLU B 279 74.100 63.332 17.917 1.00 33.64 O
-ATOM 3049 CB GLU B 279 74.939 62.115 15.381 1.00 51.90 C
-ATOM 3050 CG GLU B 279 75.696 61.330 14.314 1.00 73.72 C
-ATOM 3051 CD GLU B 279 75.993 62.135 13.068 1.00 83.44 C
-ATOM 3052 OE1 GLU B 279 75.087 62.858 12.601 1.00 87.47 O
-ATOM 3053 OE2 GLU B 279 77.129 62.034 12.553 1.00 86.16 O
-ATOM 3054 N THR B 280 73.146 61.343 18.334 1.00 40.43 N
-ATOM 3055 CA THR B 280 72.194 61.854 19.304 1.00 37.13 C
-ATOM 3056 C THR B 280 72.490 61.123 20.609 1.00 38.77 C
-ATOM 3057 O THR B 280 71.958 61.456 21.665 1.00 35.72 O
-ATOM 3058 CB THR B 280 70.745 61.578 18.846 1.00 39.27 C
-ATOM 3059 OG1 THR B 280 70.429 62.421 17.730 1.00 47.57 O
-ATOM 3060 CG2 THR B 280 69.769 61.864 19.957 1.00 49.31 C
-ATOM 3061 N LYS B 281 73.376 60.135 20.527 1.00 43.68 N
-ATOM 3062 CA LYS B 281 73.751 59.335 21.685 1.00 45.87 C
-ATOM 3063 C LYS B 281 72.482 58.708 22.261 1.00 45.08 C
-ATOM 3064 O LYS B 281 72.383 58.440 23.457 1.00 45.40 O
-ATOM 3065 CB LYS B 281 74.454 60.220 22.720 1.00 51.30 C
-ATOM 3066 CG LYS B 281 75.735 60.880 22.201 1.00 62.19 C
-ATOM 3067 CD LYS B 281 76.982 60.421 22.977 1.00 67.78 C
-ATOM 3068 CE LYS B 281 78.260 61.108 22.474 1.00 69.13 C
-ATOM 3069 NZ LYS B 281 79.510 60.688 23.190 1.00 68.42 N
-ATOM 3070 N CYS B 282 71.524 58.460 21.372 1.00 44.69 N
-ATOM 3071 CA CYS B 282 70.225 57.895 21.728 1.00 43.41 C
-ATOM 3072 C CYS B 282 70.198 56.383 21.908 1.00 46.14 C
-ATOM 3073 O CYS B 282 70.397 55.630 20.965 1.00 42.02 O
-ATOM 3074 CB CYS B 282 69.192 58.290 20.679 1.00 41.14 C
-ATOM 3075 SG CYS B 282 67.557 57.665 21.058 1.00 43.83 S
-ATOM 3076 N ASP B 283 69.907 55.953 23.130 1.00 49.59 N
-ATOM 3077 CA ASP B 283 69.860 54.531 23.492 1.00 50.83 C
-ATOM 3078 C ASP B 283 68.426 54.072 23.785 1.00 49.49 C
-ATOM 3079 O ASP B 283 68.194 52.926 24.178 1.00 41.18 O
-ATOM 3080 CB ASP B 283 70.735 54.319 24.727 1.00 63.58 C
-ATOM 3081 CG ASP B 283 70.372 55.270 25.853 1.00 82.71 C
-ATOM 3082 OD1 ASP B 283 69.388 54.992 26.570 1.00 92.88 O
-ATOM 3083 OD2 ASP B 283 71.054 56.307 26.009 1.00 92.28 O
-ATOM 3084 N ASP B 284 67.478 54.986 23.587 1.00 45.03 N
-ATOM 3085 CA ASP B 284 66.058 54.732 23.823 1.00 40.02 C
-ATOM 3086 C ASP B 284 65.371 54.385 22.496 1.00 36.23 C
-ATOM 3087 O ASP B 284 65.298 55.222 21.590 1.00 32.64 O
-ATOM 3088 CB ASP B 284 65.411 55.987 24.421 1.00 47.17 C
-ATOM 3089 CG ASP B 284 64.082 55.705 25.109 1.00 57.74 C
-ATOM 3090 OD1 ASP B 284 63.261 54.925 24.577 1.00 62.39 O
-ATOM 3091 OD2 ASP B 284 63.855 56.294 26.187 1.00 63.79 O
-ATOM 3092 N VAL B 285 64.868 53.158 22.384 1.00 32.04 N
-ATOM 3093 CA VAL B 285 64.196 52.718 21.168 1.00 28.26 C
-ATOM 3094 C VAL B 285 62.923 53.504 20.901 1.00 28.27 C
-ATOM 3095 O VAL B 285 62.726 54.038 19.813 1.00 28.51 O
-ATOM 3096 CB VAL B 285 63.831 51.241 21.238 1.00 25.00 C
-ATOM 3097 CG1 VAL B 285 63.281 50.805 19.909 1.00 22.67 C
-ATOM 3098 CG2 VAL B 285 65.057 50.425 21.604 1.00 23.69 C
-ATOM 3099 N LEU B 286 62.039 53.550 21.886 1.00 31.33 N
-ATOM 3100 CA LEU B 286 60.812 54.303 21.726 1.00 33.74 C
-ATOM 3101 C LEU B 286 61.144 55.762 21.406 1.00 33.70 C
-ATOM 3102 O LEU B 286 60.540 56.364 20.521 1.00 35.93 O
-ATOM 3103 CB LEU B 286 59.959 54.224 22.995 1.00 35.23 C
-ATOM 3104 CG LEU B 286 59.062 52.995 23.124 1.00 35.60 C
-ATOM 3105 CD1 LEU B 286 58.140 53.178 24.314 1.00 36.20 C
-ATOM 3106 CD2 LEU B 286 58.249 52.818 21.864 1.00 33.97 C
-ATOM 3107 N LEU B 287 62.103 56.333 22.126 1.00 31.94 N
-ATOM 3108 CA LEU B 287 62.493 57.713 21.875 1.00 30.42 C
-ATOM 3109 C LEU B 287 63.063 57.893 20.454 1.00 30.62 C
-ATOM 3110 O LEU B 287 62.723 58.853 19.762 1.00 30.82 O
-ATOM 3111 CB LEU B 287 63.511 58.171 22.916 1.00 26.17 C
-ATOM 3112 CG LEU B 287 63.963 59.633 22.852 1.00 22.88 C
-ATOM 3113 CD1 LEU B 287 62.757 60.592 22.887 1.00 22.43 C
-ATOM 3114 CD2 LEU B 287 64.890 59.883 24.022 1.00 20.85 C
-ATOM 3115 N LEU B 288 63.916 56.978 20.009 1.00 30.82 N
-ATOM 3116 CA LEU B 288 64.471 57.084 18.665 1.00 31.86 C
-ATOM 3117 C LEU B 288 63.334 57.110 17.653 1.00 32.56 C
-ATOM 3118 O LEU B 288 63.267 57.993 16.793 1.00 32.73 O
-ATOM 3119 CB LEU B 288 65.375 55.897 18.348 1.00 32.38 C
-ATOM 3120 CG LEU B 288 65.996 55.946 16.950 1.00 32.76 C
-ATOM 3121 CD1 LEU B 288 66.849 57.216 16.805 1.00 33.91 C
-ATOM 3122 CD2 LEU B 288 66.839 54.700 16.722 1.00 33.34 C
-ATOM 3123 N LEU B 289 62.456 56.118 17.754 1.00 33.96 N
-ATOM 3124 CA LEU B 289 61.308 56.021 16.872 1.00 35.96 C
-ATOM 3125 C LEU B 289 60.522 57.338 16.879 1.00 36.83 C
-ATOM 3126 O LEU B 289 60.176 57.877 15.827 1.00 37.25 O
-ATOM 3127 CB LEU B 289 60.395 54.890 17.339 1.00 37.04 C
-ATOM 3128 CG LEU B 289 59.044 54.812 16.624 1.00 39.40 C
-ATOM 3129 CD1 LEU B 289 59.255 54.328 15.198 1.00 40.10 C
-ATOM 3130 CD2 LEU B 289 58.109 53.887 17.369 1.00 38.85 C
-ATOM 3131 N GLY B 290 60.237 57.847 18.073 1.00 37.23 N
-ATOM 3132 CA GLY B 290 59.488 59.084 18.193 1.00 36.45 C
-ATOM 3133 C GLY B 290 60.171 60.234 17.488 1.00 36.87 C
-ATOM 3134 O GLY B 290 59.538 60.975 16.733 1.00 35.41 O
-ATOM 3135 N MET B 291 61.465 60.391 17.735 1.00 36.79 N
-ATOM 3136 CA MET B 291 62.217 61.463 17.111 1.00 37.44 C
-ATOM 3137 C MET B 291 62.156 61.357 15.587 1.00 37.26 C
-ATOM 3138 O MET B 291 61.709 62.280 14.892 1.00 37.80 O
-ATOM 3139 CB MET B 291 63.686 61.419 17.540 1.00 40.47 C
-ATOM 3140 CG MET B 291 63.960 61.701 19.001 1.00 46.97 C
-ATOM 3141 SD MET B 291 63.247 63.246 19.528 1.00 50.44 S
-ATOM 3142 CE MET B 291 64.092 64.451 18.429 1.00 51.21 C
-ATOM 3143 N TYR B 292 62.591 60.217 15.067 1.00 34.81 N
-ATOM 3144 CA TYR B 292 62.641 60.028 13.633 1.00 32.12 C
-ATOM 3145 C TYR B 292 61.337 60.248 12.880 1.00 32.36 C
-ATOM 3146 O TYR B 292 61.348 60.789 11.771 1.00 31.76 O
-ATOM 3147 CB TYR B 292 63.207 58.648 13.304 1.00 29.07 C
-ATOM 3148 CG TYR B 292 64.091 58.666 12.078 1.00 27.00 C
-ATOM 3149 CD1 TYR B 292 65.304 59.355 12.079 1.00 25.14 C
-ATOM 3150 CD2 TYR B 292 63.701 58.020 10.905 1.00 26.70 C
-ATOM 3151 CE1 TYR B 292 66.108 59.395 10.946 1.00 25.08 C
-ATOM 3152 CE2 TYR B 292 64.498 58.053 9.762 1.00 26.55 C
-ATOM 3153 CZ TYR B 292 65.697 58.742 9.787 1.00 25.16 C
-ATOM 3154 OH TYR B 292 66.483 58.770 8.655 1.00 24.14 O
-ATOM 3155 N LEU B 293 60.215 59.841 13.463 1.00 32.96 N
-ATOM 3156 CA LEU B 293 58.936 60.009 12.792 1.00 34.10 C
-ATOM 3157 C LEU B 293 58.524 61.466 12.609 1.00 35.67 C
-ATOM 3158 O LEU B 293 57.543 61.757 11.930 1.00 34.88 O
-ATOM 3159 CB LEU B 293 57.855 59.236 13.537 1.00 34.85 C
-ATOM 3160 CG LEU B 293 57.934 57.730 13.271 1.00 38.35 C
-ATOM 3161 CD1 LEU B 293 57.021 56.955 14.206 1.00 38.90 C
-ATOM 3162 CD2 LEU B 293 57.555 57.467 11.814 1.00 39.60 C
-ATOM 3163 N GLU B 294 59.276 62.387 13.193 1.00 37.48 N
-ATOM 3164 CA GLU B 294 58.943 63.798 13.045 1.00 38.99 C
-ATOM 3165 C GLU B 294 59.543 64.360 11.768 1.00 39.03 C
-ATOM 3166 O GLU B 294 59.090 65.379 11.250 1.00 38.64 O
-ATOM 3167 CB GLU B 294 59.476 64.604 14.215 1.00 42.19 C
-ATOM 3168 CG GLU B 294 59.108 64.033 15.541 1.00 50.29 C
-ATOM 3169 CD GLU B 294 59.314 65.017 16.654 1.00 53.28 C
-ATOM 3170 OE1 GLU B 294 60.406 65.619 16.727 1.00 55.56 O
-ATOM 3171 OE2 GLU B 294 58.377 65.185 17.462 1.00 56.22 O
-ATOM 3172 N PHE B 295 60.576 63.701 11.267 1.00 37.85 N
-ATOM 3173 CA PHE B 295 61.225 64.171 10.063 1.00 35.94 C
-ATOM 3174 C PHE B 295 60.489 63.760 8.802 1.00 36.20 C
-ATOM 3175 O PHE B 295 60.932 64.077 7.709 1.00 37.56 O
-ATOM 3176 CB PHE B 295 62.662 63.640 9.971 1.00 36.00 C
-ATOM 3177 CG PHE B 295 63.500 63.895 11.192 1.00 33.88 C
-ATOM 3178 CD1 PHE B 295 63.299 65.027 11.979 1.00 34.40 C
-ATOM 3179 CD2 PHE B 295 64.526 63.016 11.527 1.00 33.37 C
-ATOM 3180 CE1 PHE B 295 64.113 65.279 13.082 1.00 35.16 C
-ATOM 3181 CE2 PHE B 295 65.348 63.254 12.625 1.00 34.75 C
-ATOM 3182 CZ PHE B 295 65.147 64.388 13.408 1.00 34.92 C
-ATOM 3183 N GLN B 296 59.379 63.053 8.936 1.00 39.46 N
-ATOM 3184 CA GLN B 296 58.646 62.614 7.748 1.00 43.33 C
-ATOM 3185 C GLN B 296 57.928 63.754 7.030 1.00 45.50 C
-ATOM 3186 O GLN B 296 57.604 63.647 5.842 1.00 46.04 O
-ATOM 3187 CB GLN B 296 57.622 61.552 8.123 1.00 43.36 C
-ATOM 3188 CG GLN B 296 56.541 62.073 9.028 1.00 43.08 C
-ATOM 3189 CD GLN B 296 55.501 61.033 9.292 1.00 43.93 C
-ATOM 3190 OE1 GLN B 296 55.816 59.937 9.743 1.00 45.16 O
-ATOM 3191 NE2 GLN B 296 54.249 61.359 9.008 1.00 45.76 N
-ATOM 3192 N TYR B 297 57.675 64.832 7.765 1.00 49.91 N
-ATOM 3193 CA TYR B 297 56.995 66.003 7.232 1.00 52.28 C
-ATOM 3194 C TYR B 297 57.998 66.907 6.535 1.00 52.85 C
-ATOM 3195 O TYR B 297 59.174 66.924 6.891 1.00 52.37 O
-ATOM 3196 CB TYR B 297 56.306 66.765 8.366 1.00 55.46 C
-ATOM 3197 CG TYR B 297 55.411 65.893 9.226 1.00 60.11 C
-ATOM 3198 CD1 TYR B 297 54.387 65.131 8.658 1.00 60.32 C
-ATOM 3199 CD2 TYR B 297 55.617 65.793 10.602 1.00 61.87 C
-ATOM 3200 CE1 TYR B 297 53.597 64.287 9.439 1.00 61.37 C
-ATOM 3201 CE2 TYR B 297 54.831 64.950 11.394 1.00 61.93 C
-ATOM 3202 CZ TYR B 297 53.827 64.195 10.807 1.00 61.80 C
-ATOM 3203 OH TYR B 297 53.084 63.318 11.576 1.00 61.03 O
-ATOM 3204 N SER B 298 57.535 67.657 5.536 1.00 54.55 N
-ATOM 3205 CA SER B 298 58.420 68.564 4.807 1.00 54.26 C
-ATOM 3206 C SER B 298 59.022 69.543 5.804 1.00 57.78 C
-ATOM 3207 O SER B 298 58.315 70.094 6.659 1.00 53.69 O
-ATOM 3208 CB SER B 298 57.649 69.328 3.729 1.00 51.76 C
-ATOM 3209 OG SER B 298 56.776 70.280 4.307 1.00 51.11 O
-ATOM 3210 N PHE B 299 60.330 69.744 5.699 1.00 67.50 N
-ATOM 3211 CA PHE B 299 61.035 70.642 6.605 1.00 75.16 C
-ATOM 3212 C PHE B 299 60.907 72.101 6.148 1.00 76.58 C
-ATOM 3213 O PHE B 299 61.306 73.027 6.868 1.00 79.85 O
-ATOM 3214 CB PHE B 299 62.517 70.244 6.689 1.00 81.03 C
-ATOM 3215 CG PHE B 299 63.399 71.022 5.766 1.00 89.07 C
-ATOM 3216 CD1 PHE B 299 64.220 72.031 6.259 1.00 91.52 C
-ATOM 3217 CD2 PHE B 299 63.357 70.793 4.394 1.00 92.58 C
-ATOM 3218 CE1 PHE B 299 64.985 72.804 5.401 1.00 93.46 C
-ATOM 3219 CE2 PHE B 299 64.118 71.563 3.523 1.00 94.19 C
-ATOM 3220 CZ PHE B 299 64.934 72.573 4.028 1.00 94.38 C
-ATOM 3221 N GLU B 300 60.358 72.291 4.950 1.00 82.55 N
-ATOM 3222 CA GLU B 300 60.172 73.624 4.387 1.00 88.29 C
-ATOM 3223 C GLU B 300 59.367 74.511 5.327 1.00 91.18 C
-ATOM 3224 O GLU B 300 59.786 75.618 5.659 1.00 97.37 O
-ATOM 3225 CB GLU B 300 59.472 73.530 3.033 1.00 88.10 C
-ATOM 3226 CG GLU B 300 60.354 72.977 1.928 1.00 83.41 C
-ATOM 3227 CD GLU B 300 59.783 71.726 1.281 1.00 80.11 C
-ATOM 3228 OE1 GLU B 300 58.698 71.808 0.662 1.00 78.42 O
-ATOM 3229 OE2 GLU B 300 60.426 70.660 1.395 1.00 77.59 O
-ATOM 3230 N MET B 301 58.208 74.031 5.754 1.00 92.84 N
-ATOM 3231 CA MET B 301 57.391 74.809 6.671 1.00 92.01 C
-ATOM 3232 C MET B 301 57.487 74.216 8.077 1.00 88.96 C
-ATOM 3233 O MET B 301 56.523 74.278 8.856 1.00 84.33 O
-ATOM 3234 CB MET B 301 55.927 74.834 6.208 1.00 97.69 C
-ATOM 3235 CG MET B 301 55.674 75.604 4.911 1.00105.22 C
-ATOM 3236 SD MET B 301 56.053 74.670 3.406 1.00108.78 S
-ATOM 3237 CE MET B 301 54.460 73.900 3.081 1.00108.86 C
-ATOM 3238 N CYS B 302 58.647 73.639 8.402 1.00 79.72 N
-ATOM 3239 CA CYS B 302 58.841 73.048 9.723 1.00 70.14 C
-ATOM 3240 C CYS B 302 58.966 74.149 10.768 1.00 66.23 C
-ATOM 3241 O CYS B 302 59.919 74.926 10.758 1.00 63.11 O
-ATOM 3242 CB CYS B 302 60.086 72.149 9.752 1.00 65.55 C
-ATOM 3243 SG CYS B 302 60.689 71.769 11.439 1.00 61.97 S
-ATOM 3244 N LEU B 303 57.988 74.208 11.665 1.00 62.86 N
-ATOM 3245 CA LEU B 303 57.983 75.211 12.714 1.00 64.49 C
-ATOM 3246 C LEU B 303 59.033 74.891 13.768 1.00 66.76 C
-ATOM 3247 O LEU B 303 59.713 75.787 14.275 1.00 69.86 O
-ATOM 3248 CB LEU B 303 56.595 75.288 13.350 1.00 61.91 C
-ATOM 3249 CG LEU B 303 55.454 75.620 12.383 1.00 57.69 C
-ATOM 3250 CD1 LEU B 303 54.133 75.686 13.152 1.00 54.85 C
-ATOM 3251 CD2 LEU B 303 55.741 76.952 11.682 1.00 53.50 C
-ATOM 3252 N LYS B 304 59.163 73.609 14.094 1.00 67.18 N
-ATOM 3253 CA LYS B 304 60.136 73.178 15.086 1.00 65.15 C
-ATOM 3254 C LYS B 304 61.512 73.645 14.668 1.00 64.15 C
-ATOM 3255 O LYS B 304 62.286 74.130 15.488 1.00 60.14 O
-ATOM 3256 CB LYS B 304 60.106 71.654 15.240 1.00 66.27 C
-ATOM 3257 CG LYS B 304 58.852 71.176 15.954 1.00 70.91 C
-ATOM 3258 CD LYS B 304 58.809 69.676 16.184 1.00 72.65 C
-ATOM 3259 CE LYS B 304 57.549 69.307 16.957 1.00 73.53 C
-ATOM 3260 NZ LYS B 304 57.318 67.843 16.974 1.00 74.13 N
-ATOM 3261 N CYS B 305 61.804 73.510 13.381 1.00 63.82 N
-ATOM 3262 CA CYS B 305 63.086 73.936 12.838 1.00 64.62 C
-ATOM 3263 C CYS B 305 63.086 75.460 12.767 1.00 65.05 C
-ATOM 3264 O CYS B 305 63.988 76.116 13.280 1.00 68.09 O
-ATOM 3265 CB CYS B 305 63.280 73.363 11.436 1.00 61.96 C
-ATOM 3266 SG CYS B 305 62.726 71.645 11.243 1.00 60.59 S
-ATOM 3267 N ILE B 306 62.064 76.009 12.115 1.00 68.13 N
-ATOM 3268 CA ILE B 306 61.915 77.451 11.969 1.00 75.66 C
-ATOM 3269 C ILE B 306 62.060 78.149 13.319 1.00 75.47 C
-ATOM 3270 O ILE B 306 62.648 79.232 13.404 1.00 75.04 O
-ATOM 3271 CB ILE B 306 60.532 77.816 11.351 1.00 79.19 C
-ATOM 3272 CG1 ILE B 306 60.521 77.459 9.862 1.00 83.79 C
-ATOM 3273 CG2 ILE B 306 60.239 79.298 11.548 1.00 83.04 C
-ATOM 3274 CD1 ILE B 306 59.170 77.620 9.190 1.00 83.47 C
-ATOM 3275 N LYS B 307 61.532 77.531 14.371 1.00 73.50 N
-ATOM 3276 CA LYS B 307 61.623 78.120 15.697 1.00 66.14 C
-ATOM 3277 C LYS B 307 62.810 77.624 16.502 1.00 62.00 C
-ATOM 3278 O LYS B 307 62.996 78.043 17.638 1.00 57.14 O
-ATOM 3279 CB LYS B 307 60.345 77.861 16.484 1.00 64.25 C
-ATOM 3280 CG LYS B 307 59.165 78.677 16.016 1.00 69.33 C
-ATOM 3281 CD LYS B 307 58.076 78.661 17.073 1.00 73.69 C
-ATOM 3282 CE LYS B 307 57.023 79.732 16.813 1.00 76.00 C
-ATOM 3283 NZ LYS B 307 56.037 79.829 17.937 1.00 76.84 N
-ATOM 3284 N LYS B 308 63.603 76.733 15.910 1.00 58.98 N
-ATOM 3285 CA LYS B 308 64.784 76.143 16.551 1.00 61.13 C
-ATOM 3286 C LYS B 308 64.573 75.794 18.026 1.00 64.93 C
-ATOM 3287 O LYS B 308 65.315 76.231 18.907 1.00 67.09 O
-ATOM 3288 CB LYS B 308 65.992 77.065 16.366 1.00 59.90 C
-ATOM 3289 CG LYS B 308 66.350 77.223 14.899 1.00 57.27 C
-ATOM 3290 CD LYS B 308 67.739 77.796 14.673 1.00 55.65 C
-ATOM 3291 CE LYS B 308 68.118 77.714 13.188 1.00 54.38 C
-ATOM 3292 NZ LYS B 308 69.533 78.114 12.928 1.00 54.05 N
-ATOM 3293 N GLU B 309 63.556 74.968 18.259 1.00 69.75 N
-ATOM 3294 CA GLU B 309 63.146 74.522 19.582 1.00 69.05 C
-ATOM 3295 C GLU B 309 63.874 73.272 20.094 1.00 66.42 C
-ATOM 3296 O GLU B 309 63.865 73.004 21.298 1.00 64.00 O
-ATOM 3297 CB GLU B 309 61.633 74.273 19.561 1.00 71.21 C
-ATOM 3298 CG GLU B 309 60.889 75.271 18.673 1.00 81.59 C
-ATOM 3299 CD GLU B 309 59.409 74.953 18.488 1.00 86.43 C
-ATOM 3300 OE1 GLU B 309 59.074 73.797 18.157 1.00 88.15 O
-ATOM 3301 OE2 GLU B 309 58.578 75.872 18.656 1.00 88.22 O
-ATOM 3302 N GLN B 310 64.493 72.500 19.200 1.00 62.07 N
-ATOM 3303 CA GLN B 310 65.213 71.292 19.620 1.00 61.01 C
-ATOM 3304 C GLN B 310 66.362 70.904 18.704 1.00 61.01 C
-ATOM 3305 O GLN B 310 66.152 70.576 17.538 1.00 64.40 O
-ATOM 3306 CB GLN B 310 64.263 70.109 19.721 1.00 61.85 C
-ATOM 3307 CG GLN B 310 63.392 70.115 20.956 1.00 60.20 C
-ATOM 3308 CD GLN B 310 64.181 69.953 22.234 1.00 58.49 C
-ATOM 3309 OE1 GLN B 310 65.065 69.096 22.333 1.00 58.28 O
-ATOM 3310 NE2 GLN B 310 63.854 70.765 23.233 1.00 57.04 N
-ATOM 3311 N PRO B 311 67.596 70.915 19.231 1.00 53.33 N
-ATOM 3312 CA PRO B 311 68.781 70.562 18.443 1.00 54.66 C
-ATOM 3313 C PRO B 311 68.675 69.156 17.859 1.00 54.84 C
-ATOM 3314 O PRO B 311 68.970 68.934 16.682 1.00 49.90 O
-ATOM 3315 CB PRO B 311 69.919 70.680 19.458 1.00 53.22 C
-ATOM 3316 CG PRO B 311 69.403 71.697 20.436 1.00 53.21 C
-ATOM 3317 CD PRO B 311 67.974 71.265 20.612 1.00 55.97 C
-ATOM 3318 N SER B 312 68.245 68.215 18.696 1.00 52.30 N
-ATOM 3319 CA SER B 312 68.092 66.824 18.290 1.00 50.49 C
-ATOM 3320 C SER B 312 67.088 66.712 17.152 1.00 48.57 C
-ATOM 3321 O SER B 312 66.842 65.632 16.623 1.00 46.34 O
-ATOM 3322 CB SER B 312 67.623 65.986 19.477 1.00 52.39 C
-ATOM 3323 OG SER B 312 66.447 66.532 20.041 1.00 60.03 O
-ATOM 3324 N HIS B 313 66.515 67.842 16.771 1.00 47.09 N
-ATOM 3325 CA HIS B 313 65.543 67.843 15.704 1.00 46.06 C
-ATOM 3326 C HIS B 313 65.917 68.737 14.532 1.00 46.44 C
-ATOM 3327 O HIS B 313 66.131 68.247 13.420 1.00 49.98 O
-ATOM 3328 CB HIS B 313 64.190 68.278 16.233 1.00 41.80 C
-ATOM 3329 CG HIS B 313 63.181 68.493 15.154 1.00 37.90 C
-ATOM 3330 ND1 HIS B 313 62.443 67.466 14.610 1.00 37.56 N
-ATOM 3331 CD2 HIS B 313 62.844 69.606 14.463 1.00 37.06 C
-ATOM 3332 CE1 HIS B 313 61.695 67.935 13.628 1.00 35.54 C
-ATOM 3333 NE2 HIS B 313 61.921 69.231 13.518 1.00 35.85 N
-ATOM 3334 N TYR B 314 65.995 70.045 14.782 1.00 48.21 N
-ATOM 3335 CA TYR B 314 66.297 71.003 13.722 1.00 50.55 C
-ATOM 3336 C TYR B 314 67.650 70.840 13.036 1.00 50.42 C
-ATOM 3337 O TYR B 314 67.812 71.242 11.879 1.00 52.24 O
-ATOM 3338 CB TYR B 314 66.110 72.448 14.226 1.00 49.89 C
-ATOM 3339 CG TYR B 314 67.114 72.970 15.244 1.00 47.78 C
-ATOM 3340 CD1 TYR B 314 68.456 73.137 14.912 1.00 46.23 C
-ATOM 3341 CD2 TYR B 314 66.700 73.373 16.520 1.00 46.18 C
-ATOM 3342 CE1 TYR B 314 69.362 73.696 15.818 1.00 45.52 C
-ATOM 3343 CE2 TYR B 314 67.600 73.933 17.437 1.00 44.56 C
-ATOM 3344 CZ TYR B 314 68.931 74.094 17.080 1.00 45.38 C
-ATOM 3345 OH TYR B 314 69.835 74.661 17.964 1.00 43.74 O
-ATOM 3346 N LYS B 315 68.609 70.236 13.734 1.00 47.12 N
-ATOM 3347 CA LYS B 315 69.936 70.016 13.165 1.00 42.83 C
-ATOM 3348 C LYS B 315 69.995 68.802 12.244 1.00 41.78 C
-ATOM 3349 O LYS B 315 71.008 68.572 11.603 1.00 40.97 O
-ATOM 3350 CB LYS B 315 70.976 69.832 14.272 1.00 39.23 C
-ATOM 3351 CG LYS B 315 71.369 71.099 15.012 1.00 35.30 C
-ATOM 3352 CD LYS B 315 72.241 70.770 16.213 1.00 35.35 C
-ATOM 3353 CE LYS B 315 73.383 69.814 15.827 1.00 38.50 C
-ATOM 3354 NZ LYS B 315 74.257 69.364 16.978 1.00 39.22 N
-ATOM 3355 N TYR B 316 68.926 68.017 12.171 1.00 40.36 N
-ATOM 3356 CA TYR B 316 68.955 66.839 11.310 1.00 40.25 C
-ATOM 3357 C TYR B 316 67.728 66.607 10.430 1.00 40.84 C
-ATOM 3358 O TYR B 316 67.746 65.730 9.569 1.00 44.03 O
-ATOM 3359 CB TYR B 316 69.180 65.580 12.148 1.00 39.03 C
-ATOM 3360 CG TYR B 316 70.244 65.701 13.219 1.00 37.49 C
-ATOM 3361 CD1 TYR B 316 69.998 66.416 14.395 1.00 36.49 C
-ATOM 3362 CD2 TYR B 316 71.489 65.088 13.068 1.00 35.85 C
-ATOM 3363 CE1 TYR B 316 70.961 66.512 15.400 1.00 35.10 C
-ATOM 3364 CE2 TYR B 316 72.458 65.178 14.066 1.00 36.39 C
-ATOM 3365 CZ TYR B 316 72.187 65.894 15.228 1.00 35.46 C
-ATOM 3366 OH TYR B 316 73.139 65.990 16.216 1.00 35.68 O
-ATOM 3367 N HIS B 317 66.662 67.376 10.630 1.00 43.49 N
-ATOM 3368 CA HIS B 317 65.446 67.180 9.839 1.00 45.61 C
-ATOM 3369 C HIS B 317 65.678 67.142 8.329 1.00 49.92 C
-ATOM 3370 O HIS B 317 65.214 66.223 7.656 1.00 50.12 O
-ATOM 3371 CB HIS B 317 64.407 68.256 10.185 1.00 42.50 C
-ATOM 3372 CG HIS B 317 63.042 67.994 9.613 1.00 38.56 C
-ATOM 3373 ND1 HIS B 317 61.952 68.788 9.897 1.00 37.03 N
-ATOM 3374 CD2 HIS B 317 62.589 67.024 8.787 1.00 36.40 C
-ATOM 3375 CE1 HIS B 317 60.886 68.318 9.274 1.00 34.43 C
-ATOM 3376 NE2 HIS B 317 61.246 67.247 8.593 1.00 35.39 N
-ATOM 3377 N GLU B 318 66.410 68.115 7.797 1.00 54.61 N
-ATOM 3378 CA GLU B 318 66.633 68.155 6.361 1.00 56.76 C
-ATOM 3379 C GLU B 318 67.372 66.943 5.809 1.00 54.56 C
-ATOM 3380 O GLU B 318 66.913 66.311 4.862 1.00 51.51 O
-ATOM 3381 CB GLU B 318 67.373 69.432 5.966 1.00 65.07 C
-ATOM 3382 CG GLU B 318 66.974 69.938 4.584 1.00 80.29 C
-ATOM 3383 CD GLU B 318 67.888 71.029 4.053 1.00 87.12 C
-ATOM 3384 OE1 GLU B 318 68.064 72.059 4.741 1.00 89.59 O
-ATOM 3385 OE2 GLU B 318 68.426 70.854 2.937 1.00 89.60 O
-ATOM 3386 N LYS B 319 68.513 66.607 6.394 1.00 50.20 N
-ATOM 3387 CA LYS B 319 69.288 65.458 5.917 1.00 45.94 C
-ATOM 3388 C LYS B 319 68.540 64.141 6.047 1.00 43.27 C
-ATOM 3389 O LYS B 319 69.017 63.114 5.584 1.00 42.55 O
-ATOM 3390 CB LYS B 319 70.623 65.346 6.677 1.00 46.28 C
-ATOM 3391 CG LYS B 319 71.459 64.118 6.303 1.00 49.81 C
-ATOM 3392 CD LYS B 319 72.929 64.279 6.697 1.00 52.72 C
-ATOM 3393 CE LYS B 319 73.820 63.252 5.984 1.00 54.35 C
-ATOM 3394 NZ LYS B 319 75.269 63.642 5.961 1.00 52.69 N
-ATOM 3395 N HIS B 320 67.367 64.166 6.665 1.00 39.44 N
-ATOM 3396 CA HIS B 320 66.624 62.933 6.872 1.00 36.27 C
-ATOM 3397 C HIS B 320 65.230 62.896 6.278 1.00 38.06 C
-ATOM 3398 O HIS B 320 64.614 61.831 6.211 1.00 33.79 O
-ATOM 3399 CB HIS B 320 66.559 62.634 8.374 1.00 31.18 C
-ATOM 3400 CG HIS B 320 67.882 62.246 8.964 1.00 26.63 C
-ATOM 3401 ND1 HIS B 320 68.464 61.017 8.745 1.00 25.13 N
-ATOM 3402 CD2 HIS B 320 68.762 62.952 9.709 1.00 25.44 C
-ATOM 3403 CE1 HIS B 320 69.650 60.983 9.325 1.00 24.49 C
-ATOM 3404 NE2 HIS B 320 69.857 62.147 9.917 1.00 25.01 N
-ATOM 3405 N TYR B 321 64.731 64.048 5.843 1.00 41.58 N
-ATOM 3406 CA TYR B 321 63.396 64.099 5.272 1.00 44.15 C
-ATOM 3407 C TYR B 321 63.152 62.855 4.433 1.00 43.01 C
-ATOM 3408 O TYR B 321 62.391 61.969 4.819 1.00 42.61 O
-ATOM 3409 CB TYR B 321 63.217 65.333 4.387 1.00 52.00 C
-ATOM 3410 CG TYR B 321 61.856 65.373 3.732 1.00 62.58 C
-ATOM 3411 CD1 TYR B 321 60.722 65.700 4.466 1.00 67.30 C
-ATOM 3412 CD2 TYR B 321 61.692 65.014 2.394 1.00 67.18 C
-ATOM 3413 CE1 TYR B 321 59.454 65.665 3.889 1.00 69.56 C
-ATOM 3414 CE2 TYR B 321 60.427 64.974 1.807 1.00 69.38 C
-ATOM 3415 CZ TYR B 321 59.311 65.301 2.562 1.00 69.87 C
-ATOM 3416 OH TYR B 321 58.052 65.263 2.000 1.00 70.45 O
-ATOM 3417 N ALA B 322 63.823 62.799 3.291 1.00 41.01 N
-ATOM 3418 CA ALA B 322 63.691 61.691 2.361 1.00 39.13 C
-ATOM 3419 C ALA B 322 63.559 60.345 3.052 1.00 39.76 C
-ATOM 3420 O ALA B 322 62.574 59.636 2.871 1.00 40.55 O
-ATOM 3421 CB ALA B 322 64.883 61.670 1.424 1.00 37.37 C
-ATOM 3422 N ASN B 323 64.559 59.994 3.848 1.00 40.66 N
-ATOM 3423 CA ASN B 323 64.553 58.714 4.534 1.00 40.52 C
-ATOM 3424 C ASN B 323 63.325 58.560 5.437 1.00 38.72 C
-ATOM 3425 O ASN B 323 62.603 57.567 5.351 1.00 38.53 O
-ATOM 3426 CB ASN B 323 65.853 58.562 5.335 1.00 43.51 C
-ATOM 3427 CG ASN B 323 66.192 57.111 5.641 1.00 46.70 C
-ATOM 3428 OD1 ASN B 323 66.229 56.266 4.747 1.00 48.85 O
-ATOM 3429 ND2 ASN B 323 66.452 56.821 6.910 1.00 49.44 N
-ATOM 3430 N ALA B 324 63.078 59.556 6.282 1.00 35.14 N
-ATOM 3431 CA ALA B 324 61.950 59.525 7.207 1.00 33.14 C
-ATOM 3432 C ALA B 324 60.616 59.284 6.506 1.00 33.80 C
-ATOM 3433 O ALA B 324 59.802 58.492 6.967 1.00 33.01 O
-ATOM 3434 CB ALA B 324 61.900 60.833 8.003 1.00 28.88 C
-ATOM 3435 N ALA B 325 60.395 59.977 5.395 1.00 36.17 N
-ATOM 3436 CA ALA B 325 59.156 59.834 4.638 1.00 37.55 C
-ATOM 3437 C ALA B 325 58.941 58.395 4.190 1.00 38.25 C
-ATOM 3438 O ALA B 325 57.800 57.957 4.036 1.00 37.94 O
-ATOM 3439 CB ALA B 325 59.170 60.760 3.426 1.00 38.98 C
-ATOM 3440 N ILE B 326 60.032 57.665 3.965 1.00 38.88 N
-ATOM 3441 CA ILE B 326 59.937 56.262 3.552 1.00 40.33 C
-ATOM 3442 C ILE B 326 59.763 55.389 4.794 1.00 39.45 C
-ATOM 3443 O ILE B 326 59.061 54.373 4.767 1.00 39.20 O
-ATOM 3444 CB ILE B 326 61.209 55.802 2.795 1.00 40.92 C
-ATOM 3445 CG1 ILE B 326 61.465 56.728 1.607 1.00 42.37 C
-ATOM 3446 CG2 ILE B 326 61.043 54.377 2.302 1.00 40.24 C
-ATOM 3447 CD1 ILE B 326 62.680 56.352 0.793 1.00 42.77 C
-ATOM 3448 N PHE B 327 60.417 55.813 5.873 1.00 38.70 N
-ATOM 3449 CA PHE B 327 60.382 55.130 7.157 1.00 36.97 C
-ATOM 3450 C PHE B 327 58.941 55.072 7.634 1.00 35.76 C
-ATOM 3451 O PHE B 327 58.491 54.060 8.172 1.00 36.30 O
-ATOM 3452 CB PHE B 327 61.235 55.909 8.156 1.00 35.76 C
-ATOM 3453 CG PHE B 327 61.344 55.263 9.511 1.00 33.77 C
-ATOM 3454 CD1 PHE B 327 62.111 54.112 9.691 1.00 33.17 C
-ATOM 3455 CD2 PHE B 327 60.714 55.832 10.621 1.00 32.44 C
-ATOM 3456 CE1 PHE B 327 62.251 53.547 10.956 1.00 31.28 C
-ATOM 3457 CE2 PHE B 327 60.852 55.269 11.886 1.00 32.11 C
-ATOM 3458 CZ PHE B 327 61.621 54.129 12.053 1.00 30.41 C
-ATOM 3459 N ALA B 328 58.226 56.168 7.407 1.00 36.03 N
-ATOM 3460 CA ALA B 328 56.829 56.310 7.802 1.00 38.07 C
-ATOM 3461 C ALA B 328 55.878 55.271 7.182 1.00 42.88 C
-ATOM 3462 O ALA B 328 54.810 54.983 7.749 1.00 42.32 O
-ATOM 3463 CB ALA B 328 56.359 57.719 7.464 1.00 34.21 C
-ATOM 3464 N ASP B 329 56.267 54.720 6.028 1.00 48.12 N
-ATOM 3465 CA ASP B 329 55.467 53.715 5.320 1.00 51.93 C
-ATOM 3466 C ASP B 329 56.080 52.315 5.411 1.00 52.24 C
-ATOM 3467 O ASP B 329 55.639 51.391 4.726 1.00 47.12 O
-ATOM 3468 CB ASP B 329 55.320 54.097 3.842 1.00 62.48 C
-ATOM 3469 CG ASP B 329 54.373 55.271 3.623 1.00 77.08 C
-ATOM 3470 OD1 ASP B 329 53.148 55.098 3.813 1.00 84.40 O
-ATOM 3471 OD2 ASP B 329 54.856 56.367 3.258 1.00 83.83 O
-ATOM 3472 N SER B 330 57.103 52.171 6.249 1.00 52.10 N
-ATOM 3473 CA SER B 330 57.787 50.898 6.449 1.00 49.40 C
-ATOM 3474 C SER B 330 57.034 50.044 7.466 1.00 47.75 C
-ATOM 3475 O SER B 330 56.465 50.563 8.429 1.00 46.70 O
-ATOM 3476 CB SER B 330 59.210 51.149 6.940 1.00 50.11 C
-ATOM 3477 OG SER B 330 59.866 49.925 7.214 1.00 59.43 O
-ATOM 3478 N LYS B 331 57.048 48.731 7.265 1.00 47.20 N
-ATOM 3479 CA LYS B 331 56.336 47.817 8.154 1.00 48.09 C
-ATOM 3480 C LYS B 331 57.020 47.406 9.457 1.00 49.60 C
-ATOM 3481 O LYS B 331 56.365 46.897 10.367 1.00 50.18 O
-ATOM 3482 CB LYS B 331 55.929 46.568 7.378 1.00 49.27 C
-ATOM 3483 CG LYS B 331 54.793 46.816 6.419 1.00 52.46 C
-ATOM 3484 CD LYS B 331 54.638 45.666 5.447 1.00 53.69 C
-ATOM 3485 CE LYS B 331 53.451 45.917 4.539 1.00 54.40 C
-ATOM 3486 NZ LYS B 331 53.455 47.327 4.063 1.00 54.52 N
-ATOM 3487 N ASN B 332 58.326 47.613 9.563 1.00 49.40 N
-ATOM 3488 CA ASN B 332 59.018 47.249 10.792 1.00 47.18 C
-ATOM 3489 C ASN B 332 59.894 48.392 11.315 1.00 44.74 C
-ATOM 3490 O ASN B 332 61.114 48.271 11.434 1.00 39.15 O
-ATOM 3491 CB ASN B 332 59.830 45.970 10.570 1.00 53.46 C
-ATOM 3492 CG ASN B 332 60.832 46.099 9.445 1.00 63.24 C
-ATOM 3493 OD1 ASN B 332 60.642 46.878 8.509 1.00 67.50 O
-ATOM 3494 ND2 ASN B 332 61.903 45.318 9.520 1.00 68.90 N
-ATOM 3495 N GLN B 333 59.243 49.510 11.618 1.00 39.07 N
-ATOM 3496 CA GLN B 333 59.911 50.696 12.146 1.00 34.64 C
-ATOM 3497 C GLN B 333 60.655 50.329 13.438 1.00 34.56 C
-ATOM 3498 O GLN B 333 61.814 50.694 13.630 1.00 30.29 O
-ATOM 3499 CB GLN B 333 58.875 51.789 12.430 1.00 35.07 C
-ATOM 3500 CG GLN B 333 58.169 52.351 11.204 1.00 37.13 C
-ATOM 3501 CD GLN B 333 57.029 53.284 11.577 1.00 39.05 C
-ATOM 3502 OE1 GLN B 333 56.555 54.065 10.757 1.00 41.74 O
-ATOM 3503 NE2 GLN B 333 56.574 53.195 12.820 1.00 39.34 N
-ATOM 3504 N LYS B 334 59.972 49.596 14.313 1.00 34.56 N
-ATOM 3505 CA LYS B 334 60.526 49.147 15.590 1.00 33.53 C
-ATOM 3506 C LYS B 334 61.849 48.383 15.399 1.00 32.50 C
-ATOM 3507 O LYS B 334 62.865 48.694 16.025 1.00 29.12 O
-ATOM 3508 CB LYS B 334 59.499 48.251 16.291 1.00 37.90 C
-ATOM 3509 CG LYS B 334 59.924 47.691 17.636 1.00 47.19 C
-ATOM 3510 CD LYS B 334 59.567 48.617 18.792 1.00 52.16 C
-ATOM 3511 CE LYS B 334 59.937 47.975 20.123 1.00 54.06 C
-ATOM 3512 NZ LYS B 334 59.619 48.844 21.287 1.00 55.05 N
-ATOM 3513 N THR B 335 61.837 47.380 14.531 1.00 31.48 N
-ATOM 3514 CA THR B 335 63.034 46.593 14.290 1.00 30.28 C
-ATOM 3515 C THR B 335 64.204 47.459 13.798 1.00 28.26 C
-ATOM 3516 O THR B 335 65.340 47.291 14.249 1.00 29.50 O
-ATOM 3517 CB THR B 335 62.731 45.464 13.291 1.00 32.26 C
-ATOM 3518 OG1 THR B 335 61.695 44.635 13.836 1.00 35.83 O
-ATOM 3519 CG2 THR B 335 63.973 44.608 13.036 1.00 33.46 C
-ATOM 3520 N ILE B 336 63.931 48.381 12.880 1.00 27.09 N
-ATOM 3521 CA ILE B 336 64.969 49.273 12.371 1.00 27.40 C
-ATOM 3522 C ILE B 336 65.602 50.021 13.564 1.00 28.54 C
-ATOM 3523 O ILE B 336 66.824 49.997 13.764 1.00 29.79 O
-ATOM 3524 CB ILE B 336 64.361 50.298 11.363 1.00 22.80 C
-ATOM 3525 CG1 ILE B 336 63.792 49.566 10.154 1.00 18.69 C
-ATOM 3526 CG2 ILE B 336 65.403 51.281 10.891 1.00 17.17 C
-ATOM 3527 CD1 ILE B 336 63.104 50.482 9.171 1.00 15.36 C
-ATOM 3528 N CYS B 337 64.759 50.667 14.367 1.00 31.20 N
-ATOM 3529 CA CYS B 337 65.227 51.411 15.535 1.00 34.00 C
-ATOM 3530 C CYS B 337 66.065 50.564 16.482 1.00 35.43 C
-ATOM 3531 O CYS B 337 66.986 51.068 17.114 1.00 35.01 O
-ATOM 3532 CB CYS B 337 64.045 51.992 16.310 1.00 32.98 C
-ATOM 3533 SG CYS B 337 63.171 53.316 15.443 1.00 37.16 S
-ATOM 3534 N GLN B 338 65.734 49.282 16.591 1.00 38.08 N
-ATOM 3535 CA GLN B 338 66.468 48.381 17.466 1.00 39.30 C
-ATOM 3536 C GLN B 338 67.931 48.354 17.112 1.00 37.85 C
-ATOM 3537 O GLN B 338 68.782 48.654 17.937 1.00 39.68 O
-ATOM 3538 CB GLN B 338 65.919 46.961 17.370 1.00 43.87 C
-ATOM 3539 CG GLN B 338 64.886 46.623 18.423 1.00 51.44 C
-ATOM 3540 CD GLN B 338 65.357 46.954 19.823 1.00 53.05 C
-ATOM 3541 OE1 GLN B 338 66.547 47.184 20.053 1.00 52.69 O
-ATOM 3542 NE2 GLN B 338 64.422 46.972 20.773 1.00 53.74 N
-ATOM 3543 N GLN B 339 68.214 47.988 15.873 1.00 35.50 N
-ATOM 3544 CA GLN B 339 69.583 47.905 15.390 1.00 32.70 C
-ATOM 3545 C GLN B 339 70.329 49.216 15.575 1.00 32.12 C
-ATOM 3546 O GLN B 339 71.527 49.222 15.872 1.00 33.21 O
-ATOM 3547 CB GLN B 339 69.597 47.527 13.910 1.00 31.03 C
-ATOM 3548 CG GLN B 339 70.984 47.315 13.350 1.00 27.08 C
-ATOM 3549 CD GLN B 339 70.953 46.595 12.023 1.00 26.96 C
-ATOM 3550 OE1 GLN B 339 71.117 47.210 10.971 1.00 27.76 O
-ATOM 3551 NE2 GLN B 339 70.729 45.279 12.063 1.00 24.84 N
-ATOM 3552 N ALA B 340 69.625 50.325 15.383 1.00 31.05 N
-ATOM 3553 CA ALA B 340 70.240 51.633 15.531 1.00 30.70 C
-ATOM 3554 C ALA B 340 70.646 51.857 16.981 1.00 31.49 C
-ATOM 3555 O ALA B 340 71.630 52.536 17.267 1.00 33.94 O
-ATOM 3556 CB ALA B 340 69.269 52.704 15.094 1.00 29.70 C
-ATOM 3557 N VAL B 341 69.877 51.277 17.891 1.00 30.39 N
-ATOM 3558 CA VAL B 341 70.130 51.411 19.317 1.00 30.71 C
-ATOM 3559 C VAL B 341 71.216 50.444 19.774 1.00 32.21 C
-ATOM 3560 O VAL B 341 72.079 50.798 20.576 1.00 28.62 O
-ATOM 3561 CB VAL B 341 68.829 51.164 20.127 1.00 31.56 C
-ATOM 3562 CG1 VAL B 341 69.128 51.172 21.635 1.00 31.69 C
-ATOM 3563 CG2 VAL B 341 67.806 52.231 19.779 1.00 30.26 C
-ATOM 3564 N ASP B 342 71.164 49.222 19.267 1.00 32.62 N
-ATOM 3565 CA ASP B 342 72.164 48.233 19.614 1.00 33.29 C
-ATOM 3566 C ASP B 342 73.529 48.766 19.180 1.00 32.48 C
-ATOM 3567 O ASP B 342 74.560 48.431 19.766 1.00 31.50 O
-ATOM 3568 CB ASP B 342 71.852 46.907 18.913 1.00 37.58 C
-ATOM 3569 CG ASP B 342 70.712 46.150 19.579 1.00 45.30 C
-ATOM 3570 OD1 ASP B 342 69.935 46.785 20.325 1.00 48.91 O
-ATOM 3571 OD2 ASP B 342 70.581 44.924 19.356 1.00 49.09 O
-ATOM 3572 N THR B 343 73.518 49.609 18.151 1.00 32.53 N
-ATOM 3573 CA THR B 343 74.738 50.191 17.617 1.00 33.32 C
-ATOM 3574 C THR B 343 75.275 51.195 18.600 1.00 34.53 C
-ATOM 3575 O THR B 343 76.479 51.294 18.795 1.00 35.65 O
-ATOM 3576 CB THR B 343 74.492 50.931 16.288 1.00 33.35 C
-ATOM 3577 OG1 THR B 343 74.164 49.986 15.259 1.00 33.16 O
-ATOM 3578 CG2 THR B 343 75.729 51.727 15.888 1.00 32.79 C
-ATOM 3579 N VAL B 344 74.379 51.957 19.211 1.00 35.21 N
-ATOM 3580 CA VAL B 344 74.803 52.958 20.170 1.00 34.09 C
-ATOM 3581 C VAL B 344 75.256 52.261 21.437 1.00 32.68 C
-ATOM 3582 O VAL B 344 76.235 52.663 22.045 1.00 30.76 O
-ATOM 3583 CB VAL B 344 73.665 53.946 20.481 1.00 37.18 C
-ATOM 3584 CG1 VAL B 344 74.111 54.942 21.522 1.00 39.83 C
-ATOM 3585 CG2 VAL B 344 73.256 54.673 19.206 1.00 39.69 C
-ATOM 3586 N LEU B 345 74.551 51.210 21.833 1.00 31.33 N
-ATOM 3587 CA LEU B 345 74.933 50.466 23.027 1.00 30.01 C
-ATOM 3588 C LEU B 345 76.246 49.749 22.754 1.00 29.83 C
-ATOM 3589 O LEU B 345 77.065 49.567 23.658 1.00 30.36 O
-ATOM 3590 CB LEU B 345 73.863 49.435 23.407 1.00 29.53 C
-ATOM 3591 CG LEU B 345 72.501 49.978 23.857 1.00 30.06 C
-ATOM 3592 CD1 LEU B 345 71.563 48.827 24.094 1.00 29.20 C
-ATOM 3593 CD2 LEU B 345 72.645 50.793 25.138 1.00 30.75 C
-ATOM 3594 N ALA B 346 76.446 49.345 21.501 1.00 29.79 N
-ATOM 3595 CA ALA B 346 77.665 48.643 21.115 1.00 29.54 C
-ATOM 3596 C ALA B 346 78.877 49.572 21.183 1.00 31.30 C
-ATOM 3597 O ALA B 346 79.975 49.159 21.570 1.00 30.44 O
-ATOM 3598 CB ALA B 346 77.518 48.083 19.720 1.00 26.97 C
-ATOM 3599 N LYS B 347 78.675 50.830 20.808 1.00 33.83 N
-ATOM 3600 CA LYS B 347 79.750 51.806 20.834 1.00 35.39 C
-ATOM 3601 C LYS B 347 80.087 52.097 22.295 1.00 36.26 C
-ATOM 3602 O LYS B 347 81.250 52.262 22.655 1.00 33.16 O
-ATOM 3603 CB LYS B 347 79.323 53.085 20.096 1.00 37.67 C
-ATOM 3604 CG LYS B 347 80.354 54.207 20.099 1.00 43.63 C
-ATOM 3605 CD LYS B 347 81.694 53.751 19.545 1.00 47.72 C
-ATOM 3606 CE LYS B 347 82.795 54.786 19.777 1.00 48.27 C
-ATOM 3607 NZ LYS B 347 84.165 54.220 19.504 1.00 48.67 N
-ATOM 3608 N LYS B 348 79.066 52.124 23.142 1.00 38.54 N
-ATOM 3609 CA LYS B 348 79.281 52.391 24.554 1.00 40.37 C
-ATOM 3610 C LYS B 348 79.996 51.242 25.239 1.00 42.08 C
-ATOM 3611 O LYS B 348 80.681 51.436 26.244 1.00 38.28 O
-ATOM 3612 CB LYS B 348 77.950 52.682 25.249 1.00 43.59 C
-ATOM 3613 CG LYS B 348 77.339 53.996 24.807 1.00 53.33 C
-ATOM 3614 CD LYS B 348 76.104 54.352 25.612 1.00 58.30 C
-ATOM 3615 CE LYS B 348 75.608 55.749 25.266 1.00 59.02 C
-ATOM 3616 NZ LYS B 348 74.437 56.117 26.109 1.00 60.12 N
-ATOM 3617 N ARG B 349 79.832 50.042 24.698 1.00 44.90 N
-ATOM 3618 CA ARG B 349 80.487 48.871 25.254 1.00 44.81 C
-ATOM 3619 C ARG B 349 81.959 48.897 24.826 1.00 42.98 C
-ATOM 3620 O ARG B 349 82.850 48.404 25.529 1.00 42.59 O
-ATOM 3621 CB ARG B 349 79.802 47.602 24.744 1.00 47.90 C
-ATOM 3622 CG ARG B 349 80.517 46.326 25.123 1.00 60.28 C
-ATOM 3623 CD ARG B 349 80.859 46.297 26.604 1.00 67.20 C
-ATOM 3624 NE ARG B 349 80.132 45.256 27.327 1.00 70.34 N
-ATOM 3625 CZ ARG B 349 78.808 45.213 27.472 1.00 70.31 C
-ATOM 3626 NH1 ARG B 349 78.038 46.158 26.945 1.00 70.03 N
-ATOM 3627 NH2 ARG B 349 78.249 44.218 28.150 1.00 69.88 N
-ATOM 3628 N VAL B 350 82.215 49.494 23.671 1.00 41.99 N
-ATOM 3629 CA VAL B 350 83.570 49.574 23.162 1.00 42.89 C
-ATOM 3630 C VAL B 350 84.382 50.624 23.908 1.00 42.33 C
-ATOM 3631 O VAL B 350 85.553 50.411 24.200 1.00 45.20 O
-ATOM 3632 CB VAL B 350 83.570 49.897 21.651 1.00 42.12 C
-ATOM 3633 CG1 VAL B 350 84.978 50.240 21.187 1.00 41.20 C
-ATOM 3634 CG2 VAL B 350 83.035 48.703 20.867 1.00 39.28 C
-ATOM 3635 N ASP B 351 83.764 51.756 24.222 1.00 41.66 N
-ATOM 3636 CA ASP B 351 84.471 52.814 24.927 1.00 40.28 C
-ATOM 3637 C ASP B 351 84.756 52.423 26.366 1.00 40.20 C
-ATOM 3638 O ASP B 351 85.732 52.881 26.969 1.00 35.85 O
-ATOM 3639 CB ASP B 351 83.666 54.105 24.886 1.00 40.64 C
-ATOM 3640 CG ASP B 351 83.540 54.652 23.498 1.00 42.17 C
-ATOM 3641 OD1 ASP B 351 84.480 54.434 22.703 1.00 44.45 O
-ATOM 3642 OD2 ASP B 351 82.514 55.308 23.210 1.00 43.39 O
-ATOM 3643 N SER B 352 83.894 51.574 26.909 1.00 39.00 N
-ATOM 3644 CA SER B 352 84.062 51.092 28.269 1.00 39.31 C
-ATOM 3645 C SER B 352 85.386 50.362 28.358 1.00 37.56 C
-ATOM 3646 O SER B 352 86.174 50.578 29.269 1.00 37.89 O
-ATOM 3647 CB SER B 352 82.943 50.114 28.648 1.00 41.62 C
-ATOM 3648 OG SER B 352 81.742 50.788 28.970 1.00 49.00 O
-ATOM 3649 N LEU B 353 85.638 49.506 27.385 1.00 35.98 N
-ATOM 3650 CA LEU B 353 86.855 48.729 27.399 1.00 35.71 C
-ATOM 3651 C LEU B 353 88.065 49.306 26.687 1.00 35.63 C
-ATOM 3652 O LEU B 353 89.122 48.672 26.680 1.00 39.17 O
-ATOM 3653 CB LEU B 353 86.552 47.342 26.845 1.00 34.84 C
-ATOM 3654 CG LEU B 353 85.559 46.567 27.701 1.00 32.99 C
-ATOM 3655 CD1 LEU B 353 85.137 45.313 26.974 1.00 31.38 C
-ATOM 3656 CD2 LEU B 353 86.216 46.235 29.039 1.00 32.04 C
-ATOM 3657 N GLN B 354 87.945 50.496 26.107 1.00 34.01 N
-ATOM 3658 CA GLN B 354 89.077 51.062 25.380 1.00 32.72 C
-ATOM 3659 C GLN B 354 89.514 52.481 25.692 1.00 31.82 C
-ATOM 3660 O GLN B 354 90.638 52.851 25.380 1.00 33.53 O
-ATOM 3661 CB GLN B 354 88.836 50.969 23.875 1.00 30.21 C
-ATOM 3662 CG GLN B 354 88.243 49.657 23.467 1.00 30.42 C
-ATOM 3663 CD GLN B 354 88.562 49.283 22.039 1.00 31.22 C
-ATOM 3664 OE1 GLN B 354 88.504 50.121 21.123 1.00 31.76 O
-ATOM 3665 NE2 GLN B 354 88.891 48.009 21.833 1.00 30.51 N
-ATOM 3666 N LEU B 355 88.658 53.301 26.274 1.00 30.07 N
-ATOM 3667 CA LEU B 355 89.100 54.656 26.543 1.00 30.74 C
-ATOM 3668 C LEU B 355 89.788 54.783 27.893 1.00 31.26 C
-ATOM 3669 O LEU B 355 89.479 54.053 28.843 1.00 31.32 O
-ATOM 3670 CB LEU B 355 87.922 55.619 26.469 1.00 30.80 C
-ATOM 3671 CG LEU B 355 87.202 55.581 25.129 1.00 29.10 C
-ATOM 3672 CD1 LEU B 355 86.028 56.522 25.155 1.00 28.35 C
-ATOM 3673 CD2 LEU B 355 88.174 55.959 24.029 1.00 29.41 C
-ATOM 3674 N THR B 356 90.748 55.698 27.963 1.00 30.32 N
-ATOM 3675 CA THR B 356 91.451 55.956 29.210 1.00 27.99 C
-ATOM 3676 C THR B 356 90.441 56.769 29.983 1.00 27.19 C
-ATOM 3677 O THR B 356 89.513 57.323 29.388 1.00 27.63 O
-ATOM 3678 CB THR B 356 92.685 56.811 28.985 1.00 27.25 C
-ATOM 3679 OG1 THR B 356 92.303 58.065 28.376 1.00 22.76 O
-ATOM 3680 CG2 THR B 356 93.671 56.061 28.103 1.00 24.43 C
-ATOM 3681 N ARG B 357 90.600 56.848 31.293 1.00 27.80 N
-ATOM 3682 CA ARG B 357 89.645 57.605 32.068 1.00 31.82 C
-ATOM 3683 C ARG B 357 89.606 59.082 31.655 1.00 39.66 C
-ATOM 3684 O ARG B 357 88.529 59.702 31.642 1.00 36.19 O
-ATOM 3685 CB ARG B 357 89.938 57.441 33.554 1.00 27.00 C
-ATOM 3686 CG ARG B 357 89.729 56.014 34.042 1.00 22.61 C
-ATOM 3687 CD ARG B 357 90.095 55.866 35.507 1.00 21.02 C
-ATOM 3688 NE ARG B 357 89.191 56.622 36.368 1.00 23.50 N
-ATOM 3689 CZ ARG B 357 87.917 56.304 36.584 1.00 22.05 C
-ATOM 3690 NH1 ARG B 357 87.383 55.237 36.004 1.00 22.06 N
-ATOM 3691 NH2 ARG B 357 87.175 57.057 37.383 1.00 22.73 N
-ATOM 3692 N GLU B 358 90.755 59.646 31.283 1.00 48.78 N
-ATOM 3693 CA GLU B 358 90.751 61.039 30.875 1.00 54.17 C
-ATOM 3694 C GLU B 358 89.879 61.210 29.631 1.00 50.56 C
-ATOM 3695 O GLU B 358 89.065 62.134 29.575 1.00 44.95 O
-ATOM 3696 CB GLU B 358 92.170 61.562 30.615 1.00 70.81 C
-ATOM 3697 CG GLU B 358 92.263 63.089 30.789 1.00102.33 C
-ATOM 3698 CD GLU B 358 93.674 63.645 30.666 1.00115.30 C
-ATOM 3699 OE1 GLU B 358 94.589 63.108 31.329 1.00119.65 O
-ATOM 3700 OE2 GLU B 358 93.862 64.631 29.917 1.00119.28 O
-ATOM 3701 N GLN B 359 90.027 60.325 28.643 1.00 43.72 N
-ATOM 3702 CA GLN B 359 89.208 60.423 27.432 1.00 35.07 C
-ATOM 3703 C GLN B 359 87.743 60.367 27.850 1.00 30.94 C
-ATOM 3704 O GLN B 359 86.893 61.071 27.289 1.00 28.83 O
-ATOM 3705 CB GLN B 359 89.507 59.282 26.469 1.00 32.53 C
-ATOM 3706 CG GLN B 359 90.969 59.120 26.154 1.00 34.68 C
-ATOM 3707 CD GLN B 359 91.224 57.948 25.221 1.00 37.16 C
-ATOM 3708 OE1 GLN B 359 90.667 56.855 25.396 1.00 35.83 O
-ATOM 3709 NE2 GLN B 359 92.075 58.168 24.223 1.00 37.58 N
-ATOM 3710 N MET B 360 87.454 59.527 28.843 1.00 27.62 N
-ATOM 3711 CA MET B 360 86.095 59.408 29.373 1.00 26.56 C
-ATOM 3712 C MET B 360 85.663 60.779 29.912 1.00 27.50 C
-ATOM 3713 O MET B 360 84.619 61.323 29.511 1.00 26.72 O
-ATOM 3714 CB MET B 360 86.036 58.372 30.515 1.00 22.82 C
-ATOM 3715 CG MET B 360 85.872 56.906 30.093 1.00 17.31 C
-ATOM 3716 SD MET B 360 85.841 55.762 31.514 1.00 15.67 S
-ATOM 3717 CE MET B 360 87.195 54.760 31.176 1.00 14.26 C
-ATOM 3718 N LEU B 361 86.481 61.341 30.807 1.00 26.92 N
-ATOM 3719 CA LEU B 361 86.171 62.634 31.401 1.00 26.64 C
-ATOM 3720 C LEU B 361 86.007 63.735 30.363 1.00 26.61 C
-ATOM 3721 O LEU B 361 85.213 64.651 30.562 1.00 25.27 O
-ATOM 3722 CB LEU B 361 87.249 63.058 32.408 1.00 27.64 C
-ATOM 3723 CG LEU B 361 86.838 63.711 33.752 1.00 27.55 C
-ATOM 3724 CD1 LEU B 361 87.946 64.652 34.224 1.00 24.80 C
-ATOM 3725 CD2 LEU B 361 85.513 64.472 33.622 1.00 26.29 C
-ATOM 3726 N THR B 362 86.748 63.665 29.260 1.00 28.11 N
-ATOM 3727 CA THR B 362 86.627 64.704 28.234 1.00 31.93 C
-ATOM 3728 C THR B 362 85.309 64.602 27.455 1.00 33.70 C
-ATOM 3729 O THR B 362 84.704 65.622 27.106 1.00 34.11 O
-ATOM 3730 CB THR B 362 87.781 64.661 27.234 1.00 31.36 C
-ATOM 3731 OG1 THR B 362 89.021 64.783 27.934 1.00 32.92 O
-ATOM 3732 CG2 THR B 362 87.661 65.813 26.255 1.00 32.58 C
-ATOM 3733 N ASN B 363 84.861 63.381 27.173 1.00 34.86 N
-ATOM 3734 CA ASN B 363 83.599 63.223 26.471 1.00 34.56 C
-ATOM 3735 C ASN B 363 82.530 63.846 27.352 1.00 34.02 C
-ATOM 3736 O ASN B 363 81.655 64.557 26.877 1.00 33.97 O
-ATOM 3737 CB ASN B 363 83.278 61.751 26.245 1.00 36.57 C
-ATOM 3738 CG ASN B 363 84.315 61.057 25.394 1.00 38.97 C
-ATOM 3739 OD1 ASN B 363 84.997 61.686 24.588 1.00 39.94 O
-ATOM 3740 ND2 ASN B 363 84.430 59.746 25.561 1.00 40.98 N
-ATOM 3741 N ARG B 364 82.624 63.589 28.650 1.00 33.79 N
-ATOM 3742 CA ARG B 364 81.668 64.138 29.601 1.00 34.11 C
-ATOM 3743 C ARG B 364 81.672 65.657 29.491 1.00 33.81 C
-ATOM 3744 O ARG B 364 80.621 66.286 29.392 1.00 34.79 O
-ATOM 3745 CB ARG B 364 82.039 63.710 31.025 1.00 34.92 C
-ATOM 3746 CG ARG B 364 81.113 64.224 32.100 1.00 35.24 C
-ATOM 3747 CD ARG B 364 79.720 63.681 31.944 1.00 35.27 C
-ATOM 3748 NE ARG B 364 78.778 64.409 32.784 1.00 37.20 N
-ATOM 3749 CZ ARG B 364 77.477 64.144 32.850 1.00 38.31 C
-ATOM 3750 NH1 ARG B 364 76.962 63.160 32.127 1.00 39.70 N
-ATOM 3751 NH2 ARG B 364 76.684 64.871 33.620 1.00 37.31 N
-ATOM 3752 N PHE B 365 82.862 66.244 29.496 1.00 32.52 N
-ATOM 3753 CA PHE B 365 82.991 67.692 29.394 1.00 31.25 C
-ATOM 3754 C PHE B 365 82.386 68.232 28.104 1.00 31.75 C
-ATOM 3755 O PHE B 365 81.663 69.240 28.121 1.00 29.40 O
-ATOM 3756 CB PHE B 365 84.463 68.087 29.517 1.00 30.06 C
-ATOM 3757 CG PHE B 365 84.936 68.179 30.934 1.00 30.36 C
-ATOM 3758 CD1 PHE B 365 84.235 67.545 31.959 1.00 31.72 C
-ATOM 3759 CD2 PHE B 365 86.079 68.900 31.253 1.00 29.41 C
-ATOM 3760 CE1 PHE B 365 84.667 67.630 33.285 1.00 30.86 C
-ATOM 3761 CE2 PHE B 365 86.523 68.993 32.568 1.00 29.08 C
-ATOM 3762 CZ PHE B 365 85.818 68.357 33.588 1.00 30.67 C
-ATOM 3763 N ASN B 366 82.671 67.561 26.989 1.00 30.81 N
-ATOM 3764 CA ASN B 366 82.127 67.987 25.712 1.00 30.95 C
-ATOM 3765 C ASN B 366 80.615 68.018 25.790 1.00 33.38 C
-ATOM 3766 O ASN B 366 79.973 68.962 25.314 1.00 30.44 O
-ATOM 3767 CB ASN B 366 82.573 67.052 24.598 1.00 29.44 C
-ATOM 3768 CG ASN B 366 83.985 67.329 24.156 1.00 29.88 C
-ATOM 3769 OD1 ASN B 366 84.327 68.471 23.875 1.00 30.77 O
-ATOM 3770 ND2 ASN B 366 84.817 66.288 24.090 1.00 31.26 N
-ATOM 3771 N ASP B 367 80.047 66.995 26.415 1.00 37.78 N
-ATOM 3772 CA ASP B 367 78.603 66.926 26.562 1.00 41.01 C
-ATOM 3773 C ASP B 367 78.072 68.084 27.391 1.00 39.56 C
-ATOM 3774 O ASP B 367 77.196 68.822 26.939 1.00 38.85 O
-ATOM 3775 CB ASP B 367 78.198 65.587 27.174 1.00 48.84 C
-ATOM 3776 CG ASP B 367 78.341 64.434 26.187 1.00 60.70 C
-ATOM 3777 OD1 ASP B 367 77.619 64.428 25.166 1.00 66.84 O
-ATOM 3778 OD2 ASP B 367 79.180 63.540 26.420 1.00 67.04 O
-ATOM 3779 N LEU B 368 78.600 68.267 28.594 1.00 35.98 N
-ATOM 3780 CA LEU B 368 78.132 69.375 29.413 1.00 31.25 C
-ATOM 3781 C LEU B 368 78.281 70.658 28.608 1.00 28.73 C
-ATOM 3782 O LEU B 368 77.414 71.526 28.647 1.00 26.95 O
-ATOM 3783 CB LEU B 368 78.928 69.473 30.715 1.00 32.07 C
-ATOM 3784 CG LEU B 368 78.741 68.322 31.712 1.00 33.32 C
-ATOM 3785 CD1 LEU B 368 79.473 68.666 33.002 1.00 32.58 C
-ATOM 3786 CD2 LEU B 368 77.251 68.084 31.981 1.00 32.94 C
-ATOM 3787 N LEU B 369 79.373 70.777 27.862 1.00 28.21 N
-ATOM 3788 CA LEU B 369 79.560 71.969 27.054 1.00 28.53 C
-ATOM 3789 C LEU B 369 78.444 72.025 26.019 1.00 31.16 C
-ATOM 3790 O LEU B 369 77.818 73.077 25.832 1.00 33.08 O
-ATOM 3791 CB LEU B 369 80.928 71.971 26.359 1.00 21.52 C
-ATOM 3792 CG LEU B 369 82.155 72.464 27.146 1.00 16.34 C
-ATOM 3793 CD1 LEU B 369 83.349 72.569 26.186 1.00 12.51 C
-ATOM 3794 CD2 LEU B 369 81.877 73.836 27.781 1.00 13.17 C
-ATOM 3795 N ASP B 370 78.183 70.898 25.358 1.00 36.36 N
-ATOM 3796 CA ASP B 370 77.125 70.853 24.356 1.00 40.75 C
-ATOM 3797 C ASP B 370 75.882 71.552 24.916 1.00 42.57 C
-ATOM 3798 O ASP B 370 75.249 72.355 24.229 1.00 44.78 O
-ATOM 3799 CB ASP B 370 76.795 69.400 23.965 1.00 43.02 C
-ATOM 3800 CG ASP B 370 77.877 68.756 23.073 1.00 48.21 C
-ATOM 3801 OD1 ASP B 370 78.292 69.386 22.068 1.00 50.27 O
-ATOM 3802 OD2 ASP B 370 78.310 67.613 23.366 1.00 50.04 O
-ATOM 3803 N ARG B 371 75.549 71.271 26.174 1.00 43.01 N
-ATOM 3804 CA ARG B 371 74.384 71.888 26.807 1.00 42.46 C
-ATOM 3805 C ARG B 371 74.542 73.386 26.963 1.00 41.54 C
-ATOM 3806 O ARG B 371 73.631 74.160 26.664 1.00 42.36 O
-ATOM 3807 CB ARG B 371 74.160 71.346 28.206 1.00 43.84 C
-ATOM 3808 CG ARG B 371 73.765 69.930 28.310 1.00 45.50 C
-ATOM 3809 CD ARG B 371 73.346 69.746 29.731 1.00 47.79 C
-ATOM 3810 NE ARG B 371 73.457 68.365 30.170 1.00 51.73 N
-ATOM 3811 CZ ARG B 371 73.344 67.990 31.439 1.00 51.00 C
-ATOM 3812 NH1 ARG B 371 73.119 68.909 32.375 1.00 47.19 N
-ATOM 3813 NH2 ARG B 371 73.450 66.704 31.767 1.00 51.17 N
-ATOM 3814 N MET B 372 75.697 73.779 27.486 1.00 39.37 N
-ATOM 3815 CA MET B 372 75.987 75.180 27.715 1.00 37.56 C
-ATOM 3816 C MET B 372 75.759 76.012 26.457 1.00 37.35 C
-ATOM 3817 O MET B 372 75.131 77.072 26.524 1.00 38.99 O
-ATOM 3818 CB MET B 372 77.423 75.337 28.239 1.00 34.77 C
-ATOM 3819 CG MET B 372 77.597 74.865 29.706 1.00 27.50 C
-ATOM 3820 SD MET B 372 79.306 74.596 30.190 1.00 19.75 S
-ATOM 3821 CE MET B 372 79.791 76.258 30.566 1.00 22.14 C
-ATOM 3822 N ASP B 373 76.238 75.538 25.309 1.00 37.88 N
-ATOM 3823 CA ASP B 373 76.029 76.291 24.073 1.00 40.62 C
-ATOM 3824 C ASP B 373 74.527 76.564 23.927 1.00 42.73 C
-ATOM 3825 O ASP B 373 74.115 77.661 23.550 1.00 44.89 O
-ATOM 3826 CB ASP B 373 76.536 75.514 22.852 1.00 37.14 C
-ATOM 3827 CG ASP B 373 78.034 75.274 22.895 1.00 34.93 C
-ATOM 3828 OD1 ASP B 373 78.748 76.081 23.532 1.00 34.98 O
-ATOM 3829 OD2 ASP B 373 78.507 74.286 22.286 1.00 32.01 O
-ATOM 3830 N ILE B 374 73.711 75.568 24.251 1.00 42.40 N
-ATOM 3831 CA ILE B 374 72.273 75.726 24.160 1.00 41.74 C
-ATOM 3832 C ILE B 374 71.657 76.545 25.291 1.00 40.51 C
-ATOM 3833 O ILE B 374 70.911 77.479 25.016 1.00 40.48 O
-ATOM 3834 CB ILE B 374 71.579 74.377 24.111 1.00 43.36 C
-ATOM 3835 CG1 ILE B 374 72.114 73.584 22.927 1.00 45.31 C
-ATOM 3836 CG2 ILE B 374 70.077 74.577 23.998 1.00 43.88 C
-ATOM 3837 CD1 ILE B 374 71.606 72.159 22.878 1.00 48.19 C
-ATOM 3838 N MET B 375 71.939 76.191 26.548 1.00 37.53 N
-ATOM 3839 CA MET B 375 71.389 76.935 27.693 1.00 36.20 C
-ATOM 3840 C MET B 375 71.649 78.425 27.548 1.00 36.07 C
-ATOM 3841 O MET B 375 70.754 79.258 27.747 1.00 36.64 O
-ATOM 3842 CB MET B 375 72.053 76.539 29.010 1.00 33.12 C
-ATOM 3843 CG MET B 375 71.789 75.165 29.530 1.00 32.29 C
-ATOM 3844 SD MET B 375 73.032 74.915 30.784 1.00 27.50 S
-ATOM 3845 CE MET B 375 72.519 76.117 32.007 1.00 27.30 C
-ATOM 3846 N PHE B 376 72.903 78.748 27.240 1.00 37.69 N
-ATOM 3847 CA PHE B 376 73.336 80.130 27.103 1.00 39.07 C
-ATOM 3848 C PHE B 376 73.245 80.650 25.682 1.00 40.59 C
-ATOM 3849 O PHE B 376 73.580 81.800 25.421 1.00 43.00 O
-ATOM 3850 CB PHE B 376 74.766 80.278 27.645 1.00 35.86 C
-ATOM 3851 CG PHE B 376 74.918 79.797 29.068 1.00 30.20 C
-ATOM 3852 CD1 PHE B 376 74.176 80.378 30.094 1.00 26.27 C
-ATOM 3853 CD2 PHE B 376 75.784 78.742 29.377 1.00 29.57 C
-ATOM 3854 CE1 PHE B 376 74.289 79.915 31.409 1.00 27.89 C
-ATOM 3855 CE2 PHE B 376 75.908 78.270 30.690 1.00 26.94 C
-ATOM 3856 CZ PHE B 376 75.158 78.859 31.706 1.00 27.89 C
-ATOM 3857 N GLY B 377 72.795 79.803 24.765 1.00 43.72 N
-ATOM 3858 CA GLY B 377 72.654 80.247 23.392 1.00 46.64 C
-ATOM 3859 C GLY B 377 71.498 81.228 23.283 1.00 47.84 C
-ATOM 3860 O GLY B 377 70.863 81.566 24.300 1.00 47.76 O
-ATOM 3861 N SER B 378 71.214 81.684 22.060 1.00 48.61 N
-ATOM 3862 CA SER B 378 70.118 82.632 21.830 1.00 51.26 C
-ATOM 3863 C SER B 378 68.749 81.961 21.943 1.00 54.56 C
-ATOM 3864 O SER B 378 67.722 82.641 21.957 1.00 51.94 O
-ATOM 3865 CB SER B 378 70.226 83.252 20.447 1.00 49.77 C
-ATOM 3866 OG SER B 378 69.770 82.333 19.476 1.00 49.66 O
-ATOM 3867 N THR B 379 68.747 80.629 22.006 1.00 59.08 N
-ATOM 3868 CA THR B 379 67.517 79.847 22.123 1.00 60.19 C
-ATOM 3869 C THR B 379 67.300 79.401 23.564 1.00 58.26 C
-ATOM 3870 O THR B 379 66.171 79.187 23.991 1.00 54.54 O
-ATOM 3871 CB THR B 379 67.558 78.588 21.228 1.00 68.23 C
-ATOM 3872 OG1 THR B 379 67.627 78.981 19.854 1.00 80.85 O
-ATOM 3873 CG2 THR B 379 66.315 77.740 21.437 1.00 79.96 C
-ATOM 3874 N GLY B 380 68.388 79.257 24.308 1.00 54.69 N
-ATOM 3875 CA GLY B 380 68.275 78.838 25.689 1.00 50.12 C
-ATOM 3876 C GLY B 380 67.628 79.907 26.545 1.00 47.71 C
-ATOM 3877 O GLY B 380 67.400 81.019 26.082 1.00 47.07 O
-ATOM 3878 N SER B 381 67.344 79.568 27.800 1.00 46.66 N
-ATOM 3879 CA SER B 381 66.711 80.488 28.743 1.00 49.51 C
-ATOM 3880 C SER B 381 67.627 80.854 29.915 1.00 50.63 C
-ATOM 3881 O SER B 381 67.268 81.669 30.770 1.00 53.75 O
-ATOM 3882 CB SER B 381 65.434 79.851 29.284 1.00 49.16 C
-ATOM 3883 OG SER B 381 65.707 78.543 29.751 1.00 44.63 O
-ATOM 3884 N ALA B 382 68.814 80.257 29.944 1.00 48.60 N
-ATOM 3885 CA ALA B 382 69.768 80.495 31.019 1.00 46.12 C
-ATOM 3886 C ALA B 382 70.404 81.887 31.044 1.00 45.61 C
-ATOM 3887 O ALA B 382 70.750 82.455 30.002 1.00 40.04 O
-ATOM 3888 CB ALA B 382 70.857 79.430 30.971 1.00 44.23 C
-ATOM 3889 N ASP B 383 70.554 82.416 32.258 1.00 42.31 N
-ATOM 3890 CA ASP B 383 71.162 83.725 32.493 1.00 40.08 C
-ATOM 3891 C ASP B 383 72.584 83.438 32.954 1.00 38.79 C
-ATOM 3892 O ASP B 383 72.813 82.977 34.075 1.00 35.84 O
-ATOM 3893 CB ASP B 383 70.408 84.473 33.596 1.00 45.25 C
-ATOM 3894 CG ASP B 383 70.929 85.884 33.814 1.00 52.61 C
-ATOM 3895 OD1 ASP B 383 72.162 86.090 33.786 1.00 57.72 O
-ATOM 3896 OD2 ASP B 383 70.100 86.791 34.032 1.00 57.22 O
-ATOM 3897 N ILE B 384 73.547 83.710 32.089 1.00 36.75 N
-ATOM 3898 CA ILE B 384 74.928 83.442 32.434 1.00 36.63 C
-ATOM 3899 C ILE B 384 75.405 84.209 33.668 1.00 42.65 C
-ATOM 3900 O ILE B 384 76.306 83.747 34.377 1.00 36.77 O
-ATOM 3901 CB ILE B 384 75.848 83.730 31.249 1.00 33.86 C
-ATOM 3902 CG1 ILE B 384 77.226 83.147 31.536 1.00 34.30 C
-ATOM 3903 CG2 ILE B 384 75.906 85.218 30.986 1.00 33.71 C
-ATOM 3904 CD1 ILE B 384 78.171 83.278 30.382 1.00 37.84 C
-ATOM 3905 N GLU B 385 74.812 85.376 33.925 1.00 50.34 N
-ATOM 3906 CA GLU B 385 75.180 86.160 35.104 1.00 54.17 C
-ATOM 3907 C GLU B 385 74.835 85.359 36.356 1.00 51.51 C
-ATOM 3908 O GLU B 385 75.583 85.356 37.336 1.00 44.78 O
-ATOM 3909 CB GLU B 385 74.411 87.478 35.164 1.00 69.17 C
-ATOM 3910 CG GLU B 385 74.851 88.533 34.185 1.00100.62 C
-ATOM 3911 CD GLU B 385 74.730 89.925 34.780 1.00113.92 C
-ATOM 3912 OE1 GLU B 385 73.719 90.187 35.472 1.00117.90 O
-ATOM 3913 OE2 GLU B 385 75.642 90.754 34.554 1.00118.68 O
-ATOM 3914 N GLU B 386 73.690 84.683 36.311 1.00 45.21 N
-ATOM 3915 CA GLU B 386 73.226 83.893 37.439 1.00 38.46 C
-ATOM 3916 C GLU B 386 74.071 82.651 37.655 1.00 36.10 C
-ATOM 3917 O GLU B 386 74.249 82.195 38.796 1.00 33.10 O
-ATOM 3918 CB GLU B 386 71.753 83.526 37.252 1.00 39.98 C
-ATOM 3919 CG GLU B 386 70.809 84.678 37.565 1.00 47.18 C
-ATOM 3920 CD GLU B 386 69.354 84.315 37.354 1.00 52.36 C
-ATOM 3921 OE1 GLU B 386 68.952 83.218 37.795 1.00 53.77 O
-ATOM 3922 OE2 GLU B 386 68.606 85.127 36.757 1.00 54.49 O
-ATOM 3923 N TRP B 387 74.610 82.111 36.564 1.00 33.02 N
-ATOM 3924 CA TRP B 387 75.458 80.930 36.657 1.00 30.12 C
-ATOM 3925 C TRP B 387 76.887 81.302 37.081 1.00 28.35 C
-ATOM 3926 O TRP B 387 77.689 80.440 37.469 1.00 26.70 O
-ATOM 3927 CB TRP B 387 75.449 80.169 35.327 1.00 31.31 C
-ATOM 3928 CG TRP B 387 74.214 79.364 35.177 1.00 35.49 C
-ATOM 3929 CD1 TRP B 387 72.984 79.808 34.777 1.00 37.06 C
-ATOM 3930 CD2 TRP B 387 74.043 77.992 35.546 1.00 36.75 C
-ATOM 3931 NE1 TRP B 387 72.057 78.796 34.880 1.00 37.94 N
-ATOM 3932 CE2 TRP B 387 72.681 77.671 35.347 1.00 37.24 C
-ATOM 3933 CE3 TRP B 387 74.912 77.001 36.025 1.00 37.30 C
-ATOM 3934 CZ2 TRP B 387 72.165 76.402 35.618 1.00 37.27 C
-ATOM 3935 CZ3 TRP B 387 74.398 75.736 36.294 1.00 37.95 C
-ATOM 3936 CH2 TRP B 387 73.037 75.448 36.088 1.00 37.83 C
-ATOM 3937 N MET B 388 77.203 82.590 37.000 1.00 27.61 N
-ATOM 3938 CA MET B 388 78.513 83.061 37.413 1.00 27.95 C
-ATOM 3939 C MET B 388 78.359 83.515 38.872 1.00 27.72 C
-ATOM 3940 O MET B 388 79.336 83.695 39.603 1.00 29.42 O
-ATOM 3941 CB MET B 388 78.978 84.218 36.513 1.00 26.24 C
-ATOM 3942 CG MET B 388 79.756 83.789 35.246 1.00 22.25 C
-ATOM 3943 SD MET B 388 81.445 83.155 35.517 1.00 14.78 S
-ATOM 3944 CE MET B 388 81.235 81.674 34.892 1.00 18.81 C
-ATOM 3945 N ALA B 389 77.116 83.692 39.295 1.00 28.99 N
-ATOM 3946 CA ALA B 389 76.859 84.082 40.669 1.00 29.51 C
-ATOM 3947 C ALA B 389 77.015 82.770 41.406 1.00 29.60 C
-ATOM 3948 O ALA B 389 77.330 82.733 42.604 1.00 28.45 O
-ATOM 3949 CB ALA B 389 75.429 84.618 40.817 1.00 29.44 C
-ATOM 3950 N GLY B 390 76.792 81.687 40.661 1.00 28.44 N
-ATOM 3951 CA GLY B 390 76.907 80.361 41.234 1.00 27.86 C
-ATOM 3952 C GLY B 390 78.346 79.969 41.506 1.00 26.72 C
-ATOM 3953 O GLY B 390 78.653 79.373 42.549 1.00 26.18 O
-ATOM 3954 N VAL B 391 79.231 80.305 40.565 1.00 25.12 N
-ATOM 3955 CA VAL B 391 80.654 79.999 40.701 1.00 22.35 C
-ATOM 3956 C VAL B 391 81.158 80.742 41.915 1.00 21.36 C
-ATOM 3957 O VAL B 391 81.850 80.186 42.753 1.00 21.06 O
-ATOM 3958 CB VAL B 391 81.454 80.457 39.460 1.00 21.90 C
-ATOM 3959 CG1 VAL B 391 82.905 80.083 39.594 1.00 18.60 C
-ATOM 3960 CG2 VAL B 391 80.879 79.807 38.219 1.00 22.35 C
-ATOM 3961 N ALA B 392 80.776 82.006 42.011 1.00 20.19 N
-ATOM 3962 CA ALA B 392 81.196 82.841 43.119 1.00 20.99 C
-ATOM 3963 C ALA B 392 80.753 82.257 44.463 1.00 21.88 C
-ATOM 3964 O ALA B 392 81.548 82.163 45.412 1.00 22.07 O
-ATOM 3965 CB ALA B 392 80.634 84.256 42.937 1.00 19.27 C
-ATOM 3966 N TRP B 393 79.485 81.874 44.552 1.00 23.98 N
-ATOM 3967 CA TRP B 393 79.004 81.312 45.795 1.00 26.79 C
-ATOM 3968 C TRP B 393 79.793 80.046 46.066 1.00 27.18 C
-ATOM 3969 O TRP B 393 80.424 79.916 47.115 1.00 28.78 O
-ATOM 3970 CB TRP B 393 77.517 80.976 45.721 1.00 28.13 C
-ATOM 3971 CG TRP B 393 76.949 80.598 47.053 1.00 28.90 C
-ATOM 3972 CD1 TRP B 393 76.435 81.441 47.995 1.00 29.54 C
-ATOM 3973 CD2 TRP B 393 76.869 79.282 47.610 1.00 29.83 C
-ATOM 3974 NE1 TRP B 393 76.035 80.733 49.108 1.00 29.88 N
-ATOM 3975 CE2 TRP B 393 76.290 79.404 48.897 1.00 30.35 C
-ATOM 3976 CE3 TRP B 393 77.231 78.011 47.150 1.00 29.12 C
-ATOM 3977 CZ2 TRP B 393 76.064 78.294 49.728 1.00 29.04 C
-ATOM 3978 CZ3 TRP B 393 77.007 76.912 47.978 1.00 28.95 C
-ATOM 3979 CH2 TRP B 393 76.430 77.062 49.250 1.00 27.79 C
-ATOM 3980 N LEU B 394 79.769 79.116 45.116 1.00 26.88 N
-ATOM 3981 CA LEU B 394 80.507 77.868 45.285 1.00 26.43 C
-ATOM 3982 C LEU B 394 81.983 78.112 45.652 1.00 26.41 C
-ATOM 3983 O LEU B 394 82.591 77.326 46.384 1.00 26.77 O
-ATOM 3984 CB LEU B 394 80.411 77.022 44.014 1.00 25.18 C
-ATOM 3985 CG LEU B 394 79.186 76.112 43.910 1.00 27.18 C
-ATOM 3986 CD1 LEU B 394 79.067 75.525 42.509 1.00 27.42 C
-ATOM 3987 CD2 LEU B 394 79.304 74.991 44.952 1.00 30.90 C
-ATOM 3988 N HIS B 395 82.546 79.221 45.184 1.00 26.80 N
-ATOM 3989 CA HIS B 395 83.936 79.517 45.466 1.00 27.58 C
-ATOM 3990 C HIS B 395 84.127 80.050 46.886 1.00 29.81 C
-ATOM 3991 O HIS B 395 85.260 80.315 47.318 1.00 33.66 O
-ATOM 3992 CB HIS B 395 84.469 80.501 44.412 1.00 27.68 C
-ATOM 3993 CG HIS B 395 85.959 80.458 44.231 1.00 26.49 C
-ATOM 3994 ND1 HIS B 395 86.832 81.140 45.052 1.00 24.54 N
-ATOM 3995 CD2 HIS B 395 86.728 79.790 43.338 1.00 25.64 C
-ATOM 3996 CE1 HIS B 395 88.073 80.893 44.675 1.00 25.33 C
-ATOM 3997 NE2 HIS B 395 88.042 80.075 43.636 1.00 23.82 N
-ATOM 3998 N CYS B 396 83.026 80.206 47.618 1.00 32.44 N
-ATOM 3999 CA CYS B 396 83.103 80.687 49.003 1.00 33.22 C
-ATOM 4000 C CYS B 396 82.759 79.559 49.973 1.00 31.28 C
-ATOM 4001 O CYS B 396 82.844 79.721 51.188 1.00 32.73 O
-ATOM 4002 CB CYS B 396 82.165 81.882 49.225 1.00 33.37 C
-ATOM 4003 SG CYS B 396 82.703 83.458 48.456 1.00 32.20 S
-ATOM 4004 N LEU B 397 82.389 78.409 49.414 1.00 30.03 N
-ATOM 4005 CA LEU B 397 82.030 77.234 50.193 1.00 29.91 C
-ATOM 4006 C LEU B 397 83.278 76.533 50.746 1.00 31.11 C
-ATOM 4007 O LEU B 397 83.223 75.915 51.806 1.00 33.59 O
-ATOM 4008 CB LEU B 397 81.221 76.272 49.319 1.00 25.95 C
-ATOM 4009 CG LEU B 397 80.639 74.987 49.941 1.00 23.46 C
-ATOM 4010 CD1 LEU B 397 79.659 75.348 51.058 1.00 18.81 C
-ATOM 4011 CD2 LEU B 397 79.940 74.154 48.860 1.00 17.88 C
-ATOM 4012 N LEU B 398 84.401 76.647 50.036 1.00 30.63 N
-ATOM 4013 CA LEU B 398 85.657 76.031 50.453 1.00 29.96 C
-ATOM 4014 C LEU B 398 86.843 76.866 50.001 1.00 30.06 C
-ATOM 4015 O LEU B 398 86.779 77.587 48.995 1.00 29.42 O
-ATOM 4016 CB LEU B 398 85.812 74.640 49.849 1.00 30.26 C
-ATOM 4017 CG LEU B 398 85.488 73.351 50.596 1.00 28.60 C
-ATOM 4018 CD1 LEU B 398 84.200 73.462 51.357 1.00 29.62 C
-ATOM 4019 CD2 LEU B 398 85.396 72.234 49.571 1.00 29.56 C
-ATOM 4020 N PRO B 399 87.952 76.776 50.744 1.00 36.38 N
-ATOM 4021 CA PRO B 399 89.182 77.511 50.442 1.00 36.28 C
-ATOM 4022 C PRO B 399 89.838 76.882 49.220 1.00 39.84 C
-ATOM 4023 O PRO B 399 89.938 75.656 49.147 1.00 39.96 O
-ATOM 4024 CB PRO B 399 90.021 77.308 51.700 1.00 35.60 C
-ATOM 4025 CG PRO B 399 88.976 77.057 52.778 1.00 36.60 C
-ATOM 4026 CD PRO B 399 88.029 76.146 52.072 1.00 34.07 C
-ATOM 4027 N LYS B 400 90.288 77.714 48.278 1.00 44.16 N
-ATOM 4028 CA LYS B 400 90.932 77.257 47.038 1.00 44.01 C
-ATOM 4029 C LYS B 400 90.087 76.189 46.342 1.00 38.78 C
-ATOM 4030 O LYS B 400 90.597 75.156 45.918 1.00 34.94 O
-ATOM 4031 CB LYS B 400 92.338 76.714 47.327 1.00 53.19 C
-ATOM 4032 CG LYS B 400 93.235 77.700 48.070 1.00 70.95 C
-ATOM 4033 CD LYS B 400 94.708 77.294 48.076 1.00 80.04 C
-ATOM 4034 CE LYS B 400 95.360 77.515 46.710 1.00 83.91 C
-ATOM 4035 NZ LYS B 400 96.831 77.231 46.703 1.00 84.24 N
-ATOM 4036 N MET B 401 88.795 76.475 46.206 1.00 30.38 N
-ATOM 4037 CA MET B 401 87.833 75.556 45.618 1.00 24.59 C
-ATOM 4038 C MET B 401 88.135 75.068 44.204 1.00 23.45 C
-ATOM 4039 O MET B 401 87.888 73.907 43.879 1.00 23.40 O
-ATOM 4040 CB MET B 401 86.422 76.174 45.675 1.00 19.51 C
-ATOM 4041 CG MET B 401 85.328 75.293 45.067 1.00 12.14 C
-ATOM 4042 SD MET B 401 85.121 73.773 45.954 1.00 6.69 S
-ATOM 4043 CE MET B 401 83.678 74.146 46.984 1.00 7.33 C
-ATOM 4044 N ASP B 402 88.654 75.938 43.354 1.00 22.60 N
-ATOM 4045 CA ASP B 402 88.970 75.519 41.996 1.00 23.23 C
-ATOM 4046 C ASP B 402 90.124 74.520 41.978 1.00 22.55 C
-ATOM 4047 O ASP B 402 90.184 73.652 41.108 1.00 22.31 O
-ATOM 4048 CB ASP B 402 89.283 76.737 41.104 1.00 23.95 C
-ATOM 4049 CG ASP B 402 90.457 77.554 41.602 1.00 26.30 C
-ATOM 4050 OD1 ASP B 402 91.611 77.327 41.146 1.00 26.64 O
-ATOM 4051 OD2 ASP B 402 90.208 78.429 42.458 1.00 27.75 O
-ATOM 4052 N SER B 403 91.034 74.646 42.940 1.00 21.07 N
-ATOM 4053 CA SER B 403 92.179 73.754 43.039 1.00 19.49 C
-ATOM 4054 C SER B 403 91.631 72.476 43.656 1.00 19.95 C
-ATOM 4055 O SER B 403 92.106 71.383 43.387 1.00 20.21 O
-ATOM 4056 CB SER B 403 93.259 74.365 43.936 1.00 17.92 C
-ATOM 4057 OG SER B 403 93.552 75.703 43.568 1.00 19.10 O
-ATOM 4058 N VAL B 404 90.606 72.620 44.478 1.00 21.49 N
-ATOM 4059 CA VAL B 404 89.993 71.465 45.087 1.00 23.64 C
-ATOM 4060 C VAL B 404 89.284 70.655 44.007 1.00 22.90 C
-ATOM 4061 O VAL B 404 89.448 69.443 43.933 1.00 25.74 O
-ATOM 4062 CB VAL B 404 88.976 71.872 46.176 1.00 25.78 C
-ATOM 4063 CG1 VAL B 404 88.138 70.663 46.585 1.00 28.47 C
-ATOM 4064 CG2 VAL B 404 89.717 72.423 47.385 1.00 27.06 C
-ATOM 4065 N VAL B 405 88.493 71.322 43.171 1.00 22.93 N
-ATOM 4066 CA VAL B 405 87.784 70.624 42.107 1.00 23.74 C
-ATOM 4067 C VAL B 405 88.766 69.938 41.167 1.00 25.13 C
-ATOM 4068 O VAL B 405 88.593 68.768 40.804 1.00 25.85 O
-ATOM 4069 CB VAL B 405 86.922 71.578 41.272 1.00 20.21 C
-ATOM 4070 CG1 VAL B 405 86.400 70.849 40.031 1.00 17.52 C
-ATOM 4071 CG2 VAL B 405 85.765 72.086 42.102 1.00 15.99 C
-ATOM 4072 N TYR B 406 89.787 70.681 40.762 1.00 27.11 N
-ATOM 4073 CA TYR B 406 90.809 70.164 39.870 1.00 29.13 C
-ATOM 4074 C TYR B 406 91.416 68.876 40.436 1.00 29.32 C
-ATOM 4075 O TYR B 406 91.453 67.842 39.758 1.00 27.58 O
-ATOM 4076 CB TYR B 406 91.888 71.230 39.662 1.00 32.47 C
-ATOM 4077 CG TYR B 406 93.121 70.746 38.933 1.00 38.98 C
-ATOM 4078 CD1 TYR B 406 93.054 70.282 37.612 1.00 40.68 C
-ATOM 4079 CD2 TYR B 406 94.360 70.751 39.563 1.00 39.36 C
-ATOM 4080 CE1 TYR B 406 94.201 69.831 36.945 1.00 41.20 C
-ATOM 4081 CE2 TYR B 406 95.501 70.308 38.912 1.00 40.84 C
-ATOM 4082 CZ TYR B 406 95.423 69.854 37.609 1.00 40.66 C
-ATOM 4083 OH TYR B 406 96.576 69.430 36.994 1.00 40.25 O
-ATOM 4084 N ASP B 407 91.884 68.933 41.679 1.00 27.56 N
-ATOM 4085 CA ASP B 407 92.473 67.761 42.295 1.00 26.28 C
-ATOM 4086 C ASP B 407 91.540 66.553 42.255 1.00 25.90 C
-ATOM 4087 O ASP B 407 91.917 65.475 41.784 1.00 25.12 O
-ATOM 4088 CB ASP B 407 92.865 68.062 43.742 1.00 28.19 C
-ATOM 4089 CG ASP B 407 94.025 69.029 43.841 1.00 31.96 C
-ATOM 4090 OD1 ASP B 407 94.975 68.907 43.044 1.00 35.67 O
-ATOM 4091 OD2 ASP B 407 94.000 69.908 44.724 1.00 32.88 O
-ATOM 4092 N PHE B 408 90.326 66.731 42.759 1.00 23.91 N
-ATOM 4093 CA PHE B 408 89.359 65.652 42.777 1.00 21.79 C
-ATOM 4094 C PHE B 408 89.429 64.957 41.422 1.00 20.53 C
-ATOM 4095 O PHE B 408 89.528 63.741 41.342 1.00 17.94 O
-ATOM 4096 CB PHE B 408 87.951 66.218 43.022 1.00 23.22 C
-ATOM 4097 CG PHE B 408 86.874 65.163 43.157 1.00 24.94 C
-ATOM 4098 CD1 PHE B 408 86.855 64.309 44.247 1.00 23.90 C
-ATOM 4099 CD2 PHE B 408 85.879 65.027 42.176 1.00 25.89 C
-ATOM 4100 CE1 PHE B 408 85.855 63.327 44.361 1.00 27.42 C
-ATOM 4101 CE2 PHE B 408 84.874 64.052 42.279 1.00 25.04 C
-ATOM 4102 CZ PHE B 408 84.862 63.201 43.370 1.00 25.97 C
-ATOM 4103 N LEU B 409 89.387 65.747 40.358 1.00 20.67 N
-ATOM 4104 CA LEU B 409 89.439 65.220 39.000 1.00 21.08 C
-ATOM 4105 C LEU B 409 90.695 64.382 38.777 1.00 23.30 C
-ATOM 4106 O LEU B 409 90.614 63.236 38.336 1.00 20.40 O
-ATOM 4107 CB LEU B 409 89.373 66.374 37.988 1.00 19.20 C
-ATOM 4108 CG LEU B 409 88.064 67.175 38.044 1.00 20.21 C
-ATOM 4109 CD1 LEU B 409 88.050 68.302 37.021 1.00 19.29 C
-ATOM 4110 CD2 LEU B 409 86.906 66.227 37.790 1.00 19.92 C
-ATOM 4111 N LYS B 410 91.859 64.944 39.073 1.00 27.46 N
-ATOM 4112 CA LYS B 410 93.070 64.177 38.884 1.00 30.34 C
-ATOM 4113 C LYS B 410 92.900 62.884 39.663 1.00 29.97 C
-ATOM 4114 O LYS B 410 93.220 61.791 39.177 1.00 28.52 O
-ATOM 4115 CB LYS B 410 94.293 64.943 39.385 1.00 36.27 C
-ATOM 4116 CG LYS B 410 94.772 66.012 38.425 1.00 49.56 C
-ATOM 4117 CD LYS B 410 94.942 65.458 37.013 1.00 55.70 C
-ATOM 4118 CE LYS B 410 95.218 66.568 36.000 1.00 58.66 C
-ATOM 4119 NZ LYS B 410 95.179 66.104 34.582 1.00 58.35 N
-ATOM 4120 N CYS B 411 92.378 63.009 40.874 1.00 29.32 N
-ATOM 4121 CA CYS B 411 92.163 61.844 41.705 1.00 28.44 C
-ATOM 4122 C CYS B 411 91.304 60.816 40.952 1.00 26.76 C
-ATOM 4123 O CYS B 411 91.727 59.688 40.724 1.00 30.38 O
-ATOM 4124 CB CYS B 411 91.479 62.265 43.000 1.00 28.05 C
-ATOM 4125 SG CYS B 411 91.452 61.020 44.289 1.00 31.02 S
-ATOM 4126 N MET B 412 90.112 61.221 40.539 1.00 24.91 N
-ATOM 4127 CA MET B 412 89.201 60.330 39.842 1.00 25.36 C
-ATOM 4128 C MET B 412 89.762 59.737 38.543 1.00 25.86 C
-ATOM 4129 O MET B 412 89.548 58.555 38.237 1.00 27.54 O
-ATOM 4130 CB MET B 412 87.880 61.063 39.554 1.00 22.85 C
-ATOM 4131 CG MET B 412 87.088 61.490 40.794 1.00 16.96 C
-ATOM 4132 SD MET B 412 86.667 60.141 41.922 1.00 10.65 S
-ATOM 4133 CE MET B 412 87.945 60.265 43.088 1.00 10.78 C
-ATOM 4134 N VAL B 413 90.463 60.554 37.769 1.00 23.19 N
-ATOM 4135 CA VAL B 413 91.024 60.080 36.522 1.00 21.94 C
-ATOM 4136 C VAL B 413 92.172 59.115 36.819 1.00 25.81 C
-ATOM 4137 O VAL B 413 92.282 58.062 36.195 1.00 24.95 O
-ATOM 4138 CB VAL B 413 91.542 61.255 35.679 1.00 18.49 C
-ATOM 4139 CG1 VAL B 413 92.507 60.753 34.621 1.00 16.54 C
-ATOM 4140 CG2 VAL B 413 90.388 61.975 35.022 1.00 15.60 C
-ATOM 4141 N TYR B 414 93.014 59.455 37.790 1.00 29.70 N
-ATOM 4142 CA TYR B 414 94.163 58.613 38.125 1.00 32.15 C
-ATOM 4143 C TYR B 414 93.781 57.296 38.754 1.00 32.13 C
-ATOM 4144 O TYR B 414 94.536 56.337 38.668 1.00 31.56 O
-ATOM 4145 CB TYR B 414 95.136 59.361 39.048 1.00 38.69 C
-ATOM 4146 CG TYR B 414 95.925 60.470 38.370 1.00 47.72 C
-ATOM 4147 CD1 TYR B 414 95.579 60.925 37.099 1.00 51.92 C
-ATOM 4148 CD2 TYR B 414 96.991 61.090 39.019 1.00 52.00 C
-ATOM 4149 CE1 TYR B 414 96.267 61.965 36.488 1.00 53.30 C
-ATOM 4150 CE2 TYR B 414 97.691 62.141 38.416 1.00 54.28 C
-ATOM 4151 CZ TYR B 414 97.317 62.573 37.148 1.00 54.23 C
-ATOM 4152 OH TYR B 414 97.979 63.614 36.538 1.00 54.09 O
-ATOM 4153 N ASN B 415 92.608 57.259 39.380 1.00 33.32 N
-ATOM 4154 CA ASN B 415 92.090 56.058 40.041 1.00 33.30 C
-ATOM 4155 C ASN B 415 93.201 55.144 40.569 1.00 32.57 C
-ATOM 4156 O ASN B 415 93.353 54.013 40.120 1.00 33.11 O
-ATOM 4157 CB ASN B 415 91.197 55.280 39.074 1.00 33.28 C
-ATOM 4158 CG ASN B 415 90.386 54.215 39.765 1.00 35.68 C
-ATOM 4159 OD1 ASN B 415 89.926 53.281 39.131 1.00 39.48 O
-ATOM 4160 ND2 ASN B 415 90.198 54.352 41.066 1.00 36.02 N
-ATOM 4161 N ILE B 416 93.961 55.638 41.538 1.00 31.18 N
-ATOM 4162 CA ILE B 416 95.067 54.885 42.103 1.00 29.37 C
-ATOM 4163 C ILE B 416 94.754 54.194 43.438 1.00 28.85 C
-ATOM 4164 O ILE B 416 94.235 54.809 44.362 1.00 29.17 O
-ATOM 4165 CB ILE B 416 96.291 55.831 42.242 1.00 30.86 C
-ATOM 4166 CG1 ILE B 416 96.840 56.133 40.843 1.00 30.56 C
-ATOM 4167 CG2 ILE B 416 97.343 55.236 43.169 1.00 29.05 C
-ATOM 4168 CD1 ILE B 416 97.799 57.284 40.797 1.00 32.19 C
-ATOM 4169 N PRO B 417 95.085 52.900 43.552 1.00 28.06 N
-ATOM 4170 CA PRO B 417 94.852 52.101 44.761 1.00 27.75 C
-ATOM 4171 C PRO B 417 95.007 52.842 46.092 1.00 28.92 C
-ATOM 4172 O PRO B 417 96.052 53.441 46.366 1.00 30.18 O
-ATOM 4173 CB PRO B 417 95.864 50.960 44.616 1.00 25.31 C
-ATOM 4174 CG PRO B 417 95.834 50.712 43.150 1.00 22.69 C
-ATOM 4175 CD PRO B 417 95.865 52.127 42.568 1.00 24.91 C
-ATOM 4176 N LYS B 418 93.953 52.778 46.906 1.00 31.96 N
-ATOM 4177 CA LYS B 418 93.911 53.397 48.230 1.00 35.22 C
-ATOM 4178 C LYS B 418 93.975 54.924 48.248 1.00 36.92 C
-ATOM 4179 O LYS B 418 94.081 55.531 49.319 1.00 36.57 O
-ATOM 4180 CB LYS B 418 95.025 52.816 49.110 1.00 37.80 C
-ATOM 4181 CG LYS B 418 94.870 51.325 49.384 1.00 42.47 C
-ATOM 4182 CD LYS B 418 95.941 50.790 50.316 1.00 43.77 C
-ATOM 4183 CE LYS B 418 95.678 49.324 50.671 1.00 45.28 C
-ATOM 4184 NZ LYS B 418 96.764 48.725 51.511 1.00 45.48 N
-ATOM 4185 N LYS B 419 93.903 55.544 47.071 1.00 34.73 N
-ATOM 4186 CA LYS B 419 93.940 57.000 46.965 1.00 30.63 C
-ATOM 4187 C LYS B 419 92.845 57.468 46.012 1.00 28.61 C
-ATOM 4188 O LYS B 419 93.065 58.335 45.164 1.00 23.59 O
-ATOM 4189 CB LYS B 419 95.302 57.441 46.442 1.00 33.32 C
-ATOM 4190 CG LYS B 419 96.475 56.969 47.285 1.00 40.51 C
-ATOM 4191 CD LYS B 419 97.782 57.349 46.617 1.00 45.23 C
-ATOM 4192 CE LYS B 419 98.985 56.964 47.454 1.00 46.69 C
-ATOM 4193 NZ LYS B 419 100.258 57.360 46.771 1.00 48.03 N
-ATOM 4194 N ARG B 420 91.656 56.893 46.163 1.00 25.51 N
-ATOM 4195 CA ARG B 420 90.539 57.238 45.285 1.00 23.49 C
-ATOM 4196 C ARG B 420 89.234 57.634 45.978 1.00 22.11 C
-ATOM 4197 O ARG B 420 88.225 57.874 45.304 1.00 21.73 O
-ATOM 4198 CB ARG B 420 90.271 56.071 44.325 1.00 22.85 C
-ATOM 4199 CG ARG B 420 90.907 54.778 44.777 1.00 21.96 C
-ATOM 4200 CD ARG B 420 90.600 53.686 43.812 1.00 23.48 C
-ATOM 4201 NE ARG B 420 89.461 52.913 44.281 1.00 23.14 N
-ATOM 4202 CZ ARG B 420 88.648 52.233 43.486 1.00 22.90 C
-ATOM 4203 NH1 ARG B 420 88.844 52.238 42.171 1.00 23.14 N
-ATOM 4204 NH2 ARG B 420 87.652 51.539 44.008 1.00 19.90 N
-ATOM 4205 N TYR B 421 89.254 57.705 47.308 1.00 21.45 N
-ATOM 4206 CA TYR B 421 88.062 58.075 48.045 1.00 21.99 C
-ATOM 4207 C TYR B 421 88.190 59.262 48.961 1.00 23.49 C
-ATOM 4208 O TYR B 421 89.078 59.315 49.808 1.00 25.96 O
-ATOM 4209 CB TYR B 421 87.516 56.894 48.846 1.00 19.53 C
-ATOM 4210 CG TYR B 421 86.541 56.092 48.041 1.00 18.10 C
-ATOM 4211 CD1 TYR B 421 86.984 55.079 47.191 1.00 18.07 C
-ATOM 4212 CD2 TYR B 421 85.184 56.438 48.020 1.00 17.47 C
-ATOM 4213 CE1 TYR B 421 86.106 54.427 46.326 1.00 17.87 C
-ATOM 4214 CE2 TYR B 421 84.290 55.804 47.158 1.00 17.64 C
-ATOM 4215 CZ TYR B 421 84.763 54.801 46.306 1.00 18.55 C
-ATOM 4216 OH TYR B 421 83.920 54.221 45.389 1.00 16.71 O
-ATOM 4217 N TRP B 422 87.280 60.213 48.768 1.00 23.70 N
-ATOM 4218 CA TRP B 422 87.209 61.416 49.573 1.00 22.97 C
-ATOM 4219 C TRP B 422 86.018 61.261 50.499 1.00 24.21 C
-ATOM 4220 O TRP B 422 85.016 60.622 50.162 1.00 21.72 O
-ATOM 4221 CB TRP B 422 87.013 62.635 48.689 1.00 21.55 C
-ATOM 4222 CG TRP B 422 88.213 62.972 47.923 1.00 22.57 C
-ATOM 4223 CD1 TRP B 422 89.218 62.124 47.568 1.00 23.47 C
-ATOM 4224 CD2 TRP B 422 88.571 64.263 47.408 1.00 22.88 C
-ATOM 4225 NE1 TRP B 422 90.188 62.802 46.866 1.00 23.93 N
-ATOM 4226 CE2 TRP B 422 89.817 64.117 46.751 1.00 23.38 C
-ATOM 4227 CE3 TRP B 422 87.958 65.525 47.441 1.00 20.94 C
-ATOM 4228 CZ2 TRP B 422 90.470 65.187 46.127 1.00 22.32 C
-ATOM 4229 CZ3 TRP B 422 88.602 66.588 46.826 1.00 21.75 C
-ATOM 4230 CH2 TRP B 422 89.852 66.412 46.175 1.00 23.52 C
-ATOM 4231 N LEU B 423 86.148 61.862 51.669 1.00 27.32 N
-ATOM 4232 CA LEU B 423 85.124 61.809 52.679 1.00 30.01 C
-ATOM 4233 C LEU B 423 84.595 63.210 52.924 1.00 29.64 C
-ATOM 4234 O LEU B 423 85.335 64.080 53.382 1.00 30.70 O
-ATOM 4235 CB LEU B 423 85.710 61.258 53.984 1.00 31.97 C
-ATOM 4236 CG LEU B 423 84.697 61.192 55.126 1.00 34.79 C
-ATOM 4237 CD1 LEU B 423 83.769 60.025 54.853 1.00 34.51 C
-ATOM 4238 CD2 LEU B 423 85.389 61.035 56.477 1.00 35.42 C
-ATOM 4239 N PHE B 424 83.327 63.436 52.603 1.00 30.55 N
-ATOM 4240 CA PHE B 424 82.716 64.739 52.856 1.00 30.60 C
-ATOM 4241 C PHE B 424 81.980 64.571 54.165 1.00 31.42 C
-ATOM 4242 O PHE B 424 80.929 63.933 54.224 1.00 31.85 O
-ATOM 4243 CB PHE B 424 81.744 65.132 51.744 1.00 28.61 C
-ATOM 4244 CG PHE B 424 82.421 65.606 50.480 1.00 27.26 C
-ATOM 4245 CD1 PHE B 424 83.801 65.479 50.312 1.00 27.28 C
-ATOM 4246 CD2 PHE B 424 81.672 66.183 49.448 1.00 27.55 C
-ATOM 4247 CE1 PHE B 424 84.423 65.922 49.137 1.00 28.10 C
-ATOM 4248 CE2 PHE B 424 82.279 66.627 48.270 1.00 25.97 C
-ATOM 4249 CZ PHE B 424 83.661 66.496 48.115 1.00 26.62 C
-ATOM 4250 N LYS B 425 82.561 65.113 55.225 1.00 33.92 N
-ATOM 4251 CA LYS B 425 81.962 64.992 56.537 1.00 35.95 C
-ATOM 4252 C LYS B 425 81.437 66.348 56.997 1.00 37.29 C
-ATOM 4253 O LYS B 425 82.160 67.347 57.012 1.00 37.80 O
-ATOM 4254 CB LYS B 425 82.992 64.438 57.524 1.00 36.30 C
-ATOM 4255 CG LYS B 425 82.418 63.495 58.565 1.00 37.17 C
-ATOM 4256 CD LYS B 425 83.525 62.989 59.474 1.00 38.59 C
-ATOM 4257 CE LYS B 425 82.970 62.276 60.687 1.00 38.47 C
-ATOM 4258 NZ LYS B 425 83.997 62.255 61.765 1.00 38.51 N
-ATOM 4259 N GLY B 426 80.162 66.392 57.353 1.00 39.53 N
-ATOM 4260 CA GLY B 426 79.609 67.649 57.800 1.00 39.73 C
-ATOM 4261 C GLY B 426 78.213 67.482 58.345 1.00 38.71 C
-ATOM 4262 O GLY B 426 77.588 66.426 58.174 1.00 41.97 O
-ATOM 4263 N PRO B 427 77.708 68.509 59.040 1.00 44.32 N
-ATOM 4264 CA PRO B 427 76.366 68.475 59.613 1.00 43.94 C
-ATOM 4265 C PRO B 427 75.367 68.355 58.486 1.00 45.46 C
-ATOM 4266 O PRO B 427 75.478 67.488 57.624 1.00 49.43 O
-ATOM 4267 CB PRO B 427 76.263 69.819 60.320 1.00 41.75 C
-ATOM 4268 CG PRO B 427 77.660 70.061 60.762 1.00 40.93 C
-ATOM 4269 CD PRO B 427 78.455 69.675 59.536 1.00 42.09 C
-ATOM 4270 N ILE B 428 74.402 69.255 58.493 1.00 50.37 N
-ATOM 4271 CA ILE B 428 73.358 69.275 57.484 1.00 53.16 C
-ATOM 4272 C ILE B 428 73.241 70.731 57.034 1.00 58.56 C
-ATOM 4273 O ILE B 428 73.452 71.653 57.828 1.00 52.38 O
-ATOM 4274 CB ILE B 428 72.036 68.763 58.094 1.00 54.51 C
-ATOM 4275 CG1 ILE B 428 71.083 68.318 56.996 1.00 57.04 C
-ATOM 4276 CG2 ILE B 428 71.405 69.845 58.952 1.00 57.18 C
-ATOM 4277 CD1 ILE B 428 69.930 67.495 57.515 1.00 58.80 C
-ATOM 4278 N ASP B 429 72.926 70.938 55.761 1.00 62.79 N
-ATOM 4279 CA ASP B 429 72.826 72.286 55.217 1.00 63.60 C
-ATOM 4280 C ASP B 429 74.192 72.902 55.403 1.00 58.80 C
-ATOM 4281 O ASP B 429 74.313 74.080 55.699 1.00 54.89 O
-ATOM 4282 CB ASP B 429 71.784 73.111 55.973 1.00 81.05 C
-ATOM 4283 CG ASP B 429 70.428 72.452 55.985 1.00105.52 C
-ATOM 4284 OD1 ASP B 429 70.316 71.344 56.550 1.00118.22 O
-ATOM 4285 OD2 ASP B 429 69.475 73.037 55.429 1.00117.76 O
-ATOM 4286 N SER B 430 75.222 72.081 55.244 1.00 51.30 N
-ATOM 4287 CA SER B 430 76.603 72.530 55.394 1.00 43.99 C
-ATOM 4288 C SER B 430 77.370 72.618 54.071 1.00 40.98 C
-ATOM 4289 O SER B 430 78.511 73.078 54.047 1.00 38.97 O
-ATOM 4290 CB SER B 430 77.344 71.602 56.360 1.00 43.06 C
-ATOM 4291 OG SER B 430 77.010 70.248 56.118 1.00 45.54 O
-ATOM 4292 N GLY B 431 76.743 72.171 52.982 1.00 38.44 N
-ATOM 4293 CA GLY B 431 77.375 72.217 51.674 1.00 35.10 C
-ATOM 4294 C GLY B 431 77.799 70.891 51.050 1.00 34.36 C
-ATOM 4295 O GLY B 431 77.748 70.744 49.818 1.00 33.05 O
-ATOM 4296 N LYS B 432 78.212 69.926 51.878 1.00 32.12 N
-ATOM 4297 CA LYS B 432 78.668 68.634 51.368 1.00 32.02 C
-ATOM 4298 C LYS B 432 77.734 68.008 50.346 1.00 31.35 C
-ATOM 4299 O LYS B 432 78.172 67.533 49.291 1.00 31.31 O
-ATOM 4300 CB LYS B 432 78.902 67.658 52.512 1.00 30.97 C
-ATOM 4301 CG LYS B 432 77.945 67.806 53.651 1.00 33.97 C
-ATOM 4302 CD LYS B 432 78.114 66.665 54.642 1.00 33.09 C
-ATOM 4303 CE LYS B 432 77.045 65.613 54.420 1.00 32.65 C
-ATOM 4304 NZ LYS B 432 75.701 66.159 54.715 1.00 32.69 N
-ATOM 4305 N THR B 433 76.445 67.998 50.655 1.00 28.74 N
-ATOM 4306 CA THR B 433 75.472 67.434 49.737 1.00 26.58 C
-ATOM 4307 C THR B 433 75.498 68.196 48.414 1.00 25.74 C
-ATOM 4308 O THR B 433 75.522 67.600 47.345 1.00 21.86 O
-ATOM 4309 CB THR B 433 74.053 67.456 50.373 1.00 25.90 C
-ATOM 4310 OG1 THR B 433 73.934 66.355 51.290 1.00 26.30 O
-ATOM 4311 CG2 THR B 433 72.974 67.351 49.319 1.00 25.35 C
-ATOM 4312 N THR B 434 75.528 69.518 48.492 1.00 24.32 N
-ATOM 4313 CA THR B 434 75.550 70.343 47.289 1.00 23.06 C
-ATOM 4314 C THR B 434 76.789 70.101 46.420 1.00 24.94 C
-ATOM 4315 O THR B 434 76.662 69.809 45.222 1.00 22.10 O
-ATOM 4316 CB THR B 434 75.451 71.836 47.660 1.00 25.01 C
-ATOM 4317 OG1 THR B 434 74.106 72.116 48.055 1.00 28.10 O
-ATOM 4318 CG2 THR B 434 75.831 72.733 46.486 1.00 26.86 C
-ATOM 4319 N LEU B 435 77.977 70.205 47.023 1.00 27.02 N
-ATOM 4320 CA LEU B 435 79.232 70.003 46.300 1.00 27.60 C
-ATOM 4321 C LEU B 435 79.374 68.595 45.714 1.00 26.87 C
-ATOM 4322 O LEU B 435 79.900 68.425 44.613 1.00 28.49 O
-ATOM 4323 CB LEU B 435 80.425 70.297 47.208 1.00 28.49 C
-ATOM 4324 CG LEU B 435 81.783 70.347 46.489 1.00 28.74 C
-ATOM 4325 CD1 LEU B 435 81.724 71.363 45.356 1.00 30.45 C
-ATOM 4326 CD2 LEU B 435 82.872 70.733 47.479 1.00 29.41 C
-ATOM 4327 N ALA B 436 78.908 67.593 46.454 1.00 26.25 N
-ATOM 4328 CA ALA B 436 78.971 66.210 45.992 1.00 26.41 C
-ATOM 4329 C ALA B 436 78.030 66.035 44.814 1.00 26.58 C
-ATOM 4330 O ALA B 436 78.283 65.228 43.916 1.00 27.34 O
-ATOM 4331 CB ALA B 436 78.575 65.255 47.108 1.00 24.13 C
-ATOM 4332 N ALA B 437 76.938 66.792 44.822 1.00 25.59 N
-ATOM 4333 CA ALA B 437 75.967 66.714 43.741 1.00 26.14 C
-ATOM 4334 C ALA B 437 76.566 67.340 42.484 1.00 27.25 C
-ATOM 4335 O ALA B 437 76.436 66.804 41.380 1.00 27.20 O
-ATOM 4336 CB ALA B 437 74.687 67.442 44.129 1.00 26.75 C
-ATOM 4337 N ALA B 438 77.221 68.479 42.656 1.00 25.80 N
-ATOM 4338 CA ALA B 438 77.835 69.158 41.531 1.00 26.37 C
-ATOM 4339 C ALA B 438 78.969 68.305 40.965 1.00 26.13 C
-ATOM 4340 O ALA B 438 79.121 68.176 39.754 1.00 26.01 O
-ATOM 4341 CB ALA B 438 78.368 70.512 41.974 1.00 26.85 C
-ATOM 4342 N LEU B 439 79.768 67.725 41.852 1.00 26.17 N
-ATOM 4343 CA LEU B 439 80.891 66.898 41.426 1.00 25.76 C
-ATOM 4344 C LEU B 439 80.371 65.665 40.713 1.00 26.00 C
-ATOM 4345 O LEU B 439 80.954 65.219 39.717 1.00 24.83 O
-ATOM 4346 CB LEU B 439 81.746 66.490 42.638 1.00 25.13 C
-ATOM 4347 CG LEU B 439 82.685 67.553 43.231 1.00 24.09 C
-ATOM 4348 CD1 LEU B 439 83.330 67.028 44.498 1.00 22.23 C
-ATOM 4349 CD2 LEU B 439 83.741 67.941 42.208 1.00 23.38 C
-ATOM 4350 N LEU B 440 79.259 65.136 41.230 1.00 27.70 N
-ATOM 4351 CA LEU B 440 78.621 63.954 40.666 1.00 28.33 C
-ATOM 4352 C LEU B 440 78.238 64.223 39.223 1.00 30.13 C
-ATOM 4353 O LEU B 440 78.543 63.421 38.343 1.00 30.22 O
-ATOM 4354 CB LEU B 440 77.376 63.567 41.481 1.00 27.63 C
-ATOM 4355 CG LEU B 440 76.653 62.216 41.255 1.00 26.65 C
-ATOM 4356 CD1 LEU B 440 75.523 62.367 40.254 1.00 25.80 C
-ATOM 4357 CD2 LEU B 440 77.640 61.154 40.801 1.00 26.90 C
-ATOM 4358 N GLU B 441 77.603 65.367 38.974 1.00 31.94 N
-ATOM 4359 CA GLU B 441 77.181 65.716 37.622 1.00 33.09 C
-ATOM 4360 C GLU B 441 78.347 66.116 36.712 1.00 30.87 C
-ATOM 4361 O GLU B 441 78.337 65.851 35.513 1.00 30.94 O
-ATOM 4362 CB GLU B 441 76.145 66.842 37.665 1.00 37.61 C
-ATOM 4363 CG GLU B 441 75.619 67.228 36.288 1.00 46.88 C
-ATOM 4364 CD GLU B 441 74.299 67.969 36.338 1.00 51.32 C
-ATOM 4365 OE1 GLU B 441 74.231 69.035 36.993 1.00 53.39 O
-ATOM 4366 OE2 GLU B 441 73.329 67.481 35.715 1.00 53.42 O
-ATOM 4367 N LEU B 442 79.364 66.739 37.282 1.00 27.62 N
-ATOM 4368 CA LEU B 442 80.515 67.165 36.499 1.00 24.36 C
-ATOM 4369 C LEU B 442 81.257 65.989 35.895 1.00 25.62 C
-ATOM 4370 O LEU B 442 81.726 66.077 34.768 1.00 24.18 O
-ATOM 4371 CB LEU B 442 81.479 67.972 37.370 1.00 20.75 C
-ATOM 4372 CG LEU B 442 82.749 68.466 36.685 1.00 18.25 C
-ATOM 4373 CD1 LEU B 442 82.422 69.620 35.764 1.00 16.40 C
-ATOM 4374 CD2 LEU B 442 83.761 68.893 37.735 1.00 18.89 C
-ATOM 4375 N CYS B 443 81.357 64.888 36.638 1.00 29.46 N
-ATOM 4376 CA CYS B 443 82.073 63.691 36.170 1.00 32.36 C
-ATOM 4377 C CYS B 443 81.265 62.531 35.608 1.00 34.25 C
-ATOM 4378 O CYS B 443 81.818 61.668 34.921 1.00 33.09 O
-ATOM 4379 CB CYS B 443 82.903 63.122 37.302 1.00 31.81 C
-ATOM 4380 SG CYS B 443 84.072 64.275 37.898 1.00 37.05 S
-ATOM 4381 N GLY B 444 79.969 62.511 35.906 1.00 37.65 N
-ATOM 4382 CA GLY B 444 79.121 61.410 35.491 1.00 42.32 C
-ATOM 4383 C GLY B 444 79.126 60.505 36.717 1.00 43.98 C
-ATOM 4384 O GLY B 444 79.887 60.753 37.649 1.00 49.06 O
-ATOM 4385 N GLY B 445 78.294 59.474 36.757 1.00 44.74 N
-ATOM 4386 CA GLY B 445 78.305 58.604 37.923 1.00 42.92 C
-ATOM 4387 C GLY B 445 76.979 58.466 38.649 1.00 42.71 C
-ATOM 4388 O GLY B 445 76.021 59.181 38.359 1.00 41.85 O
-ATOM 4389 N LYS B 446 76.932 57.542 39.607 1.00 42.71 N
-ATOM 4390 CA LYS B 446 75.719 57.285 40.384 1.00 40.08 C
-ATOM 4391 C LYS B 446 75.871 57.449 41.894 1.00 38.23 C
-ATOM 4392 O LYS B 446 76.948 57.237 42.461 1.00 36.96 O
-ATOM 4393 CB LYS B 446 75.218 55.867 40.099 1.00 40.85 C
-ATOM 4394 CG LYS B 446 74.698 55.631 38.689 1.00 43.95 C
-ATOM 4395 CD LYS B 446 73.378 56.343 38.438 1.00 46.70 C
-ATOM 4396 CE LYS B 446 72.712 55.855 37.154 1.00 47.61 C
-ATOM 4397 NZ LYS B 446 71.339 56.435 36.994 1.00 48.16 N
-ATOM 4398 N ALA B 447 74.776 57.832 42.538 1.00 37.92 N
-ATOM 4399 CA ALA B 447 74.757 57.984 43.986 1.00 38.85 C
-ATOM 4400 C ALA B 447 74.339 56.605 44.490 1.00 40.12 C
-ATOM 4401 O ALA B 447 73.619 55.889 43.783 1.00 43.35 O
-ATOM 4402 CB ALA B 447 73.727 59.041 44.399 1.00 39.61 C
-ATOM 4403 N LEU B 448 74.795 56.219 45.683 1.00 38.67 N
-ATOM 4404 CA LEU B 448 74.439 54.911 46.234 1.00 37.24 C
-ATOM 4405 C LEU B 448 74.055 54.971 47.704 1.00 39.96 C
-ATOM 4406 O LEU B 448 74.699 55.666 48.497 1.00 35.95 O
-ATOM 4407 CB LEU B 448 75.597 53.920 46.089 1.00 35.87 C
-ATOM 4408 CG LEU B 448 76.155 53.591 44.709 1.00 34.46 C
-ATOM 4409 CD1 LEU B 448 77.257 52.560 44.848 1.00 35.05 C
-ATOM 4410 CD2 LEU B 448 75.061 53.076 43.830 1.00 34.46 C
-ATOM 4411 N ASN B 449 73.014 54.227 48.066 1.00 41.60 N
-ATOM 4412 CA ASN B 449 72.569 54.173 49.452 1.00 42.60 C
-ATOM 4413 C ASN B 449 72.973 52.831 50.030 1.00 41.43 C
-ATOM 4414 O ASN B 449 72.490 51.791 49.600 1.00 39.25 O
-ATOM 4415 CB ASN B 449 71.057 54.350 49.557 1.00 50.00 C
-ATOM 4416 CG ASN B 449 70.582 54.297 50.986 1.00 60.69 C
-ATOM 4417 OD1 ASN B 449 70.625 53.245 51.619 1.00 68.36 O
-ATOM 4418 ND2 ASN B 449 70.152 55.434 51.516 1.00 65.68 N
-ATOM 4419 N VAL B 450 73.869 52.867 51.008 1.00 42.39 N
-ATOM 4420 CA VAL B 450 74.370 51.657 51.626 1.00 43.90 C
-ATOM 4421 C VAL B 450 73.790 51.452 53.019 1.00 46.33 C
-ATOM 4422 O VAL B 450 74.101 50.469 53.691 1.00 47.15 O
-ATOM 4423 CB VAL B 450 75.911 51.687 51.657 1.00 43.01 C
-ATOM 4424 CG1 VAL B 450 76.458 50.457 52.309 1.00 45.62 C
-ATOM 4425 CG2 VAL B 450 76.435 51.755 50.251 1.00 44.17 C
-ATOM 4426 N ASN B 451 72.953 52.384 53.465 1.00 50.97 N
-ATOM 4427 CA ASN B 451 72.301 52.212 54.753 1.00 52.38 C
-ATOM 4428 C ASN B 451 71.175 51.257 54.384 1.00 52.69 C
-ATOM 4429 O ASN B 451 70.050 51.685 54.139 1.00 50.17 O
-ATOM 4430 CB ASN B 451 71.692 53.515 55.248 1.00 58.27 C
-ATOM 4431 CG ASN B 451 72.593 54.692 55.030 1.00 66.62 C
-ATOM 4432 OD1 ASN B 451 73.686 54.765 55.591 1.00 70.41 O
-ATOM 4433 ND2 ASN B 451 72.142 55.633 54.207 1.00 71.80 N
-ATOM 4434 N LEU B 452 71.482 49.969 54.304 1.00 57.13 N
-ATOM 4435 CA LEU B 452 70.473 48.987 53.930 1.00 60.61 C
-ATOM 4436 C LEU B 452 70.716 47.659 54.647 1.00 63.75 C
-ATOM 4437 O LEU B 452 71.607 47.555 55.497 1.00 69.41 O
-ATOM 4438 CB LEU B 452 70.514 48.758 52.414 1.00 54.90 C
-ATOM 4439 CG LEU B 452 70.287 49.905 51.427 1.00 50.44 C
-ATOM 4440 CD1 LEU B 452 70.412 49.368 50.014 1.00 48.18 C
-ATOM 4441 CD2 LEU B 452 68.918 50.519 51.626 1.00 48.56 C
-ATOM 4442 N PRO B 453 69.898 46.636 54.340 1.00 83.32 N
-ATOM 4443 CA PRO B 453 70.080 45.326 54.977 1.00 84.65 C
-ATOM 4444 C PRO B 453 71.356 44.721 54.394 1.00 83.91 C
-ATOM 4445 O PRO B 453 71.498 44.651 53.173 1.00 88.85 O
-ATOM 4446 CB PRO B 453 68.836 44.557 54.543 1.00 90.04 C
-ATOM 4447 CG PRO B 453 67.809 45.645 54.357 1.00 91.36 C
-ATOM 4448 CD PRO B 453 68.601 46.699 53.642 1.00 84.86 C
-ATOM 4449 N LEU B 454 72.275 44.288 55.254 1.00 83.57 N
-ATOM 4450 CA LEU B 454 73.542 43.727 54.788 1.00 79.96 C
-ATOM 4451 C LEU B 454 73.403 42.727 53.638 1.00 82.24 C
-ATOM 4452 O LEU B 454 74.405 42.295 53.067 1.00 77.88 O
-ATOM 4453 CB LEU B 454 74.303 43.066 55.941 1.00 73.50 C
-ATOM 4454 CG LEU B 454 75.708 42.564 55.575 1.00 68.39 C
-ATOM 4455 CD1 LEU B 454 76.704 43.723 55.579 1.00 65.47 C
-ATOM 4456 CD2 LEU B 454 76.139 41.494 56.560 1.00 67.29 C
-ATOM 4457 N ASP B 455 72.172 42.358 53.294 1.00 87.31 N
-ATOM 4458 CA ASP B 455 71.953 41.418 52.198 1.00 92.70 C
-ATOM 4459 C ASP B 455 71.318 42.099 50.986 1.00 95.57 C
-ATOM 4460 O ASP B 455 71.501 41.666 49.845 1.00 94.38 O
-ATOM 4461 CB ASP B 455 71.097 40.238 52.676 1.00 98.07 C
-ATOM 4462 CG ASP B 455 71.942 39.090 53.243 1.00105.29 C
-ATOM 4463 OD1 ASP B 455 72.820 39.342 54.099 1.00109.17 O
-ATOM 4464 OD2 ASP B 455 71.723 37.929 52.833 1.00109.15 O
-ATOM 4465 N ARG B 456 70.573 43.168 51.237 1.00100.41 N
-ATOM 4466 CA ARG B 456 69.951 43.920 50.158 1.00103.49 C
-ATOM 4467 C ARG B 456 70.958 44.984 49.724 1.00 99.71 C
-ATOM 4468 O ARG B 456 70.591 46.055 49.233 1.00101.80 O
-ATOM 4469 CB ARG B 456 68.651 44.562 50.647 1.00112.19 C
-ATOM 4470 CG ARG B 456 67.580 43.533 50.974 1.00125.10 C
-ATOM 4471 CD ARG B 456 66.300 44.166 51.506 1.00130.45 C
-ATOM 4472 NE ARG B 456 65.248 43.166 51.696 1.00131.93 N
-ATOM 4473 CZ ARG B 456 64.065 43.413 52.254 1.00132.20 C
-ATOM 4474 NH1 ARG B 456 63.776 44.633 52.684 1.00132.19 N
-ATOM 4475 NH2 ARG B 456 63.169 42.442 52.379 1.00131.91 N
-ATOM 4476 N LEU B 457 72.236 44.656 49.910 1.00 90.72 N
-ATOM 4477 CA LEU B 457 73.353 45.535 49.576 1.00 81.96 C
-ATOM 4478 C LEU B 457 73.847 45.320 48.140 1.00 79.50 C
-ATOM 4479 O LEU B 457 73.909 46.270 47.352 1.00 75.68 O
-ATOM 4480 CB LEU B 457 74.494 45.298 50.575 1.00 76.38 C
-ATOM 4481 CG LEU B 457 75.725 46.208 50.574 1.00 70.67 C
-ATOM 4482 CD1 LEU B 457 75.283 47.654 50.694 1.00 69.03 C
-ATOM 4483 CD2 LEU B 457 76.650 45.837 51.731 1.00 67.15 C
-ATOM 4484 N ASN B 458 74.197 44.079 47.802 1.00 73.08 N
-ATOM 4485 CA ASN B 458 74.678 43.755 46.456 1.00 69.84 C
-ATOM 4486 C ASN B 458 73.827 44.447 45.395 1.00 71.95 C
-ATOM 4487 O ASN B 458 74.339 44.882 44.357 1.00 63.80 O
-ATOM 4488 CB ASN B 458 74.643 42.243 46.225 1.00 70.04 C
-ATOM 4489 CG ASN B 458 75.586 41.492 47.144 1.00 73.90 C
-ATOM 4490 OD1 ASN B 458 76.799 41.710 47.124 1.00 76.91 O
-ATOM 4491 ND2 ASN B 458 75.031 40.598 47.955 1.00 76.37 N
-ATOM 4492 N PHE B 459 72.526 44.528 45.676 1.00 72.95 N
-ATOM 4493 CA PHE B 459 71.537 45.172 44.807 1.00 72.96 C
-ATOM 4494 C PHE B 459 72.080 46.535 44.373 1.00 71.07 C
-ATOM 4495 O PHE B 459 72.323 46.776 43.186 1.00 62.90 O
-ATOM 4496 CB PHE B 459 70.227 45.367 45.597 1.00 85.95 C
-ATOM 4497 CG PHE B 459 69.121 46.068 44.832 1.00106.24 C
-ATOM 4498 CD1 PHE B 459 68.191 45.335 44.096 1.00114.37 C
-ATOM 4499 CD2 PHE B 459 68.989 47.457 44.879 1.00114.03 C
-ATOM 4500 CE1 PHE B 459 67.143 45.975 43.421 1.00117.48 C
-ATOM 4501 CE2 PHE B 459 67.948 48.104 44.208 1.00117.01 C
-ATOM 4502 CZ PHE B 459 67.025 47.361 43.479 1.00118.06 C
-ATOM 4503 N GLU B 460 72.281 47.411 45.358 1.00 67.66 N
-ATOM 4504 CA GLU B 460 72.761 48.767 45.124 1.00 62.79 C
-ATOM 4505 C GLU B 460 74.187 48.828 44.578 1.00 56.97 C
-ATOM 4506 O GLU B 460 74.464 49.536 43.609 1.00 54.32 O
-ATOM 4507 CB GLU B 460 72.666 49.580 46.422 1.00 67.31 C
-ATOM 4508 CG GLU B 460 72.275 51.038 46.204 1.00 77.67 C
-ATOM 4509 CD GLU B 460 70.783 51.226 46.004 1.00 82.26 C
-ATOM 4510 OE1 GLU B 460 70.139 50.355 45.383 1.00 83.76 O
-ATOM 4511 OE2 GLU B 460 70.255 52.256 46.464 1.00 84.48 O
-ATOM 4512 N LEU B 461 75.094 48.090 45.201 1.00 49.44 N
-ATOM 4513 CA LEU B 461 76.473 48.093 44.745 1.00 45.10 C
-ATOM 4514 C LEU B 461 76.559 47.792 43.251 1.00 43.19 C
-ATOM 4515 O LEU B 461 77.472 48.253 42.566 1.00 42.65 O
-ATOM 4516 CB LEU B 461 77.294 47.074 45.536 1.00 40.94 C
-ATOM 4517 CG LEU B 461 77.476 47.360 47.032 1.00 37.84 C
-ATOM 4518 CD1 LEU B 461 78.447 46.319 47.604 1.00 33.59 C
-ATOM 4519 CD2 LEU B 461 78.002 48.798 47.265 1.00 34.26 C
-ATOM 4520 N GLY B 462 75.603 47.019 42.750 1.00 41.64 N
-ATOM 4521 CA GLY B 462 75.594 46.679 41.340 1.00 40.36 C
-ATOM 4522 C GLY B 462 75.323 47.877 40.447 1.00 41.30 C
-ATOM 4523 O GLY B 462 75.616 47.837 39.254 1.00 38.56 O
-ATOM 4524 N VAL B 463 74.764 48.943 41.014 1.00 42.70 N
-ATOM 4525 CA VAL B 463 74.469 50.144 40.234 1.00 44.21 C
-ATOM 4526 C VAL B 463 75.757 50.797 39.751 1.00 43.35 C
-ATOM 4527 O VAL B 463 75.762 51.528 38.752 1.00 44.46 O
-ATOM 4528 CB VAL B 463 73.705 51.198 41.067 1.00 48.30 C
-ATOM 4529 CG1 VAL B 463 73.341 52.401 40.188 1.00 51.37 C
-ATOM 4530 CG2 VAL B 463 72.464 50.577 41.679 1.00 52.22 C
-ATOM 4531 N ALA B 464 76.841 50.516 40.473 1.00 41.37 N
-ATOM 4532 CA ALA B 464 78.160 51.073 40.190 1.00 39.33 C
-ATOM 4533 C ALA B 464 78.782 50.578 38.897 1.00 41.81 C
-ATOM 4534 O ALA B 464 79.767 51.145 38.421 1.00 44.34 O
-ATOM 4535 CB ALA B 464 79.087 50.775 41.347 1.00 35.00 C
-ATOM 4536 N ILE B 465 78.200 49.522 38.337 1.00 46.92 N
-ATOM 4537 CA ILE B 465 78.684 48.910 37.107 1.00 51.40 C
-ATOM 4538 C ILE B 465 78.954 49.895 35.985 1.00 55.54 C
-ATOM 4539 O ILE B 465 78.053 50.612 35.559 1.00 55.70 O
-ATOM 4540 CB ILE B 465 77.683 47.857 36.625 1.00 52.72 C
-ATOM 4541 CG1 ILE B 465 77.791 46.628 37.532 1.00 55.93 C
-ATOM 4542 CG2 ILE B 465 77.926 47.524 35.161 1.00 54.61 C
-ATOM 4543 CD1 ILE B 465 76.741 45.567 37.301 1.00 57.56 C
-ATOM 4544 N ASP B 466 80.199 49.918 35.513 1.00 59.32 N
-ATOM 4545 CA ASP B 466 80.621 50.804 34.426 1.00 61.25 C
-ATOM 4546 C ASP B 466 80.513 52.305 34.719 1.00 58.62 C
-ATOM 4547 O ASP B 466 80.692 53.126 33.814 1.00 57.13 O
-ATOM 4548 CB ASP B 466 79.833 50.492 33.146 1.00 70.78 C
-ATOM 4549 CG ASP B 466 80.149 49.123 32.582 1.00 83.85 C
-ATOM 4550 OD1 ASP B 466 81.128 48.506 33.049 1.00 90.84 O
-ATOM 4551 OD2 ASP B 466 79.425 48.670 31.666 1.00 89.90 O
-ATOM 4552 N GLN B 467 80.215 52.669 35.964 1.00 52.29 N
-ATOM 4553 CA GLN B 467 80.107 54.079 36.334 1.00 45.89 C
-ATOM 4554 C GLN B 467 81.499 54.680 36.527 1.00 42.21 C
-ATOM 4555 O GLN B 467 82.383 54.042 37.088 1.00 41.59 O
-ATOM 4556 CB GLN B 467 79.295 54.229 37.624 1.00 45.56 C
-ATOM 4557 CG GLN B 467 77.801 53.982 37.465 1.00 45.85 C
-ATOM 4558 CD GLN B 467 77.185 54.879 36.406 1.00 45.76 C
-ATOM 4559 OE1 GLN B 467 77.309 54.615 35.216 1.00 45.91 O
-ATOM 4560 NE2 GLN B 467 76.537 55.955 36.834 1.00 45.38 N
-ATOM 4561 N PHE B 468 81.690 55.904 36.059 1.00 35.95 N
-ATOM 4562 CA PHE B 468 82.977 56.580 36.190 1.00 31.78 C
-ATOM 4563 C PHE B 468 83.375 56.845 37.648 1.00 30.75 C
-ATOM 4564 O PHE B 468 84.530 56.672 38.017 1.00 31.28 O
-ATOM 4565 CB PHE B 468 82.933 57.889 35.419 1.00 30.08 C
-ATOM 4566 CG PHE B 468 84.199 58.681 35.494 1.00 27.67 C
-ATOM 4567 CD1 PHE B 468 85.318 58.292 34.761 1.00 26.08 C
-ATOM 4568 CD2 PHE B 468 84.266 59.832 36.280 1.00 25.96 C
-ATOM 4569 CE1 PHE B 468 86.488 59.036 34.803 1.00 26.77 C
-ATOM 4570 CE2 PHE B 468 85.424 60.583 36.332 1.00 26.67 C
-ATOM 4571 CZ PHE B 468 86.544 60.188 35.591 1.00 27.18 C
-ATOM 4572 N LEU B 469 82.433 57.297 38.468 1.00 27.72 N
-ATOM 4573 CA LEU B 469 82.717 57.536 39.881 1.00 27.26 C
-ATOM 4574 C LEU B 469 81.433 57.280 40.648 1.00 28.57 C
-ATOM 4575 O LEU B 469 80.335 57.310 40.084 1.00 29.37 O
-ATOM 4576 CB LEU B 469 83.205 58.973 40.148 1.00 25.26 C
-ATOM 4577 CG LEU B 469 82.244 60.152 40.402 1.00 23.80 C
-ATOM 4578 CD1 LEU B 469 81.416 59.922 41.665 1.00 23.69 C
-ATOM 4579 CD2 LEU B 469 83.050 61.442 40.574 1.00 24.39 C
-ATOM 4580 N VAL B 470 81.563 57.048 41.942 1.00 27.95 N
-ATOM 4581 CA VAL B 470 80.403 56.769 42.749 1.00 27.32 C
-ATOM 4582 C VAL B 470 80.290 57.690 43.944 1.00 26.11 C
-ATOM 4583 O VAL B 470 81.289 58.207 44.445 1.00 27.79 O
-ATOM 4584 CB VAL B 470 80.459 55.304 43.229 1.00 27.94 C
-ATOM 4585 CG1 VAL B 470 79.753 55.139 44.567 1.00 27.17 C
-ATOM 4586 CG2 VAL B 470 79.831 54.414 42.181 1.00 27.45 C
-ATOM 4587 N VAL B 471 79.061 57.910 44.391 1.00 24.64 N
-ATOM 4588 CA VAL B 471 78.860 58.719 45.571 1.00 24.06 C
-ATOM 4589 C VAL B 471 77.912 58.015 46.544 1.00 23.72 C
-ATOM 4590 O VAL B 471 76.757 57.742 46.220 1.00 24.86 O
-ATOM 4591 CB VAL B 471 78.308 60.122 45.231 1.00 21.44 C
-ATOM 4592 CG1 VAL B 471 77.979 60.877 46.537 1.00 14.48 C
-ATOM 4593 CG2 VAL B 471 79.334 60.912 44.424 1.00 12.41 C
-ATOM 4594 N PHE B 472 78.442 57.687 47.720 1.00 25.75 N
-ATOM 4595 CA PHE B 472 77.679 57.055 48.795 1.00 29.45 C
-ATOM 4596 C PHE B 472 77.100 58.227 49.584 1.00 35.97 C
-ATOM 4597 O PHE B 472 77.811 58.856 50.377 1.00 31.82 O
-ATOM 4598 CB PHE B 472 78.605 56.253 49.707 1.00 27.11 C
-ATOM 4599 CG PHE B 472 79.238 55.043 49.048 1.00 25.45 C
-ATOM 4600 CD1 PHE B 472 78.652 53.790 49.165 1.00 23.46 C
-ATOM 4601 CD2 PHE B 472 80.440 55.152 48.353 1.00 22.28 C
-ATOM 4602 CE1 PHE B 472 79.250 52.672 48.608 1.00 21.89 C
-ATOM 4603 CE2 PHE B 472 81.041 54.035 47.796 1.00 21.71 C
-ATOM 4604 CZ PHE B 472 80.450 52.800 47.923 1.00 22.09 C
-ATOM 4605 N GLU B 473 75.822 58.521 49.349 1.00 43.95 N
-ATOM 4606 CA GLU B 473 75.158 59.630 50.008 1.00 50.62 C
-ATOM 4607 C GLU B 473 74.627 59.356 51.403 1.00 52.29 C
-ATOM 4608 O GLU B 473 73.969 58.351 51.641 1.00 46.85 O
-ATOM 4609 CB GLU B 473 74.028 60.174 49.134 1.00 62.20 C
-ATOM 4610 CG GLU B 473 74.264 61.590 48.622 1.00 87.71 C
-ATOM 4611 CD GLU B 473 74.395 62.622 49.737 1.00 98.31 C
-ATOM 4612 OE1 GLU B 473 73.475 62.717 50.580 1.00101.96 O
-ATOM 4613 OE2 GLU B 473 75.416 63.344 49.768 1.00101.31 O
-ATOM 4614 N ASP B 474 74.922 60.282 52.313 1.00 53.04 N
-ATOM 4615 CA ASP B 474 74.506 60.225 53.705 1.00 49.97 C
-ATOM 4616 C ASP B 474 74.629 58.864 54.371 1.00 45.96 C
-ATOM 4617 O ASP B 474 73.642 58.284 54.813 1.00 42.30 O
-ATOM 4618 CB ASP B 474 73.075 60.730 53.853 1.00 59.21 C
-ATOM 4619 CG ASP B 474 72.955 61.796 54.909 1.00 74.74 C
-ATOM 4620 OD1 ASP B 474 72.014 61.717 55.723 1.00 83.31 O
-ATOM 4621 OD2 ASP B 474 73.803 62.715 54.919 1.00 82.54 O
-ATOM 4622 N VAL B 475 75.852 58.360 54.440 1.00 42.61 N
-ATOM 4623 CA VAL B 475 76.109 57.091 55.081 1.00 39.96 C
-ATOM 4624 C VAL B 475 75.802 57.316 56.560 1.00 40.87 C
-ATOM 4625 O VAL B 475 76.142 58.363 57.111 1.00 40.16 O
-ATOM 4626 CB VAL B 475 77.580 56.706 54.907 1.00 37.46 C
-ATOM 4627 CG1 VAL B 475 77.783 55.251 55.268 1.00 37.24 C
-ATOM 4628 CG2 VAL B 475 78.009 56.978 53.482 1.00 36.08 C
-ATOM 4629 N LYS B 476 75.144 56.350 57.197 1.00 44.18 N
-ATOM 4630 CA LYS B 476 74.802 56.475 58.614 1.00 45.22 C
-ATOM 4631 C LYS B 476 75.451 55.378 59.439 1.00 45.90 C
-ATOM 4632 O LYS B 476 75.638 54.261 58.954 1.00 43.93 O
-ATOM 4633 CB LYS B 476 73.288 56.420 58.802 1.00 47.29 C
-ATOM 4634 CG LYS B 476 72.550 57.537 58.106 1.00 51.09 C
-ATOM 4635 CD LYS B 476 71.057 57.304 58.117 1.00 53.28 C
-ATOM 4636 CE LYS B 476 70.380 58.208 57.110 1.00 54.71 C
-ATOM 4637 NZ LYS B 476 68.907 58.071 57.150 1.00 55.63 N
-ATOM 4638 N GLY B 477 75.794 55.705 60.682 1.00 49.06 N
-ATOM 4639 CA GLY B 477 76.426 54.733 61.555 1.00 53.66 C
-ATOM 4640 C GLY B 477 75.653 54.486 62.831 1.00 58.13 C
-ATOM 4641 O GLY B 477 74.948 55.368 63.315 1.00 55.95 O
-ATOM 4642 N THR B 478 75.776 53.275 63.366 1.00 67.05 N
-ATOM 4643 CA THR B 478 75.095 52.913 64.602 1.00 73.80 C
-ATOM 4644 C THR B 478 75.719 53.745 65.710 1.00 75.48 C
-ATOM 4645 O THR B 478 75.022 54.451 66.440 1.00 76.87 O
-ATOM 4646 CB THR B 478 75.288 51.426 64.947 1.00 78.75 C
-ATOM 4647 OG1 THR B 478 74.915 50.620 63.824 1.00 85.98 O
-ATOM 4648 CG2 THR B 478 74.422 51.046 66.144 1.00 85.99 C
-ATOM 4649 N GLY B 479 77.039 53.645 65.836 1.00 78.60 N
-ATOM 4650 CA GLY B 479 77.730 54.418 66.846 1.00 80.24 C
-ATOM 4651 C GLY B 479 77.216 55.833 66.693 1.00 81.02 C
-ATOM 4652 O GLY B 479 76.970 56.281 65.572 1.00 82.07 O
-ATOM 4653 N GLY B 480 77.031 56.536 67.802 1.00 81.00 N
-ATOM 4654 CA GLY B 480 76.529 57.893 67.719 1.00 82.35 C
-ATOM 4655 C GLY B 480 75.017 57.884 67.669 1.00 86.16 C
-ATOM 4656 O GLY B 480 74.412 57.153 66.888 1.00 83.18 O
-ATOM 4657 N GLU B 481 74.406 58.724 68.490 1.00 91.11 N
-ATOM 4658 CA GLU B 481 72.957 58.793 68.573 1.00 89.75 C
-ATOM 4659 C GLU B 481 72.574 59.978 69.444 1.00 85.74 C
-ATOM 4660 O GLU B 481 71.595 60.677 69.183 1.00 81.96 O
-ATOM 4661 CB GLU B 481 72.443 57.499 69.197 1.00 95.75 C
-ATOM 4662 CG GLU B 481 73.279 57.063 70.393 1.00112.64 C
-ATOM 4663 CD GLU B 481 72.901 55.694 70.915 1.00120.77 C
-ATOM 4664 OE1 GLU B 481 71.763 55.538 71.407 1.00123.88 O
-ATOM 4665 OE2 GLU B 481 73.743 54.773 70.832 1.00124.11 O
-ATOM 4666 N SER B 482 73.361 60.194 70.490 1.00 82.96 N
-ATOM 4667 CA SER B 482 73.121 61.295 71.403 1.00 83.45 C
-ATOM 4668 C SER B 482 72.944 62.604 70.635 1.00 85.33 C
-ATOM 4669 O SER B 482 71.917 63.264 70.766 1.00 90.55 O
-ATOM 4670 CB SER B 482 74.277 61.407 72.403 1.00 81.55 C
-ATOM 4671 OG SER B 482 75.532 61.215 71.768 1.00 74.27 O
-ATOM 4672 N ARG B 483 73.927 62.963 69.813 1.00 86.74 N
-ATOM 4673 CA ARG B 483 73.865 64.206 69.044 1.00 86.80 C
-ATOM 4674 C ARG B 483 72.710 64.339 68.029 1.00 87.00 C
-ATOM 4675 O ARG B 483 72.752 65.199 67.144 1.00 79.05 O
-ATOM 4676 CB ARG B 483 75.218 64.473 68.358 1.00 90.48 C
-ATOM 4677 CG ARG B 483 75.842 63.281 67.640 1.00 97.49 C
-ATOM 4678 CD ARG B 483 76.573 62.325 68.588 1.00100.20 C
-ATOM 4679 NE ARG B 483 77.886 62.818 69.008 1.00100.82 N
-ATOM 4680 CZ ARG B 483 78.728 62.138 69.787 1.00101.45 C
-ATOM 4681 NH1 ARG B 483 78.400 60.931 70.236 1.00101.17 N
-ATOM 4682 NH2 ARG B 483 79.904 62.664 70.119 1.00101.05 N
-ATOM 4683 N ASP B 484 71.684 63.497 68.174 1.00 82.10 N
-ATOM 4684 CA ASP B 484 70.489 63.530 67.319 1.00 75.79 C
-ATOM 4685 C ASP B 484 70.583 62.845 65.957 1.00 71.38 C
-ATOM 4686 O ASP B 484 69.709 63.016 65.098 1.00 63.51 O
-ATOM 4687 CB ASP B 484 70.033 64.978 67.104 1.00 83.33 C
-ATOM 4688 CG ASP B 484 69.816 65.721 68.404 1.00 96.30 C
-ATOM 4689 OD1 ASP B 484 69.208 65.135 69.323 1.00103.78 O
-ATOM 4690 OD2 ASP B 484 70.242 66.892 68.502 1.00104.24 O
-ATOM 4691 N LEU B 485 71.628 62.057 65.759 1.00 66.69 N
-ATOM 4692 CA LEU B 485 71.809 61.375 64.490 1.00 63.92 C
-ATOM 4693 C LEU B 485 71.226 59.967 64.512 1.00 62.94 C
-ATOM 4694 O LEU B 485 71.479 59.196 65.442 1.00 65.22 O
-ATOM 4695 CB LEU B 485 73.296 61.313 64.156 1.00 64.76 C
-ATOM 4696 CG LEU B 485 74.006 62.665 64.247 1.00 65.73 C
-ATOM 4697 CD1 LEU B 485 75.500 62.499 64.012 1.00 66.40 C
-ATOM 4698 CD2 LEU B 485 73.396 63.612 63.227 1.00 66.43 C
-ATOM 4699 N PRO B 486 70.427 59.618 63.486 1.00 65.55 N
-ATOM 4700 CA PRO B 486 69.776 58.312 63.325 1.00 65.96 C
-ATOM 4701 C PRO B 486 70.731 57.125 63.441 1.00 66.83 C
-ATOM 4702 O PRO B 486 71.912 57.300 63.747 1.00 68.29 O
-ATOM 4703 CB PRO B 486 69.138 58.424 61.944 1.00 65.64 C
-ATOM 4704 CG PRO B 486 68.702 59.851 61.925 1.00 65.07 C
-ATOM 4705 CD PRO B 486 69.925 60.569 62.476 1.00 64.97 C
-ATOM 4706 N SER B 487 70.224 55.924 63.180 1.00 67.36 N
-ATOM 4707 CA SER B 487 71.043 54.721 63.288 1.00 67.47 C
-ATOM 4708 C SER B 487 71.738 54.315 61.983 1.00 65.37 C
-ATOM 4709 O SER B 487 72.943 54.554 61.814 1.00 62.70 O
-ATOM 4710 CB SER B 487 70.189 53.565 63.807 1.00 71.90 C
-ATOM 4711 OG SER B 487 70.984 52.428 64.094 1.00 80.65 O
-ATOM 4712 N GLY B 488 70.992 53.694 61.068 1.00 59.63 N
-ATOM 4713 CA GLY B 488 71.576 53.279 59.798 1.00 53.38 C
-ATOM 4714 C GLY B 488 72.781 52.351 59.909 1.00 51.19 C
-ATOM 4715 O GLY B 488 73.483 52.347 60.920 1.00 46.11 O
-ATOM 4716 N GLN B 489 73.033 51.574 58.860 1.00 51.47 N
-ATOM 4717 CA GLN B 489 74.152 50.635 58.853 1.00 52.08 C
-ATOM 4718 C GLN B 489 75.220 50.920 57.792 1.00 51.27 C
-ATOM 4719 O GLN B 489 76.103 50.095 57.561 1.00 50.23 O
-ATOM 4720 CB GLN B 489 73.625 49.209 58.664 1.00 54.93 C
-ATOM 4721 CG GLN B 489 72.834 48.668 59.842 1.00 61.98 C
-ATOM 4722 CD GLN B 489 73.708 48.338 61.039 1.00 65.32 C
-ATOM 4723 OE1 GLN B 489 74.681 47.586 60.922 1.00 66.90 O
-ATOM 4724 NE2 GLN B 489 73.358 48.886 62.203 1.00 66.19 N
-ATOM 4725 N GLY B 490 75.141 52.079 57.146 1.00 49.30 N
-ATOM 4726 CA GLY B 490 76.116 52.414 56.121 1.00 47.25 C
-ATOM 4727 C GLY B 490 77.573 52.287 56.540 1.00 45.97 C
-ATOM 4728 O GLY B 490 78.335 51.556 55.902 1.00 46.10 O
-ATOM 4729 N ILE B 491 77.962 52.997 57.602 1.00 43.06 N
-ATOM 4730 CA ILE B 491 79.342 52.958 58.094 1.00 38.17 C
-ATOM 4731 C ILE B 491 79.738 51.501 58.314 1.00 40.89 C
-ATOM 4732 O ILE B 491 80.859 51.077 58.006 1.00 35.68 O
-ATOM 4733 CB ILE B 491 79.498 53.700 59.443 1.00 36.14 C
-ATOM 4734 CG1 ILE B 491 78.787 55.051 59.399 1.00 34.17 C
-ATOM 4735 CG2 ILE B 491 80.972 53.915 59.748 1.00 32.76 C
-ATOM 4736 CD1 ILE B 491 79.441 56.072 58.518 1.00 35.07 C
-ATOM 4737 N ASN B 492 78.793 50.739 58.847 1.00 44.31 N
-ATOM 4738 CA ASN B 492 79.012 49.330 59.109 1.00 47.14 C
-ATOM 4739 C ASN B 492 79.320 48.627 57.797 1.00 47.48 C
-ATOM 4740 O ASN B 492 80.295 47.888 57.692 1.00 48.00 O
-ATOM 4741 CB ASN B 492 77.760 48.712 59.717 1.00 54.60 C
-ATOM 4742 CG ASN B 492 78.075 47.734 60.811 1.00 63.99 C
-ATOM 4743 OD1 ASN B 492 78.156 48.108 61.983 1.00 69.01 O
-ATOM 4744 ND2 ASN B 492 78.269 46.470 60.441 1.00 67.45 N
-ATOM 4745 N ASN B 493 78.483 48.871 56.794 1.00 47.26 N
-ATOM 4746 CA ASN B 493 78.651 48.239 55.495 1.00 44.97 C
-ATOM 4747 C ASN B 493 79.909 48.680 54.767 1.00 43.91 C
-ATOM 4748 O ASN B 493 80.635 47.848 54.218 1.00 41.65 O
-ATOM 4749 CB ASN B 493 77.429 48.502 54.613 1.00 45.91 C
-ATOM 4750 CG ASN B 493 76.176 47.838 55.144 1.00 47.47 C
-ATOM 4751 OD1 ASN B 493 76.125 46.624 55.295 1.00 49.98 O
-ATOM 4752 ND2 ASN B 493 75.160 48.634 55.432 1.00 49.48 N
-ATOM 4753 N LEU B 494 80.168 49.984 54.762 1.00 43.52 N
-ATOM 4754 CA LEU B 494 81.348 50.498 54.082 1.00 44.12 C
-ATOM 4755 C LEU B 494 82.577 49.761 54.561 1.00 46.33 C
-ATOM 4756 O LEU B 494 83.437 49.395 53.762 1.00 45.35 O
-ATOM 4757 CB LEU B 494 81.523 52.006 54.323 1.00 42.56 C
-ATOM 4758 CG LEU B 494 80.578 52.959 53.570 1.00 41.07 C
-ATOM 4759 CD1 LEU B 494 80.966 54.377 53.896 1.00 39.22 C
-ATOM 4760 CD2 LEU B 494 80.644 52.724 52.051 1.00 39.99 C
-ATOM 4761 N ASP B 495 82.652 49.522 55.864 1.00 51.79 N
-ATOM 4762 CA ASP B 495 83.805 48.830 56.413 1.00 55.06 C
-ATOM 4763 C ASP B 495 83.959 47.398 55.899 1.00 55.70 C
-ATOM 4764 O ASP B 495 85.048 46.820 55.981 1.00 53.90 O
-ATOM 4765 CB ASP B 495 83.760 48.831 57.934 1.00 60.63 C
-ATOM 4766 CG ASP B 495 85.138 48.986 58.541 1.00 69.57 C
-ATOM 4767 OD1 ASP B 495 86.057 48.243 58.127 1.00 74.01 O
-ATOM 4768 OD2 ASP B 495 85.306 49.853 59.425 1.00 73.94 O
-ATOM 4769 N ASN B 496 82.880 46.832 55.360 1.00 57.46 N
-ATOM 4770 CA ASN B 496 82.918 45.473 54.820 1.00 56.65 C
-ATOM 4771 C ASN B 496 83.121 45.484 53.311 1.00 53.89 C
-ATOM 4772 O ASN B 496 82.941 44.467 52.640 1.00 56.25 O
-ATOM 4773 CB ASN B 496 81.623 44.735 55.131 1.00 58.74 C
-ATOM 4774 CG ASN B 496 81.326 44.697 56.603 1.00 62.52 C
-ATOM 4775 OD1 ASN B 496 82.175 44.324 57.415 1.00 63.47 O
-ATOM 4776 ND2 ASN B 496 80.112 45.083 56.962 1.00 65.34 N
-ATOM 4777 N LEU B 497 83.494 46.643 52.781 1.00 51.11 N
-ATOM 4778 CA LEU B 497 83.710 46.786 51.353 1.00 52.26 C
-ATOM 4779 C LEU B 497 85.083 47.399 51.066 1.00 58.79 C
-ATOM 4780 O LEU B 497 85.283 48.020 50.024 1.00 55.73 O
-ATOM 4781 CB LEU B 497 82.606 47.661 50.758 1.00 45.55 C
-ATOM 4782 CG LEU B 497 81.159 47.225 51.020 1.00 37.73 C
-ATOM 4783 CD1 LEU B 497 80.201 48.377 50.737 1.00 32.55 C
-ATOM 4784 CD2 LEU B 497 80.833 46.023 50.162 1.00 33.77 C
-ATOM 4785 N ARG B 498 86.025 47.219 51.991 1.00 63.77 N
-ATOM 4786 CA ARG B 498 87.377 47.746 51.829 1.00 63.57 C
-ATOM 4787 C ARG B 498 87.965 47.385 50.465 1.00 59.66 C
-ATOM 4788 O ARG B 498 88.796 48.107 49.937 1.00 49.04 O
-ATOM 4789 CB ARG B 498 88.277 47.223 52.948 1.00 74.69 C
-ATOM 4790 CG ARG B 498 88.318 45.721 53.019 1.00101.51 C
-ATOM 4791 CD ARG B 498 89.087 45.230 54.222 1.00115.21 C
-ATOM 4792 NE ARG B 498 89.292 43.784 54.154 1.00120.19 N
-ATOM 4793 CZ ARG B 498 89.944 43.074 55.069 1.00121.23 C
-ATOM 4794 NH1 ARG B 498 90.457 43.678 56.132 1.00121.28 N
-ATOM 4795 NH2 ARG B 498 90.091 41.763 54.916 1.00120.71 N
-ATOM 4796 N ASP B 499 87.515 46.281 49.884 1.00 55.47 N
-ATOM 4797 CA ASP B 499 88.019 45.849 48.584 1.00 52.62 C
-ATOM 4798 C ASP B 499 87.423 46.629 47.424 1.00 51.25 C
-ATOM 4799 O ASP B 499 88.051 46.787 46.369 1.00 53.70 O
-ATOM 4800 CB ASP B 499 87.758 44.358 48.393 1.00 53.32 C
-ATOM 4801 CG ASP B 499 88.850 43.502 48.995 1.00 56.79 C
-ATOM 4802 OD1 ASP B 499 89.484 43.935 49.981 1.00 58.87 O
-ATOM 4803 OD2 ASP B 499 89.072 42.388 48.487 1.00 60.25 O
-ATOM 4804 N TYR B 500 86.203 47.106 47.616 1.00 51.40 N
-ATOM 4805 CA TYR B 500 85.542 47.886 46.588 1.00 51.59 C
-ATOM 4806 C TYR B 500 86.115 49.299 46.635 1.00 49.07 C
-ATOM 4807 O TYR B 500 86.291 49.947 45.611 1.00 52.55 O
-ATOM 4808 CB TYR B 500 84.033 47.963 46.850 1.00 53.59 C
-ATOM 4809 CG TYR B 500 83.310 46.638 46.867 1.00 54.20 C
-ATOM 4810 CD1 TYR B 500 83.570 45.691 47.855 1.00 54.00 C
-ATOM 4811 CD2 TYR B 500 82.354 46.337 45.896 1.00 53.99 C
-ATOM 4812 CE1 TYR B 500 82.896 44.477 47.877 1.00 53.45 C
-ATOM 4813 CE2 TYR B 500 81.674 45.131 45.910 1.00 53.33 C
-ATOM 4814 CZ TYR B 500 81.951 44.204 46.901 1.00 53.46 C
-ATOM 4815 OH TYR B 500 81.288 43.000 46.910 1.00 54.64 O
-ATOM 4816 N LEU B 501 86.418 49.765 47.839 1.00 41.44 N
-ATOM 4817 CA LEU B 501 86.922 51.113 48.024 1.00 36.83 C
-ATOM 4818 C LEU B 501 88.330 51.418 47.545 1.00 40.39 C
-ATOM 4819 O LEU B 501 88.506 52.299 46.710 1.00 33.96 O
-ATOM 4820 CB LEU B 501 86.785 51.522 49.489 1.00 28.32 C
-ATOM 4821 CG LEU B 501 85.355 51.721 49.984 1.00 21.97 C
-ATOM 4822 CD1 LEU B 501 85.384 52.019 51.467 1.00 20.79 C
-ATOM 4823 CD2 LEU B 501 84.686 52.856 49.229 1.00 19.33 C
-ATOM 4824 N ASP B 502 89.334 50.711 48.055 1.00 42.25 N
-ATOM 4825 CA ASP B 502 90.706 51.007 47.634 1.00 43.10 C
-ATOM 4826 C ASP B 502 91.096 50.429 46.289 1.00 39.26 C
-ATOM 4827 O ASP B 502 92.149 50.755 45.738 1.00 32.66 O
-ATOM 4828 CB ASP B 502 91.727 50.612 48.714 1.00 58.00 C
-ATOM 4829 CG ASP B 502 91.299 49.420 49.525 1.00 76.04 C
-ATOM 4830 OD1 ASP B 502 91.052 48.357 48.923 1.00 87.21 O
-ATOM 4831 OD2 ASP B 502 91.219 49.548 50.768 1.00 85.36 O
-ATOM 4832 N GLY B 503 90.220 49.586 45.765 1.00 35.81 N
-ATOM 4833 CA GLY B 503 90.419 48.993 44.459 1.00 32.50 C
-ATOM 4834 C GLY B 503 91.773 48.453 44.060 1.00 31.96 C
-ATOM 4835 O GLY B 503 92.281 48.807 42.993 1.00 29.22 O
-ATOM 4836 N SER B 504 92.352 47.588 44.896 1.00 34.73 N
-ATOM 4837 CA SER B 504 93.643 46.974 44.589 1.00 35.94 C
-ATOM 4838 C SER B 504 93.405 45.872 43.573 1.00 36.94 C
-ATOM 4839 O SER B 504 94.191 45.686 42.650 1.00 38.91 O
-ATOM 4840 CB SER B 504 94.274 46.366 45.839 1.00 36.35 C
-ATOM 4841 OG SER B 504 94.745 47.366 46.723 1.00 37.14 O
-ATOM 4842 N VAL B 505 92.308 45.145 43.751 1.00 38.67 N
-ATOM 4843 CA VAL B 505 91.955 44.057 42.848 1.00 39.92 C
-ATOM 4844 C VAL B 505 90.508 44.225 42.385 1.00 39.99 C
-ATOM 4845 O VAL B 505 89.773 45.047 42.936 1.00 41.32 O
-ATOM 4846 CB VAL B 505 92.125 42.673 43.540 1.00 39.41 C
-ATOM 4847 CG1 VAL B 505 91.978 41.548 42.508 1.00 38.17 C
-ATOM 4848 CG2 VAL B 505 93.494 42.582 44.208 1.00 36.74 C
-ATOM 4849 N LYS B 506 90.107 43.457 41.369 1.00 40.90 N
-ATOM 4850 CA LYS B 506 88.743 43.529 40.838 1.00 41.58 C
-ATOM 4851 C LYS B 506 87.656 43.030 41.799 1.00 41.04 C
-ATOM 4852 O LYS B 506 87.934 42.430 42.838 1.00 43.09 O
-ATOM 4853 CB LYS B 506 88.623 42.742 39.539 1.00 39.44 C
-ATOM 4854 CG LYS B 506 89.467 43.246 38.384 1.00 36.22 C
-ATOM 4855 CD LYS B 506 88.660 43.157 37.084 1.00 34.18 C
-ATOM 4856 CE LYS B 506 89.543 43.113 35.850 1.00 32.63 C
-ATOM 4857 NZ LYS B 506 90.077 41.747 35.649 1.00 35.22 N
-ATOM 4858 N VAL B 507 86.408 43.273 41.418 1.00 41.71 N
-ATOM 4859 CA VAL B 507 85.258 42.893 42.223 1.00 43.67 C
-ATOM 4860 C VAL B 507 84.055 42.491 41.331 1.00 48.45 C
-ATOM 4861 O VAL B 507 83.954 42.896 40.165 1.00 44.17 O
-ATOM 4862 CB VAL B 507 84.916 44.073 43.173 1.00 38.61 C
-ATOM 4863 CG1 VAL B 507 83.492 44.020 43.609 1.00 37.67 C
-ATOM 4864 CG2 VAL B 507 85.805 44.021 44.389 1.00 34.88 C
-ATOM 4865 N ASN B 508 83.155 41.672 41.873 1.00 54.86 N
-ATOM 4866 CA ASN B 508 81.984 41.222 41.114 1.00 57.53 C
-ATOM 4867 C ASN B 508 80.697 41.945 41.524 1.00 56.62 C
-ATOM 4868 O ASN B 508 80.258 41.843 42.666 1.00 47.40 O
-ATOM 4869 CB ASN B 508 81.815 39.707 41.270 1.00 70.65 C
-ATOM 4870 CG ASN B 508 83.047 38.929 40.812 1.00 89.37 C
-ATOM 4871 OD1 ASN B 508 82.995 37.711 40.646 1.00 99.61 O
-ATOM 4872 ND2 ASN B 508 84.158 39.631 40.615 1.00 99.06 N
-ATOM 4873 N LEU B 509 80.100 42.660 40.570 1.00 55.71 N
-ATOM 4874 CA LEU B 509 78.883 43.448 40.792 1.00 54.87 C
-ATOM 4875 C LEU B 509 77.583 42.768 40.331 1.00 59.16 C
-ATOM 4876 O LEU B 509 77.522 42.193 39.247 1.00 52.40 O
-ATOM 4877 CB LEU B 509 79.034 44.809 40.092 1.00 59.48 C
-ATOM 4878 CG LEU B 509 79.910 45.917 40.712 1.00 68.14 C
-ATOM 4879 CD1 LEU B 509 80.983 45.336 41.618 1.00 72.38 C
-ATOM 4880 CD2 LEU B 509 80.534 46.751 39.592 1.00 72.66 C
-ATOM 4881 N GLU B 510 76.540 42.862 41.155 1.00 71.31 N
-ATOM 4882 CA GLU B 510 75.240 42.242 40.858 1.00 75.95 C
-ATOM 4883 C GLU B 510 74.146 43.177 40.339 1.00 75.52 C
-ATOM 4884 O GLU B 510 73.752 44.126 41.014 1.00 77.97 O
-ATOM 4885 CB GLU B 510 74.684 41.540 42.103 1.00 82.26 C
-ATOM 4886 CG GLU B 510 75.286 40.189 42.427 1.00 98.76 C
-ATOM 4887 CD GLU B 510 74.412 39.394 43.390 1.00106.36 C
-ATOM 4888 OE1 GLU B 510 74.139 39.896 44.502 1.00108.51 O
-ATOM 4889 OE2 GLU B 510 73.993 38.270 43.032 1.00109.66 O
-ATOM 4890 N LYS B 511 73.631 42.869 39.153 1.00 82.43 N
-ATOM 4891 CA LYS B 511 72.565 43.652 38.534 1.00 90.15 C
-ATOM 4892 C LYS B 511 71.707 42.671 37.722 1.00 95.24 C
-ATOM 4893 O LYS B 511 72.178 41.586 37.375 1.00104.88 O
-ATOM 4894 CB LYS B 511 73.174 44.723 37.624 1.00 89.47 C
-ATOM 4895 CG LYS B 511 72.188 45.741 37.086 1.00 80.69 C
-ATOM 4896 CD LYS B 511 72.816 46.578 35.974 1.00 74.66 C
-ATOM 4897 CE LYS B 511 71.763 47.407 35.260 1.00 72.51 C
-ATOM 4898 NZ LYS B 511 72.267 47.961 33.980 1.00 71.63 N
-ATOM 4899 N LYS B 512 70.460 43.033 37.419 1.00104.09 N
-ATOM 4900 CA LYS B 512 69.577 42.140 36.662 1.00107.50 C
-ATOM 4901 C LYS B 512 69.266 40.901 37.496 1.00112.77 C
-ATOM 4902 O LYS B 512 68.702 39.925 36.994 1.00109.18 O
-ATOM 4903 CB LYS B 512 70.239 41.705 35.346 1.00102.99 C
-ATOM 4904 CG LYS B 512 69.734 42.424 34.104 1.00 98.78 C
-ATOM 4905 CD LYS B 512 68.296 42.036 33.786 1.00 96.92 C
-ATOM 4906 CE LYS B 512 67.801 42.740 32.531 1.00 96.42 C
-ATOM 4907 NZ LYS B 512 66.380 42.422 32.240 1.00 96.32 N
-ATOM 4908 N HIS B 513 69.651 40.959 38.769 1.00122.75 N
-ATOM 4909 CA HIS B 513 69.449 39.873 39.726 1.00130.20 C
-ATOM 4910 C HIS B 513 70.374 38.690 39.444 1.00127.83 C
-ATOM 4911 O HIS B 513 69.954 37.532 39.502 1.00133.51 O
-ATOM 4912 CB HIS B 513 67.988 39.407 39.714 1.00141.01 C
-ATOM 4913 CG HIS B 513 67.591 38.642 40.940 1.00153.93 C
-ATOM 4914 ND1 HIS B 513 68.193 37.461 41.312 1.00158.69 N
-ATOM 4915 CD2 HIS B 513 66.663 38.907 41.893 1.00158.71 C
-ATOM 4916 CE1 HIS B 513 67.657 37.028 42.439 1.00160.58 C
-ATOM 4917 NE2 HIS B 513 66.726 37.889 42.813 1.00160.70 N
-ATOM 4918 N LEU B 514 71.635 38.994 39.147 1.00125.51 N
-ATOM 4919 CA LEU B 514 72.646 37.978 38.850 1.00123.61 C
-ATOM 4920 C LEU B 514 74.042 38.609 38.935 1.00121.42 C
-ATOM 4921 O LEU B 514 74.190 39.732 39.426 1.00129.84 O
-ATOM 4922 CB LEU B 514 72.421 37.403 37.443 1.00114.80 C
-ATOM 4923 CG LEU B 514 71.203 36.501 37.205 1.00100.99 C
-ATOM 4924 CD1 LEU B 514 70.921 36.382 35.711 1.00 92.56 C
-ATOM 4925 CD2 LEU B 514 71.449 35.132 37.837 1.00 92.50 C
-ATOM 4926 N ASN B 515 75.059 37.889 38.461 1.00114.82 N
-ATOM 4927 CA ASN B 515 76.433 38.401 38.482 1.00110.58 C
-ATOM 4928 C ASN B 515 76.914 38.879 37.112 1.00106.87 C
-ATOM 4929 O ASN B 515 77.419 38.095 36.309 1.00104.06 O
-ATOM 4930 CB ASN B 515 77.406 37.338 39.014 1.00107.23 C
-ATOM 4931 CG ASN B 515 77.504 37.334 40.536 1.00 99.67 C
-ATOM 4932 OD1 ASN B 515 76.576 36.917 41.230 1.00 95.55 O
-ATOM 4933 ND2 ASN B 515 78.633 37.807 41.058 1.00 94.60 N
-ATOM 4934 N LYS B 516 76.748 40.173 36.855 1.00 93.76 N
-ATOM 4935 CA LYS B 516 77.176 40.767 35.595 1.00 83.07 C
-ATOM 4936 C LYS B 516 78.666 41.051 35.727 1.00 80.31 C
-ATOM 4937 O LYS B 516 79.439 40.211 36.193 1.00 70.49 O
-ATOM 4938 CB LYS B 516 76.457 42.097 35.331 1.00 78.96 C
-ATOM 4939 CG LYS B 516 75.028 42.189 35.835 1.00 77.75 C
-ATOM 4940 CD LYS B 516 74.083 41.323 35.028 1.00 78.92 C
-ATOM 4941 CE LYS B 516 74.003 41.774 33.581 1.00 78.76 C
-ATOM 4942 NZ LYS B 516 72.988 40.972 32.845 1.00 79.11 N
-ATOM 4943 N ARG B 517 79.038 42.267 35.346 1.00 73.19 N
-ATOM 4944 CA ARG B 517 80.412 42.741 35.375 1.00 70.93 C
-ATOM 4945 C ARG B 517 81.301 42.469 36.592 1.00 71.67 C
-ATOM 4946 O ARG B 517 80.860 42.494 37.749 1.00 64.37 O
-ATOM 4947 CB ARG B 517 80.439 44.247 35.091 1.00 75.07 C
-ATOM 4948 CG ARG B 517 80.790 44.597 33.659 1.00 85.90 C
-ATOM 4949 CD ARG B 517 81.931 45.604 33.615 1.00 91.17 C
-ATOM 4950 NE ARG B 517 82.559 45.666 32.296 1.00 93.46 N
-ATOM 4951 CZ ARG B 517 83.551 46.490 31.974 1.00 93.61 C
-ATOM 4952 NH1 ARG B 517 84.039 47.334 32.875 1.00 93.21 N
-ATOM 4953 NH2 ARG B 517 84.053 46.471 30.747 1.00 93.07 N
-ATOM 4954 N THR B 518 82.572 42.221 36.274 1.00 71.23 N
-ATOM 4955 CA THR B 518 83.656 41.975 37.222 1.00 67.21 C
-ATOM 4956 C THR B 518 84.582 43.135 36.876 1.00 64.40 C
-ATOM 4957 O THR B 518 85.112 43.184 35.771 1.00 61.53 O
-ATOM 4958 CB THR B 518 84.409 40.672 36.901 1.00 72.54 C
-ATOM 4959 OG1 THR B 518 83.475 39.602 36.714 1.00 82.37 O
-ATOM 4960 CG2 THR B 518 85.374 40.328 38.027 1.00 82.39 C
-ATOM 4961 N GLN B 519 84.778 44.071 37.795 1.00 58.29 N
-ATOM 4962 CA GLN B 519 85.613 45.232 37.489 1.00 54.00 C
-ATOM 4963 C GLN B 519 86.198 45.877 38.730 1.00 50.82 C
-ATOM 4964 O GLN B 519 85.890 45.495 39.856 1.00 51.13 O
-ATOM 4965 CB GLN B 519 84.766 46.296 36.777 1.00 55.88 C
-ATOM 4966 CG GLN B 519 83.695 46.895 37.706 1.00 57.00 C
-ATOM 4967 CD GLN B 519 82.912 48.040 37.089 1.00 57.44 C
-ATOM 4968 OE1 GLN B 519 82.079 47.835 36.206 1.00 56.56 O
-ATOM 4969 NE2 GLN B 519 83.179 49.259 37.558 1.00 56.62 N
-ATOM 4970 N ILE B 520 87.054 46.865 38.513 1.00 42.67 N
-ATOM 4971 CA ILE B 520 87.598 47.599 39.632 1.00 34.90 C
-ATOM 4972 C ILE B 520 86.409 48.478 40.036 1.00 33.07 C
-ATOM 4973 O ILE B 520 85.796 49.124 39.184 1.00 28.62 O
-ATOM 4974 CB ILE B 520 88.758 48.513 39.207 1.00 35.11 C
-ATOM 4975 CG1 ILE B 520 89.901 47.689 38.601 1.00 32.53 C
-ATOM 4976 CG2 ILE B 520 89.244 49.319 40.421 1.00 32.71 C
-ATOM 4977 CD1 ILE B 520 90.838 47.089 39.631 1.00 31.26 C
-ATOM 4978 N PHE B 521 86.052 48.483 41.315 1.00 27.60 N
-ATOM 4979 CA PHE B 521 84.931 49.311 41.754 1.00 26.96 C
-ATOM 4980 C PHE B 521 85.292 50.784 41.518 1.00 29.17 C
-ATOM 4981 O PHE B 521 86.440 51.187 41.698 1.00 26.49 O
-ATOM 4982 CB PHE B 521 84.641 49.077 43.231 1.00 22.67 C
-ATOM 4983 CG PHE B 521 83.277 49.505 43.637 1.00 22.37 C
-ATOM 4984 CD1 PHE B 521 82.161 48.832 43.151 1.00 22.27 C
-ATOM 4985 CD2 PHE B 521 83.096 50.573 44.512 1.00 23.26 C
-ATOM 4986 CE1 PHE B 521 80.879 49.215 43.534 1.00 22.78 C
-ATOM 4987 CE2 PHE B 521 81.811 50.970 44.905 1.00 22.74 C
-ATOM 4988 CZ PHE B 521 80.702 50.288 44.415 1.00 23.77 C
-ATOM 4989 N PRO B 522 84.312 51.608 41.118 1.00 28.76 N
-ATOM 4990 CA PRO B 522 84.634 53.021 40.876 1.00 27.89 C
-ATOM 4991 C PRO B 522 85.091 53.823 42.099 1.00 25.12 C
-ATOM 4992 O PRO B 522 84.781 53.460 43.229 1.00 23.86 O
-ATOM 4993 CB PRO B 522 83.335 53.574 40.269 1.00 31.25 C
-ATOM 4994 CG PRO B 522 82.737 52.373 39.584 1.00 31.91 C
-ATOM 4995 CD PRO B 522 82.957 51.292 40.637 1.00 30.13 C
-ATOM 4996 N PRO B 523 85.854 54.914 41.868 1.00 25.34 N
-ATOM 4997 CA PRO B 523 86.396 55.838 42.867 1.00 22.77 C
-ATOM 4998 C PRO B 523 85.244 56.787 43.190 1.00 21.78 C
-ATOM 4999 O PRO B 523 84.205 56.742 42.531 1.00 27.07 O
-ATOM 5000 CB PRO B 523 87.490 56.585 42.104 1.00 20.38 C
-ATOM 5001 CG PRO B 523 87.648 55.837 40.813 1.00 19.05 C
-ATOM 5002 CD PRO B 523 86.283 55.336 40.530 1.00 20.82 C
-ATOM 5003 N GLY B 524 85.406 57.653 44.178 1.00 21.40 N
-ATOM 5004 CA GLY B 524 84.319 58.563 44.464 1.00 22.26 C
-ATOM 5005 C GLY B 524 84.332 59.282 45.785 1.00 23.31 C
-ATOM 5006 O GLY B 524 85.385 59.516 46.372 1.00 23.22 O
-ATOM 5007 N ILE B 525 83.141 59.635 46.254 1.00 23.81 N
-ATOM 5008 CA ILE B 525 83.006 60.357 47.506 1.00 24.35 C
-ATOM 5009 C ILE B 525 82.097 59.600 48.485 1.00 24.14 C
-ATOM 5010 O ILE B 525 81.291 58.738 48.110 1.00 23.44 O
-ATOM 5011 CB ILE B 525 82.350 61.747 47.276 1.00 24.66 C
-ATOM 5012 CG1 ILE B 525 82.919 62.405 46.025 1.00 24.73 C
-ATOM 5013 CG2 ILE B 525 82.551 62.646 48.499 1.00 23.87 C
-ATOM 5014 CD1 ILE B 525 82.054 63.587 45.515 1.00 23.92 C
-ATOM 5015 N VAL B 526 82.242 59.933 49.754 1.00 24.02 N
-ATOM 5016 CA VAL B 526 81.395 59.369 50.774 1.00 25.08 C
-ATOM 5017 C VAL B 526 80.932 60.598 51.526 1.00 29.69 C
-ATOM 5018 O VAL B 526 81.744 61.326 52.097 1.00 26.11 O
-ATOM 5019 CB VAL B 526 82.156 58.422 51.718 1.00 21.33 C
-ATOM 5020 CG1 VAL B 526 81.392 58.252 53.018 1.00 17.28 C
-ATOM 5021 CG2 VAL B 526 82.305 57.069 51.068 1.00 18.53 C
-ATOM 5022 N THR B 527 79.629 60.858 51.454 1.00 35.18 N
-ATOM 5023 CA THR B 527 79.024 61.992 52.145 1.00 36.85 C
-ATOM 5024 C THR B 527 78.553 61.441 53.496 1.00 34.89 C
-ATOM 5025 O THR B 527 77.903 60.402 53.563 1.00 32.03 O
-ATOM 5026 CB THR B 527 77.854 62.557 51.330 1.00 44.77 C
-ATOM 5027 OG1 THR B 527 77.167 63.551 52.094 1.00 58.56 O
-ATOM 5028 CG2 THR B 527 76.921 61.478 50.967 1.00 57.44 C
-ATOM 5029 N MET B 528 78.886 62.133 54.573 1.00 32.94 N
-ATOM 5030 CA MET B 528 78.547 61.633 55.891 1.00 31.02 C
-ATOM 5031 C MET B 528 78.064 62.736 56.801 1.00 33.51 C
-ATOM 5032 O MET B 528 78.397 63.903 56.595 1.00 34.33 O
-ATOM 5033 CB MET B 528 79.791 60.970 56.465 1.00 27.78 C
-ATOM 5034 CG MET B 528 79.594 60.172 57.717 1.00 24.05 C
-ATOM 5035 SD MET B 528 81.178 59.620 58.243 1.00 15.70 S
-ATOM 5036 CE MET B 528 81.403 58.327 57.168 1.00 19.12 C
-ATOM 5037 N ASN B 529 77.318 62.361 57.837 1.00 40.76 N
-ATOM 5038 CA ASN B 529 76.739 63.342 58.750 1.00 46.59 C
-ATOM 5039 C ASN B 529 77.375 63.607 60.117 1.00 49.12 C
-ATOM 5040 O ASN B 529 76.793 64.331 60.922 1.00 50.16 O
-ATOM 5041 CB ASN B 529 75.260 63.020 58.955 1.00 50.36 C
-ATOM 5042 CG ASN B 529 74.403 64.264 59.027 1.00 54.97 C
-ATOM 5043 OD1 ASN B 529 74.661 65.166 59.831 1.00 56.38 O
-ATOM 5044 ND2 ASN B 529 73.373 64.324 58.182 1.00 56.71 N
-ATOM 5045 N GLU B 530 78.549 63.043 60.379 1.00 55.63 N
-ATOM 5046 CA GLU B 530 79.264 63.246 61.649 1.00 59.39 C
-ATOM 5047 C GLU B 530 79.108 62.165 62.703 1.00 60.38 C
-ATOM 5048 O GLU B 530 78.735 62.443 63.845 1.00 64.07 O
-ATOM 5049 CB GLU B 530 78.915 64.590 62.300 1.00 58.24 C
-ATOM 5050 CG GLU B 530 79.654 65.769 61.724 1.00 58.91 C
-ATOM 5051 CD GLU B 530 79.680 66.941 62.680 1.00 59.79 C
-ATOM 5052 OE1 GLU B 530 78.590 67.454 63.018 1.00 59.81 O
-ATOM 5053 OE2 GLU B 530 80.790 67.345 63.098 1.00 60.50 O
-ATOM 5054 N TYR B 531 79.414 60.933 62.314 1.00 64.49 N
-ATOM 5055 CA TYR B 531 79.349 59.796 63.218 1.00 67.51 C
-ATOM 5056 C TYR B 531 80.783 59.475 63.625 1.00 68.81 C
-ATOM 5057 O TYR B 531 81.684 60.298 63.456 1.00 72.21 O
-ATOM 5058 CB TYR B 531 78.740 58.589 62.505 1.00 67.47 C
-ATOM 5059 CG TYR B 531 77.312 58.783 62.053 1.00 63.74 C
-ATOM 5060 CD1 TYR B 531 76.998 59.676 61.039 1.00 61.45 C
-ATOM 5061 CD2 TYR B 531 76.277 58.056 62.634 1.00 62.54 C
-ATOM 5062 CE1 TYR B 531 75.682 59.839 60.609 1.00 61.78 C
-ATOM 5063 CE2 TYR B 531 74.961 58.212 62.216 1.00 61.73 C
-ATOM 5064 CZ TYR B 531 74.665 59.103 61.202 1.00 61.32 C
-ATOM 5065 OH TYR B 531 73.357 59.248 60.779 1.00 61.16 O
-ATOM 5066 N SER B 532 80.988 58.285 64.176 1.00 68.73 N
-ATOM 5067 CA SER B 532 82.323 57.848 64.562 1.00 65.58 C
-ATOM 5068 C SER B 532 82.750 56.908 63.457 1.00 61.68 C
-ATOM 5069 O SER B 532 82.059 55.929 63.163 1.00 61.98 O
-ATOM 5070 CB SER B 532 82.299 57.100 65.897 1.00 64.61 C
-ATOM 5071 OG SER B 532 82.015 57.983 66.969 1.00 65.04 O
-ATOM 5072 N VAL B 533 83.877 57.210 62.829 1.00 54.21 N
-ATOM 5073 CA VAL B 533 84.351 56.375 61.744 1.00 52.41 C
-ATOM 5074 C VAL B 533 85.524 55.492 62.165 1.00 50.55 C
-ATOM 5075 O VAL B 533 86.591 55.985 62.537 1.00 52.89 O
-ATOM 5076 CB VAL B 533 84.747 57.242 60.525 1.00 50.60 C
-ATOM 5077 CG1 VAL B 533 85.333 56.359 59.421 1.00 45.37 C
-ATOM 5078 CG2 VAL B 533 83.527 57.990 60.009 1.00 44.45 C
-ATOM 5079 N PRO B 534 85.330 54.165 62.119 1.00 41.78 N
-ATOM 5080 CA PRO B 534 86.344 53.172 62.483 1.00 43.63 C
-ATOM 5081 C PRO B 534 87.662 53.473 61.780 1.00 44.32 C
-ATOM 5082 O PRO B 534 87.671 53.833 60.602 1.00 40.60 O
-ATOM 5083 CB PRO B 534 85.728 51.861 62.005 1.00 41.09 C
-ATOM 5084 CG PRO B 534 84.286 52.087 62.193 1.00 40.63 C
-ATOM 5085 CD PRO B 534 84.086 53.505 61.688 1.00 45.14 C
-ATOM 5086 N LYS B 535 88.768 53.326 62.504 1.00 43.32 N
-ATOM 5087 CA LYS B 535 90.084 53.592 61.937 1.00 42.84 C
-ATOM 5088 C LYS B 535 90.273 52.797 60.640 1.00 41.84 C
-ATOM 5089 O LYS B 535 90.882 53.277 59.675 1.00 38.25 O
-ATOM 5090 CB LYS B 535 91.193 53.211 62.921 1.00 46.54 C
-ATOM 5091 CG LYS B 535 92.521 53.824 62.528 1.00 55.47 C
-ATOM 5092 CD LYS B 535 93.714 53.109 63.118 1.00 59.84 C
-ATOM 5093 CE LYS B 535 94.986 53.672 62.494 1.00 61.40 C
-ATOM 5094 NZ LYS B 535 96.181 52.840 62.777 1.00 63.11 N
-ATOM 5095 N THR B 536 89.741 51.582 60.618 1.00 39.34 N
-ATOM 5096 CA THR B 536 89.861 50.753 59.437 1.00 38.15 C
-ATOM 5097 C THR B 536 89.117 51.391 58.255 1.00 37.18 C
-ATOM 5098 O THR B 536 89.494 51.205 57.096 1.00 37.79 O
-ATOM 5099 CB THR B 536 89.324 49.328 59.715 1.00 40.52 C
-ATOM 5100 OG1 THR B 536 88.099 49.409 60.456 1.00 45.16 O
-ATOM 5101 CG2 THR B 536 90.334 48.527 60.515 1.00 42.30 C
-ATOM 5102 N LEU B 537 88.071 52.155 58.546 1.00 35.98 N
-ATOM 5103 CA LEU B 537 87.314 52.810 57.485 1.00 34.50 C
-ATOM 5104 C LEU B 537 87.987 54.128 57.115 1.00 33.99 C
-ATOM 5105 O LEU B 537 88.121 54.472 55.939 1.00 34.34 O
-ATOM 5106 CB LEU B 537 85.881 53.084 57.948 1.00 33.87 C
-ATOM 5107 CG LEU B 537 84.917 53.635 56.898 1.00 32.31 C
-ATOM 5108 CD1 LEU B 537 84.872 52.691 55.695 1.00 31.47 C
-ATOM 5109 CD2 LEU B 537 83.529 53.793 57.511 1.00 31.93 C
-ATOM 5110 N GLN B 538 88.418 54.858 58.136 1.00 32.26 N
-ATOM 5111 CA GLN B 538 89.069 56.144 57.945 1.00 32.32 C
-ATOM 5112 C GLN B 538 90.267 56.028 57.020 1.00 32.28 C
-ATOM 5113 O GLN B 538 90.510 56.903 56.192 1.00 33.63 O
-ATOM 5114 CB GLN B 538 89.530 56.692 59.290 1.00 33.05 C
-ATOM 5115 CG GLN B 538 90.060 58.104 59.233 1.00 30.86 C
-ATOM 5116 CD GLN B 538 88.969 59.117 58.995 1.00 31.61 C
-ATOM 5117 OE1 GLN B 538 87.961 59.127 59.700 1.00 31.47 O
-ATOM 5118 NE2 GLN B 538 89.164 59.986 58.006 1.00 30.90 N
-ATOM 5119 N ALA B 539 91.013 54.937 57.174 1.00 31.18 N
-ATOM 5120 CA ALA B 539 92.210 54.667 56.374 1.00 29.27 C
-ATOM 5121 C ALA B 539 91.867 54.468 54.905 1.00 30.15 C
-ATOM 5122 O ALA B 539 92.739 54.399 54.044 1.00 28.56 O
-ATOM 5123 CB ALA B 539 92.918 53.425 56.918 1.00 25.48 C
-ATOM 5124 N ARG B 540 90.577 54.379 54.632 1.00 33.32 N
-ATOM 5125 CA ARG B 540 90.106 54.179 53.283 1.00 36.18 C
-ATOM 5126 C ARG B 540 90.018 55.472 52.486 1.00 36.77 C
-ATOM 5127 O ARG B 540 89.957 55.435 51.258 1.00 37.56 O
-ATOM 5128 CB ARG B 540 88.749 53.488 53.329 1.00 38.71 C
-ATOM 5129 CG ARG B 540 88.849 52.085 53.885 1.00 44.47 C
-ATOM 5130 CD ARG B 540 89.539 51.167 52.888 1.00 47.50 C
-ATOM 5131 NE ARG B 540 90.207 50.030 53.518 1.00 49.43 N
-ATOM 5132 CZ ARG B 540 91.434 50.062 54.032 1.00 48.57 C
-ATOM 5133 NH1 ARG B 540 92.150 51.177 53.996 1.00 46.65 N
-ATOM 5134 NH2 ARG B 540 91.945 48.970 54.582 1.00 48.87 N
-ATOM 5135 N PHE B 541 90.039 56.613 53.168 1.00 35.50 N
-ATOM 5136 CA PHE B 541 89.924 57.891 52.470 1.00 35.11 C
-ATOM 5137 C PHE B 541 91.221 58.665 52.398 1.00 34.09 C
-ATOM 5138 O PHE B 541 91.826 58.958 53.422 1.00 34.77 O
-ATOM 5139 CB PHE B 541 88.864 58.761 53.140 1.00 35.63 C
-ATOM 5140 CG PHE B 541 87.568 58.040 53.391 1.00 36.31 C
-ATOM 5141 CD1 PHE B 541 87.249 57.588 54.664 1.00 34.86 C
-ATOM 5142 CD2 PHE B 541 86.701 57.761 52.340 1.00 35.27 C
-ATOM 5143 CE1 PHE B 541 86.091 56.868 54.885 1.00 34.78 C
-ATOM 5144 CE2 PHE B 541 85.546 57.043 52.546 1.00 34.36 C
-ATOM 5145 CZ PHE B 541 85.237 56.592 53.822 1.00 36.27 C
-ATOM 5146 N VAL B 542 91.628 59.013 51.181 1.00 30.39 N
-ATOM 5147 CA VAL B 542 92.854 59.754 50.960 1.00 28.60 C
-ATOM 5148 C VAL B 542 92.746 61.241 51.318 1.00 29.50 C
-ATOM 5149 O VAL B 542 93.755 61.923 51.515 1.00 27.64 O
-ATOM 5150 CB VAL B 542 93.281 59.649 49.510 1.00 27.70 C
-ATOM 5151 CG1 VAL B 542 92.278 60.399 48.635 1.00 27.33 C
-ATOM 5152 CG2 VAL B 542 94.708 60.192 49.351 1.00 26.49 C
-ATOM 5153 N LYS B 543 91.521 61.744 51.384 1.00 27.31 N
-ATOM 5154 CA LYS B 543 91.286 63.139 51.730 1.00 25.57 C
-ATOM 5155 C LYS B 543 89.950 63.245 52.464 1.00 25.33 C
-ATOM 5156 O LYS B 543 89.035 62.471 52.200 1.00 22.37 O
-ATOM 5157 CB LYS B 543 91.259 64.002 50.464 1.00 27.69 C
-ATOM 5158 CG LYS B 543 91.029 65.476 50.733 1.00 34.80 C
-ATOM 5159 CD LYS B 543 90.902 66.279 49.441 1.00 38.58 C
-ATOM 5160 CE LYS B 543 90.855 67.790 49.709 1.00 40.40 C
-ATOM 5161 NZ LYS B 543 92.128 68.308 50.301 1.00 41.48 N
-ATOM 5162 N GLN B 544 89.850 64.179 53.403 1.00 25.10 N
-ATOM 5163 CA GLN B 544 88.606 64.380 54.140 1.00 23.94 C
-ATOM 5164 C GLN B 544 88.330 65.867 54.257 1.00 25.40 C
-ATOM 5165 O GLN B 544 89.189 66.631 54.694 1.00 22.78 O
-ATOM 5166 CB GLN B 544 88.673 63.772 55.542 1.00 25.63 C
-ATOM 5167 CG GLN B 544 87.452 64.118 56.391 1.00 29.62 C
-ATOM 5168 CD GLN B 544 87.459 63.466 57.771 1.00 31.02 C
-ATOM 5169 OE1 GLN B 544 86.727 63.893 58.672 1.00 30.20 O
-ATOM 5170 NE2 GLN B 544 88.278 62.426 57.940 1.00 31.34 N
-ATOM 5171 N ILE B 545 87.124 66.270 53.862 1.00 29.80 N
-ATOM 5172 CA ILE B 545 86.715 67.674 53.906 1.00 29.89 C
-ATOM 5173 C ILE B 545 85.609 67.856 54.940 1.00 32.00 C
-ATOM 5174 O ILE B 545 84.626 67.122 54.924 1.00 29.60 O
-ATOM 5175 CB ILE B 545 86.172 68.149 52.528 1.00 31.30 C
-ATOM 5176 CG1 ILE B 545 87.212 67.884 51.438 1.00 32.75 C
-ATOM 5177 CG2 ILE B 545 85.807 69.627 52.590 1.00 32.59 C
-ATOM 5178 CD1 ILE B 545 86.769 68.287 50.056 1.00 34.28 C
-ATOM 5179 N ASP B 546 85.786 68.822 55.840 1.00 39.18 N
-ATOM 5180 CA ASP B 546 84.789 69.108 56.859 1.00 42.46 C
-ATOM 5181 C ASP B 546 84.006 70.321 56.422 1.00 42.27 C
-ATOM 5182 O ASP B 546 84.588 71.366 56.131 1.00 47.75 O
-ATOM 5183 CB ASP B 546 85.435 69.407 58.207 1.00 43.52 C
-ATOM 5184 CG ASP B 546 86.190 68.229 58.758 1.00 46.19 C
-ATOM 5185 OD1 ASP B 546 85.612 67.124 58.839 1.00 44.39 O
-ATOM 5186 OD2 ASP B 546 87.370 68.415 59.117 1.00 49.16 O
-ATOM 5187 N PHE B 547 82.690 70.174 56.348 1.00 43.59 N
-ATOM 5188 CA PHE B 547 81.841 71.290 55.970 1.00 46.11 C
-ATOM 5189 C PHE B 547 81.136 71.751 57.234 1.00 49.70 C
-ATOM 5190 O PHE B 547 80.546 70.935 57.946 1.00 50.27 O
-ATOM 5191 CB PHE B 547 80.793 70.874 54.933 1.00 40.95 C
-ATOM 5192 CG PHE B 547 81.365 70.506 53.597 1.00 33.68 C
-ATOM 5193 CD1 PHE B 547 82.060 69.320 53.432 1.00 30.47 C
-ATOM 5194 CD2 PHE B 547 81.221 71.357 52.506 1.00 30.85 C
-ATOM 5195 CE1 PHE B 547 82.608 68.986 52.196 1.00 30.66 C
-ATOM 5196 CE2 PHE B 547 81.760 71.036 51.274 1.00 29.43 C
-ATOM 5197 CZ PHE B 547 82.457 69.849 51.114 1.00 29.76 C
-ATOM 5198 N ARG B 548 81.226 73.048 57.524 1.00 52.34 N
-ATOM 5199 CA ARG B 548 80.577 73.634 58.696 1.00 52.60 C
-ATOM 5200 C ARG B 548 79.680 74.748 58.177 1.00 51.10 C
-ATOM 5201 O ARG B 548 80.120 75.578 57.387 1.00 47.22 O
-ATOM 5202 CB ARG B 548 81.625 74.173 59.676 1.00 55.79 C
-ATOM 5203 CG ARG B 548 82.181 73.106 60.618 1.00 65.04 C
-ATOM 5204 CD ARG B 548 83.385 73.596 61.394 1.00 70.23 C
-ATOM 5205 NE ARG B 548 84.646 73.309 60.709 1.00 72.67 N
-ATOM 5206 CZ ARG B 548 85.807 73.898 60.997 1.00 73.68 C
-ATOM 5207 NH1 ARG B 548 85.871 74.817 61.957 1.00 74.03 N
-ATOM 5208 NH2 ARG B 548 86.910 73.568 60.335 1.00 73.16 N
-ATOM 5209 N PRO B 549 78.401 74.765 58.596 1.00 50.55 N
-ATOM 5210 CA PRO B 549 77.461 75.795 58.141 1.00 49.15 C
-ATOM 5211 C PRO B 549 78.010 77.201 58.322 1.00 51.07 C
-ATOM 5212 O PRO B 549 78.617 77.523 59.348 1.00 49.36 O
-ATOM 5213 CB PRO B 549 76.222 75.540 59.001 1.00 47.80 C
-ATOM 5214 CG PRO B 549 76.280 74.091 59.280 1.00 47.86 C
-ATOM 5215 CD PRO B 549 77.756 73.895 59.595 1.00 49.19 C
-ATOM 5216 N LYS B 550 77.801 78.038 57.316 1.00 53.39 N
-ATOM 5217 CA LYS B 550 78.277 79.411 57.383 1.00 55.81 C
-ATOM 5218 C LYS B 550 77.091 80.351 57.190 1.00 56.51 C
-ATOM 5219 O LYS B 550 76.328 80.222 56.230 1.00 49.91 O
-ATOM 5220 CB LYS B 550 79.346 79.656 56.311 1.00 62.73 C
-ATOM 5221 CG LYS B 550 80.576 78.748 56.414 1.00 76.31 C
-ATOM 5222 CD LYS B 550 81.472 78.955 55.204 1.00 83.34 C
-ATOM 5223 CE LYS B 550 82.633 77.982 55.150 1.00 84.36 C
-ATOM 5224 NZ LYS B 550 83.429 78.213 53.906 1.00 84.47 N
-ATOM 5225 N ASP B 551 76.946 81.294 58.114 1.00 54.75 N
-ATOM 5226 CA ASP B 551 75.852 82.248 58.086 1.00 51.19 C
-ATOM 5227 C ASP B 551 75.741 83.088 56.819 1.00 47.04 C
-ATOM 5228 O ASP B 551 74.661 83.185 56.224 1.00 40.45 O
-ATOM 5229 CB ASP B 551 75.943 83.151 59.311 1.00 62.13 C
-ATOM 5230 CG ASP B 551 75.846 82.370 60.597 1.00 78.14 C
-ATOM 5231 OD1 ASP B 551 74.795 81.735 60.823 1.00 86.26 O
-ATOM 5232 OD2 ASP B 551 76.825 82.380 61.372 1.00 87.51 O
-ATOM 5233 N TYR B 552 76.842 83.697 56.399 1.00 41.33 N
-ATOM 5234 CA TYR B 552 76.788 84.515 55.200 1.00 35.84 C
-ATOM 5235 C TYR B 552 76.318 83.699 54.005 1.00 32.55 C
-ATOM 5236 O TYR B 552 75.519 84.177 53.207 1.00 33.74 O
-ATOM 5237 CB TYR B 552 78.151 85.177 54.928 1.00 35.09 C
-ATOM 5238 CG TYR B 552 79.346 84.242 54.947 1.00 37.73 C
-ATOM 5239 CD1 TYR B 552 79.933 83.793 53.757 1.00 36.64 C
-ATOM 5240 CD2 TYR B 552 79.924 83.842 56.158 1.00 37.97 C
-ATOM 5241 CE1 TYR B 552 81.066 82.983 53.779 1.00 36.21 C
-ATOM 5242 CE2 TYR B 552 81.058 83.032 56.186 1.00 35.26 C
-ATOM 5243 CZ TYR B 552 81.624 82.612 54.998 1.00 35.39 C
-ATOM 5244 OH TYR B 552 82.768 81.853 55.034 1.00 35.21 O
-ATOM 5245 N LEU B 553 76.787 82.462 53.892 1.00 29.99 N
-ATOM 5246 CA LEU B 553 76.378 81.619 52.777 1.00 30.34 C
-ATOM 5247 C LEU B 553 74.876 81.367 52.821 1.00 32.24 C
-ATOM 5248 O LEU B 553 74.211 81.329 51.787 1.00 32.95 O
-ATOM 5249 CB LEU B 553 77.125 80.283 52.806 1.00 26.05 C
-ATOM 5250 CG LEU B 553 78.627 80.302 52.514 1.00 21.61 C
-ATOM 5251 CD1 LEU B 553 79.167 78.866 52.451 1.00 18.01 C
-ATOM 5252 CD2 LEU B 553 78.872 81.016 51.207 1.00 19.21 C
-ATOM 5253 N LYS B 554 74.350 81.187 54.024 1.00 32.80 N
-ATOM 5254 CA LYS B 554 72.933 80.937 54.202 1.00 34.14 C
-ATOM 5255 C LYS B 554 72.129 82.202 53.865 1.00 35.04 C
-ATOM 5256 O LYS B 554 71.263 82.188 52.971 1.00 30.04 O
-ATOM 5257 CB LYS B 554 72.679 80.521 55.645 1.00 38.40 C
-ATOM 5258 CG LYS B 554 71.237 80.266 55.992 1.00 46.99 C
-ATOM 5259 CD LYS B 554 71.100 80.174 57.493 1.00 51.44 C
-ATOM 5260 CE LYS B 554 69.655 80.017 57.902 1.00 54.33 C
-ATOM 5261 NZ LYS B 554 69.509 80.097 59.384 1.00 55.41 N
-ATOM 5262 N HIS B 555 72.410 83.299 54.565 1.00 35.90 N
-ATOM 5263 CA HIS B 555 71.687 84.542 54.299 1.00 36.37 C
-ATOM 5264 C HIS B 555 71.730 84.828 52.811 1.00 35.55 C
-ATOM 5265 O HIS B 555 70.704 85.085 52.181 1.00 34.65 O
-ATOM 5266 CB HIS B 555 72.317 85.721 55.036 1.00 41.13 C
-ATOM 5267 CG HIS B 555 72.494 85.495 56.505 1.00 48.83 C
-ATOM 5268 ND1 HIS B 555 71.498 84.969 57.301 1.00 50.74 N
-ATOM 5269 CD2 HIS B 555 73.547 85.730 57.321 1.00 51.91 C
-ATOM 5270 CE1 HIS B 555 71.935 84.889 58.545 1.00 53.22 C
-ATOM 5271 NE2 HIS B 555 73.174 85.344 58.586 1.00 52.57 N
-ATOM 5272 N CYS B 556 72.939 84.770 52.264 1.00 35.92 N
-ATOM 5273 CA CYS B 556 73.174 85.012 50.849 1.00 34.28 C
-ATOM 5274 C CYS B 556 72.158 84.310 49.957 1.00 33.23 C
-ATOM 5275 O CYS B 556 71.621 84.909 49.028 1.00 33.41 O
-ATOM 5276 CB CYS B 556 74.580 84.559 50.472 1.00 32.10 C
-ATOM 5277 SG CYS B 556 74.988 85.019 48.804 1.00 33.74 S
-ATOM 5278 N LEU B 557 71.898 83.037 50.235 1.00 34.45 N
-ATOM 5279 CA LEU B 557 70.937 82.287 49.438 1.00 35.25 C
-ATOM 5280 C LEU B 557 69.559 82.894 49.655 1.00 36.39 C
-ATOM 5281 O LEU B 557 68.800 83.091 48.701 1.00 35.72 O
-ATOM 5282 CB LEU B 557 70.925 80.796 49.829 1.00 33.45 C
-ATOM 5283 CG LEU B 557 72.191 79.964 49.599 1.00 30.17 C
-ATOM 5284 CD1 LEU B 557 71.996 78.548 50.100 1.00 27.41 C
-ATOM 5285 CD2 LEU B 557 72.517 79.950 48.118 1.00 28.79 C
-ATOM 5286 N GLU B 558 69.246 83.204 50.913 1.00 38.89 N
-ATOM 5287 CA GLU B 558 67.947 83.795 51.241 1.00 40.45 C
-ATOM 5288 C GLU B 558 67.691 84.977 50.308 1.00 40.75 C
-ATOM 5289 O GLU B 558 66.576 85.173 49.817 1.00 38.31 O
-ATOM 5290 CB GLU B 558 67.919 84.259 52.703 1.00 40.89 C
-ATOM 5291 CG GLU B 558 68.288 83.149 53.691 1.00 45.66 C
-ATOM 5292 CD GLU B 558 68.167 83.552 55.167 1.00 46.54 C
-ATOM 5293 OE1 GLU B 558 68.550 84.695 55.511 1.00 47.65 O
-ATOM 5294 OE2 GLU B 558 67.705 82.712 55.983 1.00 44.57 O
-ATOM 5295 N ARG B 559 68.748 85.740 50.048 1.00 42.94 N
-ATOM 5296 CA ARG B 559 68.665 86.906 49.181 1.00 43.00 C
-ATOM 5297 C ARG B 559 69.026 86.607 47.722 1.00 41.72 C
-ATOM 5298 O ARG B 559 68.899 87.475 46.856 1.00 43.36 O
-ATOM 5299 CB ARG B 559 69.558 88.013 49.741 1.00 43.49 C
-ATOM 5300 CG ARG B 559 69.150 88.474 51.125 1.00 44.54 C
-ATOM 5301 CD ARG B 559 70.102 89.539 51.632 1.00 47.06 C
-ATOM 5302 NE ARG B 559 69.674 90.139 52.896 1.00 48.94 N
-ATOM 5303 CZ ARG B 559 69.542 89.481 54.047 1.00 48.42 C
-ATOM 5304 NH1 ARG B 559 69.806 88.182 54.110 1.00 48.01 N
-ATOM 5305 NH2 ARG B 559 69.141 90.127 55.138 1.00 46.78 N
-ATOM 5306 N SER B 560 69.457 85.376 47.453 1.00 40.36 N
-ATOM 5307 CA SER B 560 69.817 84.971 46.096 1.00 41.52 C
-ATOM 5308 C SER B 560 69.064 83.702 45.691 1.00 46.91 C
-ATOM 5309 O SER B 560 69.626 82.768 45.101 1.00 42.40 O
-ATOM 5310 CB SER B 560 71.324 84.738 45.994 1.00 39.41 C
-ATOM 5311 OG SER B 560 72.033 85.836 46.536 1.00 34.84 O
-ATOM 5312 N GLU B 561 67.780 83.692 46.021 1.00 50.89 N
-ATOM 5313 CA GLU B 561 66.883 82.588 45.718 1.00 50.98 C
-ATOM 5314 C GLU B 561 67.168 81.901 44.384 1.00 46.02 C
-ATOM 5315 O GLU B 561 67.228 80.673 44.317 1.00 40.13 O
-ATOM 5316 CB GLU B 561 65.430 83.082 45.719 1.00 62.52 C
-ATOM 5317 CG GLU B 561 65.242 84.569 46.067 1.00 87.76 C
-ATOM 5318 CD GLU B 561 65.939 85.530 45.094 1.00 98.33 C
-ATOM 5319 OE1 GLU B 561 65.742 85.401 43.866 1.00102.12 O
-ATOM 5320 OE2 GLU B 561 66.678 86.426 45.560 1.00101.30 O
-ATOM 5321 N PHE B 562 67.354 82.686 43.325 1.00 39.42 N
-ATOM 5322 CA PHE B 562 67.586 82.112 41.998 1.00 34.47 C
-ATOM 5323 C PHE B 562 68.663 81.035 41.963 1.00 32.75 C
-ATOM 5324 O PHE B 562 68.687 80.209 41.047 1.00 33.76 O
-ATOM 5325 CB PHE B 562 67.902 83.213 40.967 1.00 32.25 C
-ATOM 5326 CG PHE B 562 69.270 83.835 41.115 1.00 31.72 C
-ATOM 5327 CD1 PHE B 562 70.405 83.199 40.604 1.00 30.49 C
-ATOM 5328 CD2 PHE B 562 69.426 85.062 41.764 1.00 31.44 C
-ATOM 5329 CE1 PHE B 562 71.665 83.770 40.735 1.00 30.13 C
-ATOM 5330 CE2 PHE B 562 70.687 85.638 41.900 1.00 31.42 C
-ATOM 5331 CZ PHE B 562 71.807 84.988 41.382 1.00 30.92 C
-ATOM 5332 N LEU B 563 69.543 81.030 42.959 1.00 31.64 N
-ATOM 5333 CA LEU B 563 70.592 80.037 42.987 1.00 31.20 C
-ATOM 5334 C LEU B 563 70.047 78.649 43.303 1.00 31.79 C
-ATOM 5335 O LEU B 563 70.505 77.648 42.743 1.00 31.86 O
-ATOM 5336 CB LEU B 563 71.652 80.425 44.008 1.00 28.93 C
-ATOM 5337 CG LEU B 563 72.595 81.533 43.568 1.00 26.46 C
-ATOM 5338 CD1 LEU B 563 73.719 81.651 44.603 1.00 22.95 C
-ATOM 5339 CD2 LEU B 563 73.158 81.210 42.177 1.00 24.98 C
-ATOM 5340 N LEU B 564 69.075 78.590 44.209 1.00 33.29 N
-ATOM 5341 CA LEU B 564 68.467 77.320 44.596 1.00 34.99 C
-ATOM 5342 C LEU B 564 67.283 76.989 43.696 1.00 38.54 C
-ATOM 5343 O LEU B 564 67.078 75.835 43.316 1.00 33.31 O
-ATOM 5344 CB LEU B 564 68.013 77.377 46.062 1.00 35.22 C
-ATOM 5345 CG LEU B 564 69.131 77.585 47.092 1.00 37.51 C
-ATOM 5346 CD1 LEU B 564 68.580 77.476 48.491 1.00 37.23 C
-ATOM 5347 CD2 LEU B 564 70.217 76.540 46.882 1.00 38.77 C
-ATOM 5348 N GLU B 565 66.529 78.020 43.335 1.00 41.18 N
-ATOM 5349 CA GLU B 565 65.355 77.858 42.497 1.00 41.24 C
-ATOM 5350 C GLU B 565 65.656 77.362 41.087 1.00 38.17 C
-ATOM 5351 O GLU B 565 64.828 76.702 40.462 1.00 32.32 O
-ATOM 5352 CB GLU B 565 64.564 79.171 42.474 1.00 51.88 C
-ATOM 5353 CG GLU B 565 64.073 79.567 43.869 1.00 74.96 C
-ATOM 5354 CD GLU B 565 63.045 80.687 43.864 1.00 85.67 C
-ATOM 5355 OE1 GLU B 565 63.383 81.811 43.435 1.00 89.25 O
-ATOM 5356 OE2 GLU B 565 61.894 80.443 44.298 1.00 89.23 O
-ATOM 5357 N LYS B 566 66.837 77.659 40.571 1.00 32.85 N
-ATOM 5358 CA LYS B 566 67.155 77.180 39.236 1.00 27.92 C
-ATOM 5359 C LYS B 566 68.180 76.057 39.312 1.00 26.60 C
-ATOM 5360 O LYS B 566 68.826 75.728 38.319 1.00 23.45 O
-ATOM 5361 CB LYS B 566 67.661 78.319 38.354 1.00 29.50 C
-ATOM 5362 CG LYS B 566 66.592 79.341 38.044 1.00 33.82 C
-ATOM 5363 CD LYS B 566 67.145 80.458 37.197 1.00 38.26 C
-ATOM 5364 CE LYS B 566 66.333 81.740 37.386 1.00 40.14 C
-ATOM 5365 NZ LYS B 566 66.894 82.892 36.605 1.00 40.42 N
-ATOM 5366 N ARG B 567 68.317 75.477 40.502 1.00 26.25 N
-ATOM 5367 CA ARG B 567 69.228 74.361 40.720 1.00 26.90 C
-ATOM 5368 C ARG B 567 70.610 74.616 40.132 1.00 27.23 C
-ATOM 5369 O ARG B 567 71.184 73.742 39.477 1.00 27.17 O
-ATOM 5370 CB ARG B 567 68.630 73.092 40.099 1.00 28.45 C
-ATOM 5371 CG ARG B 567 67.252 72.734 40.641 1.00 30.55 C
-ATOM 5372 CD ARG B 567 66.667 71.510 39.957 1.00 32.66 C
-ATOM 5373 NE ARG B 567 65.473 70.977 40.634 1.00 33.99 N
-ATOM 5374 CZ ARG B 567 64.270 71.556 40.639 1.00 33.17 C
-ATOM 5375 NH1 ARG B 567 64.067 72.703 40.005 1.00 32.79 N
-ATOM 5376 NH2 ARG B 567 63.261 70.983 41.278 1.00 33.35 N
-ATOM 5377 N ILE B 568 71.144 75.806 40.391 1.00 28.39 N
-ATOM 5378 CA ILE B 568 72.446 76.213 39.872 1.00 29.40 C
-ATOM 5379 C ILE B 568 73.681 75.784 40.680 1.00 28.96 C
-ATOM 5380 O ILE B 568 74.673 75.327 40.105 1.00 30.88 O
-ATOM 5381 CB ILE B 568 72.502 77.742 39.701 1.00 29.39 C
-ATOM 5382 CG1 ILE B 568 71.299 78.220 38.890 1.00 28.01 C
-ATOM 5383 CG2 ILE B 568 73.797 78.142 38.984 1.00 28.68 C
-ATOM 5384 CD1 ILE B 568 71.215 79.723 38.806 1.00 26.78 C
-ATOM 5385 N ILE B 569 73.634 75.927 41.999 1.00 28.37 N
-ATOM 5386 CA ILE B 569 74.787 75.562 42.799 1.00 28.27 C
-ATOM 5387 C ILE B 569 75.073 74.072 42.876 1.00 29.36 C
-ATOM 5388 O ILE B 569 76.201 73.695 43.214 1.00 29.73 O
-ATOM 5389 CB ILE B 569 74.698 76.122 44.232 1.00 27.13 C
-ATOM 5390 CG1 ILE B 569 73.429 75.648 44.920 1.00 26.59 C
-ATOM 5391 CG2 ILE B 569 74.703 77.633 44.196 1.00 27.10 C
-ATOM 5392 CD1 ILE B 569 73.352 76.081 46.370 1.00 25.04 C
-ATOM 5393 N GLN B 570 74.083 73.221 42.579 1.00 30.71 N
-ATOM 5394 CA GLN B 570 74.312 71.773 42.615 1.00 30.81 C
-ATOM 5395 C GLN B 570 74.601 71.256 41.216 1.00 30.45 C
-ATOM 5396 O GLN B 570 74.623 70.052 40.991 1.00 31.16 O
-ATOM 5397 CB GLN B 570 73.111 70.984 43.140 1.00 32.52 C
-ATOM 5398 CG GLN B 570 72.205 71.682 44.099 1.00 39.62 C
-ATOM 5399 CD GLN B 570 70.986 72.251 43.395 1.00 41.89 C
-ATOM 5400 OE1 GLN B 570 71.080 73.231 42.652 1.00 41.56 O
-ATOM 5401 NE2 GLN B 570 69.836 71.627 43.614 1.00 42.79 N
-ATOM 5402 N SER B 571 74.810 72.154 40.269 1.00 28.18 N
-ATOM 5403 CA SER B 571 75.089 71.723 38.917 1.00 26.50 C
-ATOM 5404 C SER B 571 76.561 71.549 38.627 1.00 26.14 C
-ATOM 5405 O SER B 571 77.394 72.392 38.980 1.00 24.48 O
-ATOM 5406 CB SER B 571 74.519 72.701 37.896 1.00 27.79 C
-ATOM 5407 OG SER B 571 74.958 72.344 36.594 1.00 28.15 O
-ATOM 5408 N GLY B 572 76.871 70.442 37.967 1.00 24.87 N
-ATOM 5409 CA GLY B 572 78.236 70.179 37.584 1.00 23.27 C
-ATOM 5410 C GLY B 572 78.566 71.226 36.542 1.00 23.63 C
-ATOM 5411 O GLY B 572 79.738 71.498 36.284 1.00 24.31 O
-ATOM 5412 N ILE B 573 77.536 71.817 35.935 1.00 23.38 N
-ATOM 5413 CA ILE B 573 77.760 72.851 34.928 1.00 23.54 C
-ATOM 5414 C ILE B 573 78.314 74.088 35.602 1.00 24.08 C
-ATOM 5415 O ILE B 573 79.091 74.843 35.006 1.00 25.62 O
-ATOM 5416 CB ILE B 573 76.470 73.221 34.168 1.00 25.15 C
-ATOM 5417 CG1 ILE B 573 76.270 72.234 33.015 1.00 23.27 C
-ATOM 5418 CG2 ILE B 573 76.539 74.674 33.649 1.00 23.92 C
-ATOM 5419 CD1 ILE B 573 75.128 72.571 32.118 1.00 23.54 C
-ATOM 5420 N ALA B 574 77.917 74.292 36.851 1.00 24.78 N
-ATOM 5421 CA ALA B 574 78.413 75.426 37.599 1.00 24.39 C
-ATOM 5422 C ALA B 574 79.897 75.170 37.817 1.00 24.43 C
-ATOM 5423 O ALA B 574 80.715 76.086 37.741 1.00 26.69 O
-ATOM 5424 CB ALA B 574 77.687 75.534 38.935 1.00 24.17 C
-ATOM 5425 N LEU B 575 80.244 73.912 38.075 1.00 24.36 N
-ATOM 5426 CA LEU B 575 81.635 73.548 38.313 1.00 23.92 C
-ATOM 5427 C LEU B 575 82.493 73.534 37.061 1.00 24.82 C
-ATOM 5428 O LEU B 575 83.705 73.715 37.149 1.00 27.38 O
-ATOM 5429 CB LEU B 575 81.741 72.190 39.014 1.00 20.23 C
-ATOM 5430 CG LEU B 575 81.392 72.206 40.504 1.00 13.79 C
-ATOM 5431 CD1 LEU B 575 81.688 70.840 41.117 1.00 11.67 C
-ATOM 5432 CD2 LEU B 575 82.210 73.274 41.189 1.00 10.18 C
-ATOM 5433 N LEU B 576 81.886 73.319 35.898 1.00 27.18 N
-ATOM 5434 CA LEU B 576 82.668 73.335 34.664 1.00 29.56 C
-ATOM 5435 C LEU B 576 82.973 74.789 34.318 1.00 29.77 C
-ATOM 5436 O LEU B 576 84.008 75.094 33.722 1.00 30.81 O
-ATOM 5437 CB LEU B 576 81.915 72.677 33.500 1.00 30.15 C
-ATOM 5438 CG LEU B 576 82.714 72.613 32.190 1.00 29.10 C
-ATOM 5439 CD1 LEU B 576 84.107 72.032 32.446 1.00 27.96 C
-ATOM 5440 CD2 LEU B 576 81.949 71.784 31.171 1.00 28.76 C
-ATOM 5441 N LEU B 577 82.064 75.682 34.698 1.00 29.22 N
-ATOM 5442 CA LEU B 577 82.256 77.092 34.448 1.00 28.48 C
-ATOM 5443 C LEU B 577 83.354 77.612 35.357 1.00 27.38 C
-ATOM 5444 O LEU B 577 84.090 78.522 34.972 1.00 30.99 O
-ATOM 5445 CB LEU B 577 80.970 77.872 34.713 1.00 26.43 C
-ATOM 5446 CG LEU B 577 80.093 78.201 33.503 1.00 25.60 C
-ATOM 5447 CD1 LEU B 577 78.754 78.735 33.978 1.00 24.76 C
-ATOM 5448 CD2 LEU B 577 80.806 79.225 32.614 1.00 22.63 C
-ATOM 5449 N MET B 578 83.468 77.050 36.561 1.00 25.06 N
-ATOM 5450 CA MET B 578 84.488 77.508 37.497 1.00 25.14 C
-ATOM 5451 C MET B 578 85.902 77.172 37.022 1.00 26.24 C
-ATOM 5452 O MET B 578 86.848 77.937 37.237 1.00 28.66 O
-ATOM 5453 CB MET B 578 84.258 76.892 38.872 1.00 20.36 C
-ATOM 5454 CG MET B 578 85.180 77.463 39.967 1.00 12.03 C
-ATOM 5455 SD MET B 578 85.012 76.614 41.551 1.00 4.67 S
-ATOM 5456 CE MET B 578 86.018 75.416 41.210 1.00 6.52 C
-ATOM 5457 N LEU B 579 86.042 76.020 36.381 1.00 25.53 N
-ATOM 5458 CA LEU B 579 87.334 75.577 35.879 1.00 25.16 C
-ATOM 5459 C LEU B 579 87.745 76.403 34.668 1.00 23.79 C
-ATOM 5460 O LEU B 579 88.891 76.804 34.536 1.00 23.14 O
-ATOM 5461 CB LEU B 579 87.263 74.095 35.493 1.00 27.02 C
-ATOM 5462 CG LEU B 579 86.997 73.035 36.559 1.00 26.12 C
-ATOM 5463 CD1 LEU B 579 86.828 71.682 35.888 1.00 28.03 C
-ATOM 5464 CD2 LEU B 579 88.145 72.993 37.541 1.00 27.24 C
-ATOM 5465 N ILE B 580 86.794 76.644 33.781 1.00 21.37 N
-ATOM 5466 CA ILE B 580 87.049 77.423 32.588 1.00 21.06 C
-ATOM 5467 C ILE B 580 87.415 78.855 32.977 1.00 21.89 C
-ATOM 5468 O ILE B 580 88.192 79.517 32.284 1.00 20.80 O
-ATOM 5469 CB ILE B 580 85.789 77.497 31.683 1.00 22.89 C
-ATOM 5470 CG1 ILE B 580 85.308 76.090 31.317 1.00 24.33 C
-ATOM 5471 CG2 ILE B 580 86.101 78.319 30.428 1.00 21.57 C
-ATOM 5472 CD1 ILE B 580 83.963 76.060 30.571 1.00 22.68 C
-ATOM 5473 N TRP B 581 86.846 79.324 34.085 1.00 22.42 N
-ATOM 5474 CA TRP B 581 87.074 80.684 34.556 1.00 23.19 C
-ATOM 5475 C TRP B 581 88.310 80.905 35.423 1.00 23.60 C
-ATOM 5476 O TRP B 581 88.788 82.033 35.524 1.00 24.88 O
-ATOM 5477 CB TRP B 581 85.819 81.175 35.292 1.00 24.82 C
-ATOM 5478 CG TRP B 581 85.962 82.519 35.975 1.00 29.26 C
-ATOM 5479 CD1 TRP B 581 86.281 82.744 37.292 1.00 30.84 C
-ATOM 5480 CD2 TRP B 581 85.806 83.814 35.377 1.00 29.86 C
-ATOM 5481 NE1 TRP B 581 86.332 84.098 37.546 1.00 31.52 N
-ATOM 5482 CE2 TRP B 581 86.046 84.777 36.390 1.00 31.13 C
-ATOM 5483 CE3 TRP B 581 85.485 84.255 34.089 1.00 29.33 C
-ATOM 5484 CZ2 TRP B 581 85.977 86.157 36.146 1.00 30.40 C
-ATOM 5485 CZ3 TRP B 581 85.417 85.631 33.850 1.00 29.24 C
-ATOM 5486 CH2 TRP B 581 85.661 86.561 34.876 1.00 30.05 C
-ATOM 5487 N TYR B 582 88.834 79.839 36.032 1.00 22.92 N
-ATOM 5488 CA TYR B 582 90.003 79.927 36.917 1.00 20.44 C
-ATOM 5489 C TYR B 582 91.236 79.229 36.401 1.00 21.35 C
-ATOM 5490 O TYR B 582 92.362 79.678 36.601 1.00 19.93 O
-ATOM 5491 CB TYR B 582 89.696 79.287 38.261 1.00 18.43 C
-ATOM 5492 CG TYR B 582 89.131 80.204 39.293 1.00 18.94 C
-ATOM 5493 CD1 TYR B 582 87.758 80.280 39.512 1.00 20.16 C
-ATOM 5494 CD2 TYR B 582 89.970 80.999 40.061 1.00 19.37 C
-ATOM 5495 CE1 TYR B 582 87.224 81.140 40.481 1.00 19.75 C
-ATOM 5496 CE2 TYR B 582 89.459 81.855 41.028 1.00 21.17 C
-ATOM 5497 CZ TYR B 582 88.080 81.921 41.234 1.00 20.39 C
-ATOM 5498 OH TYR B 582 87.577 82.762 42.193 1.00 21.34 O
-ATOM 5499 N ARG B 583 91.009 78.113 35.731 1.00 23.58 N
-ATOM 5500 CA ARG B 583 92.079 77.265 35.251 1.00 23.71 C
-ATOM 5501 C ARG B 583 92.697 77.542 33.883 1.00 23.19 C
-ATOM 5502 O ARG B 583 92.039 78.055 32.985 1.00 24.52 O
-ATOM 5503 CB ARG B 583 91.565 75.827 35.332 1.00 25.54 C
-ATOM 5504 CG ARG B 583 91.256 75.428 36.760 1.00 25.11 C
-ATOM 5505 CD ARG B 583 92.579 75.184 37.434 1.00 28.37 C
-ATOM 5506 NE ARG B 583 92.601 75.424 38.868 1.00 27.98 N
-ATOM 5507 CZ ARG B 583 93.646 75.123 39.634 1.00 25.73 C
-ATOM 5508 NH1 ARG B 583 94.729 74.574 39.094 1.00 21.57 N
-ATOM 5509 NH2 ARG B 583 93.609 75.371 40.935 1.00 27.15 N
-ATOM 5510 N PRO B 584 93.989 77.213 33.722 1.00 28.96 N
-ATOM 5511 CA PRO B 584 94.671 77.432 32.440 1.00 29.39 C
-ATOM 5512 C PRO B 584 94.357 76.329 31.431 1.00 29.56 C
-ATOM 5513 O PRO B 584 94.208 75.163 31.797 1.00 32.28 O
-ATOM 5514 CB PRO B 584 96.154 77.474 32.827 1.00 27.91 C
-ATOM 5515 CG PRO B 584 96.217 76.578 34.036 1.00 25.93 C
-ATOM 5516 CD PRO B 584 94.959 76.940 34.802 1.00 27.78 C
-ATOM 5517 N VAL B 585 94.258 76.716 30.164 1.00 31.08 N
-ATOM 5518 CA VAL B 585 93.967 75.800 29.073 1.00 29.30 C
-ATOM 5519 C VAL B 585 94.782 74.502 29.024 1.00 28.14 C
-ATOM 5520 O VAL B 585 94.218 73.433 28.771 1.00 28.31 O
-ATOM 5521 CB VAL B 585 94.108 76.532 27.730 1.00 28.15 C
-ATOM 5522 CG1 VAL B 585 94.282 75.549 26.601 1.00 29.76 C
-ATOM 5523 CG2 VAL B 585 92.871 77.351 27.489 1.00 29.19 C
-ATOM 5524 N ALA B 586 96.091 74.582 29.262 1.00 26.75 N
-ATOM 5525 CA ALA B 586 96.947 73.390 29.213 1.00 27.32 C
-ATOM 5526 C ALA B 586 96.569 72.335 30.228 1.00 29.91 C
-ATOM 5527 O ALA B 586 97.070 71.214 30.181 1.00 32.05 O
-ATOM 5528 CB ALA B 586 98.398 73.766 29.422 1.00 23.87 C
-ATOM 5529 N GLU B 587 95.699 72.696 31.160 1.00 33.59 N
-ATOM 5530 CA GLU B 587 95.286 71.760 32.176 1.00 35.68 C
-ATOM 5531 C GLU B 587 94.198 70.861 31.640 1.00 36.19 C
-ATOM 5532 O GLU B 587 93.933 69.819 32.218 1.00 38.86 O
-ATOM 5533 CB GLU B 587 94.788 72.511 33.400 1.00 38.20 C
-ATOM 5534 CG GLU B 587 95.550 72.195 34.666 1.00 42.29 C
-ATOM 5535 CD GLU B 587 95.101 73.054 35.820 1.00 45.86 C
-ATOM 5536 OE1 GLU B 587 93.871 73.166 36.011 1.00 46.03 O
-ATOM 5537 OE2 GLU B 587 95.969 73.608 36.534 1.00 45.93 O
-ATOM 5538 N PHE B 588 93.564 71.269 30.541 1.00 35.95 N
-ATOM 5539 CA PHE B 588 92.501 70.476 29.913 1.00 36.51 C
-ATOM 5540 C PHE B 588 93.118 69.511 28.918 1.00 37.14 C
-ATOM 5541 O PHE B 588 94.292 69.633 28.593 1.00 38.75 O
-ATOM 5542 CB PHE B 588 91.518 71.368 29.150 1.00 36.45 C
-ATOM 5543 CG PHE B 588 90.634 72.197 30.026 1.00 36.21 C
-ATOM 5544 CD1 PHE B 588 91.146 73.273 30.737 1.00 36.75 C
-ATOM 5545 CD2 PHE B 588 89.283 71.918 30.118 1.00 36.37 C
-ATOM 5546 CE1 PHE B 588 90.328 74.065 31.522 1.00 36.72 C
-ATOM 5547 CE2 PHE B 588 88.447 72.704 30.905 1.00 38.29 C
-ATOM 5548 CZ PHE B 588 88.970 73.781 31.608 1.00 37.81 C
-ATOM 5549 N ALA B 589 92.328 68.566 28.420 1.00 37.77 N
-ATOM 5550 CA ALA B 589 92.827 67.607 27.435 1.00 38.57 C
-ATOM 5551 C ALA B 589 93.009 68.335 26.105 1.00 41.86 C
-ATOM 5552 O ALA B 589 92.155 69.122 25.704 1.00 37.72 O
-ATOM 5553 CB ALA B 589 91.842 66.461 27.271 1.00 36.76 C
-ATOM 5554 N GLN B 590 94.124 68.070 25.428 1.00 46.88 N
-ATOM 5555 CA GLN B 590 94.427 68.707 24.149 1.00 50.35 C
-ATOM 5556 C GLN B 590 93.180 68.818 23.283 1.00 49.04 C
-ATOM 5557 O GLN B 590 92.843 69.881 22.761 1.00 45.62 O
-ATOM 5558 CB GLN B 590 95.500 67.897 23.409 1.00 61.26 C
-ATOM 5559 CG GLN B 590 95.890 68.423 22.029 1.00 81.11 C
-ATOM 5560 CD GLN B 590 96.529 69.793 22.084 1.00 89.81 C
-ATOM 5561 OE1 GLN B 590 97.215 70.129 23.049 1.00 92.97 O
-ATOM 5562 NE2 GLN B 590 96.322 70.588 21.038 1.00 93.00 N
-ATOM 5563 N SER B 591 92.494 67.695 23.153 1.00 45.69 N
-ATOM 5564 CA SER B 591 91.284 67.594 22.353 1.00 40.32 C
-ATOM 5565 C SER B 591 90.201 68.630 22.602 1.00 37.60 C
-ATOM 5566 O SER B 591 89.499 69.013 21.674 1.00 36.59 O
-ATOM 5567 CB SER B 591 90.668 66.202 22.534 1.00 41.32 C
-ATOM 5568 OG SER B 591 89.274 66.236 22.263 1.00 46.79 O
-ATOM 5569 N ILE B 592 90.055 69.083 23.841 1.00 35.41 N
-ATOM 5570 CA ILE B 592 88.992 70.025 24.163 1.00 33.59 C
-ATOM 5571 C ILE B 592 89.405 71.496 24.291 1.00 34.17 C
-ATOM 5572 O ILE B 592 88.600 72.393 24.058 1.00 33.80 O
-ATOM 5573 CB ILE B 592 88.292 69.577 25.458 1.00 30.85 C
-ATOM 5574 CG1 ILE B 592 86.824 69.941 25.390 1.00 30.49 C
-ATOM 5575 CG2 ILE B 592 88.913 70.248 26.671 1.00 30.28 C
-ATOM 5576 CD1 ILE B 592 86.090 69.588 26.654 1.00 31.95 C
-ATOM 5577 N GLN B 593 90.663 71.729 24.652 1.00 36.82 N
-ATOM 5578 CA GLN B 593 91.206 73.078 24.846 1.00 38.37 C
-ATOM 5579 C GLN B 593 90.673 74.152 23.909 1.00 40.75 C
-ATOM 5580 O GLN B 593 90.234 75.203 24.357 1.00 41.38 O
-ATOM 5581 CB GLN B 593 92.730 73.050 24.738 1.00 34.56 C
-ATOM 5582 CG GLN B 593 93.382 71.997 25.611 1.00 32.36 C
-ATOM 5583 CD GLN B 593 94.881 72.137 25.664 1.00 31.57 C
-ATOM 5584 OE1 GLN B 593 95.469 72.958 24.950 1.00 32.41 O
-ATOM 5585 NE2 GLN B 593 95.518 71.332 26.511 1.00 30.62 N
-ATOM 5586 N SER B 594 90.724 73.899 22.609 1.00 46.33 N
-ATOM 5587 CA SER B 594 90.251 74.884 21.646 1.00 51.04 C
-ATOM 5588 C SER B 594 88.816 75.304 21.928 1.00 50.54 C
-ATOM 5589 O SER B 594 88.433 76.441 21.663 1.00 54.54 O
-ATOM 5590 CB SER B 594 90.364 74.336 20.223 1.00 54.78 C
-ATOM 5591 OG SER B 594 91.715 74.041 19.914 1.00 60.74 O
-ATOM 5592 N ARG B 595 88.029 74.391 22.482 1.00 47.62 N
-ATOM 5593 CA ARG B 595 86.636 74.682 22.784 1.00 44.29 C
-ATOM 5594 C ARG B 595 86.509 75.472 24.090 1.00 41.28 C
-ATOM 5595 O ARG B 595 85.581 76.263 24.262 1.00 43.76 O
-ATOM 5596 CB ARG B 595 85.866 73.371 22.873 1.00 42.18 C
-ATOM 5597 CG ARG B 595 84.379 73.502 22.688 1.00 38.08 C
-ATOM 5598 CD ARG B 595 83.708 72.136 22.690 1.00 36.56 C
-ATOM 5599 NE ARG B 595 82.251 72.250 22.631 1.00 35.93 N
-ATOM 5600 CZ ARG B 595 81.410 71.237 22.817 1.00 34.80 C
-ATOM 5601 NH1 ARG B 595 81.872 70.018 23.081 1.00 36.66 N
-ATOM 5602 NH2 ARG B 595 80.103 71.443 22.737 1.00 35.66 N
-ATOM 5603 N ILE B 596 87.447 75.246 25.005 1.00 36.49 N
-ATOM 5604 CA ILE B 596 87.475 75.937 26.296 1.00 33.41 C
-ATOM 5605 C ILE B 596 87.909 77.396 26.063 1.00 33.42 C
-ATOM 5606 O ILE B 596 87.276 78.335 26.558 1.00 32.93 O
-ATOM 5607 CB ILE B 596 88.490 75.262 27.277 1.00 28.37 C
-ATOM 5608 CG1 ILE B 596 88.040 73.836 27.617 1.00 21.47 C
-ATOM 5609 CG2 ILE B 596 88.658 76.117 28.530 1.00 21.60 C
-ATOM 5610 CD1 ILE B 596 86.697 73.763 28.281 1.00 16.92 C
-ATOM 5611 N VAL B 597 88.994 77.566 25.304 1.00 31.42 N
-ATOM 5612 CA VAL B 597 89.533 78.885 24.980 1.00 33.14 C
-ATOM 5613 C VAL B 597 88.401 79.727 24.419 1.00 36.88 C
-ATOM 5614 O VAL B 597 88.237 80.900 24.753 1.00 35.01 O
-ATOM 5615 CB VAL B 597 90.642 78.799 23.908 1.00 31.52 C
-ATOM 5616 CG1 VAL B 597 90.962 80.204 23.387 1.00 30.13 C
-ATOM 5617 CG2 VAL B 597 91.886 78.148 24.492 1.00 28.29 C
-ATOM 5618 N GLU B 598 87.632 79.089 23.552 1.00 41.56 N
-ATOM 5619 CA GLU B 598 86.475 79.671 22.892 1.00 43.15 C
-ATOM 5620 C GLU B 598 85.555 80.264 23.969 1.00 41.41 C
-ATOM 5621 O GLU B 598 85.078 81.399 23.855 1.00 38.47 O
-ATOM 5622 CB GLU B 598 85.777 78.542 22.134 1.00 49.15 C
-ATOM 5623 CG GLU B 598 84.906 78.923 20.971 1.00 61.07 C
-ATOM 5624 CD GLU B 598 84.336 77.686 20.289 1.00 67.18 C
-ATOM 5625 OE1 GLU B 598 85.117 76.904 19.699 1.00 68.26 O
-ATOM 5626 OE2 GLU B 598 83.106 77.485 20.358 1.00 69.86 O
-ATOM 5627 N TRP B 599 85.329 79.480 25.020 1.00 39.44 N
-ATOM 5628 CA TRP B 599 84.470 79.888 26.127 1.00 37.87 C
-ATOM 5629 C TRP B 599 85.083 80.967 27.033 1.00 36.96 C
-ATOM 5630 O TRP B 599 84.391 81.901 27.462 1.00 35.95 O
-ATOM 5631 CB TRP B 599 84.094 78.661 26.972 1.00 33.82 C
-ATOM 5632 CG TRP B 599 82.751 78.111 26.631 1.00 30.33 C
-ATOM 5633 CD1 TRP B 599 82.477 76.989 25.904 1.00 27.18 C
-ATOM 5634 CD2 TRP B 599 81.486 78.690 26.975 1.00 29.48 C
-ATOM 5635 NE1 TRP B 599 81.122 76.833 25.775 1.00 27.46 N
-ATOM 5636 CE2 TRP B 599 80.485 77.858 26.422 1.00 27.42 C
-ATOM 5637 CE3 TRP B 599 81.102 79.836 27.698 1.00 29.96 C
-ATOM 5638 CZ2 TRP B 599 79.111 78.129 26.564 1.00 28.46 C
-ATOM 5639 CZ3 TRP B 599 79.726 80.116 27.844 1.00 29.63 C
-ATOM 5640 CH2 TRP B 599 78.749 79.257 27.277 1.00 30.20 C
-ATOM 5641 N LYS B 600 86.373 80.817 27.336 1.00 36.77 N
-ATOM 5642 CA LYS B 600 87.087 81.770 28.182 1.00 37.21 C
-ATOM 5643 C LYS B 600 86.883 83.156 27.621 1.00 38.67 C
-ATOM 5644 O LYS B 600 86.468 84.079 28.322 1.00 36.86 O
-ATOM 5645 CB LYS B 600 88.584 81.467 28.196 1.00 36.77 C
-ATOM 5646 CG LYS B 600 88.959 80.195 28.914 1.00 38.05 C
-ATOM 5647 CD LYS B 600 90.457 79.984 28.942 1.00 37.15 C
-ATOM 5648 CE LYS B 600 90.785 78.806 29.841 1.00 37.66 C
-ATOM 5649 NZ LYS B 600 90.263 79.046 31.219 1.00 35.97 N
-ATOM 5650 N GLU B 601 87.181 83.281 26.337 1.00 40.16 N
-ATOM 5651 CA GLU B 601 87.033 84.535 25.634 1.00 40.04 C
-ATOM 5652 C GLU B 601 85.612 85.067 25.775 1.00 39.49 C
-ATOM 5653 O GLU B 601 85.400 86.240 26.086 1.00 39.08 O
-ATOM 5654 CB GLU B 601 87.406 84.325 24.168 1.00 41.16 C
-ATOM 5655 CG GLU B 601 88.907 84.104 23.976 1.00 46.01 C
-ATOM 5656 CD GLU B 601 89.275 83.676 22.571 1.00 49.04 C
-ATOM 5657 OE1 GLU B 601 88.543 84.041 21.624 1.00 50.51 O
-ATOM 5658 OE2 GLU B 601 90.310 82.989 22.417 1.00 50.28 O
-ATOM 5659 N ARG B 602 84.636 84.199 25.568 1.00 40.02 N
-ATOM 5660 CA ARG B 602 83.257 84.618 25.681 1.00 40.79 C
-ATOM 5661 C ARG B 602 83.029 85.140 27.092 1.00 41.63 C
-ATOM 5662 O ARG B 602 82.469 86.220 27.287 1.00 45.68 O
-ATOM 5663 CB ARG B 602 82.340 83.434 25.391 1.00 42.15 C
-ATOM 5664 CG ARG B 602 80.884 83.786 25.200 1.00 41.54 C
-ATOM 5665 CD ARG B 602 80.168 83.834 26.521 1.00 43.37 C
-ATOM 5666 NE ARG B 602 78.726 83.973 26.351 1.00 45.92 N
-ATOM 5667 CZ ARG B 602 77.967 83.121 25.667 1.00 45.85 C
-ATOM 5668 NH1 ARG B 602 78.511 82.056 25.081 1.00 45.69 N
-ATOM 5669 NH2 ARG B 602 76.659 83.332 25.571 1.00 44.44 N
-ATOM 5670 N LEU B 603 83.496 84.380 28.075 1.00 42.62 N
-ATOM 5671 CA LEU B 603 83.323 84.742 29.477 1.00 42.96 C
-ATOM 5672 C LEU B 603 84.104 85.990 29.886 1.00 46.39 C
-ATOM 5673 O LEU B 603 83.606 86.814 30.666 1.00 44.55 O
-ATOM 5674 CB LEU B 603 83.721 83.554 30.350 1.00 38.78 C
-ATOM 5675 CG LEU B 603 82.715 83.088 31.408 1.00 35.66 C
-ATOM 5676 CD1 LEU B 603 81.282 83.232 30.930 1.00 31.14 C
-ATOM 5677 CD2 LEU B 603 83.036 81.631 31.745 1.00 34.19 C
-ATOM 5678 N ASP B 604 85.326 86.117 29.363 1.00 51.12 N
-ATOM 5679 CA ASP B 604 86.195 87.262 29.650 1.00 53.46 C
-ATOM 5680 C ASP B 604 85.687 88.526 28.958 1.00 52.08 C
-ATOM 5681 O ASP B 604 86.035 89.640 29.354 1.00 50.81 O
-ATOM 5682 CB ASP B 604 87.640 86.980 29.207 1.00 60.84 C
-ATOM 5683 CG ASP B 604 88.454 86.252 30.270 1.00 71.18 C
-ATOM 5684 OD1 ASP B 604 88.614 86.801 31.380 1.00 76.81 O
-ATOM 5685 OD2 ASP B 604 88.940 85.133 29.998 1.00 76.01 O
-ATOM 5686 N LYS B 605 84.870 88.348 27.921 1.00 48.81 N
-ATOM 5687 CA LYS B 605 84.289 89.473 27.196 1.00 46.95 C
-ATOM 5688 C LYS B 605 83.033 89.936 27.934 1.00 50.30 C
-ATOM 5689 O LYS B 605 82.627 91.089 27.823 1.00 45.03 O
-ATOM 5690 CB LYS B 605 83.931 89.050 25.769 1.00 45.44 C
-ATOM 5691 CG LYS B 605 83.128 90.076 24.972 1.00 47.62 C
-ATOM 5692 CD LYS B 605 82.743 89.536 23.588 1.00 49.53 C
-ATOM 5693 CE LYS B 605 81.765 90.456 22.843 1.00 48.76 C
-ATOM 5694 NZ LYS B 605 80.397 90.531 23.459 1.00 48.91 N
-ATOM 5695 N GLU B 606 82.448 89.030 28.711 1.00 52.42 N
-ATOM 5696 CA GLU B 606 81.224 89.297 29.468 1.00 50.67 C
-ATOM 5697 C GLU B 606 81.386 89.799 30.902 1.00 44.45 C
-ATOM 5698 O GLU B 606 80.542 90.556 31.392 1.00 35.95 O
-ATOM 5699 CB GLU B 606 80.362 88.036 29.502 1.00 63.61 C
-ATOM 5700 CG GLU B 606 79.649 87.735 28.206 1.00 91.14 C
-ATOM 5701 CD GLU B 606 78.147 87.801 28.367 1.00103.32 C
-ATOM 5702 OE1 GLU B 606 77.661 88.797 28.949 1.00107.69 O
-ATOM 5703 OE2 GLU B 606 77.457 86.865 27.911 1.00107.53 O
-ATOM 5704 N PHE B 607 82.441 89.371 31.589 1.00 35.20 N
-ATOM 5705 CA PHE B 607 82.620 89.788 32.972 1.00 28.14 C
-ATOM 5706 C PHE B 607 84.026 90.236 33.273 1.00 26.21 C
-ATOM 5707 O PHE B 607 84.980 89.634 32.804 1.00 27.06 O
-ATOM 5708 CB PHE B 607 82.265 88.640 33.932 1.00 26.96 C
-ATOM 5709 CG PHE B 607 80.912 88.036 33.684 1.00 25.80 C
-ATOM 5710 CD1 PHE B 607 80.767 86.958 32.819 1.00 24.19 C
-ATOM 5711 CD2 PHE B 607 79.772 88.600 34.256 1.00 26.34 C
-ATOM 5712 CE1 PHE B 607 79.499 86.451 32.516 1.00 24.69 C
-ATOM 5713 CE2 PHE B 607 78.502 88.108 33.966 1.00 24.79 C
-ATOM 5714 CZ PHE B 607 78.363 87.028 33.089 1.00 25.18 C
-ATOM 5715 N SER B 608 84.148 91.287 34.076 1.00 26.77 N
-ATOM 5716 CA SER B 608 85.450 91.798 34.475 1.00 26.54 C
-ATOM 5717 C SER B 608 85.782 91.134 35.803 1.00 28.17 C
-ATOM 5718 O SER B 608 84.891 90.800 36.585 1.00 27.35 O
-ATOM 5719 CB SER B 608 85.406 93.320 34.670 1.00 26.10 C
-ATOM 5720 OG SER B 608 84.706 93.671 35.862 1.00 25.22 O
-ATOM 5721 N LEU B 609 87.067 90.948 36.058 1.00 30.12 N
-ATOM 5722 CA LEU B 609 87.507 90.329 37.290 1.00 31.09 C
-ATOM 5723 C LEU B 609 86.915 91.055 38.491 1.00 31.11 C
-ATOM 5724 O LEU B 609 86.553 90.418 39.482 1.00 32.27 O
-ATOM 5725 CB LEU B 609 89.036 90.353 37.375 1.00 32.84 C
-ATOM 5726 CG LEU B 609 89.648 89.255 38.246 1.00 34.53 C
-ATOM 5727 CD1 LEU B 609 89.329 89.455 39.704 1.00 35.64 C
-ATOM 5728 CD2 LEU B 609 89.085 87.931 37.773 1.00 37.19 C
-ATOM 5729 N SER B 610 86.816 92.382 38.401 1.00 31.01 N
-ATOM 5730 CA SER B 610 86.284 93.200 39.495 1.00 31.60 C
-ATOM 5731 C SER B 610 84.805 92.936 39.761 1.00 31.17 C
-ATOM 5732 O SER B 610 84.356 92.966 40.912 1.00 31.88 O
-ATOM 5733 CB SER B 610 86.505 94.691 39.205 1.00 32.62 C
-ATOM 5734 OG SER B 610 86.038 95.042 37.913 1.00 35.41 O
-ATOM 5735 N VAL B 611 84.053 92.670 38.696 1.00 28.31 N
-ATOM 5736 CA VAL B 611 82.633 92.386 38.820 1.00 24.67 C
-ATOM 5737 C VAL B 611 82.460 91.069 39.554 1.00 25.13 C
-ATOM 5738 O VAL B 611 81.620 90.936 40.450 1.00 24.12 O
-ATOM 5739 CB VAL B 611 81.991 92.287 37.442 1.00 22.21 C
-ATOM 5740 CG1 VAL B 611 80.583 91.738 37.559 1.00 19.87 C
-ATOM 5741 CG2 VAL B 611 81.975 93.666 36.796 1.00 21.68 C
-ATOM 5742 N TYR B 612 83.272 90.096 39.166 1.00 26.41 N
-ATOM 5743 CA TYR B 612 83.235 88.789 39.779 1.00 28.10 C
-ATOM 5744 C TYR B 612 83.660 88.880 41.231 1.00 29.60 C
-ATOM 5745 O TYR B 612 83.066 88.236 42.099 1.00 31.02 O
-ATOM 5746 CB TYR B 612 84.171 87.836 39.045 1.00 29.82 C
-ATOM 5747 CG TYR B 612 84.346 86.526 39.764 1.00 32.12 C
-ATOM 5748 CD1 TYR B 612 83.330 85.578 39.783 1.00 33.78 C
-ATOM 5749 CD2 TYR B 612 85.517 86.243 40.449 1.00 33.26 C
-ATOM 5750 CE1 TYR B 612 83.476 84.366 40.469 1.00 33.67 C
-ATOM 5751 CE2 TYR B 612 85.673 85.039 41.141 1.00 35.34 C
-ATOM 5752 CZ TYR B 612 84.650 84.102 41.147 1.00 34.28 C
-ATOM 5753 OH TYR B 612 84.804 82.911 41.828 1.00 31.38 O
-ATOM 5754 N GLN B 613 84.694 89.670 41.494 1.00 29.32 N
-ATOM 5755 CA GLN B 613 85.189 89.819 42.852 1.00 30.30 C
-ATOM 5756 C GLN B 613 84.146 90.443 43.763 1.00 30.67 C
-ATOM 5757 O GLN B 613 84.081 90.118 44.949 1.00 27.92 O
-ATOM 5758 CB GLN B 613 86.460 90.657 42.869 1.00 32.65 C
-ATOM 5759 CG GLN B 613 87.692 89.903 42.393 1.00 38.10 C
-ATOM 5760 CD GLN B 613 88.025 88.713 43.277 1.00 39.29 C
-ATOM 5761 OE1 GLN B 613 88.140 88.848 44.491 1.00 40.19 O
-ATOM 5762 NE2 GLN B 613 88.184 87.544 42.669 1.00 40.63 N
-ATOM 5763 N LYS B 614 83.320 91.329 43.211 1.00 30.74 N
-ATOM 5764 CA LYS B 614 82.269 91.966 44.003 1.00 29.95 C
-ATOM 5765 C LYS B 614 81.247 90.888 44.387 1.00 27.41 C
-ATOM 5766 O LYS B 614 80.696 90.886 45.495 1.00 26.44 O
-ATOM 5767 CB LYS B 614 81.600 93.085 43.189 1.00 33.43 C
-ATOM 5768 CG LYS B 614 80.596 93.947 43.964 1.00 38.42 C
-ATOM 5769 CD LYS B 614 80.313 95.240 43.194 1.00 43.26 C
-ATOM 5770 CE LYS B 614 79.358 96.179 43.912 1.00 43.23 C
-ATOM 5771 NZ LYS B 614 77.946 95.725 43.782 1.00 43.87 N
-ATOM 5772 N MET B 615 81.016 89.966 43.455 1.00 24.00 N
-ATOM 5773 CA MET B 615 80.089 88.879 43.677 1.00 21.33 C
-ATOM 5774 C MET B 615 80.554 88.079 44.889 1.00 22.27 C
-ATOM 5775 O MET B 615 79.753 87.765 45.761 1.00 23.33 O
-ATOM 5776 CB MET B 615 79.997 87.988 42.429 1.00 17.34 C
-ATOM 5777 CG MET B 615 79.224 88.587 41.252 1.00 8.89 C
-ATOM 5778 SD MET B 615 78.923 87.349 39.957 1.00 6.32 S
-ATOM 5779 CE MET B 615 80.223 87.587 38.908 1.00 11.47 C
-ATOM 5780 N LYS B 616 81.844 87.766 44.969 1.00 24.19 N
-ATOM 5781 CA LYS B 616 82.335 87.006 46.122 1.00 26.58 C
-ATOM 5782 C LYS B 616 82.242 87.863 47.369 1.00 28.53 C
-ATOM 5783 O LYS B 616 81.872 87.381 48.430 1.00 28.60 O
-ATOM 5784 CB LYS B 616 83.796 86.546 45.940 1.00 26.18 C
-ATOM 5785 CG LYS B 616 84.000 85.438 44.912 1.00 26.63 C
-ATOM 5786 CD LYS B 616 85.435 84.879 44.944 1.00 25.69 C
-ATOM 5787 CE LYS B 616 85.681 84.032 46.199 1.00 25.83 C
-ATOM 5788 NZ LYS B 616 87.084 83.551 46.303 1.00 25.31 N
-ATOM 5789 N PHE B 617 82.594 89.140 47.240 1.00 31.53 N
-ATOM 5790 CA PHE B 617 82.543 90.054 48.374 1.00 32.38 C
-ATOM 5791 C PHE B 617 81.129 90.033 48.939 1.00 32.68 C
-ATOM 5792 O PHE B 617 80.929 90.027 50.160 1.00 32.97 O
-ATOM 5793 CB PHE B 617 82.885 91.474 47.941 1.00 33.30 C
-ATOM 5794 CG PHE B 617 82.682 92.487 49.022 1.00 35.32 C
-ATOM 5795 CD1 PHE B 617 83.612 92.627 50.045 1.00 35.64 C
-ATOM 5796 CD2 PHE B 617 81.536 93.275 49.044 1.00 36.93 C
-ATOM 5797 CE1 PHE B 617 83.403 93.534 51.075 1.00 37.00 C
-ATOM 5798 CE2 PHE B 617 81.316 94.187 50.069 1.00 37.37 C
-ATOM 5799 CZ PHE B 617 82.251 94.318 51.087 1.00 37.39 C
-ATOM 5800 N ASN B 618 80.151 90.031 48.035 1.00 34.06 N
-ATOM 5801 CA ASN B 618 78.750 89.993 48.428 1.00 34.93 C
-ATOM 5802 C ASN B 618 78.441 88.721 49.206 1.00 33.90 C
-ATOM 5803 O ASN B 618 77.898 88.779 50.309 1.00 36.07 O
-ATOM 5804 CB ASN B 618 77.841 90.096 47.203 1.00 33.90 C
-ATOM 5805 CG ASN B 618 77.658 91.522 46.749 1.00 33.27 C
-ATOM 5806 OD1 ASN B 618 77.869 92.456 47.532 1.00 34.38 O
-ATOM 5807 ND2 ASN B 618 77.254 91.710 45.489 1.00 32.50 N
-ATOM 5808 N VAL B 619 78.784 87.575 48.632 1.00 31.33 N
-ATOM 5809 CA VAL B 619 78.555 86.302 49.303 1.00 29.38 C
-ATOM 5810 C VAL B 619 79.203 86.385 50.691 1.00 30.70 C
-ATOM 5811 O VAL B 619 78.677 85.870 51.673 1.00 30.97 O
-ATOM 5812 CB VAL B 619 79.183 85.140 48.488 1.00 26.01 C
-ATOM 5813 CG1 VAL B 619 79.149 83.850 49.279 1.00 21.70 C
-ATOM 5814 CG2 VAL B 619 78.438 84.970 47.177 1.00 18.61 C
-ATOM 5815 N ALA B 620 80.337 87.074 50.760 1.00 33.11 N
-ATOM 5816 CA ALA B 620 81.082 87.240 52.005 1.00 35.77 C
-ATOM 5817 C ALA B 620 80.307 88.044 53.047 1.00 36.45 C
-ATOM 5818 O ALA B 620 80.327 87.706 54.231 1.00 38.86 O
-ATOM 5819 CB ALA B 620 82.412 87.911 51.714 1.00 35.97 C
-ATOM 5820 N MET B 621 79.635 89.107 52.601 1.00 38.27 N
-ATOM 5821 CA MET B 621 78.840 89.963 53.484 1.00 39.15 C
-ATOM 5822 C MET B 621 77.419 89.428 53.636 1.00 39.31 C
-ATOM 5823 O MET B 621 76.571 90.085 54.243 1.00 40.32 O
-ATOM 5824 CB MET B 621 78.763 91.386 52.930 1.00 38.75 C
-ATOM 5825 CG MET B 621 80.075 92.175 52.961 1.00 39.00 C
-ATOM 5826 SD MET B 621 80.749 92.490 54.610 1.00 36.57 S
-ATOM 5827 CE MET B 621 82.241 91.479 54.575 1.00 35.60 C
-ATOM 5828 N GLY B 622 77.168 88.245 53.069 1.00 37.36 N
-ATOM 5829 CA GLY B 622 75.855 87.619 53.137 1.00 32.75 C
-ATOM 5830 C GLY B 622 74.714 88.447 52.577 1.00 30.81 C
-ATOM 5831 O GLY B 622 73.750 88.693 53.278 1.00 29.49 O
-ATOM 5832 N ILE B 623 74.793 88.851 51.314 1.00 29.09 N
-ATOM 5833 CA ILE B 623 73.747 89.679 50.733 1.00 29.02 C
-ATOM 5834 C ILE B 623 73.365 89.411 49.288 1.00 30.68 C
-ATOM 5835 O ILE B 623 72.973 90.323 48.579 1.00 32.19 O
-ATOM 5836 CB ILE B 623 74.121 91.173 50.797 1.00 29.79 C
-ATOM 5837 CG1 ILE B 623 75.523 91.368 50.204 1.00 29.85 C
-ATOM 5838 CG2 ILE B 623 74.019 91.688 52.229 1.00 28.46 C
-ATOM 5839 CD1 ILE B 623 75.850 92.788 49.797 1.00 26.72 C
-ATOM 5840 N GLY B 624 73.455 88.189 48.809 1.00 32.90 N
-ATOM 5841 CA GLY B 624 73.054 88.010 47.426 1.00 35.64 C
-ATOM 5842 C GLY B 624 74.039 88.607 46.440 1.00 37.71 C
-ATOM 5843 O GLY B 624 74.286 89.819 46.413 1.00 35.07 O
-ATOM 5844 N VAL B 625 74.592 87.715 45.624 1.00 39.89 N
-ATOM 5845 CA VAL B 625 75.590 88.035 44.618 1.00 40.45 C
-ATOM 5846 C VAL B 625 75.357 89.171 43.635 1.00 40.19 C
-ATOM 5847 O VAL B 625 76.303 89.883 43.300 1.00 40.65 O
-ATOM 5848 CB VAL B 625 75.914 86.797 43.793 1.00 41.40 C
-ATOM 5849 CG1 VAL B 625 77.163 86.157 44.308 1.00 45.21 C
-ATOM 5850 CG2 VAL B 625 74.774 85.821 43.883 1.00 43.70 C
-ATOM 5851 N LEU B 626 74.128 89.358 43.168 1.00 39.16 N
-ATOM 5852 CA LEU B 626 73.886 90.402 42.176 1.00 38.52 C
-ATOM 5853 C LEU B 626 73.542 91.802 42.660 1.00 39.66 C
-ATOM 5854 O LEU B 626 73.046 92.614 41.877 1.00 41.72 O
-ATOM 5855 CB LEU B 626 72.817 89.937 41.188 1.00 35.12 C
-ATOM 5856 CG LEU B 626 73.160 88.620 40.494 1.00 33.02 C
-ATOM 5857 CD1 LEU B 626 72.094 88.294 39.461 1.00 31.33 C
-ATOM 5858 CD2 LEU B 626 74.545 88.729 39.838 1.00 32.12 C
-ATOM 5859 N ASP B 627 73.800 92.100 43.931 1.00 44.14 N
-ATOM 5860 CA ASP B 627 73.501 93.431 44.459 1.00 48.27 C
-ATOM 5861 C ASP B 627 74.465 94.495 43.903 1.00 50.64 C
-ATOM 5862 O ASP B 627 75.657 94.161 43.670 1.00 54.13 O
-ATOM 5863 CB ASP B 627 73.582 93.429 45.994 1.00 49.55 C
-ATOM 5864 CG ASP B 627 72.259 93.058 46.661 1.00 48.92 C
-ATOM 5865 OD1 ASP B 627 71.836 93.789 47.591 1.00 47.20 O
-ATOM 5866 OD2 ASP B 627 71.646 92.040 46.265 1.00 47.20 O
-ATOM 5867 OXT ASP B 627 74.022 95.662 43.729 1.00 54.20 O
-TER 5868 ASP B 627
-HETATM 5869 ZN ZN A 700 30.663 53.669 11.494 1.00 56.10 ZN
-HETATM 5870 ZN ZN B 700 61.548 69.963 11.448 1.00 53.72 ZN
-MASTER 304 0 2 44 14 0 0 6 5868 2 0 58
-END
diff --git a/data/carotid.vtk b/data/carotid.vtk
deleted file mode 100644
index 458ebab..0000000
--- a/data/carotid.vtk
+++ /dev/null
@@ -1,111734 +0,0 @@
-# vtk DataFile Version 1.0
-Carotid arteries with flow vectors and speed scalars
-ASCII
-DATASET STRUCTURED_POINTS
-DIMENSIONS 76 49 45
-ORIGIN 100.0 80.0 1.0
-ASPECT_RATIO 1.0 1.0 1.0
-
-POINT_DATA 167580
-SCALARS scalars float
-LOOKUP_TABLE default
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diff --git a/data/gktbhFA.vtk b/data/gktbhFA.vtk
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index deb9d67..0000000
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diff --git a/data/gktbhL123.vtk b/data/gktbhL123.vtk
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diff --git a/data/head.120.vtk b/data/head.120.vtk
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index a3e7489..0000000
--- a/data/head.120.vtk
+++ /dev/null
@@ -1,91541 +0,0 @@
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\ No newline at end of file
diff --git a/data/pdb.pdb b/data/pdb.pdb
deleted file mode 100644
index 4cf3e1f..0000000
--- a/data/pdb.pdb
+++ /dev/null
@@ -1,3025 +0,0 @@
-HEADER LYASE 23-MAR-06 2DH6
-TITLE CRYSTAL STRUCTURE OF E. COLI APO-TRPB
-COMPND MOL_ID: 1;
-COMPND 2 MOLECULE: TRYPTOPHAN SYNTHASE BETA SUBUNIT;
-COMPND 3 CHAIN: A;
-COMPND 4 SYNONYM: TRYPTOPHAN SYNTHASE BETA-CHAIN;
-COMPND 5 EC: 4.2.1.20;
-COMPND 6 ENGINEERED: YES
-SOURCE MOL_ID: 1;
-SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
-SOURCE 3 ORGANISM_COMMON: BACTERIA;
-SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
-SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA;
-SOURCE 6 EXPRESSION_SYSTEM_STRAIN: CB149;
-SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
-SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PSTECOTB
-KEYWDS TRYPTOPHAN SYNTHASE, BETA-CHAIN, PLP
-EXPDTA X-RAY DIFFRACTION
-AUTHOR K.NISHIO,Y.MORIMOTO,K.OGASAHARA,N.YASUOKA,K.YUTANI,
-AUTHOR 2 T.TSUKIHARA
-REVDAT 1 24-APR-07 2DH6 0
-JRNL AUTH K.NISHIO,Y.MORIMOTO,K.OGASAHARA,N.YASUOKA,K.YUTANI,
-JRNL AUTH 2 T.TSUKIHARA
-JRNL TITL CRYSTAL STRUCTURE OF TRYPTOPHAN SYNTHASE
-JRNL TITL 2 BETA-SUBUNIT FROM ESCHERICHIA COLI
-JRNL REF TO BE PUBLISHED
-JRNL REFN
-REMARK 1
-REMARK 2
-REMARK 2 RESOLUTION. 3.00 ANGSTROMS.
-REMARK 3
-REMARK 3 REFINEMENT.
-REMARK 3 PROGRAM : CNS 1.1
-REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
-REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
-REMARK 3 : READ,RICE,SIMONSON,WARREN
-REMARK 3
-REMARK 3 REFINEMENT TARGET : NULL
-REMARK 3
-REMARK 3 DATA USED IN REFINEMENT.
-REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00
-REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.82
-REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
-REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1425358.900
-REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
-REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6
-REMARK 3 NUMBER OF REFLECTIONS : 13244
-REMARK 3
-REMARK 3 FIT TO DATA USED IN REFINEMENT.
-REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
-REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
-REMARK 3 R VALUE (WORKING SET) : 0.206
-REMARK 3 FREE R VALUE : 0.254
-REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
-REMARK 3 FREE R VALUE TEST SET COUNT : 659
-REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010
-REMARK 3
-REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
-REMARK 3 TOTAL NUMBER OF BINS USED : 6
-REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00
-REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19
-REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00
-REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2072
-REMARK 3 BIN R VALUE (WORKING SET) : 0.3140
-REMARK 3 BIN FREE R VALUE : 0.3610
-REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.00
-REMARK 3 BIN FREE R VALUE TEST SET COUNT : 87
-REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.039
-REMARK 3
-REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
-REMARK 3 PROTEIN ATOMS : 2514
-REMARK 3 NUCLEIC ACID ATOMS : 0
-REMARK 3 HETEROGEN ATOMS : 15
-REMARK 3 SOLVENT ATOMS : 23
-REMARK 3
-REMARK 3 B VALUES.
-REMARK 3 FROM WILSON PLOT (A**2) : 85.41
-REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.30
-REMARK 3 OVERALL ANISOTROPIC B VALUE.
-REMARK 3 B11 (A**2) : -0.80000
-REMARK 3 B22 (A**2) : -0.80000
-REMARK 3 B33 (A**2) : 1.61000
-REMARK 3 B12 (A**2) : 0.00000
-REMARK 3 B13 (A**2) : 0.00000
-REMARK 3 B23 (A**2) : 0.00000
-REMARK 3
-REMARK 3 ESTIMATED COORDINATE ERROR.
-REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32
-REMARK 3 ESD FROM SIGMAA (A) : 0.44
-REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
-REMARK 3
-REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
-REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41
-REMARK 3 ESD FROM C-V SIGMAA (A) : 0.55
-REMARK 3
-REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
-REMARK 3 BOND LENGTHS (A) : 0.012
-REMARK 3 BOND ANGLES (DEGREES) : 1.70
-REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80
-REMARK 3 IMPROPER ANGLES (DEGREES) : 0.98
-REMARK 3
-REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
-REMARK 3
-REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
-REMARK 3 MAIN-CHAIN BOND (A**2) : 1.800 ; 1.500
-REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.030 ; 2.000
-REMARK 3 SIDE-CHAIN BOND (A**2) : 3.050 ; 2.000
-REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.620 ; 2.500
-REMARK 3
-REMARK 3 BULK SOLVENT MODELING.
-REMARK 3 METHOD USED : FLAT MODEL
-REMARK 3 KSOL : 0.38
-REMARK 3 BSOL : 52.95
-REMARK 3
-REMARK 3 NCS MODEL : NULL
-REMARK 3
-REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
-REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
-REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
-REMARK 3
-REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
-REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM
-REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
-REMARK 3 PARAMETER FILE 4 : ION.PARAM
-REMARK 3 PARAMETER FILE 5 : LIGAND.PARAM
-REMARK 3 PARAMETER FILE 6 : NULL
-REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
-REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP
-REMARK 3 TOPOLOGY FILE 3 : WATER.TOP
-REMARK 3 TOPOLOGY FILE 4 : ION.TOP
-REMARK 3 TOPOLOGY FILE 5 : LIGAND.TOP
-REMARK 3 TOPOLOGY FILE 6 : NULL
-REMARK 3
-REMARK 3 OTHER REFINEMENT REMARKS: NULL
-REMARK 4
-REMARK 4 2DH6 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
-REMARK 100
-REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-2006.
-REMARK 100 THE RCSB ID CODE IS RCSB025414.
-REMARK 200
-REMARK 200 EXPERIMENTAL DETAILS
-REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
-REMARK 200 DATE OF DATA COLLECTION : 26-OCT-2003
-REMARK 200 TEMPERATURE (KELVIN) : 100.0
-REMARK 200 PH : 6.50
-REMARK 200 NUMBER OF CRYSTALS USED : 2
-REMARK 200
-REMARK 200 SYNCHROTRON (Y/N) : Y
-REMARK 200 RADIATION SOURCE : SPRING-8
-REMARK 200 BEAMLINE : BL44XU
-REMARK 200 X-RAY GENERATOR MODEL : NULL
-REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
-REMARK 200 WAVELENGTH OR RANGE (A) : 0.9
-REMARK 200 MONOCHROMATOR : MIRROR
-REMARK 200 OPTICS : NULL
-REMARK 200
-REMARK 200 DETECTOR TYPE : IMAGE PLATE
-REMARK 200 DETECTOR MANUFACTURER : DIP 6040
-REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
-REMARK 200 DATA SCALING SOFTWARE : SCALA
-REMARK 200
-REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13266
-REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000
-REMARK 200 RESOLUTION RANGE LOW (A) : 46.410
-REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.800
-REMARK 200
-REMARK 200 OVERALL.
-REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
-REMARK 200 DATA REDUNDANCY : 5.200
-REMARK 200 R MERGE (I) : 0.07400
-REMARK 200 R SYM (I) : NULL
-REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
-REMARK 200
-REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
-REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00
-REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16
-REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
-REMARK 200 DATA REDUNDANCY IN SHELL : 5.30
-REMARK 200 R MERGE FOR SHELL (I) : 0.38900
-REMARK 200 R SYM FOR SHELL (I) : NULL
-REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
-REMARK 200
-REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
-REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
-REMARK 200 SOFTWARE USED: CNS
-REMARK 200 STARTING MODEL: CHAIN B OF 1BKS
-REMARK 200
-REMARK 200 REMARK: NULL
-REMARK 280
-REMARK 280 CRYSTAL
-REMARK 280 SOLVENT CONTENT, VS (%): 66.29
-REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.65
-REMARK 280
-REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE, PH 6.5, VAPOR
-REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 288K
-REMARK 290
-REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
-REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2
-REMARK 290
-REMARK 290 SYMOP SYMMETRY
-REMARK 290 NNNMMM OPERATOR
-REMARK 290 1555 X,Y,Z
-REMARK 290 2555 -X,-Y,1/2+Z
-REMARK 290 3555 -Y,X,3/4+Z
-REMARK 290 4555 Y,-X,1/4+Z
-REMARK 290 5555 -X,Y,-Z
-REMARK 290 6555 X,-Y,1/2-Z
-REMARK 290 7555 Y,X,1/4-Z
-REMARK 290 8555 -Y,-X,3/4-Z
-REMARK 290
-REMARK 290 WHERE NNN -> OPERATOR NUMBER
-REMARK 290 MMM -> TRANSLATION VECTOR
-REMARK 290
-REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
-REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
-REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
-REMARK 290 RELATED MOLECULES.
-REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
-REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
-REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
-REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.10650
-REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
-REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 76.65975
-REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000
-REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.55325
-REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000
-REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000
-REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000
-REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.10650
-REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
-REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 25.55325
-REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
-REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
-REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 76.65975
-REMARK 290
-REMARK 290 REMARK: NULL
-REMARK 300
-REMARK 300 BIOMOLECULE: 1
-REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
-REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR
-REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
-REMARK 350
-REMARK 350 GENERATING THE BIOMOLECULE
-REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
-REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
-REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
-REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
-REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
-REMARK 350
-REMARK 350 BIOMOLECULE: 1
-REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
-REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
-REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
-REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
-REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 110.88600
-REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
-REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
-REMARK 465
-REMARK 465 MISSING RESIDUES
-REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
-REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
-REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
-REMARK 465
-REMARK 465 M RES C SSSEQI
-REMARK 465 MET A 1
-REMARK 465 THR A 2
-REMARK 465 THR A 3
-REMARK 465 LEU A 4
-REMARK 465 LEU A 5
-REMARK 465 ASN A 6
-REMARK 465 PRO A 7
-REMARK 465 TYR A 8
-REMARK 465 PHE A 9
-REMARK 465 GLY A 10
-REMARK 465 GLU A 11
-REMARK 465 PHE A 12
-REMARK 465 GLY A 13
-REMARK 465 GLY A 14
-REMARK 465 MET A 15
-REMARK 465 TYR A 16
-REMARK 465 GLY A 259
-REMARK 465 HIS A 260
-REMARK 465 GLY A 261
-REMARK 465 ILE A 262
-REMARK 465 GLU A 263
-REMARK 465 THR A 264
-REMARK 465 GLY A 265
-REMARK 465 GLU A 266
-REMARK 465 HIS A 267
-REMARK 465 GLY A 268
-REMARK 465 ALA A 269
-REMARK 465 PRO A 270
-REMARK 465 LEU A 271
-REMARK 465 LYS A 272
-REMARK 465 HIS A 273
-REMARK 465 GLY A 274
-REMARK 465 ARG A 275
-REMARK 465 VAL A 276
-REMARK 465 GLY A 277
-REMARK 465 ILE A 278
-REMARK 465 TYR A 279
-REMARK 465 PHE A 280
-REMARK 465 GLY A 281
-REMARK 465 MET A 282
-REMARK 465 LYS A 283
-REMARK 465 ALA A 284
-REMARK 465 PRO A 285
-REMARK 465 MET A 286
-REMARK 465 MET A 287
-REMARK 465 GLN A 288
-REMARK 465 THR A 289
-REMARK 465 GLU A 290
-REMARK 465 ASP A 291
-REMARK 465 GLY A 292
-REMARK 465 GLN A 293
-REMARK 465 ILE A 294
-REMARK 465 GLU A 295
-REMARK 465 GLU A 296
-REMARK 465 SER A 297
-REMARK 465 TYR A 298
-REMARK 465 SER A 299
-REMARK 465 ILE A 300
-REMARK 465 SER A 301
-REMARK 465 ALA A 302
-REMARK 465 GLY A 303
-REMARK 465 LEU A 304
-REMARK 465 ASP A 305
-REMARK 465 PHE A 306
-REMARK 465 PRO A 307
-REMARK 465 SER A 308
-REMARK 500
-REMARK 500 GEOMETRY AND STEREOCHEMISTRY
-REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
-REMARK 500
-REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
-REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
-REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
-REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
-REMARK 500
-REMARK 500 STANDARD TABLE:
-REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3)
-REMARK 500
-REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
-REMARK 500
-REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
-REMARK 500 MET A 22 SD MET A 22 CE 0.078
-REMARK 500 MET A 362 SD MET A 362 CE 0.073
-REMARK 500
-REMARK 500 GEOMETRY AND STEREOCHEMISTRY
-REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
-REMARK 500
-REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
-REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
-REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
-REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
-REMARK 500
-REMARK 500 STANDARD TABLE:
-REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
-REMARK 500
-REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
-REMARK 500
-REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
-REMARK 500 PRO A 56 C - N - CA ANGL. DEV. = 10.2 DEGREES
-REMARK 500 LEU A 59 N - CA - C ANGL. DEV. =-10.1 DEGREES
-REMARK 500 THR A 72 N - CA - C ANGL. DEV. =-10.8 DEGREES
-REMARK 500 GLY A 378 N - CA - C ANGL. DEV. = 16.7 DEGREES
-REMARK 900
-REMARK 900 RELATED ENTRIES
-REMARK 900 RELATED ID: 2DH5 RELATED DB: PDB
-REMARK 900 HOLO-TRPB
-REMARK 999
-REMARK 999 SEQUENCE
-REMARK 999 X (143) OF SEQUENCE DATABASE REFERENCE STANDS
-REMARK 999 FOR ANY RESIDUE, AND THE AUTHOR USED SER.
-DBREF 2DH6 A 1 397 GB 924784 AAA73808 1 397
-SEQADV 2DH6 SER A 143 GB 924784 X 143 SEE REMARK 999
-SEQRES 1 A 397 MET THR THR LEU LEU ASN PRO TYR PHE GLY GLU PHE GLY
-SEQRES 2 A 397 GLY MET TYR VAL PRO GLN ILE LEU MET PRO ALA LEU ARG
-SEQRES 3 A 397 GLN LEU GLU GLU ALA PHE VAL SER ALA GLN LYS ASP PRO
-SEQRES 4 A 397 GLU PHE GLN ALA GLN PHE ASN ASP LEU LEU LYS ASN TYR
-SEQRES 5 A 397 ALA GLY ARG PRO THR ALA LEU THR LYS CYS GLN ASN ILE
-SEQRES 6 A 397 THR ALA GLY THR ASN THR THR LEU TYR LEU LYS ARG GLU
-SEQRES 7 A 397 ASP LEU LEU HIS GLY GLY ALA HIS LYS THR ASN GLN VAL
-SEQRES 8 A 397 LEU GLY GLN ALA LEU LEU ALA LYS ARG MET GLY LYS THR
-SEQRES 9 A 397 GLU ILE ILE ALA GLU THR GLY ALA GLY GLN HIS GLY VAL
-SEQRES 10 A 397 ALA SER ALA LEU ALA SER ALA LEU LEU GLY LEU LYS CYS
-SEQRES 11 A 397 ARG ILE TYR MET GLY ALA LYS ASP VAL GLU ARG GLN SER
-SEQRES 12 A 397 PRO ASN VAL PHE ARG MET ARG LEU MET GLY ALA GLU VAL
-SEQRES 13 A 397 ILE PRO VAL HIS SER GLY SER ALA THR LEU LYS ASP ALA
-SEQRES 14 A 397 CYS ASN GLU ALA LEU ARG ASP TRP SER GLY SER TYR GLU
-SEQRES 15 A 397 THR ALA HIS TYR MET LEU GLY THR ALA ALA GLY PRO HIS
-SEQRES 16 A 397 PRO TYR PRO THR ILE VAL ARG GLU PHE GLN ARG MET ILE
-SEQRES 17 A 397 GLY GLU GLU THR LYS ALA GLN ILE LEU GLU ARG GLU GLY
-SEQRES 18 A 397 ARG LEU PRO ASP ALA VAL ILE ALA CYS VAL GLY GLY GLY
-SEQRES 19 A 397 SER ASN ALA ILE GLY MET PHE ALA ASP PHE ILE ASN GLU
-SEQRES 20 A 397 THR ASN VAL GLY LEU ILE GLY VAL GLU PRO GLY GLY HIS
-SEQRES 21 A 397 GLY ILE GLU THR GLY GLU HIS GLY ALA PRO LEU LYS HIS
-SEQRES 22 A 397 GLY ARG VAL GLY ILE TYR PHE GLY MET LYS ALA PRO MET
-SEQRES 23 A 397 MET GLN THR GLU ASP GLY GLN ILE GLU GLU SER TYR SER
-SEQRES 24 A 397 ILE SER ALA GLY LEU ASP PHE PRO SER VAL GLY PRO GLN
-SEQRES 25 A 397 HIS ALA TYR LEU ASN SER THR GLY ARG ALA ASP TYR VAL
-SEQRES 26 A 397 SER ILE THR ASP ASP GLU ALA LEU GLU ALA PHE LYS THR
-SEQRES 27 A 397 LEU CYS LEU HIS GLU GLY ILE ILE PRO ALA LEU GLU SER
-SEQRES 28 A 397 SER HIS ALA LEU ALA HIS ALA LEU LYS MET MET ARG GLU
-SEQRES 29 A 397 ASN PRO ASP LYS GLU GLN LEU LEU VAL VAL ASN LEU SER
-SEQRES 30 A 397 GLY ARG GLY ASP LYS ASP ILE PHE THR VAL HIS ASP ILE
-SEQRES 31 A 397 LEU LYS ALA ARG GLY GLU ILE
-HET SO4 801 5
-HET SO4 802 5
-HET SO4 803 5
-HETNAM SO4 SULFATE ION
-FORMUL 2 SO4 3(O4 S1 2-)
-FORMUL 5 HOH *23(H2 O1)
-HELIX 1 1 LEU A 21 LYS A 37 1 17
-HELIX 2 2 ASP A 38 GLY A 54 1 17
-HELIX 3 3 GLU A 78 LEU A 81 5 4
-HELIX 4 4 GLY A 84 MET A 101 1 18
-HELIX 5 5 GLY A 113 LEU A 126 1 14
-HELIX 6 6 ALA A 136 ARG A 141 1 6
-HELIX 7 7 GLN A 142 MET A 152 1 11
-HELIX 8 8 THR A 165 SER A 178 1 14
-HELIX 9 9 PRO A 196 PHE A 204 1 9
-HELIX 10 10 ARG A 206 GLY A 221 1 16
-HELIX 11 11 ASN A 236 ALA A 242 1 7
-HELIX 12 12 ASP A 243 ILE A 245 5 3
-HELIX 13 13 GLY A 310 THR A 319 1 10
-HELIX 14 14 THR A 328 GLY A 344 1 17
-HELIX 15 15 ALA A 348 ASN A 365 1 18
-HELIX 16 16 ILE A 384 ARG A 394 1 11
-SHEET 1 A 6 LEU A 59 CYS A 62 0
-SHEET 2 A 6 THR A 72 LYS A 76 -1 O LEU A 73 N CYS A 62
-SHEET 3 A 6 LEU A 371 ASN A 375 1 O VAL A 374 N TYR A 74
-SHEET 4 A 6 ALA A 226 CYS A 230 1 N ILE A 228 O VAL A 373
-SHEET 5 A 6 GLY A 251 PRO A 257 1 O GLY A 251 N VAL A 227
-SHEET 6 A 6 ALA A 322 ILE A 327 1 O VAL A 325 N GLU A 256
-SHEET 1 B 4 GLU A 155 VAL A 159 0
-SHEET 2 B 4 LYS A 129 GLY A 135 1 N ILE A 132 O GLU A 155
-SHEET 3 B 4 GLU A 105 THR A 110 1 N ILE A 106 O LYS A 129
-SHEET 4 B 4 ALA A 184 TYR A 186 1 O HIS A 185 N ILE A 107
-CISPEP 1 ARG A 55 PRO A 56 0 -0.01
-CISPEP 2 HIS A 195 PRO A 196 0 0.29
-CRYST1 110.886 110.886 102.213 90.00 90.00 90.00 P 43 2 2 8
-ORIGX1 1.000000 0.000000 0.000000 0.00000
-ORIGX2 0.000000 1.000000 0.000000 0.00000
-ORIGX3 0.000000 0.000000 1.000000 0.00000
-SCALE1 0.009018 0.000000 0.000000 0.00000
-SCALE2 0.000000 0.009018 0.000000 0.00000
-SCALE3 0.000000 0.000000 0.009783 0.00000
-ATOM 1 N VAL A 17 89.425 14.301 -18.452 1.00 86.84 N
-ATOM 2 CA VAL A 17 88.322 14.292 -19.468 1.00 86.19 C
-ATOM 3 C VAL A 17 88.787 13.881 -20.861 1.00 86.01 C
-ATOM 4 O VAL A 17 89.717 14.463 -21.413 1.00 87.98 O
-ATOM 5 CB VAL A 17 87.686 15.677 -19.604 1.00 84.80 C
-ATOM 6 CG1 VAL A 17 86.685 15.677 -20.758 1.00 84.01 C
-ATOM 7 CG2 VAL A 17 87.037 16.068 -18.302 1.00 83.68 C
-ATOM 8 N PRO A 18 88.147 12.872 -21.450 1.00 84.69 N
-ATOM 9 CA PRO A 18 88.576 12.475 -22.792 1.00 85.53 C
-ATOM 10 C PRO A 18 88.482 13.682 -23.731 1.00 86.56 C
-ATOM 11 O PRO A 18 87.465 14.378 -23.761 1.00 86.30 O
-ATOM 12 CB PRO A 18 87.591 11.369 -23.154 1.00 86.13 C
-ATOM 13 CG PRO A 18 86.366 11.713 -22.343 1.00 86.89 C
-ATOM 14 CD PRO A 18 86.951 12.132 -21.023 1.00 84.68 C
-ATOM 15 N GLN A 19 89.550 13.928 -24.486 1.00 87.56 N
-ATOM 16 CA GLN A 19 89.625 15.060 -25.415 1.00 88.01 C
-ATOM 17 C GLN A 19 88.397 15.232 -26.331 1.00 85.50 C
-ATOM 18 O GLN A 19 88.166 16.315 -26.862 1.00 84.73 O
-ATOM 19 CB GLN A 19 90.923 14.966 -26.260 1.00 91.56 C
-ATOM 20 CG GLN A 19 91.018 13.765 -27.258 1.00 97.54 C
-ATOM 21 CD GLN A 19 91.405 12.397 -26.624 1.00100.69 C
-ATOM 22 OE1 GLN A 19 91.289 11.342 -27.271 1.00 98.31 O
-ATOM 23 NE2 GLN A 19 91.876 12.423 -25.371 1.00100.62 N
-ATOM 24 N ILE A 20 87.607 14.175 -26.496 1.00 84.16 N
-ATOM 25 CA ILE A 20 86.420 14.207 -27.357 1.00 82.94 C
-ATOM 26 C ILE A 20 85.223 14.960 -26.756 1.00 83.21 C
-ATOM 27 O ILE A 20 84.353 15.465 -27.484 1.00 82.26 O
-ATOM 28 CB ILE A 20 85.962 12.767 -27.703 1.00 82.26 C
-ATOM 29 CG1 ILE A 20 84.755 12.816 -28.639 1.00 80.80 C
-ATOM 30 CG2 ILE A 20 85.604 12.013 -26.426 1.00 79.92 C
-ATOM 31 CD1 ILE A 20 84.334 11.474 -29.155 1.00 79.46 C
-ATOM 32 N LEU A 21 85.183 15.012 -25.424 1.00 82.95 N
-ATOM 33 CA LEU A 21 84.113 15.691 -24.687 1.00 81.20 C
-ATOM 34 C LEU A 21 84.422 17.159 -24.375 1.00 80.11 C
-ATOM 35 O LEU A 21 83.551 17.872 -23.884 1.00 81.43 O
-ATOM 36 CB LEU A 21 83.827 14.959 -23.366 1.00 79.37 C
-ATOM 37 CG LEU A 21 83.147 13.590 -23.412 1.00 76.91 C
-ATOM 38 CD1 LEU A 21 83.118 13.000 -22.027 1.00 74.74 C
-ATOM 39 CD2 LEU A 21 81.740 13.725 -23.945 1.00 75.83 C
-ATOM 40 N MET A 22 85.653 17.597 -24.645 1.00 77.50 N
-ATOM 41 CA MET A 22 86.065 18.971 -24.392 1.00 73.89 C
-ATOM 42 C MET A 22 85.121 19.998 -24.989 1.00 71.55 C
-ATOM 43 O MET A 22 84.723 20.944 -24.318 1.00 71.82 O
-ATOM 44 CB MET A 22 87.451 19.235 -24.955 1.00 77.66 C
-ATOM 45 CG MET A 22 88.578 18.524 -24.258 1.00 82.67 C
-ATOM 46 SD MET A 22 88.543 18.753 -22.484 1.00 89.63 S
-ATOM 47 CE MET A 22 87.967 20.522 -22.306 1.00 86.21 C
-ATOM 48 N PRO A 23 84.769 19.844 -26.273 1.00 68.13 N
-ATOM 49 CA PRO A 23 83.863 20.783 -26.937 1.00 67.51 C
-ATOM 50 C PRO A 23 82.519 20.916 -26.213 1.00 68.08 C
-ATOM 51 O PRO A 23 82.074 22.030 -25.923 1.00 70.32 O
-ATOM 52 CB PRO A 23 83.706 20.178 -28.324 1.00 65.05 C
-ATOM 53 CG PRO A 23 84.981 19.530 -28.535 1.00 64.84 C
-ATOM 54 CD PRO A 23 85.239 18.838 -27.232 1.00 66.04 C
-ATOM 55 N ALA A 24 81.881 19.774 -25.942 1.00 66.26 N
-ATOM 56 CA ALA A 24 80.593 19.721 -25.249 1.00 61.92 C
-ATOM 57 C ALA A 24 80.640 20.388 -23.872 1.00 59.13 C
-ATOM 58 O ALA A 24 79.761 21.185 -23.526 1.00 57.67 O
-ATOM 59 CB ALA A 24 80.144 18.267 -25.103 1.00 61.30 C
-ATOM 60 N LEU A 25 81.663 20.054 -23.095 1.00 54.63 N
-ATOM 61 CA LEU A 25 81.813 20.617 -21.774 1.00 55.99 C
-ATOM 62 C LEU A 25 82.079 22.120 -21.812 1.00 59.57 C
-ATOM 63 O LEU A 25 81.603 22.846 -20.942 1.00 62.38 O
-ATOM 64 CB LEU A 25 82.930 19.909 -21.025 1.00 51.33 C
-ATOM 65 CG LEU A 25 82.688 18.421 -20.821 1.00 50.95 C
-ATOM 66 CD1 LEU A 25 83.934 17.739 -20.369 1.00 49.96 C
-ATOM 67 CD2 LEU A 25 81.621 18.229 -19.801 1.00 53.70 C
-ATOM 68 N ARG A 26 82.833 22.597 -22.805 1.00 61.72 N
-ATOM 69 CA ARG A 26 83.129 24.030 -22.910 1.00 61.75 C
-ATOM 70 C ARG A 26 81.881 24.834 -23.259 1.00 63.57 C
-ATOM 71 O ARG A 26 81.614 25.872 -22.644 1.00 64.64 O
-ATOM 72 CB ARG A 26 84.214 24.294 -23.951 1.00 60.19 C
-ATOM 73 CG ARG A 26 85.489 24.848 -23.356 1.00 60.94 C
-ATOM 74 CD ARG A 26 86.049 23.883 -22.334 1.00 62.79 C
-ATOM 75 NE ARG A 26 87.373 24.255 -21.816 1.00 67.77 N
-ATOM 76 CZ ARG A 26 87.608 25.147 -20.849 1.00 68.52 C
-ATOM 77 NH1 ARG A 26 86.611 25.800 -20.264 1.00 70.21 N
-ATOM 78 NH2 ARG A 26 88.850 25.368 -20.433 1.00 68.42 N
-ATOM 79 N GLN A 27 81.118 24.364 -24.242 1.00 63.03 N
-ATOM 80 CA GLN A 27 79.897 25.048 -24.628 1.00 64.19 C
-ATOM 81 C GLN A 27 78.885 25.004 -23.484 1.00 65.40 C
-ATOM 82 O GLN A 27 78.002 25.869 -23.376 1.00 63.90 O
-ATOM 83 CB GLN A 27 79.321 24.406 -25.876 1.00 66.09 C
-ATOM 84 CG GLN A 27 79.972 24.926 -27.129 1.00 75.35 C
-ATOM 85 CD GLN A 27 80.182 23.845 -28.173 1.00 81.55 C
-ATOM 86 OE1 GLN A 27 79.214 23.294 -28.722 1.00 86.72 O
-ATOM 87 NE2 GLN A 27 81.453 23.526 -28.453 1.00 81.62 N
-ATOM 88 N LEU A 28 79.017 23.995 -22.623 1.00 64.49 N
-ATOM 89 CA LEU A 28 78.115 23.874 -21.487 1.00 61.54 C
-ATOM 90 C LEU A 28 78.508 24.949 -20.486 1.00 59.62 C
-ATOM 91 O LEU A 28 77.669 25.750 -20.074 1.00 60.71 O
-ATOM 92 CB LEU A 28 78.215 22.490 -20.824 1.00 59.14 C
-ATOM 93 CG LEU A 28 77.211 22.314 -19.677 1.00 56.51 C
-ATOM 94 CD1 LEU A 28 75.811 22.276 -20.251 1.00 53.34 C
-ATOM 95 CD2 LEU A 28 77.505 21.071 -18.890 1.00 54.29 C
-ATOM 96 N GLU A 29 79.783 24.965 -20.105 1.00 56.82 N
-ATOM 97 CA GLU A 29 80.279 25.949 -19.155 1.00 55.54 C
-ATOM 98 C GLU A 29 79.978 27.335 -19.670 1.00 54.80 C
-ATOM 99 O GLU A 29 79.617 28.224 -18.913 1.00 51.20 O
-ATOM 100 CB GLU A 29 81.775 25.792 -18.954 1.00 55.93 C
-ATOM 101 CG GLU A 29 82.431 26.996 -18.329 1.00 59.09 C
-ATOM 102 CD GLU A 29 83.904 26.760 -18.018 1.00 63.86 C
-ATOM 103 OE1 GLU A 29 84.218 26.270 -16.909 1.00 67.14 O
-ATOM 104 OE2 GLU A 29 84.753 27.049 -18.883 1.00 62.41 O
-ATOM 105 N GLU A 30 80.115 27.520 -20.972 1.00 56.15 N
-ATOM 106 CA GLU A 30 79.835 28.825 -21.538 1.00 59.26 C
-ATOM 107 C GLU A 30 78.376 29.162 -21.321 1.00 57.84 C
-ATOM 108 O GLU A 30 78.040 30.263 -20.909 1.00 59.56 O
-ATOM 109 CB GLU A 30 80.140 28.864 -23.036 1.00 62.45 C
-ATOM 110 CG GLU A 30 81.080 30.009 -23.449 1.00 69.44 C
-ATOM 111 CD GLU A 30 80.680 31.398 -22.904 1.00 72.57 C
-ATOM 112 OE1 GLU A 30 79.595 31.928 -23.276 1.00 71.44 O
-ATOM 113 OE2 GLU A 30 81.473 31.955 -22.105 1.00 71.25 O
-ATOM 114 N ALA A 31 77.502 28.215 -21.604 1.00 57.10 N
-ATOM 115 CA ALA A 31 76.088 28.470 -21.425 1.00 58.25 C
-ATOM 116 C ALA A 31 75.707 28.690 -19.951 1.00 58.23 C
-ATOM 117 O ALA A 31 74.886 29.558 -19.650 1.00 57.09 O
-ATOM 118 CB ALA A 31 75.283 27.326 -22.020 1.00 58.31 C
-ATOM 119 N PHE A 32 76.301 27.908 -19.047 1.00 57.46 N
-ATOM 120 CA PHE A 32 76.011 28.013 -17.618 1.00 58.61 C
-ATOM 121 C PHE A 32 76.327 29.397 -17.109 1.00 59.70 C
-ATOM 122 O PHE A 32 75.507 30.053 -16.460 1.00 61.36 O
-ATOM 123 CB PHE A 32 76.838 27.020 -16.809 1.00 58.37 C
-ATOM 124 CG PHE A 32 76.533 27.053 -15.340 1.00 60.38 C
-ATOM 125 CD1 PHE A 32 75.237 26.826 -14.880 1.00 60.40 C
-ATOM 126 CD2 PHE A 32 77.522 27.316 -14.415 1.00 59.98 C
-ATOM 127 CE1 PHE A 32 74.939 26.862 -13.522 1.00 57.57 C
-ATOM 128 CE2 PHE A 32 77.227 27.350 -13.049 1.00 59.81 C
-ATOM 129 CZ PHE A 32 75.932 27.122 -12.610 1.00 58.03 C
-ATOM 130 N VAL A 33 77.550 29.821 -17.392 1.00 59.99 N
-ATOM 131 CA VAL A 33 78.028 31.142 -17.010 1.00 57.76 C
-ATOM 132 C VAL A 33 77.047 32.229 -17.513 1.00 56.04 C
-ATOM 133 O VAL A 33 76.742 33.171 -16.793 1.00 54.86 O
-ATOM 134 CB VAL A 33 79.469 31.351 -17.567 1.00 55.65 C
-ATOM 135 CG1 VAL A 33 79.503 32.497 -18.585 1.00 58.67 C
-ATOM 136 CG2 VAL A 33 80.439 31.575 -16.411 1.00 55.74 C
-ATOM 137 N SER A 34 76.542 32.077 -18.732 1.00 52.93 N
-ATOM 138 CA SER A 34 75.606 33.040 -19.277 1.00 54.56 C
-ATOM 139 C SER A 34 74.281 33.045 -18.560 1.00 58.05 C
-ATOM 140 O SER A 34 73.728 34.100 -18.268 1.00 60.11 O
-ATOM 141 CB SER A 34 75.290 32.747 -20.737 1.00 54.84 C
-ATOM 142 OG SER A 34 74.068 33.383 -21.125 1.00 48.36 O
-ATOM 143 N ALA A 35 73.749 31.850 -18.334 1.00 60.74 N
-ATOM 144 CA ALA A 35 72.455 31.687 -17.699 1.00 59.46 C
-ATOM 145 C ALA A 35 72.512 32.158 -16.276 1.00 60.20 C
-ATOM 146 O ALA A 35 71.507 32.572 -15.713 1.00 60.18 O
-ATOM 147 CB ALA A 35 72.043 30.240 -17.752 1.00 59.87 C
-ATOM 148 N GLN A 36 73.695 32.106 -15.688 1.00 60.79 N
-ATOM 149 CA GLN A 36 73.822 32.537 -14.318 1.00 64.28 C
-ATOM 150 C GLN A 36 73.782 34.082 -14.258 1.00 64.43 C
-ATOM 151 O GLN A 36 73.530 34.688 -13.217 1.00 66.59 O
-ATOM 152 CB GLN A 36 75.118 31.964 -13.731 1.00 65.14 C
-ATOM 153 CG GLN A 36 74.943 31.217 -12.402 1.00 69.04 C
-ATOM 154 CD GLN A 36 76.288 31.003 -11.661 1.00 76.66 C
-ATOM 155 OE1 GLN A 36 77.177 31.886 -11.651 1.00 75.66 O
-ATOM 156 NE2 GLN A 36 76.432 29.836 -11.026 1.00 77.92 N
-ATOM 157 N LYS A 37 74.010 34.720 -15.396 1.00 64.43 N
-ATOM 158 CA LYS A 37 74.015 36.173 -15.463 1.00 61.96 C
-ATOM 159 C LYS A 37 72.684 36.637 -15.985 1.00 64.26 C
-ATOM 160 O LYS A 37 72.492 37.812 -16.236 1.00 67.65 O
-ATOM 161 CB LYS A 37 75.134 36.671 -16.398 1.00 56.55 C
-ATOM 162 CG LYS A 37 76.511 36.704 -15.756 1.00 54.61 C
-ATOM 163 CD LYS A 37 77.602 37.183 -16.701 1.00 54.92 C
-ATOM 164 CE LYS A 37 77.850 36.174 -17.825 1.00 59.16 C
-ATOM 165 NZ LYS A 37 79.027 36.460 -18.715 1.00 57.69 N
-ATOM 166 N ASP A 38 71.747 35.728 -16.169 1.00 65.81 N
-ATOM 167 CA ASP A 38 70.470 36.160 -16.684 1.00 67.40 C
-ATOM 168 C ASP A 38 69.402 36.036 -15.617 1.00 71.32 C
-ATOM 169 O ASP A 38 69.009 34.938 -15.251 1.00 73.15 O
-ATOM 170 CB ASP A 38 70.098 35.348 -17.912 1.00 66.40 C
-ATOM 171 CG ASP A 38 68.862 35.873 -18.583 1.00 68.87 C
-ATOM 172 OD1 ASP A 38 68.526 35.423 -19.705 1.00 70.33 O
-ATOM 173 OD2 ASP A 38 68.218 36.749 -17.973 1.00 69.69 O
-ATOM 174 N PRO A 39 68.914 37.172 -15.091 1.00 74.92 N
-ATOM 175 CA PRO A 39 67.879 37.132 -14.051 1.00 74.49 C
-ATOM 176 C PRO A 39 66.607 36.503 -14.606 1.00 72.70 C
-ATOM 177 O PRO A 39 65.766 36.022 -13.859 1.00 74.82 O
-ATOM 178 CB PRO A 39 67.691 38.602 -13.699 1.00 74.53 C
-ATOM 179 CG PRO A 39 69.012 39.217 -14.063 1.00 74.86 C
-ATOM 180 CD PRO A 39 69.283 38.566 -15.387 1.00 75.12 C
-ATOM 181 N GLU A 40 66.481 36.519 -15.924 1.00 69.35 N
-ATOM 182 CA GLU A 40 65.344 35.931 -16.592 1.00 68.12 C
-ATOM 183 C GLU A 40 65.425 34.406 -16.443 1.00 66.85 C
-ATOM 184 O GLU A 40 64.411 33.719 -16.383 1.00 67.22 O
-ATOM 185 CB GLU A 40 65.385 36.305 -18.061 1.00 71.30 C
-ATOM 186 CG GLU A 40 64.049 36.679 -18.606 1.00 80.03 C
-ATOM 187 CD GLU A 40 63.046 35.563 -18.449 1.00 86.12 C
-ATOM 188 OE1 GLU A 40 63.302 34.457 -18.994 1.00 89.18 O
-ATOM 189 OE2 GLU A 40 62.008 35.793 -17.781 1.00 87.92 O
-ATOM 190 N PHE A 41 66.645 33.881 -16.388 1.00 63.20 N
-ATOM 191 CA PHE A 41 66.862 32.447 -16.240 1.00 58.90 C
-ATOM 192 C PHE A 41 66.509 32.103 -14.822 1.00 58.75 C
-ATOM 193 O PHE A 41 65.574 31.354 -14.556 1.00 58.59 O
-ATOM 194 CB PHE A 41 68.329 32.091 -16.484 1.00 53.71 C
-ATOM 195 CG PHE A 41 68.631 30.631 -16.334 1.00 53.39 C
-ATOM 196 CD1 PHE A 41 68.350 29.733 -17.367 1.00 52.49 C
-ATOM 197 CD2 PHE A 41 69.208 30.139 -15.165 1.00 53.71 C
-ATOM 198 CE1 PHE A 41 68.642 28.371 -17.235 1.00 49.51 C
-ATOM 199 CE2 PHE A 41 69.505 28.772 -15.026 1.00 49.93 C
-ATOM 200 CZ PHE A 41 69.221 27.897 -16.062 1.00 47.79 C
-ATOM 201 N GLN A 42 67.276 32.675 -13.908 1.00 60.78 N
-ATOM 202 CA GLN A 42 67.068 32.449 -12.494 1.00 62.14 C
-ATOM 203 C GLN A 42 65.587 32.618 -12.162 1.00 60.05 C
-ATOM 204 O GLN A 42 65.072 32.012 -11.225 1.00 60.08 O
-ATOM 205 CB GLN A 42 67.920 33.429 -11.688 1.00 64.68 C
-ATOM 206 CG GLN A 42 69.441 33.286 -11.909 1.00 72.60 C
-ATOM 207 CD GLN A 42 70.052 32.070 -11.192 1.00 78.31 C
-ATOM 208 OE1 GLN A 42 69.787 31.833 -9.996 1.00 80.00 O
-ATOM 209 NE2 GLN A 42 70.881 31.302 -11.915 1.00 78.13 N
-ATOM 210 N ALA A 43 64.891 33.419 -12.952 1.00 55.72 N
-ATOM 211 CA ALA A 43 63.486 33.640 -12.692 1.00 55.05 C
-ATOM 212 C ALA A 43 62.680 32.406 -13.030 1.00 56.19 C
-ATOM 213 O ALA A 43 61.842 31.964 -12.252 1.00 55.99 O
-ATOM 214 CB ALA A 43 62.986 34.811 -13.506 1.00 54.28 C
-ATOM 215 N GLN A 44 62.937 31.856 -14.207 1.00 57.28 N
-ATOM 216 CA GLN A 44 62.217 30.694 -14.677 1.00 54.22 C
-ATOM 217 C GLN A 44 62.609 29.500 -13.871 1.00 52.99 C
-ATOM 218 O GLN A 44 61.796 28.607 -13.651 1.00 52.95 O
-ATOM 219 CB GLN A 44 62.540 30.427 -16.136 1.00 56.45 C
-ATOM 220 CG GLN A 44 62.528 31.649 -16.993 1.00 60.47 C
-ATOM 221 CD GLN A 44 62.236 31.318 -18.432 1.00 64.83 C
-ATOM 222 OE1 GLN A 44 62.767 30.342 -18.974 1.00 66.29 O
-ATOM 223 NE2 GLN A 44 61.387 32.133 -19.071 1.00 66.95 N
-ATOM 224 N PHE A 45 63.862 29.470 -13.439 1.00 51.22 N
-ATOM 225 CA PHE A 45 64.325 28.338 -12.656 1.00 52.59 C
-ATOM 226 C PHE A 45 63.571 28.280 -11.336 1.00 52.81 C
-ATOM 227 O PHE A 45 63.297 27.212 -10.792 1.00 53.70 O
-ATOM 228 CB PHE A 45 65.829 28.433 -12.385 1.00 51.64 C
-ATOM 229 CG PHE A 45 66.361 27.284 -11.566 1.00 51.60 C
-ATOM 230 CD1 PHE A 45 67.402 27.471 -10.669 1.00 49.53 C
-ATOM 231 CD2 PHE A 45 65.797 26.013 -11.676 1.00 52.46 C
-ATOM 232 CE1 PHE A 45 67.865 26.422 -9.900 1.00 47.80 C
-ATOM 233 CE2 PHE A 45 66.255 24.964 -10.912 1.00 49.89 C
-ATOM 234 CZ PHE A 45 67.295 25.177 -10.022 1.00 52.00 C
-ATOM 235 N ASN A 46 63.227 29.447 -10.825 1.00 54.86 N
-ATOM 236 CA ASN A 46 62.513 29.532 -9.578 1.00 56.66 C
-ATOM 237 C ASN A 46 61.053 29.178 -9.708 1.00 55.06 C
-ATOM 238 O ASN A 46 60.454 28.623 -8.800 1.00 55.54 O
-ATOM 239 CB ASN A 46 62.663 30.929 -9.006 1.00 62.52 C
-ATOM 240 CG ASN A 46 63.241 30.898 -7.626 1.00 71.44 C
-ATOM 241 OD1 ASN A 46 62.491 30.877 -6.626 1.00 76.86 O
-ATOM 242 ND2 ASN A 46 64.585 30.842 -7.541 1.00 71.19 N
-ATOM 243 N ASP A 47 60.459 29.505 -10.835 1.00 54.83 N
-ATOM 244 CA ASP A 47 59.075 29.170 -10.994 1.00 57.73 C
-ATOM 245 C ASP A 47 58.996 27.644 -11.009 1.00 56.23 C
-ATOM 246 O ASP A 47 58.166 27.056 -10.313 1.00 58.00 O
-ATOM 247 CB ASP A 47 58.526 29.758 -12.291 1.00 65.99 C
-ATOM 248 CG ASP A 47 56.993 29.794 -12.319 1.00 74.84 C
-ATOM 249 OD1 ASP A 47 56.411 29.603 -13.424 1.00 78.60 O
-ATOM 250 OD2 ASP A 47 56.371 30.020 -11.238 1.00 79.34 O
-ATOM 251 N LEU A 48 59.866 26.999 -11.787 1.00 52.41 N
-ATOM 252 CA LEU A 48 59.865 25.542 -11.855 1.00 48.73 C
-ATOM 253 C LEU A 48 60.078 24.965 -10.463 1.00 49.92 C
-ATOM 254 O LEU A 48 59.352 24.049 -10.033 1.00 51.72 O
-ATOM 255 CB LEU A 48 60.956 25.022 -12.793 1.00 42.85 C
-ATOM 256 CG LEU A 48 60.819 25.242 -14.304 1.00 40.60 C
-ATOM 257 CD1 LEU A 48 62.079 24.694 -14.979 1.00 35.46 C
-ATOM 258 CD2 LEU A 48 59.556 24.592 -14.851 1.00 30.14 C
-ATOM 259 N LEU A 49 61.063 25.503 -9.751 1.00 47.17 N
-ATOM 260 CA LEU A 49 61.356 25.034 -8.412 1.00 46.09 C
-ATOM 261 C LEU A 49 60.099 25.058 -7.497 1.00 49.46 C
-ATOM 262 O LEU A 49 59.876 24.145 -6.676 1.00 49.38 O
-ATOM 263 CB LEU A 49 62.488 25.877 -7.852 1.00 41.16 C
-ATOM 264 CG LEU A 49 63.845 25.214 -7.609 1.00 40.32 C
-ATOM 265 CD1 LEU A 49 63.954 23.918 -8.276 1.00 39.81 C
-ATOM 266 CD2 LEU A 49 64.925 26.103 -8.113 1.00 40.63 C
-ATOM 267 N LYS A 50 59.263 26.084 -7.659 1.00 50.12 N
-ATOM 268 CA LYS A 50 58.045 26.217 -6.869 1.00 50.61 C
-ATOM 269 C LYS A 50 57.019 25.227 -7.352 1.00 51.78 C
-ATOM 270 O LYS A 50 56.493 24.398 -6.622 1.00 52.91 O
-ATOM 271 CB LYS A 50 57.429 27.592 -7.044 1.00 51.18 C
-ATOM 272 CG LYS A 50 58.277 28.771 -6.638 1.00 56.28 C
-ATOM 273 CD LYS A 50 57.378 29.837 -6.001 1.00 61.70 C
-ATOM 274 CE LYS A 50 58.136 31.130 -5.721 1.00 66.69 C
-ATOM 275 NZ LYS A 50 57.302 32.109 -4.941 1.00 69.23 N
-ATOM 276 N ASN A 51 56.733 25.320 -8.627 1.00 53.73 N
-ATOM 277 CA ASN A 51 55.731 24.467 -9.192 1.00 55.14 C
-ATOM 278 C ASN A 51 56.030 22.985 -9.257 1.00 56.93 C
-ATOM 279 O ASN A 51 55.110 22.191 -9.122 1.00 59.40 O
-ATOM 280 CB ASN A 51 55.358 25.025 -10.553 1.00 53.30 C
-ATOM 281 CG ASN A 51 54.702 26.389 -10.436 1.00 55.91 C
-ATOM 282 OD1 ASN A 51 53.546 26.482 -10.012 1.00 60.67 O
-ATOM 283 ND2 ASN A 51 55.437 27.455 -10.766 1.00 50.43 N
-ATOM 284 N TYR A 52 57.288 22.578 -9.410 1.00 56.77 N
-ATOM 285 CA TYR A 52 57.537 21.137 -9.527 1.00 57.18 C
-ATOM 286 C TYR A 52 58.369 20.414 -8.491 1.00 58.44 C
-ATOM 287 O TYR A 52 58.371 19.180 -8.470 1.00 57.91 O
-ATOM 288 CB TYR A 52 58.113 20.811 -10.913 1.00 55.86 C
-ATOM 289 CG TYR A 52 57.151 21.129 -12.034 1.00 54.20 C
-ATOM 290 CD1 TYR A 52 57.144 22.387 -12.634 1.00 52.12 C
-ATOM 291 CD2 TYR A 52 56.184 20.213 -12.416 1.00 52.68 C
-ATOM 292 CE1 TYR A 52 56.203 22.726 -13.569 1.00 52.04 C
-ATOM 293 CE2 TYR A 52 55.235 20.541 -13.347 1.00 56.99 C
-ATOM 294 CZ TYR A 52 55.243 21.808 -13.922 1.00 56.74 C
-ATOM 295 OH TYR A 52 54.263 22.153 -14.826 1.00 57.42 O
-ATOM 296 N ALA A 53 59.077 21.166 -7.646 1.00 60.68 N
-ATOM 297 CA ALA A 53 59.941 20.583 -6.611 1.00 58.15 C
-ATOM 298 C ALA A 53 59.484 20.982 -5.222 1.00 57.37 C
-ATOM 299 O ALA A 53 60.234 20.855 -4.248 1.00 57.84 O
-ATOM 300 CB ALA A 53 61.368 21.031 -6.823 1.00 58.20 C
-ATOM 301 N GLY A 54 58.253 21.477 -5.154 1.00 56.65 N
-ATOM 302 CA GLY A 54 57.672 21.901 -3.901 1.00 53.81 C
-ATOM 303 C GLY A 54 58.538 22.826 -3.074 1.00 53.88 C
-ATOM 304 O GLY A 54 58.676 22.591 -1.886 1.00 57.20 O
-ATOM 305 N ARG A 55 59.115 23.874 -3.663 1.00 51.79 N
-ATOM 306 CA ARG A 55 59.950 24.799 -2.887 1.00 48.49 C
-ATOM 307 C ARG A 55 59.273 26.147 -2.628 1.00 45.84 C
-ATOM 308 O ARG A 55 58.423 26.586 -3.397 1.00 47.76 O
-ATOM 309 CB ARG A 55 61.281 25.026 -3.601 1.00 49.81 C
-ATOM 310 CG ARG A 55 62.088 23.746 -3.821 1.00 49.92 C
-ATOM 311 CD ARG A 55 63.555 24.012 -3.590 1.00 51.11 C
-ATOM 312 NE ARG A 55 63.888 24.232 -2.175 1.00 48.43 N
-ATOM 313 CZ ARG A 55 64.047 23.255 -1.287 1.00 49.80 C
-ATOM 314 NH1 ARG A 55 64.347 23.529 -0.027 1.00 46.79 N
-ATOM 315 NH2 ARG A 55 63.907 21.989 -1.667 1.00 53.87 N
-ATOM 316 N PRO A 56 59.626 26.821 -1.530 1.00 41.98 N
-ATOM 317 CA PRO A 56 60.575 26.539 -0.453 1.00 41.58 C
-ATOM 318 C PRO A 56 59.994 25.623 0.587 1.00 41.40 C
-ATOM 319 O PRO A 56 58.804 25.654 0.826 1.00 44.02 O
-ATOM 320 CB PRO A 56 60.799 27.898 0.145 1.00 38.15 C
-ATOM 321 CG PRO A 56 59.456 28.430 0.116 1.00 36.89 C
-ATOM 322 CD PRO A 56 58.977 28.110 -1.277 1.00 38.39 C
-ATOM 323 N THR A 57 60.837 24.827 1.219 1.00 40.86 N
-ATOM 324 CA THR A 57 60.381 23.937 2.260 1.00 41.23 C
-ATOM 325 C THR A 57 60.254 24.823 3.476 1.00 44.58 C
-ATOM 326 O THR A 57 60.818 25.915 3.521 1.00 46.43 O
-ATOM 327 CB THR A 57 61.409 22.885 2.540 1.00 41.75 C
-ATOM 328 OG1 THR A 57 62.662 23.529 2.793 1.00 43.67 O
-ATOM 329 CG2 THR A 57 61.570 21.972 1.344 1.00 40.14 C
-ATOM 330 N ALA A 58 59.522 24.363 4.475 1.00 46.33 N
-ATOM 331 CA ALA A 58 59.340 25.156 5.674 1.00 48.22 C
-ATOM 332 C ALA A 58 60.575 25.108 6.561 1.00 51.26 C
-ATOM 333 O ALA A 58 61.384 24.176 6.463 1.00 53.21 O
-ATOM 334 CB ALA A 58 58.138 24.637 6.446 1.00 46.31 C
-ATOM 335 N LEU A 59 60.734 26.129 7.406 1.00 52.51 N
-ATOM 336 CA LEU A 59 61.831 26.168 8.381 1.00 52.87 C
-ATOM 337 C LEU A 59 61.055 26.237 9.695 1.00 54.29 C
-ATOM 338 O LEU A 59 60.448 27.274 9.990 1.00 58.04 O
-ATOM 339 CB LEU A 59 62.701 27.417 8.234 1.00 48.74 C
-ATOM 340 CG LEU A 59 63.776 27.422 9.332 1.00 52.14 C
-ATOM 341 CD1 LEU A 59 64.878 26.415 9.012 1.00 51.02 C
-ATOM 342 CD2 LEU A 59 64.368 28.801 9.475 1.00 52.81 C
-ATOM 343 N THR A 60 61.041 25.155 10.477 1.00 51.62 N
-ATOM 344 CA THR A 60 60.255 25.196 11.696 1.00 50.31 C
-ATOM 345 C THR A 60 61.000 25.164 13.025 1.00 51.56 C
-ATOM 346 O THR A 60 61.870 24.332 13.281 1.00 50.55 O
-ATOM 347 CB THR A 60 59.108 24.125 11.652 1.00 49.96 C
-ATOM 348 OG1 THR A 60 59.470 22.951 12.367 1.00 48.78 O
-ATOM 349 CG2 THR A 60 58.823 23.730 10.233 1.00 50.81 C
-ATOM 350 N LYS A 61 60.630 26.127 13.862 1.00 52.93 N
-ATOM 351 CA LYS A 61 61.199 26.321 15.177 1.00 53.91 C
-ATOM 352 C LYS A 61 60.681 25.302 16.165 1.00 56.21 C
-ATOM 353 O LYS A 61 59.487 25.156 16.337 1.00 57.80 O
-ATOM 354 CB LYS A 61 60.837 27.713 15.685 1.00 52.42 C
-ATOM 355 CG LYS A 61 61.569 28.080 16.942 1.00 56.56 C
-ATOM 356 CD LYS A 61 60.743 28.907 17.879 1.00 59.72 C
-ATOM 357 CE LYS A 61 60.810 30.387 17.581 1.00 64.87 C
-ATOM 358 NZ LYS A 61 59.925 31.117 18.558 1.00 68.15 N
-ATOM 359 N CYS A 62 61.570 24.595 16.829 1.00 59.80 N
-ATOM 360 CA CYS A 62 61.124 23.631 17.816 1.00 64.38 C
-ATOM 361 C CYS A 62 61.143 24.311 19.175 1.00 66.34 C
-ATOM 362 O CYS A 62 62.181 24.792 19.612 1.00 70.06 O
-ATOM 363 CB CYS A 62 62.050 22.421 17.803 1.00 64.63 C
-ATOM 364 SG CYS A 62 61.980 21.554 16.213 1.00 71.99 S
-ATOM 365 N GLN A 63 60.005 24.395 19.850 1.00 68.99 N
-ATOM 366 CA GLN A 63 60.036 25.045 21.151 1.00 70.54 C
-ATOM 367 C GLN A 63 60.001 24.072 22.310 1.00 70.17 C
-ATOM 368 O GLN A 63 60.646 24.323 23.322 1.00 72.99 O
-ATOM 369 CB GLN A 63 58.919 26.081 21.293 1.00 71.47 C
-ATOM 370 CG GLN A 63 58.947 27.112 20.180 1.00 76.30 C
-ATOM 371 CD GLN A 63 58.289 28.439 20.543 1.00 78.80 C
-ATOM 372 OE1 GLN A 63 58.852 29.243 21.299 1.00 79.77 O
-ATOM 373 NE2 GLN A 63 57.093 28.678 19.999 1.00 78.40 N
-ATOM 374 N ASN A 64 59.283 22.962 22.183 1.00 67.53 N
-ATOM 375 CA ASN A 64 59.253 22.021 23.290 1.00 65.73 C
-ATOM 376 C ASN A 64 60.636 21.509 23.642 1.00 66.22 C
-ATOM 377 O ASN A 64 61.011 21.521 24.807 1.00 67.19 O
-ATOM 378 CB ASN A 64 58.335 20.848 22.991 1.00 63.50 C
-ATOM 379 CG ASN A 64 56.933 21.296 22.677 1.00 66.19 C
-ATOM 380 OD1 ASN A 64 56.438 22.267 23.251 1.00 66.35 O
-ATOM 381 ND2 ASN A 64 56.273 20.592 21.766 1.00 67.25 N
-ATOM 382 N ILE A 65 61.398 21.085 22.637 1.00 66.68 N
-ATOM 383 CA ILE A 65 62.744 20.538 22.840 1.00 64.93 C
-ATOM 384 C ILE A 65 63.768 21.469 23.504 1.00 66.77 C
-ATOM 385 O ILE A 65 64.553 21.037 24.346 1.00 67.65 O
-ATOM 386 CB ILE A 65 63.314 20.020 21.500 1.00 62.12 C
-ATOM 387 CG1 ILE A 65 62.717 18.655 21.204 1.00 63.20 C
-ATOM 388 CG2 ILE A 65 64.812 19.926 21.545 1.00 60.79 C
-ATOM 389 CD1 ILE A 65 63.453 17.895 20.131 1.00 65.90 C
-ATOM 390 N THR A 66 63.764 22.740 23.131 1.00 66.95 N
-ATOM 391 CA THR A 66 64.710 23.680 23.701 1.00 68.25 C
-ATOM 392 C THR A 66 64.223 24.216 25.043 1.00 69.93 C
-ATOM 393 O THR A 66 64.991 24.823 25.788 1.00 70.80 O
-ATOM 394 CB THR A 66 64.931 24.880 22.764 1.00 69.50 C
-ATOM 395 OG1 THR A 66 63.761 25.710 22.760 1.00 71.80 O
-ATOM 396 CG2 THR A 66 65.214 24.407 21.352 1.00 68.48 C
-ATOM 397 N ALA A 67 62.942 24.007 25.338 1.00 71.35 N
-ATOM 398 CA ALA A 67 62.348 24.478 26.589 1.00 70.37 C
-ATOM 399 C ALA A 67 63.320 24.195 27.706 1.00 70.50 C
-ATOM 400 O ALA A 67 63.885 23.105 27.779 1.00 69.55 O
-ATOM 401 CB ALA A 67 61.031 23.772 26.858 1.00 70.86 C
-ATOM 402 N GLY A 68 63.520 25.191 28.561 1.00 70.77 N
-ATOM 403 CA GLY A 68 64.448 25.048 29.662 1.00 69.52 C
-ATOM 404 C GLY A 68 65.878 25.470 29.335 1.00 69.47 C
-ATOM 405 O GLY A 68 66.738 25.391 30.207 1.00 72.58 O
-ATOM 406 N THR A 69 66.163 25.909 28.109 1.00 67.34 N
-ATOM 407 CA THR A 69 67.532 26.305 27.775 1.00 65.93 C
-ATOM 408 C THR A 69 67.545 27.524 26.883 1.00 66.51 C
-ATOM 409 O THR A 69 66.500 27.981 26.430 1.00 65.68 O
-ATOM 410 CB THR A 69 68.286 25.214 27.008 1.00 66.44 C
-ATOM 411 OG1 THR A 69 67.977 25.330 25.614 1.00 66.65 O
-ATOM 412 CG2 THR A 69 67.899 23.824 27.492 1.00 62.61 C
-ATOM 413 N ASN A 70 68.734 28.041 26.605 1.00 67.31 N
-ATOM 414 CA ASN A 70 68.825 29.218 25.755 1.00 70.86 C
-ATOM 415 C ASN A 70 69.053 28.953 24.267 1.00 71.08 C
-ATOM 416 O ASN A 70 69.286 29.894 23.493 1.00 71.62 O
-ATOM 417 CB ASN A 70 69.895 30.163 26.284 1.00 76.50 C
-ATOM 418 CG ASN A 70 69.489 30.810 27.600 1.00 80.96 C
-ATOM 419 OD1 ASN A 70 68.409 31.413 27.704 1.00 82.85 O
-ATOM 420 ND2 ASN A 70 70.347 30.688 28.615 1.00 83.12 N
-ATOM 421 N THR A 71 68.983 27.681 23.866 1.00 68.41 N
-ATOM 422 CA THR A 71 69.133 27.317 22.461 1.00 64.45 C
-ATOM 423 C THR A 71 67.803 27.576 21.752 1.00 62.62 C
-ATOM 424 O THR A 71 66.732 27.395 22.327 1.00 61.84 O
-ATOM 425 CB THR A 71 69.425 25.814 22.273 1.00 65.10 C
-ATOM 426 OG1 THR A 71 70.670 25.473 22.879 1.00 68.32 O
-ATOM 427 CG2 THR A 71 69.491 25.467 20.797 1.00 65.08 C
-ATOM 428 N THR A 72 67.872 28.025 20.508 1.00 60.70 N
-ATOM 429 CA THR A 72 66.677 28.219 19.699 1.00 57.78 C
-ATOM 430 C THR A 72 66.968 27.269 18.550 1.00 58.05 C
-ATOM 431 O THR A 72 67.902 27.506 17.777 1.00 59.97 O
-ATOM 432 CB THR A 72 66.548 29.652 19.170 1.00 54.43 C
-ATOM 433 OG1 THR A 72 66.270 30.525 20.260 1.00 52.12 O
-ATOM 434 CG2 THR A 72 65.411 29.757 18.170 1.00 53.31 C
-ATOM 435 N LEU A 73 66.212 26.177 18.458 1.00 56.11 N
-ATOM 436 CA LEU A 73 66.458 25.209 17.401 1.00 53.97 C
-ATOM 437 C LEU A 73 65.451 25.300 16.271 1.00 56.30 C
-ATOM 438 O LEU A 73 64.244 25.384 16.501 1.00 56.87 O
-ATOM 439 CB LEU A 73 66.459 23.789 17.960 1.00 47.50 C
-ATOM 440 CG LEU A 73 66.673 22.705 16.912 1.00 44.34 C
-ATOM 441 CD1 LEU A 73 68.031 22.856 16.299 1.00 40.13 C
-ATOM 442 CD2 LEU A 73 66.536 21.355 17.536 1.00 39.64 C
-ATOM 443 N TYR A 74 65.973 25.285 15.046 1.00 57.86 N
-ATOM 444 CA TYR A 74 65.175 25.334 13.823 1.00 57.11 C
-ATOM 445 C TYR A 74 65.508 24.152 12.916 1.00 56.77 C
-ATOM 446 O TYR A 74 66.690 23.876 12.658 1.00 58.37 O
-ATOM 447 CB TYR A 74 65.484 26.590 13.018 1.00 57.35 C
-ATOM 448 CG TYR A 74 64.785 27.826 13.458 1.00 57.28 C
-ATOM 449 CD1 TYR A 74 65.443 28.783 14.228 1.00 58.71 C
-ATOM 450 CD2 TYR A 74 63.472 28.065 13.077 1.00 56.00 C
-ATOM 451 CE1 TYR A 74 64.808 29.959 14.606 1.00 60.10 C
-ATOM 452 CE2 TYR A 74 62.825 29.228 13.447 1.00 58.60 C
-ATOM 453 CZ TYR A 74 63.496 30.174 14.211 1.00 60.91 C
-ATOM 454 OH TYR A 74 62.854 31.334 14.568 1.00 65.12 O
-ATOM 455 N LEU A 75 64.481 23.475 12.408 1.00 54.15 N
-ATOM 456 CA LEU A 75 64.703 22.366 11.480 1.00 51.56 C
-ATOM 457 C LEU A 75 64.278 22.840 10.082 1.00 48.56 C
-ATOM 458 O LEU A 75 63.236 23.461 9.918 1.00 47.43 O
-ATOM 459 CB LEU A 75 63.879 21.134 11.901 1.00 53.37 C
-ATOM 460 CG LEU A 75 63.782 20.803 13.410 1.00 54.98 C
-ATOM 461 CD1 LEU A 75 62.801 19.655 13.645 1.00 51.48 C
-ATOM 462 CD2 LEU A 75 65.152 20.468 13.964 1.00 52.73 C
-ATOM 463 N LYS A 76 65.115 22.592 9.086 1.00 47.80 N
-ATOM 464 CA LYS A 76 64.805 22.957 7.705 1.00 46.27 C
-ATOM 465 C LYS A 76 64.072 21.718 7.190 1.00 47.19 C
-ATOM 466 O LYS A 76 64.700 20.691 6.935 1.00 46.71 O
-ATOM 467 CB LYS A 76 66.103 23.180 6.929 1.00 45.37 C
-ATOM 468 CG LYS A 76 65.939 23.486 5.453 1.00 44.90 C
-ATOM 469 CD LYS A 76 65.056 24.692 5.219 1.00 42.70 C
-ATOM 470 CE LYS A 76 64.980 25.007 3.730 1.00 44.26 C
-ATOM 471 NZ LYS A 76 63.971 26.035 3.361 1.00 42.47 N
-ATOM 472 N ARG A 77 62.750 21.818 7.054 1.00 46.06 N
-ATOM 473 CA ARG A 77 61.914 20.700 6.640 1.00 44.01 C
-ATOM 474 C ARG A 77 62.043 20.168 5.203 1.00 46.25 C
-ATOM 475 O ARG A 77 61.120 20.289 4.404 1.00 46.31 O
-ATOM 476 CB ARG A 77 60.441 21.036 6.907 1.00 42.58 C
-ATOM 477 CG ARG A 77 60.124 21.656 8.255 1.00 41.41 C
-ATOM 478 CD ARG A 77 60.423 20.732 9.409 1.00 45.58 C
-ATOM 479 NE ARG A 77 59.854 19.391 9.246 1.00 51.06 N
-ATOM 480 CZ ARG A 77 58.600 19.046 9.538 1.00 52.13 C
-ATOM 481 NH1 ARG A 77 57.761 19.951 10.015 1.00 53.36 N
-ATOM 482 NH2 ARG A 77 58.187 17.789 9.365 1.00 50.72 N
-ATOM 483 N GLU A 78 63.174 19.564 4.863 1.00 48.14 N
-ATOM 484 CA GLU A 78 63.303 18.988 3.530 1.00 49.90 C
-ATOM 485 C GLU A 78 62.579 17.647 3.568 1.00 50.80 C
-ATOM 486 O GLU A 78 62.345 17.033 2.536 1.00 52.19 O
-ATOM 487 CB GLU A 78 64.767 18.752 3.147 1.00 48.61 C
-ATOM 488 CG GLU A 78 65.604 20.009 2.993 1.00 52.93 C
-ATOM 489 CD GLU A 78 65.060 20.985 1.957 1.00 54.42 C
-ATOM 490 OE1 GLU A 78 64.997 20.621 0.764 1.00 55.95 O
-ATOM 491 OE2 GLU A 78 64.701 22.121 2.335 1.00 53.41 O
-ATOM 492 N ASP A 79 62.227 17.212 4.777 1.00 52.10 N
-ATOM 493 CA ASP A 79 61.533 15.943 5.009 1.00 52.35 C
-ATOM 494 C ASP A 79 60.110 15.907 4.480 1.00 52.22 C
-ATOM 495 O ASP A 79 59.545 14.831 4.305 1.00 52.48 O
-ATOM 496 CB ASP A 79 61.509 15.600 6.519 1.00 54.67 C
-ATOM 497 CG ASP A 79 60.637 16.569 7.364 1.00 56.08 C
-ATOM 498 OD1 ASP A 79 60.853 17.799 7.298 1.00 55.96 O
-ATOM 499 OD2 ASP A 79 59.744 16.094 8.114 1.00 55.95 O
-ATOM 500 N LEU A 80 59.526 17.073 4.224 1.00 50.37 N
-ATOM 501 CA LEU A 80 58.162 17.103 3.741 1.00 49.08 C
-ATOM 502 C LEU A 80 58.044 17.057 2.224 1.00 50.61 C
-ATOM 503 O LEU A 80 56.946 16.948 1.690 1.00 54.55 O
-ATOM 504 CB LEU A 80 57.442 18.326 4.293 1.00 47.53 C
-ATOM 505 CG LEU A 80 57.352 18.369 5.823 1.00 48.84 C
-ATOM 506 CD1 LEU A 80 56.356 19.449 6.227 1.00 48.73 C
-ATOM 507 CD2 LEU A 80 56.917 17.020 6.386 1.00 44.55 C
-ATOM 508 N LEU A 81 59.170 17.156 1.528 1.00 50.49 N
-ATOM 509 CA LEU A 81 59.182 17.078 0.072 1.00 49.57 C
-ATOM 510 C LEU A 81 58.851 15.648 -0.293 1.00 51.66 C
-ATOM 511 O LEU A 81 58.834 14.779 0.564 1.00 51.85 O
-ATOM 512 CB LEU A 81 60.570 17.379 -0.455 1.00 45.68 C
-ATOM 513 CG LEU A 81 60.947 18.767 -0.932 1.00 44.38 C
-ATOM 514 CD1 LEU A 81 59.972 19.818 -0.462 1.00 38.08 C
-ATOM 515 CD2 LEU A 81 62.347 19.019 -0.431 1.00 43.11 C
-ATOM 516 N HIS A 82 58.582 15.390 -1.560 1.00 54.70 N
-ATOM 517 CA HIS A 82 58.310 14.028 -1.949 1.00 58.29 C
-ATOM 518 C HIS A 82 59.630 13.478 -2.387 1.00 57.89 C
-ATOM 519 O HIS A 82 60.506 14.239 -2.762 1.00 60.52 O
-ATOM 520 CB HIS A 82 57.294 13.988 -3.066 1.00 67.18 C
-ATOM 521 CG HIS A 82 55.929 13.611 -2.592 1.00 79.31 C
-ATOM 522 ND1 HIS A 82 55.692 12.455 -1.867 1.00 84.56 N
-ATOM 523 CD2 HIS A 82 54.729 14.229 -2.725 1.00 82.57 C
-ATOM 524 CE1 HIS A 82 54.402 12.379 -1.579 1.00 87.32 C
-ATOM 525 NE2 HIS A 82 53.796 13.442 -2.088 1.00 87.44 N
-ATOM 526 N GLY A 83 59.799 12.165 -2.332 1.00 59.92 N
-ATOM 527 CA GLY A 83 61.086 11.573 -2.701 1.00 58.38 C
-ATOM 528 C GLY A 83 61.562 12.042 -4.051 1.00 57.79 C
-ATOM 529 O GLY A 83 60.745 12.367 -4.915 1.00 58.15 O
-ATOM 530 N GLY A 84 62.873 12.101 -4.242 1.00 57.45 N
-ATOM 531 CA GLY A 84 63.397 12.538 -5.533 1.00 55.55 C
-ATOM 532 C GLY A 84 63.351 14.032 -5.822 1.00 53.82 C
-ATOM 533 O GLY A 84 63.904 14.486 -6.831 1.00 51.60 O
-ATOM 534 N ALA A 85 62.679 14.789 -4.954 1.00 52.11 N
-ATOM 535 CA ALA A 85 62.578 16.243 -5.093 1.00 50.22 C
-ATOM 536 C ALA A 85 63.956 16.851 -5.301 1.00 49.66 C
-ATOM 537 O ALA A 85 64.175 17.630 -6.225 1.00 48.85 O
-ATOM 538 CB ALA A 85 61.967 16.839 -3.854 1.00 50.25 C
-ATOM 539 N HIS A 86 64.888 16.490 -4.430 1.00 48.98 N
-ATOM 540 CA HIS A 86 66.224 17.017 -4.544 1.00 51.20 C
-ATOM 541 C HIS A 86 66.904 16.655 -5.867 1.00 53.49 C
-ATOM 542 O HIS A 86 67.837 17.341 -6.284 1.00 57.78 O
-ATOM 543 CB HIS A 86 67.063 16.603 -3.329 1.00 52.13 C
-ATOM 544 CG HIS A 86 66.720 17.359 -2.076 1.00 54.44 C
-ATOM 545 ND1 HIS A 86 67.364 17.150 -0.874 1.00 57.27 N
-ATOM 546 CD2 HIS A 86 65.816 18.344 -1.845 1.00 55.27 C
-ATOM 547 CE1 HIS A 86 66.873 17.972 0.040 1.00 55.44 C
-ATOM 548 NE2 HIS A 86 65.932 18.706 -0.523 1.00 53.99 N
-ATOM 549 N LYS A 87 66.442 15.610 -6.551 1.00 53.66 N
-ATOM 550 CA LYS A 87 67.040 15.262 -7.845 1.00 54.96 C
-ATOM 551 C LYS A 87 66.380 16.143 -8.872 1.00 55.25 C
-ATOM 552 O LYS A 87 67.024 16.629 -9.810 1.00 56.92 O
-ATOM 553 CB LYS A 87 66.799 13.796 -8.206 1.00 55.30 C
-ATOM 554 CG LYS A 87 67.523 12.884 -7.269 1.00 59.08 C
-ATOM 555 CD LYS A 87 67.325 11.415 -7.514 1.00 58.89 C
-ATOM 556 CE LYS A 87 68.175 10.697 -6.482 1.00 58.16 C
-ATOM 557 NZ LYS A 87 68.208 9.247 -6.704 1.00 62.56 N
-ATOM 558 N THR A 88 65.080 16.335 -8.680 1.00 52.74 N
-ATOM 559 CA THR A 88 64.282 17.159 -9.561 1.00 51.57 C
-ATOM 560 C THR A 88 64.900 18.547 -9.578 1.00 51.75 C
-ATOM 561 O THR A 88 64.871 19.245 -10.592 1.00 51.12 O
-ATOM 562 CB THR A 88 62.833 17.195 -9.059 1.00 49.93 C
-ATOM 563 OG1 THR A 88 62.376 15.847 -8.912 1.00 48.08 O
-ATOM 564 CG2 THR A 88 61.930 17.930 -10.038 1.00 46.01 C
-ATOM 565 N ASN A 89 65.474 18.927 -8.442 1.00 52.26 N
-ATOM 566 CA ASN A 89 66.145 20.208 -8.306 1.00 53.91 C
-ATOM 567 C ASN A 89 67.205 20.461 -9.379 1.00 54.46 C
-ATOM 568 O ASN A 89 67.115 21.434 -10.120 1.00 53.15 O
-ATOM 569 CB ASN A 89 66.787 20.301 -6.933 1.00 54.76 C
-ATOM 570 CG ASN A 89 65.822 20.769 -5.892 1.00 56.05 C
-ATOM 571 OD1 ASN A 89 66.088 20.678 -4.700 1.00 56.92 O
-ATOM 572 ND2 ASN A 89 64.686 21.287 -6.335 1.00 55.55 N
-ATOM 573 N GLN A 90 68.215 19.604 -9.484 1.00 55.49 N
-ATOM 574 CA GLN A 90 69.208 19.876 -10.509 1.00 57.17 C
-ATOM 575 C GLN A 90 68.747 19.563 -11.932 1.00 55.04 C
-ATOM 576 O GLN A 90 69.282 20.149 -12.877 1.00 55.43 O
-ATOM 577 CB GLN A 90 70.532 19.174 -10.207 1.00 58.11 C
-ATOM 578 CG GLN A 90 70.601 17.784 -10.676 1.00 67.31 C
-ATOM 579 CD GLN A 90 71.429 16.947 -9.739 1.00 76.61 C
-ATOM 580 OE1 GLN A 90 71.417 15.701 -9.801 1.00 81.27 O
-ATOM 581 NE2 GLN A 90 72.157 17.622 -8.841 1.00 78.98 N
-ATOM 582 N VAL A 91 67.772 18.675 -12.122 1.00 50.98 N
-ATOM 583 CA VAL A 91 67.375 18.441 -13.501 1.00 52.23 C
-ATOM 584 C VAL A 91 66.526 19.597 -14.004 1.00 50.84 C
-ATOM 585 O VAL A 91 66.594 19.952 -15.174 1.00 50.42 O
-ATOM 586 CB VAL A 91 66.607 17.110 -13.740 1.00 52.64 C
-ATOM 587 CG1 VAL A 91 67.478 15.933 -13.410 1.00 50.48 C
-ATOM 588 CG2 VAL A 91 65.335 17.099 -12.956 1.00 58.02 C
-ATOM 589 N LEU A 92 65.715 20.189 -13.138 1.00 50.75 N
-ATOM 590 CA LEU A 92 64.914 21.327 -13.580 1.00 49.99 C
-ATOM 591 C LEU A 92 65.923 22.388 -14.038 1.00 49.31 C
-ATOM 592 O LEU A 92 65.776 22.986 -15.111 1.00 46.55 O
-ATOM 593 CB LEU A 92 64.042 21.845 -12.432 1.00 47.83 C
-ATOM 594 CG LEU A 92 62.869 20.933 -12.069 1.00 47.49 C
-ATOM 595 CD1 LEU A 92 62.118 21.466 -10.855 1.00 46.32 C
-ATOM 596 CD2 LEU A 92 61.935 20.838 -13.264 1.00 45.96 C
-ATOM 597 N GLY A 93 66.958 22.585 -13.222 1.00 48.25 N
-ATOM 598 CA GLY A 93 68.009 23.525 -13.554 1.00 49.35 C
-ATOM 599 C GLY A 93 68.690 23.166 -14.876 1.00 52.32 C
-ATOM 600 O GLY A 93 68.872 24.041 -15.734 1.00 53.92 O
-ATOM 601 N GLN A 94 69.073 21.895 -15.064 1.00 51.49 N
-ATOM 602 CA GLN A 94 69.730 21.485 -16.309 1.00 48.05 C
-ATOM 603 C GLN A 94 68.790 21.400 -17.498 1.00 48.25 C
-ATOM 604 O GLN A 94 69.158 21.778 -18.601 1.00 51.29 O
-ATOM 605 CB GLN A 94 70.430 20.162 -16.131 1.00 44.84 C
-ATOM 606 CG GLN A 94 71.498 20.215 -15.111 1.00 46.83 C
-ATOM 607 CD GLN A 94 72.170 18.876 -14.947 1.00 50.62 C
-ATOM 608 OE1 GLN A 94 72.651 18.297 -15.913 1.00 49.07 O
-ATOM 609 NE2 GLN A 94 72.213 18.375 -13.718 1.00 54.74 N
-ATOM 610 N ALA A 95 67.580 20.901 -17.302 1.00 47.98 N
-ATOM 611 CA ALA A 95 66.641 20.834 -18.416 1.00 46.97 C
-ATOM 612 C ALA A 95 66.522 22.254 -18.947 1.00 46.68 C
-ATOM 613 O ALA A 95 66.614 22.476 -20.147 1.00 45.66 O
-ATOM 614 CB ALA A 95 65.268 20.325 -17.945 1.00 45.72 C
-ATOM 615 N LEU A 96 66.327 23.214 -18.041 1.00 46.93 N
-ATOM 616 CA LEU A 96 66.202 24.613 -18.429 1.00 47.28 C
-ATOM 617 C LEU A 96 67.450 25.082 -19.163 1.00 50.24 C
-ATOM 618 O LEU A 96 67.370 25.763 -20.181 1.00 51.81 O
-ATOM 619 CB LEU A 96 66.013 25.495 -17.213 1.00 46.45 C
-ATOM 620 CG LEU A 96 64.711 26.272 -17.148 1.00 46.53 C
-ATOM 621 CD1 LEU A 96 64.867 27.441 -16.227 1.00 46.61 C
-ATOM 622 CD2 LEU A 96 64.364 26.755 -18.504 1.00 47.60 C
-ATOM 623 N LEU A 97 68.615 24.721 -18.639 1.00 49.95 N
-ATOM 624 CA LEU A 97 69.865 25.111 -19.263 1.00 48.78 C
-ATOM 625 C LEU A 97 69.981 24.555 -20.685 1.00 49.98 C
-ATOM 626 O LEU A 97 70.475 25.232 -21.587 1.00 51.81 O
-ATOM 627 CB LEU A 97 71.026 24.621 -18.412 1.00 46.77 C
-ATOM 628 CG LEU A 97 72.361 25.128 -18.910 1.00 43.76 C
-ATOM 629 CD1 LEU A 97 72.262 26.622 -19.005 1.00 44.44 C
-ATOM 630 CD2 LEU A 97 73.477 24.698 -17.981 1.00 44.70 C
-ATOM 631 N ALA A 98 69.536 23.316 -20.880 1.00 49.14 N
-ATOM 632 CA ALA A 98 69.572 22.685 -22.196 1.00 49.86 C
-ATOM 633 C ALA A 98 68.663 23.438 -23.180 1.00 50.39 C
-ATOM 634 O ALA A 98 69.052 23.725 -24.309 1.00 50.36 O
-ATOM 635 CB ALA A 98 69.136 21.223 -22.090 1.00 49.24 C
-ATOM 636 N LYS A 99 67.448 23.742 -22.745 1.00 49.37 N
-ATOM 637 CA LYS A 99 66.511 24.482 -23.562 1.00 51.40 C
-ATOM 638 C LYS A 99 67.185 25.786 -23.972 1.00 53.98 C
-ATOM 639 O LYS A 99 67.073 26.242 -25.116 1.00 54.67 O
-ATOM 640 CB LYS A 99 65.279 24.797 -22.741 1.00 52.88 C
-ATOM 641 CG LYS A 99 64.020 24.178 -23.264 1.00 57.85 C
-ATOM 642 CD LYS A 99 63.241 25.151 -24.124 1.00 59.52 C
-ATOM 643 CE LYS A 99 61.967 24.489 -24.655 1.00 64.28 C
-ATOM 644 NZ LYS A 99 62.261 23.316 -25.565 1.00 64.54 N
-ATOM 645 N ARG A 100 67.888 26.390 -23.020 1.00 54.14 N
-ATOM 646 CA ARG A 100 68.577 27.633 -23.276 1.00 52.62 C
-ATOM 647 C ARG A 100 69.516 27.370 -24.415 1.00 53.32 C
-ATOM 648 O ARG A 100 69.476 28.085 -25.410 1.00 56.71 O
-ATOM 649 CB ARG A 100 69.387 28.077 -22.057 1.00 55.46 C
-ATOM 650 CG ARG A 100 69.873 29.533 -22.090 1.00 55.34 C
-ATOM 651 CD ARG A 100 69.228 30.310 -20.964 1.00 59.82 C
-ATOM 652 NE ARG A 100 69.686 31.690 -20.834 1.00 63.22 N
-ATOM 653 CZ ARG A 100 70.965 32.053 -20.792 1.00 66.13 C
-ATOM 654 NH1 ARG A 100 71.279 33.340 -20.647 1.00 62.49 N
-ATOM 655 NH2 ARG A 100 71.926 31.128 -20.927 1.00 68.02 N
-ATOM 656 N MET A 101 70.351 26.336 -24.279 1.00 52.04 N
-ATOM 657 CA MET A 101 71.337 25.999 -25.311 1.00 50.74 C
-ATOM 658 C MET A 101 70.705 25.588 -26.617 1.00 49.24 C
-ATOM 659 O MET A 101 71.409 25.262 -27.570 1.00 48.34 O
-ATOM 660 CB MET A 101 72.237 24.867 -24.859 1.00 51.65 C
-ATOM 661 CG MET A 101 73.051 25.178 -23.663 1.00 55.72 C
-ATOM 662 SD MET A 101 74.512 24.158 -23.738 1.00 59.08 S
-ATOM 663 CE MET A 101 73.891 22.676 -22.853 1.00 59.48 C
-ATOM 664 N GLY A 102 69.378 25.585 -26.650 1.00 47.55 N
-ATOM 665 CA GLY A 102 68.676 25.204 -27.853 1.00 47.25 C
-ATOM 666 C GLY A 102 68.713 23.715 -28.140 1.00 48.77 C
-ATOM 667 O GLY A 102 68.469 23.308 -29.287 1.00 48.08 O
-ATOM 668 N LYS A 103 69.022 22.907 -27.116 1.00 48.26 N
-ATOM 669 CA LYS A 103 69.071 21.452 -27.257 1.00 47.03 C
-ATOM 670 C LYS A 103 67.646 20.945 -27.475 1.00 49.28 C
-ATOM 671 O LYS A 103 66.666 21.656 -27.185 1.00 50.12 O
-ATOM 672 CB LYS A 103 69.655 20.793 -26.015 1.00 44.12 C
-ATOM 673 CG LYS A 103 71.045 21.216 -25.671 1.00 42.94 C
-ATOM 674 CD LYS A 103 72.010 20.957 -26.792 1.00 46.12 C
-ATOM 675 CE LYS A 103 73.449 21.346 -26.409 1.00 48.25 C
-ATOM 676 NZ LYS A 103 74.271 21.792 -27.606 1.00 47.96 N
-ATOM 677 N THR A 104 67.531 19.713 -27.970 1.00 49.57 N
-ATOM 678 CA THR A 104 66.224 19.125 -28.270 1.00 49.73 C
-ATOM 679 C THR A 104 66.010 17.758 -27.633 1.00 50.95 C
-ATOM 680 O THR A 104 64.882 17.293 -27.538 1.00 50.91 O
-ATOM 681 CB THR A 104 66.022 19.004 -29.812 1.00 47.33 C
-ATOM 682 OG1 THR A 104 67.251 18.598 -30.435 1.00 48.51 O
-ATOM 683 CG2 THR A 104 65.614 20.320 -30.401 1.00 46.67 C
-ATOM 684 N GLU A 105 67.093 17.105 -27.220 1.00 52.04 N
-ATOM 685 CA GLU A 105 66.979 15.801 -26.590 1.00 52.25 C
-ATOM 686 C GLU A 105 67.843 15.828 -25.348 1.00 52.04 C
-ATOM 687 O GLU A 105 68.750 16.650 -25.225 1.00 48.87 O
-ATOM 688 CB GLU A 105 67.504 14.671 -27.473 1.00 54.07 C
-ATOM 689 CG GLU A 105 67.179 14.713 -28.948 1.00 63.18 C
-ATOM 690 CD GLU A 105 68.443 14.457 -29.771 1.00 69.72 C
-ATOM 691 OE1 GLU A 105 69.295 15.375 -29.758 1.00 75.48 O
-ATOM 692 OE2 GLU A 105 68.614 13.364 -30.399 1.00 69.21 O
-ATOM 693 N ILE A 106 67.567 14.886 -24.451 1.00 52.41 N
-ATOM 694 CA ILE A 106 68.285 14.742 -23.198 1.00 51.35 C
-ATOM 695 C ILE A 106 68.695 13.275 -22.976 1.00 51.31 C
-ATOM 696 O ILE A 106 67.952 12.354 -23.311 1.00 52.69 O
-ATOM 697 CB ILE A 106 67.405 15.278 -22.051 1.00 49.76 C
-ATOM 698 CG1 ILE A 106 67.675 16.762 -21.888 1.00 46.67 C
-ATOM 699 CG2 ILE A 106 67.672 14.539 -20.772 1.00 50.66 C
-ATOM 700 CD1 ILE A 106 66.800 17.384 -20.910 1.00 48.88 C
-ATOM 701 N ILE A 107 69.891 13.083 -22.432 1.00 49.88 N
-ATOM 702 CA ILE A 107 70.446 11.761 -22.171 1.00 50.43 C
-ATOM 703 C ILE A 107 70.733 11.678 -20.675 1.00 51.80 C
-ATOM 704 O ILE A 107 71.373 12.560 -20.118 1.00 50.67 O
-ATOM 705 CB ILE A 107 71.785 11.561 -22.958 1.00 51.48 C
-ATOM 706 CG1 ILE A 107 71.500 11.440 -24.447 1.00 51.52 C
-ATOM 707 CG2 ILE A 107 72.544 10.322 -22.484 1.00 48.76 C
-ATOM 708 CD1 ILE A 107 72.730 11.706 -25.263 1.00 53.31 C
-ATOM 709 N ALA A 108 70.266 10.609 -20.040 1.00 52.48 N
-ATOM 710 CA ALA A 108 70.456 10.401 -18.615 1.00 52.94 C
-ATOM 711 C ALA A 108 70.592 8.913 -18.345 1.00 54.94 C
-ATOM 712 O ALA A 108 70.168 8.098 -19.155 1.00 57.54 O
-ATOM 713 CB ALA A 108 69.252 10.936 -17.855 1.00 49.30 C
-ATOM 714 N GLU A 109 71.200 8.566 -17.217 1.00 55.55 N
-ATOM 715 CA GLU A 109 71.313 7.178 -16.811 1.00 56.32 C
-ATOM 716 C GLU A 109 70.609 7.124 -15.458 1.00 57.80 C
-ATOM 717 O GLU A 109 70.429 8.159 -14.808 1.00 57.39 O
-ATOM 718 CB GLU A 109 72.759 6.748 -16.628 1.00 59.55 C
-ATOM 719 CG GLU A 109 73.398 7.276 -15.373 1.00 66.28 C
-ATOM 720 CD GLU A 109 74.063 8.595 -15.627 1.00 71.94 C
-ATOM 721 OE1 GLU A 109 75.047 8.572 -16.394 1.00 71.28 O
-ATOM 722 OE2 GLU A 109 73.604 9.641 -15.086 1.00 75.92 O
-ATOM 723 N THR A 110 70.225 5.925 -15.018 1.00 58.14 N
-ATOM 724 CA THR A 110 69.530 5.782 -13.740 1.00 55.24 C
-ATOM 725 C THR A 110 69.778 4.413 -13.093 1.00 55.15 C
-ATOM 726 O THR A 110 70.079 3.442 -13.776 1.00 58.80 O
-ATOM 727 CB THR A 110 68.036 6.010 -13.953 1.00 51.82 C
-ATOM 728 OG1 THR A 110 67.361 6.132 -12.696 1.00 48.23 O
-ATOM 729 CG2 THR A 110 67.473 4.873 -14.763 1.00 52.12 C
-ATOM 730 N GLY A 111 69.694 4.355 -11.768 1.00 55.41 N
-ATOM 731 CA GLY A 111 69.892 3.112 -11.042 1.00 54.73 C
-ATOM 732 C GLY A 111 68.552 2.685 -10.469 1.00 55.25 C
-ATOM 733 O GLY A 111 67.887 1.809 -10.999 1.00 56.63 O
-ATOM 734 N ALA A 112 68.145 3.317 -9.381 1.00 56.47 N
-ATOM 735 CA ALA A 112 66.866 3.018 -8.766 1.00 57.06 C
-ATOM 736 C ALA A 112 65.791 3.522 -9.708 1.00 58.71 C
-ATOM 737 O ALA A 112 64.703 2.981 -9.777 1.00 58.44 O
-ATOM 738 CB ALA A 112 66.755 3.743 -7.444 1.00 59.48 C
-ATOM 739 N GLY A 113 66.106 4.579 -10.437 1.00 60.34 N
-ATOM 740 CA GLY A 113 65.134 5.134 -11.344 1.00 60.31 C
-ATOM 741 C GLY A 113 64.682 6.511 -10.904 1.00 62.93 C
-ATOM 742 O GLY A 113 63.969 7.169 -11.656 1.00 64.06 O
-ATOM 743 N GLN A 114 65.064 6.967 -9.707 1.00 63.02 N
-ATOM 744 CA GLN A 114 64.637 8.304 -9.294 1.00 62.88 C
-ATOM 745 C GLN A 114 65.142 9.342 -10.294 1.00 60.76 C
-ATOM 746 O GLN A 114 64.342 10.061 -10.897 1.00 59.55 O
-ATOM 747 CB GLN A 114 65.133 8.659 -7.894 1.00 67.90 C
-ATOM 748 CG GLN A 114 64.336 8.036 -6.749 1.00 74.36 C
-ATOM 749 CD GLN A 114 64.755 8.585 -5.369 1.00 79.89 C
-ATOM 750 OE1 GLN A 114 65.941 8.569 -5.003 1.00 80.85 O
-ATOM 751 NE2 GLN A 114 63.773 9.072 -4.598 1.00 81.89 N
-ATOM 752 N HIS A 115 66.459 9.417 -10.484 1.00 57.94 N
-ATOM 753 CA HIS A 115 67.020 10.377 -11.438 1.00 54.19 C
-ATOM 754 C HIS A 115 66.333 10.259 -12.811 1.00 53.03 C
-ATOM 755 O HIS A 115 65.923 11.272 -13.408 1.00 50.67 O
-ATOM 756 CB HIS A 115 68.518 10.167 -11.596 1.00 51.49 C
-ATOM 757 CG HIS A 115 69.168 11.172 -12.492 1.00 54.08 C
-ATOM 758 ND1 HIS A 115 69.189 12.520 -12.208 1.00 55.53 N
-ATOM 759 CD2 HIS A 115 69.791 11.032 -13.689 1.00 57.28 C
-ATOM 760 CE1 HIS A 115 69.789 13.166 -13.193 1.00 56.75 C
-ATOM 761 NE2 HIS A 115 70.164 12.287 -14.105 1.00 55.82 N
-ATOM 762 N GLY A 116 66.206 9.032 -13.312 1.00 50.22 N
-ATOM 763 CA GLY A 116 65.533 8.849 -14.588 1.00 48.97 C
-ATOM 764 C GLY A 116 64.137 9.476 -14.620 1.00 47.08 C
-ATOM 765 O GLY A 116 63.782 10.187 -15.564 1.00 48.46 O
-ATOM 766 N VAL A 117 63.340 9.213 -13.588 1.00 43.86 N
-ATOM 767 CA VAL A 117 61.997 9.752 -13.512 1.00 41.03 C
-ATOM 768 C VAL A 117 62.061 11.257 -13.440 1.00 43.13 C
-ATOM 769 O VAL A 117 61.152 11.928 -13.898 1.00 43.82 O
-ATOM 770 CB VAL A 117 61.239 9.254 -12.267 1.00 39.62 C
-ATOM 771 CG1 VAL A 117 59.868 9.911 -12.208 1.00 35.53 C
-ATOM 772 CG2 VAL A 117 61.106 7.726 -12.289 1.00 34.51 C
-ATOM 773 N ALA A 118 63.127 11.796 -12.849 1.00 45.06 N
-ATOM 774 CA ALA A 118 63.279 13.256 -12.748 1.00 45.08 C
-ATOM 775 C ALA A 118 63.581 13.849 -14.149 1.00 46.88 C
-ATOM 776 O ALA A 118 62.997 14.873 -14.547 1.00 48.69 O
-ATOM 777 CB ALA A 118 64.387 13.615 -11.742 1.00 34.15 C
-ATOM 778 N SER A 119 64.461 13.191 -14.903 1.00 45.31 N
-ATOM 779 CA SER A 119 64.804 13.655 -16.237 1.00 45.50 C
-ATOM 780 C SER A 119 63.608 13.580 -17.193 1.00 47.92 C
-ATOM 781 O SER A 119 63.393 14.469 -18.025 1.00 47.58 O
-ATOM 782 CB SER A 119 65.935 12.816 -16.757 1.00 43.78 C
-ATOM 783 OG SER A 119 66.829 12.605 -15.697 1.00 46.90 O
-ATOM 784 N ALA A 120 62.829 12.513 -17.082 1.00 48.74 N
-ATOM 785 CA ALA A 120 61.649 12.356 -17.925 1.00 49.95 C
-ATOM 786 C ALA A 120 60.666 13.509 -17.687 1.00 50.28 C
-ATOM 787 O ALA A 120 60.184 14.144 -18.625 1.00 50.67 O
-ATOM 788 CB ALA A 120 60.971 11.028 -17.610 1.00 49.86 C
-ATOM 789 N LEU A 121 60.380 13.752 -16.412 1.00 50.85 N
-ATOM 790 CA LEU A 121 59.469 14.788 -15.966 1.00 49.71 C
-ATOM 791 C LEU A 121 59.929 16.126 -16.497 1.00 49.65 C
-ATOM 792 O LEU A 121 59.201 16.792 -17.243 1.00 49.62 O
-ATOM 793 CB LEU A 121 59.461 14.803 -14.448 1.00 53.68 C
-ATOM 794 CG LEU A 121 58.723 15.866 -13.639 1.00 56.53 C
-ATOM 795 CD1 LEU A 121 58.785 15.460 -12.180 1.00 58.69 C
-ATOM 796 CD2 LEU A 121 59.348 17.231 -13.806 1.00 56.57 C
-ATOM 797 N ALA A 122 61.142 16.523 -16.109 1.00 47.58 N
-ATOM 798 CA ALA A 122 61.696 17.795 -16.556 1.00 43.91 C
-ATOM 799 C ALA A 122 61.599 17.825 -18.063 1.00 44.93 C
-ATOM 800 O ALA A 122 61.213 18.839 -18.646 1.00 45.06 O
-ATOM 801 CB ALA A 122 63.133 17.931 -16.122 1.00 40.34 C
-ATOM 802 N SER A 123 61.922 16.693 -18.691 1.00 46.02 N
-ATOM 803 CA SER A 123 61.874 16.587 -20.147 1.00 46.55 C
-ATOM 804 C SER A 123 60.496 16.778 -20.750 1.00 47.03 C
-ATOM 805 O SER A 123 60.339 17.551 -21.685 1.00 47.72 O
-ATOM 806 CB SER A 123 62.449 15.252 -20.614 1.00 46.69 C
-ATOM 807 OG SER A 123 63.864 15.269 -20.536 1.00 47.64 O
-ATOM 808 N ALA A 124 59.484 16.101 -20.225 1.00 47.27 N
-ATOM 809 CA ALA A 124 58.159 16.258 -20.813 1.00 49.39 C
-ATOM 810 C ALA A 124 57.760 17.715 -20.752 1.00 52.13 C
-ATOM 811 O ALA A 124 57.291 18.298 -21.735 1.00 51.65 O
-ATOM 812 CB ALA A 124 57.160 15.419 -20.078 1.00 48.98 C
-ATOM 813 N LEU A 125 57.963 18.280 -19.567 1.00 54.98 N
-ATOM 814 CA LEU A 125 57.661 19.665 -19.247 1.00 54.95 C
-ATOM 815 C LEU A 125 58.218 20.644 -20.285 1.00 54.72 C
-ATOM 816 O LEU A 125 57.468 21.348 -20.950 1.00 54.08 O
-ATOM 817 CB LEU A 125 58.254 19.958 -17.879 1.00 56.33 C
-ATOM 818 CG LEU A 125 57.616 21.025 -17.026 1.00 56.16 C
-ATOM 819 CD1 LEU A 125 56.115 20.796 -17.018 1.00 58.23 C
-ATOM 820 CD2 LEU A 125 58.204 20.945 -15.620 1.00 55.97 C
-ATOM 821 N LEU A 126 59.534 20.695 -20.424 1.00 53.63 N
-ATOM 822 CA LEU A 126 60.125 21.606 -21.386 1.00 55.31 C
-ATOM 823 C LEU A 126 60.086 21.039 -22.807 1.00 56.74 C
-ATOM 824 O LEU A 126 60.758 21.552 -23.696 1.00 58.28 O
-ATOM 825 CB LEU A 126 61.575 21.895 -21.017 1.00 55.44 C
-ATOM 826 CG LEU A 126 61.822 22.196 -19.554 1.00 54.85 C
-ATOM 827 CD1 LEU A 126 63.282 22.437 -19.335 1.00 59.21 C
-ATOM 828 CD2 LEU A 126 61.056 23.402 -19.166 1.00 55.97 C
-ATOM 829 N GLY A 127 59.329 19.969 -23.017 1.00 54.99 N
-ATOM 830 CA GLY A 127 59.245 19.394 -24.345 1.00 53.74 C
-ATOM 831 C GLY A 127 60.550 18.918 -24.966 1.00 54.55 C
-ATOM 832 O GLY A 127 60.834 19.206 -26.123 1.00 57.21 O
-ATOM 833 N LEU A 128 61.356 18.182 -24.220 1.00 53.71 N
-ATOM 834 CA LEU A 128 62.602 17.666 -24.763 1.00 51.78 C
-ATOM 835 C LEU A 128 62.484 16.146 -24.934 1.00 52.26 C
-ATOM 836 O LEU A 128 61.805 15.479 -24.144 1.00 53.26 O
-ATOM 837 CB LEU A 128 63.749 18.010 -23.821 1.00 49.02 C
-ATOM 838 CG LEU A 128 64.014 19.504 -23.645 1.00 47.07 C
-ATOM 839 CD1 LEU A 128 65.041 19.714 -22.549 1.00 45.27 C
-ATOM 840 CD2 LEU A 128 64.518 20.088 -24.950 1.00 45.15 C
-ATOM 841 N LYS A 129 63.113 15.605 -25.980 1.00 52.27 N
-ATOM 842 CA LYS A 129 63.083 14.164 -26.225 1.00 52.22 C
-ATOM 843 C LYS A 129 64.086 13.556 -25.276 1.00 51.64 C
-ATOM 844 O LYS A 129 65.282 13.863 -25.318 1.00 54.34 O
-ATOM 845 CB LYS A 129 63.452 13.834 -27.666 1.00 53.99 C
-ATOM 846 CG LYS A 129 62.293 14.001 -28.600 1.00 62.36 C
-ATOM 847 CD LYS A 129 62.620 13.502 -30.015 1.00 72.50 C
-ATOM 848 CE LYS A 129 61.403 13.657 -30.987 1.00 76.91 C
-ATOM 849 NZ LYS A 129 60.114 12.997 -30.524 1.00 77.53 N
-ATOM 850 N CYS A 130 63.600 12.664 -24.433 1.00 48.23 N
-ATOM 851 CA CYS A 130 64.436 12.067 -23.413 1.00 46.24 C
-ATOM 852 C CYS A 130 64.762 10.574 -23.566 1.00 45.28 C
-ATOM 853 O CYS A 130 63.884 9.753 -23.813 1.00 45.88 O
-ATOM 854 CB CYS A 130 63.722 12.334 -22.078 1.00 46.83 C
-ATOM 855 SG CYS A 130 64.522 11.816 -20.582 1.00 51.09 S
-ATOM 856 N ARG A 131 66.031 10.215 -23.465 1.00 44.19 N
-ATOM 857 CA ARG A 131 66.364 8.801 -23.488 1.00 44.25 C
-ATOM 858 C ARG A 131 67.241 8.489 -22.268 1.00 46.99 C
-ATOM 859 O ARG A 131 68.248 9.163 -21.997 1.00 45.14 O
-ATOM 860 CB ARG A 131 67.023 8.372 -24.798 1.00 43.41 C
-ATOM 861 CG ARG A 131 68.155 9.177 -25.313 1.00 40.81 C
-ATOM 862 CD ARG A 131 68.643 8.505 -26.570 1.00 41.97 C
-ATOM 863 NE ARG A 131 69.818 9.158 -27.135 1.00 45.75 N
-ATOM 864 CZ ARG A 131 69.782 10.308 -27.788 1.00 44.38 C
-ATOM 865 NH1 ARG A 131 68.630 10.932 -27.956 1.00 45.69 N
-ATOM 866 NH2 ARG A 131 70.891 10.819 -28.281 1.00 46.34 N
-ATOM 867 N ILE A 132 66.826 7.467 -21.524 1.00 47.75 N
-ATOM 868 CA ILE A 132 67.492 7.079 -20.291 1.00 48.43 C
-ATOM 869 C ILE A 132 68.149 5.687 -20.232 1.00 50.06 C
-ATOM 870 O ILE A 132 67.457 4.665 -20.253 1.00 50.48 O
-ATOM 871 CB ILE A 132 66.478 7.181 -19.162 1.00 48.12 C
-ATOM 872 CG1 ILE A 132 65.794 8.552 -19.249 1.00 49.89 C
-ATOM 873 CG2 ILE A 132 67.154 6.914 -17.830 1.00 49.31 C
-ATOM 874 CD1 ILE A 132 64.613 8.756 -18.328 1.00 48.98 C
-ATOM 875 N TYR A 133 69.479 5.643 -20.159 1.00 49.90 N
-ATOM 876 CA TYR A 133 70.168 4.367 -20.049 1.00 49.57 C
-ATOM 877 C TYR A 133 69.979 3.860 -18.640 1.00 49.99 C
-ATOM 878 O TYR A 133 70.015 4.620 -17.686 1.00 49.74 O
-ATOM 879 CB TYR A 133 71.651 4.507 -20.363 1.00 48.70 C
-ATOM 880 CG TYR A 133 71.861 4.793 -21.817 1.00 52.69 C
-ATOM 881 CD1 TYR A 133 71.739 3.785 -22.771 1.00 51.30 C
-ATOM 882 CD2 TYR A 133 72.029 6.099 -22.262 1.00 52.68 C
-ATOM 883 CE1 TYR A 133 71.758 4.080 -24.113 1.00 51.01 C
-ATOM 884 CE2 TYR A 133 72.059 6.398 -23.606 1.00 51.12 C
-ATOM 885 CZ TYR A 133 71.915 5.393 -24.523 1.00 50.42 C
-ATOM 886 OH TYR A 133 71.890 5.724 -25.857 1.00 51.57 O
-ATOM 887 N MET A 134 69.759 2.559 -18.528 1.00 51.96 N
-ATOM 888 CA MET A 134 69.531 1.905 -17.254 1.00 51.46 C
-ATOM 889 C MET A 134 70.027 0.452 -17.345 1.00 53.83 C
-ATOM 890 O MET A 134 69.715 -0.253 -18.307 1.00 54.17 O
-ATOM 891 CB MET A 134 68.031 1.945 -16.934 1.00 46.43 C
-ATOM 892 CG MET A 134 67.686 1.383 -15.597 1.00 45.93 C
-ATOM 893 SD MET A 134 65.963 1.628 -15.158 1.00 52.98 S
-ATOM 894 CE MET A 134 66.058 1.586 -13.363 1.00 43.17 C
-ATOM 895 N GLY A 135 70.827 0.015 -16.370 1.00 55.82 N
-ATOM 896 CA GLY A 135 71.294 -1.366 -16.384 1.00 55.18 C
-ATOM 897 C GLY A 135 70.140 -2.376 -16.403 1.00 56.04 C
-ATOM 898 O GLY A 135 69.116 -2.247 -15.697 1.00 53.35 O
-ATOM 899 N ALA A 136 70.312 -3.404 -17.224 1.00 57.19 N
-ATOM 900 CA ALA A 136 69.309 -4.443 -17.381 1.00 57.18 C
-ATOM 901 C ALA A 136 68.795 -4.980 -16.049 1.00 58.66 C
-ATOM 902 O ALA A 136 67.587 -5.175 -15.879 1.00 55.54 O
-ATOM 903 CB ALA A 136 69.879 -5.549 -18.206 1.00 58.15 C
-ATOM 904 N LYS A 137 69.712 -5.219 -15.111 1.00 61.50 N
-ATOM 905 CA LYS A 137 69.344 -5.719 -13.776 1.00 64.87 C
-ATOM 906 C LYS A 137 68.414 -4.750 -13.052 1.00 65.84 C
-ATOM 907 O LYS A 137 67.438 -5.164 -12.403 1.00 67.63 O
-ATOM 908 CB LYS A 137 70.584 -5.935 -12.904 1.00 64.65 C
-ATOM 909 CG LYS A 137 71.465 -7.074 -13.361 1.00 67.98 C
-ATOM 910 CD LYS A 137 72.721 -7.152 -12.519 1.00 69.14 C
-ATOM 911 CE LYS A 137 73.659 -8.230 -13.028 1.00 69.83 C
-ATOM 912 NZ LYS A 137 74.975 -8.139 -12.340 1.00 72.91 N
-ATOM 913 N ASP A 138 68.723 -3.460 -13.163 1.00 64.83 N
-ATOM 914 CA ASP A 138 67.919 -2.443 -12.523 1.00 61.79 C
-ATOM 915 C ASP A 138 66.580 -2.342 -13.204 1.00 59.39 C
-ATOM 916 O ASP A 138 65.570 -2.158 -12.538 1.00 58.65 O
-ATOM 917 CB ASP A 138 68.631 -1.093 -12.554 1.00 65.28 C
-ATOM 918 CG ASP A 138 69.930 -1.104 -11.765 1.00 68.17 C
-ATOM 919 OD1 ASP A 138 69.911 -1.556 -10.604 1.00 69.43 O
-ATOM 920 OD2 ASP A 138 70.970 -0.656 -12.299 1.00 73.00 O
-ATOM 921 N VAL A 139 66.558 -2.478 -14.526 1.00 55.75 N
-ATOM 922 CA VAL A 139 65.293 -2.391 -15.246 1.00 54.56 C
-ATOM 923 C VAL A 139 64.321 -3.435 -14.730 1.00 56.51 C
-ATOM 924 O VAL A 139 63.112 -3.194 -14.649 1.00 54.19 O
-ATOM 925 CB VAL A 139 65.499 -2.612 -16.733 1.00 52.98 C
-ATOM 926 CG1 VAL A 139 64.206 -2.346 -17.489 1.00 48.93 C
-ATOM 927 CG2 VAL A 139 66.612 -1.711 -17.218 1.00 54.28 C
-ATOM 928 N GLU A 140 64.876 -4.599 -14.383 1.00 61.04 N
-ATOM 929 CA GLU A 140 64.129 -5.744 -13.858 1.00 62.21 C
-ATOM 930 C GLU A 140 63.643 -5.459 -12.467 1.00 62.37 C
-ATOM 931 O GLU A 140 62.448 -5.551 -12.191 1.00 62.67 O
-ATOM 932 CB GLU A 140 65.023 -6.959 -13.787 1.00 67.19 C
-ATOM 933 CG GLU A 140 64.837 -7.956 -14.895 1.00 77.76 C
-ATOM 934 CD GLU A 140 66.072 -8.836 -15.046 1.00 83.93 C
-ATOM 935 OE1 GLU A 140 66.635 -9.258 -13.992 1.00 83.57 O
-ATOM 936 OE2 GLU A 140 66.476 -9.095 -16.215 1.00 87.80 O
-ATOM 937 N ARG A 141 64.577 -5.119 -11.583 1.00 60.69 N
-ATOM 938 CA ARG A 141 64.200 -4.829 -10.219 1.00 61.61 C
-ATOM 939 C ARG A 141 63.626 -3.422 -10.095 1.00 61.77 C
-ATOM 940 O ARG A 141 63.727 -2.827 -9.040 1.00 65.58 O
-ATOM 941 CB ARG A 141 65.403 -5.025 -9.261 1.00 62.05 C
-ATOM 942 CG ARG A 141 66.546 -4.001 -9.347 1.00 71.25 C
-ATOM 943 CD ARG A 141 67.712 -4.228 -8.310 1.00 74.98 C
-ATOM 944 NE ARG A 141 68.930 -4.861 -8.877 1.00 80.88 N
-ATOM 945 CZ ARG A 141 70.143 -4.285 -8.976 1.00 82.05 C
-ATOM 946 NH1 ARG A 141 70.331 -3.043 -8.548 1.00 85.40 N
-ATOM 947 NH2 ARG A 141 71.186 -4.948 -9.492 1.00 77.91 N
-ATOM 948 N GLN A 142 62.987 -2.892 -11.137 1.00 59.77 N
-ATOM 949 CA GLN A 142 62.489 -1.518 -11.052 1.00 58.95 C
-ATOM 950 C GLN A 142 61.318 -1.148 -11.927 1.00 60.25 C
-ATOM 951 O GLN A 142 61.188 -0.005 -12.370 1.00 60.28 O
-ATOM 952 CB GLN A 142 63.617 -0.532 -11.354 1.00 58.24 C
-ATOM 953 CG GLN A 142 64.630 -0.383 -10.248 1.00 55.66 C
-ATOM 954 CD GLN A 142 63.986 0.056 -8.954 1.00 54.55 C
-ATOM 955 OE1 GLN A 142 64.630 0.062 -7.909 1.00 52.04 O
-ATOM 956 NE2 GLN A 142 62.702 0.429 -9.019 1.00 53.06 N
-ATOM 957 N SER A 143 60.452 -2.111 -12.167 1.00 62.06 N
-ATOM 958 CA SER A 143 59.278 -1.890 -12.999 1.00 61.40 C
-ATOM 959 C SER A 143 58.574 -0.550 -12.818 1.00 57.88 C
-ATOM 960 O SER A 143 58.358 0.157 -13.788 1.00 58.02 O
-ATOM 961 CB SER A 143 58.295 -3.025 -12.758 1.00 64.08 C
-ATOM 962 OG SER A 143 58.864 -3.917 -11.799 1.00 71.74 O
-ATOM 963 N PRO A 144 58.212 -0.182 -11.576 1.00 57.13 N
-ATOM 964 CA PRO A 144 57.517 1.076 -11.270 1.00 56.48 C
-ATOM 965 C PRO A 144 58.086 2.336 -11.899 1.00 56.14 C
-ATOM 966 O PRO A 144 57.398 3.009 -12.684 1.00 55.03 O
-ATOM 967 CB PRO A 144 57.557 1.119 -9.755 1.00 56.42 C
-ATOM 968 CG PRO A 144 57.419 -0.298 -9.407 1.00 56.09 C
-ATOM 969 CD PRO A 144 58.423 -0.941 -10.335 1.00 56.94 C
-ATOM 970 N ASN A 145 59.327 2.659 -11.541 1.00 54.85 N
-ATOM 971 CA ASN A 145 59.985 3.831 -12.090 1.00 53.47 C
-ATOM 972 C ASN A 145 60.160 3.709 -13.604 1.00 52.95 C
-ATOM 973 O ASN A 145 60.055 4.701 -14.332 1.00 54.54 O
-ATOM 974 CB ASN A 145 61.331 4.047 -11.410 1.00 55.16 C
-ATOM 975 CG ASN A 145 61.198 4.765 -10.084 1.00 55.97 C
-ATOM 976 OD1 ASN A 145 60.166 5.389 -9.803 1.00 58.87 O
-ATOM 977 ND2 ASN A 145 62.245 4.702 -9.268 1.00 53.66 N
-ATOM 978 N VAL A 146 60.429 2.501 -14.087 1.00 50.20 N
-ATOM 979 CA VAL A 146 60.550 2.310 -15.523 1.00 48.70 C
-ATOM 980 C VAL A 146 59.198 2.613 -16.195 1.00 49.97 C
-ATOM 981 O VAL A 146 59.153 3.250 -17.234 1.00 50.04 O
-ATOM 982 CB VAL A 146 60.996 0.870 -15.858 1.00 46.21 C
-ATOM 983 CG1 VAL A 146 60.894 0.619 -17.373 1.00 40.91 C
-ATOM 984 CG2 VAL A 146 62.437 0.660 -15.370 1.00 44.79 C
-ATOM 985 N PHE A 147 58.101 2.160 -15.585 1.00 52.49 N
-ATOM 986 CA PHE A 147 56.761 2.394 -16.108 1.00 52.40 C
-ATOM 987 C PHE A 147 56.484 3.889 -16.084 1.00 55.14 C
-ATOM 988 O PHE A 147 55.825 4.437 -16.983 1.00 55.78 O
-ATOM 989 CB PHE A 147 55.719 1.659 -15.256 1.00 50.27 C
-ATOM 990 CG PHE A 147 54.278 1.922 -15.678 1.00 50.78 C
-ATOM 991 CD1 PHE A 147 53.906 1.881 -17.014 1.00 47.73 C
-ATOM 992 CD2 PHE A 147 53.295 2.203 -14.727 1.00 48.14 C
-ATOM 993 CE1 PHE A 147 52.600 2.114 -17.389 1.00 47.07 C
-ATOM 994 CE2 PHE A 147 51.984 2.434 -15.101 1.00 45.47 C
-ATOM 995 CZ PHE A 147 51.638 2.391 -16.433 1.00 48.18 C
-ATOM 996 N ARG A 148 56.989 4.549 -15.045 1.00 55.98 N
-ATOM 997 CA ARG A 148 56.806 5.995 -14.901 1.00 56.32 C
-ATOM 998 C ARG A 148 57.543 6.767 -15.993 1.00 52.88 C
-ATOM 999 O ARG A 148 56.976 7.651 -16.640 1.00 51.49 O
-ATOM 1000 CB ARG A 148 57.313 6.477 -13.536 1.00 58.88 C
-ATOM 1001 CG ARG A 148 56.343 6.285 -12.398 1.00 60.17 C
-ATOM 1002 CD ARG A 148 56.851 6.942 -11.111 1.00 62.22 C
-ATOM 1003 NE ARG A 148 56.000 6.555 -9.993 1.00 62.87 N
-ATOM 1004 CZ ARG A 148 56.227 5.504 -9.213 1.00 65.31 C
-ATOM 1005 NH1 ARG A 148 57.303 4.739 -9.414 1.00 62.13 N
-ATOM 1006 NH2 ARG A 148 55.345 5.186 -8.267 1.00 64.75 N
-ATOM 1007 N MET A 149 58.814 6.444 -16.177 1.00 48.46 N
-ATOM 1008 CA MET A 149 59.586 7.134 -17.180 1.00 48.49 C
-ATOM 1009 C MET A 149 58.887 6.989 -18.517 1.00 49.87 C
-ATOM 1010 O MET A 149 58.688 7.970 -19.240 1.00 50.95 O
-ATOM 1011 CB MET A 149 60.999 6.563 -17.250 1.00 45.87 C
-ATOM 1012 CG MET A 149 61.741 6.652 -15.952 1.00 44.71 C
-ATOM 1013 SD MET A 149 63.428 6.145 -16.154 1.00 52.04 S
-ATOM 1014 CE MET A 149 63.490 4.657 -15.155 1.00 48.36 C
-ATOM 1015 N ARG A 150 58.490 5.763 -18.840 1.00 50.93 N
-ATOM 1016 CA ARG A 150 57.822 5.510 -20.102 1.00 49.46 C
-ATOM 1017 C ARG A 150 56.524 6.279 -20.176 1.00 48.16 C
-ATOM 1018 O ARG A 150 56.265 6.951 -21.154 1.00 46.64 O
-ATOM 1019 CB ARG A 150 57.610 4.010 -20.290 1.00 49.35 C
-ATOM 1020 CG ARG A 150 58.892 3.348 -20.759 1.00 53.64 C
-ATOM 1021 CD ARG A 150 58.809 1.840 -20.864 1.00 58.72 C
-ATOM 1022 NE ARG A 150 60.151 1.277 -21.033 1.00 65.73 N
-ATOM 1023 CZ ARG A 150 60.442 -0.017 -20.908 1.00 69.20 C
-ATOM 1024 NH1 ARG A 150 59.465 -0.879 -20.616 1.00 69.44 N
-ATOM 1025 NH2 ARG A 150 61.705 -0.446 -21.048 1.00 65.89 N
-ATOM 1026 N LEU A 151 55.728 6.205 -19.119 1.00 48.10 N
-ATOM 1027 CA LEU A 151 54.457 6.913 -19.055 1.00 48.83 C
-ATOM 1028 C LEU A 151 54.652 8.394 -19.395 1.00 51.31 C
-ATOM 1029 O LEU A 151 53.835 9.030 -20.084 1.00 50.80 O
-ATOM 1030 CB LEU A 151 53.913 6.767 -17.649 1.00 46.72 C
-ATOM 1031 CG LEU A 151 52.485 6.282 -17.457 1.00 49.67 C
-ATOM 1032 CD1 LEU A 151 51.996 5.358 -18.563 1.00 46.19 C
-ATOM 1033 CD2 LEU A 151 52.486 5.574 -16.125 1.00 50.76 C
-ATOM 1034 N MET A 152 55.764 8.926 -18.898 1.00 54.15 N
-ATOM 1035 CA MET A 152 56.145 10.316 -19.086 1.00 54.61 C
-ATOM 1036 C MET A 152 56.643 10.557 -20.511 1.00 54.06 C
-ATOM 1037 O MET A 152 56.962 11.674 -20.904 1.00 56.84 O
-ATOM 1038 CB MET A 152 57.226 10.676 -18.071 1.00 55.93 C
-ATOM 1039 CG MET A 152 56.932 11.928 -17.280 1.00 57.91 C
-ATOM 1040 SD MET A 152 56.792 11.579 -15.529 1.00 59.04 S
-ATOM 1041 CE MET A 152 58.450 11.088 -15.131 1.00 55.03 C
-ATOM 1042 N GLY A 153 56.742 9.500 -21.290 1.00 52.05 N
-ATOM 1043 CA GLY A 153 57.162 9.691 -22.657 1.00 48.08 C
-ATOM 1044 C GLY A 153 58.624 9.509 -22.919 1.00 47.34 C
-ATOM 1045 O GLY A 153 59.048 9.693 -24.042 1.00 47.45 O
-ATOM 1046 N ALA A 154 59.408 9.159 -21.909 1.00 48.51 N
-ATOM 1047 CA ALA A 154 60.835 8.981 -22.139 1.00 47.72 C
-ATOM 1048 C ALA A 154 61.006 7.602 -22.697 1.00 49.69 C
-ATOM 1049 O ALA A 154 60.067 6.813 -22.715 1.00 53.13 O
-ATOM 1050 CB ALA A 154 61.627 9.123 -20.857 1.00 43.66 C
-ATOM 1051 N GLU A 155 62.215 7.326 -23.150 1.00 51.61 N
-ATOM 1052 CA GLU A 155 62.576 6.059 -23.738 1.00 52.95 C
-ATOM 1053 C GLU A 155 63.634 5.435 -22.840 1.00 53.85 C
-ATOM 1054 O GLU A 155 64.684 6.039 -22.619 1.00 56.14 O
-ATOM 1055 CB GLU A 155 63.127 6.324 -25.130 1.00 53.61 C
-ATOM 1056 CG GLU A 155 63.742 5.138 -25.776 1.00 63.31 C
-ATOM 1057 CD GLU A 155 64.307 5.464 -27.137 1.00 68.73 C
-ATOM 1058 OE1 GLU A 155 65.089 6.446 -27.244 1.00 70.54 O
-ATOM 1059 OE2 GLU A 155 63.969 4.734 -28.103 1.00 74.48 O
-ATOM 1060 N VAL A 156 63.367 4.237 -22.322 1.00 53.99 N
-ATOM 1061 CA VAL A 156 64.311 3.563 -21.426 1.00 53.44 C
-ATOM 1062 C VAL A 156 65.137 2.519 -22.153 1.00 53.00 C
-ATOM 1063 O VAL A 156 64.629 1.496 -22.543 1.00 56.37 O
-ATOM 1064 CB VAL A 156 63.598 2.829 -20.254 1.00 53.25 C
-ATOM 1065 CG1 VAL A 156 64.641 2.365 -19.250 1.00 54.90 C
-ATOM 1066 CG2 VAL A 156 62.568 3.728 -19.574 1.00 50.42 C
-ATOM 1067 N ILE A 157 66.424 2.764 -22.300 1.00 52.26 N
-ATOM 1068 CA ILE A 157 67.314 1.837 -22.989 1.00 49.13 C
-ATOM 1069 C ILE A 157 68.007 0.934 -21.971 1.00 49.48 C
-ATOM 1070 O ILE A 157 68.807 1.398 -21.166 1.00 47.65 O
-ATOM 1071 CB ILE A 157 68.379 2.633 -23.766 1.00 47.79 C
-ATOM 1072 CG1 ILE A 157 67.688 3.502 -24.809 1.00 43.99 C
-ATOM 1073 CG2 ILE A 157 69.414 1.718 -24.348 1.00 41.35 C
-ATOM 1074 CD1 ILE A 157 68.607 4.461 -25.427 1.00 46.06 C
-ATOM 1075 N PRO A 158 67.693 -0.371 -21.977 1.00 50.07 N
-ATOM 1076 CA PRO A 158 68.361 -1.239 -21.004 1.00 48.36 C
-ATOM 1077 C PRO A 158 69.780 -1.503 -21.464 1.00 48.52 C
-ATOM 1078 O PRO A 158 70.079 -1.457 -22.653 1.00 51.27 O
-ATOM 1079 CB PRO A 158 67.496 -2.494 -21.005 1.00 46.68 C
-ATOM 1080 CG PRO A 158 67.037 -2.569 -22.418 1.00 48.18 C
-ATOM 1081 CD PRO A 158 66.685 -1.120 -22.748 1.00 49.12 C
-ATOM 1082 N VAL A 159 70.664 -1.766 -20.522 1.00 48.63 N
-ATOM 1083 CA VAL A 159 72.038 -2.031 -20.866 1.00 47.27 C
-ATOM 1084 C VAL A 159 72.456 -3.369 -20.301 1.00 51.16 C
-ATOM 1085 O VAL A 159 72.329 -3.602 -19.107 1.00 51.72 O
-ATOM 1086 CB VAL A 159 72.940 -0.987 -20.289 1.00 44.16 C
-ATOM 1087 CG1 VAL A 159 74.360 -1.264 -20.723 1.00 44.75 C
-ATOM 1088 CG2 VAL A 159 72.472 0.380 -20.694 1.00 39.97 C
-ATOM 1089 N HIS A 160 72.950 -4.254 -21.161 1.00 55.36 N
-ATOM 1090 CA HIS A 160 73.394 -5.566 -20.708 1.00 56.28 C
-ATOM 1091 C HIS A 160 74.901 -5.737 -20.756 1.00 57.26 C
-ATOM 1092 O HIS A 160 75.406 -6.725 -20.241 1.00 59.94 O
-ATOM 1093 CB HIS A 160 72.782 -6.687 -21.539 1.00 53.93 C
-ATOM 1094 CG HIS A 160 71.297 -6.682 -21.557 1.00 54.34 C
-ATOM 1095 ND1 HIS A 160 70.574 -5.782 -22.304 1.00 56.63 N
-ATOM 1096 CD2 HIS A 160 70.391 -7.486 -20.950 1.00 55.41 C
-ATOM 1097 CE1 HIS A 160 69.284 -6.035 -22.163 1.00 57.79 C
-ATOM 1098 NE2 HIS A 160 69.145 -7.063 -21.346 1.00 54.27 N
-ATOM 1099 N SER A 161 75.625 -4.814 -21.378 1.00 57.02 N
-ATOM 1100 CA SER A 161 77.070 -4.972 -21.442 1.00 59.63 C
-ATOM 1101 C SER A 161 77.620 -4.868 -20.031 1.00 61.07 C
-ATOM 1102 O SER A 161 76.895 -4.474 -19.118 1.00 63.84 O
-ATOM 1103 CB SER A 161 77.700 -3.911 -22.356 1.00 62.63 C
-ATOM 1104 OG SER A 161 77.388 -2.584 -21.954 1.00 69.49 O
-ATOM 1105 N GLY A 162 78.885 -5.241 -19.843 1.00 61.74 N
-ATOM 1106 CA GLY A 162 79.489 -5.184 -18.525 1.00 61.11 C
-ATOM 1107 C GLY A 162 78.619 -5.796 -17.434 1.00 62.45 C
-ATOM 1108 O GLY A 162 77.911 -6.777 -17.655 1.00 61.38 O
-ATOM 1109 N SER A 163 78.678 -5.208 -16.246 1.00 63.68 N
-ATOM 1110 CA SER A 163 77.906 -5.676 -15.102 1.00 64.46 C
-ATOM 1111 C SER A 163 76.384 -5.568 -15.262 1.00 63.98 C
-ATOM 1112 O SER A 163 75.629 -6.099 -14.437 1.00 60.36 O
-ATOM 1113 CB SER A 163 78.321 -4.885 -13.865 1.00 66.40 C
-ATOM 1114 OG SER A 163 77.469 -5.199 -12.777 1.00 71.79 O
-ATOM 1115 N ALA A 164 75.943 -4.872 -16.310 1.00 63.90 N
-ATOM 1116 CA ALA A 164 74.521 -4.664 -16.570 1.00 64.03 C
-ATOM 1117 C ALA A 164 73.930 -3.889 -15.419 1.00 65.23 C
-ATOM 1118 O ALA A 164 72.853 -4.221 -14.906 1.00 64.22 O
-ATOM 1119 CB ALA A 164 73.797 -5.972 -16.710 1.00 65.28 C
-ATOM 1120 N THR A 165 74.649 -2.851 -15.017 1.00 65.10 N
-ATOM 1121 CA THR A 165 74.208 -2.009 -13.925 1.00 66.70 C
-ATOM 1122 C THR A 165 74.591 -0.552 -14.149 1.00 65.70 C
-ATOM 1123 O THR A 165 75.086 -0.180 -15.211 1.00 64.21 O
-ATOM 1124 CB THR A 165 74.791 -2.477 -12.579 1.00 67.09 C
-ATOM 1125 OG1 THR A 165 76.224 -2.536 -12.662 1.00 70.16 O
-ATOM 1126 CG2 THR A 165 74.248 -3.832 -12.232 1.00 68.17 C
-ATOM 1127 N LEU A 166 74.371 0.257 -13.120 1.00 64.26 N
-ATOM 1128 CA LEU A 166 74.641 1.669 -13.191 1.00 61.67 C
-ATOM 1129 C LEU A 166 75.930 2.084 -13.892 1.00 62.08 C
-ATOM 1130 O LEU A 166 75.873 2.849 -14.858 1.00 61.93 O
-ATOM 1131 CB LEU A 166 74.589 2.279 -11.796 1.00 57.00 C
-ATOM 1132 CG LEU A 166 74.342 3.777 -11.907 1.00 53.33 C
-ATOM 1133 CD1 LEU A 166 72.989 4.080 -12.525 1.00 50.04 C
-ATOM 1134 CD2 LEU A 166 74.416 4.345 -10.555 1.00 52.62 C
-ATOM 1135 N LYS A 167 77.085 1.606 -13.432 1.00 61.72 N
-ATOM 1136 CA LYS A 167 78.328 2.022 -14.078 1.00 62.35 C
-ATOM 1137 C LYS A 167 78.236 1.743 -15.575 1.00 61.56 C
-ATOM 1138 O LYS A 167 78.745 2.493 -16.397 1.00 61.70 O
-ATOM 1139 CB LYS A 167 79.551 1.338 -13.448 1.00 62.67 C
-ATOM 1140 CG LYS A 167 79.408 -0.159 -13.167 1.00 71.96 C
-ATOM 1141 CD LYS A 167 79.086 -0.499 -11.685 1.00 75.18 C
-ATOM 1142 CE LYS A 167 77.610 -0.260 -11.316 1.00 76.94 C
-ATOM 1143 NZ LYS A 167 77.307 -0.560 -9.876 1.00 76.71 N
-ATOM 1144 N ASP A 168 77.543 0.678 -15.934 1.00 60.58 N
-ATOM 1145 CA ASP A 168 77.378 0.349 -17.336 1.00 60.65 C
-ATOM 1146 C ASP A 168 76.447 1.342 -18.034 1.00 60.19 C
-ATOM 1147 O ASP A 168 76.809 1.934 -19.055 1.00 60.17 O
-ATOM 1148 CB ASP A 168 76.824 -1.065 -17.460 1.00 62.54 C
-ATOM 1149 CG ASP A 168 77.767 -2.092 -16.901 1.00 65.21 C
-ATOM 1150 OD1 ASP A 168 78.821 -2.302 -17.541 1.00 65.37 O
-ATOM 1151 OD2 ASP A 168 77.468 -2.668 -15.826 1.00 64.98 O
-ATOM 1152 N ALA A 169 75.249 1.518 -17.484 1.00 58.37 N
-ATOM 1153 CA ALA A 169 74.277 2.429 -18.058 1.00 57.03 C
-ATOM 1154 C ALA A 169 74.898 3.802 -18.130 1.00 57.54 C
-ATOM 1155 O ALA A 169 74.631 4.572 -19.046 1.00 57.83 O
-ATOM 1156 CB ALA A 169 73.033 2.469 -17.212 1.00 57.84 C
-ATOM 1157 N CYS A 170 75.753 4.099 -17.167 1.00 57.96 N
-ATOM 1158 CA CYS A 170 76.414 5.386 -17.122 1.00 60.24 C
-ATOM 1159 C CYS A 170 77.466 5.534 -18.221 1.00 59.41 C
-ATOM 1160 O CYS A 170 77.523 6.538 -18.925 1.00 58.38 O
-ATOM 1161 CB CYS A 170 77.057 5.566 -15.760 1.00 62.38 C
-ATOM 1162 SG CYS A 170 77.555 7.257 -15.476 1.00 75.35 S
-ATOM 1163 N ASN A 171 78.306 4.521 -18.355 1.00 60.62 N
-ATOM 1164 CA ASN A 171 79.347 4.516 -19.368 1.00 60.69 C
-ATOM 1165 C ASN A 171 78.720 4.602 -20.747 1.00 59.38 C
-ATOM 1166 O ASN A 171 79.270 5.218 -21.656 1.00 56.76 O
-ATOM 1167 CB ASN A 171 80.162 3.229 -19.253 1.00 64.95 C
-ATOM 1168 CG ASN A 171 80.826 2.844 -20.561 1.00 71.53 C
-ATOM 1169 OD1 ASN A 171 81.916 3.327 -20.886 1.00 74.24 O
-ATOM 1170 ND2 ASN A 171 80.159 1.973 -21.336 1.00 75.04 N
-ATOM 1171 N GLU A 172 77.560 3.973 -20.890 1.00 59.52 N
-ATOM 1172 CA GLU A 172 76.843 3.948 -22.150 1.00 61.28 C
-ATOM 1173 C GLU A 172 76.227 5.297 -22.511 1.00 60.89 C
-ATOM 1174 O GLU A 172 76.291 5.719 -23.662 1.00 60.27 O
-ATOM 1175 CB GLU A 172 75.772 2.869 -22.088 1.00 65.87 C
-ATOM 1176 CG GLU A 172 75.667 2.021 -23.352 1.00 74.78 C
-ATOM 1177 CD GLU A 172 77.033 1.608 -23.933 1.00 80.93 C
-ATOM 1178 OE1 GLU A 172 77.863 0.987 -23.204 1.00 80.79 O
-ATOM 1179 OE2 GLU A 172 77.260 1.912 -25.140 1.00 83.75 O
-ATOM 1180 N ALA A 173 75.629 5.974 -21.531 1.00 60.87 N
-ATOM 1181 CA ALA A 173 75.028 7.292 -21.764 1.00 59.87 C
-ATOM 1182 C ALA A 173 76.116 8.240 -22.218 1.00 59.86 C
-ATOM 1183 O ALA A 173 75.956 8.969 -23.193 1.00 59.94 O
-ATOM 1184 CB ALA A 173 74.395 7.828 -20.494 1.00 57.99 C
-ATOM 1185 N LEU A 174 77.224 8.226 -21.489 1.00 60.26 N
-ATOM 1186 CA LEU A 174 78.351 9.072 -21.816 1.00 61.22 C
-ATOM 1187 C LEU A 174 78.804 8.852 -23.265 1.00 61.55 C
-ATOM 1188 O LEU A 174 79.012 9.824 -24.002 1.00 63.41 O
-ATOM 1189 CB LEU A 174 79.502 8.807 -20.843 1.00 62.63 C
-ATOM 1190 CG LEU A 174 80.266 10.064 -20.397 1.00 65.64 C
-ATOM 1191 CD1 LEU A 174 79.268 11.101 -19.826 1.00 64.42 C
-ATOM 1192 CD2 LEU A 174 81.321 9.690 -19.366 1.00 61.54 C
-ATOM 1193 N ARG A 175 78.951 7.595 -23.687 1.00 60.06 N
-ATOM 1194 CA ARG A 175 79.360 7.318 -25.066 1.00 57.52 C
-ATOM 1195 C ARG A 175 78.363 7.927 -26.013 1.00 55.42 C
-ATOM 1196 O ARG A 175 78.739 8.500 -27.021 1.00 53.14 O
-ATOM 1197 CB ARG A 175 79.438 5.825 -25.329 1.00 60.47 C
-ATOM 1198 CG ARG A 175 80.605 5.169 -24.643 1.00 66.12 C
-ATOM 1199 CD ARG A 175 80.510 3.680 -24.763 1.00 70.43 C
-ATOM 1200 NE ARG A 175 80.502 3.269 -26.159 1.00 77.95 N
-ATOM 1201 CZ ARG A 175 80.135 2.056 -26.563 1.00 82.79 C
-ATOM 1202 NH1 ARG A 175 79.745 1.154 -25.664 1.00 83.98 N
-ATOM 1203 NH2 ARG A 175 80.167 1.738 -27.856 1.00 85.11 N
-ATOM 1204 N ASP A 176 77.083 7.794 -25.674 1.00 54.91 N
-ATOM 1205 CA ASP A 176 76.014 8.353 -26.486 1.00 52.10 C
-ATOM 1206 C ASP A 176 76.210 9.863 -26.576 1.00 53.09 C
-ATOM 1207 O ASP A 176 76.283 10.425 -27.666 1.00 54.43 O
-ATOM 1208 CB ASP A 176 74.648 8.055 -25.862 1.00 48.22 C
-ATOM 1209 CG ASP A 176 73.488 8.589 -26.701 1.00 49.58 C
-ATOM 1210 OD1 ASP A 176 73.736 9.339 -27.664 1.00 49.06 O
-ATOM 1211 OD2 ASP A 176 72.319 8.272 -26.405 1.00 46.50 O
-ATOM 1212 N TRP A 177 76.321 10.526 -25.435 1.00 53.49 N
-ATOM 1213 CA TRP A 177 76.466 11.968 -25.463 1.00 54.69 C
-ATOM 1214 C TRP A 177 77.605 12.401 -26.317 1.00 54.72 C
-ATOM 1215 O TRP A 177 77.441 13.262 -27.181 1.00 55.63 O
-ATOM 1216 CB TRP A 177 76.681 12.532 -24.075 1.00 55.47 C
-ATOM 1217 CG TRP A 177 76.718 14.027 -24.028 1.00 55.71 C
-ATOM 1218 CD1 TRP A 177 75.841 14.895 -24.626 1.00 57.49 C
-ATOM 1219 CD2 TRP A 177 77.597 14.830 -23.234 1.00 56.81 C
-ATOM 1220 NE1 TRP A 177 76.116 16.196 -24.239 1.00 58.60 N
-ATOM 1221 CE2 TRP A 177 77.190 16.179 -23.386 1.00 58.32 C
-ATOM 1222 CE3 TRP A 177 78.692 14.541 -22.402 1.00 57.78 C
-ATOM 1223 CZ2 TRP A 177 77.838 17.229 -22.737 1.00 58.42 C
-ATOM 1224 CZ3 TRP A 177 79.336 15.587 -21.757 1.00 56.32 C
-ATOM 1225 CH2 TRP A 177 78.906 16.915 -21.929 1.00 58.90 C
-ATOM 1226 N SER A 178 78.758 11.790 -26.073 1.00 54.71 N
-ATOM 1227 CA SER A 178 79.982 12.135 -26.785 1.00 54.54 C
-ATOM 1228 C SER A 178 79.862 12.011 -28.268 1.00 51.91 C
-ATOM 1229 O SER A 178 80.847 12.081 -28.961 1.00 54.49 O
-ATOM 1230 CB SER A 178 81.140 11.259 -26.333 1.00 56.33 C
-ATOM 1231 OG SER A 178 80.961 9.949 -26.813 1.00 58.84 O
-ATOM 1232 N GLY A 179 78.658 11.804 -28.758 1.00 51.04 N
-ATOM 1233 CA GLY A 179 78.484 11.694 -30.180 1.00 49.81 C
-ATOM 1234 C GLY A 179 77.251 12.470 -30.531 1.00 52.83 C
-ATOM 1235 O GLY A 179 76.872 12.536 -31.694 1.00 54.04 O
-ATOM 1236 N SER A 180 76.608 13.063 -29.528 1.00 55.08 N
-ATOM 1237 CA SER A 180 75.398 13.825 -29.803 1.00 58.05 C
-ATOM 1238 C SER A 180 75.197 15.103 -29.015 1.00 58.95 C
-ATOM 1239 O SER A 180 74.094 15.670 -29.025 1.00 58.59 O
-ATOM 1240 CB SER A 180 74.158 12.929 -29.659 1.00 58.33 C
-ATOM 1241 OG SER A 180 74.237 12.095 -28.521 1.00 56.39 O
-ATOM 1242 N TYR A 181 76.253 15.578 -28.361 1.00 60.70 N
-ATOM 1243 CA TYR A 181 76.151 16.814 -27.581 1.00 63.26 C
-ATOM 1244 C TYR A 181 75.662 18.014 -28.385 1.00 62.26 C
-ATOM 1245 O TYR A 181 75.203 18.993 -27.820 1.00 62.73 O
-ATOM 1246 CB TYR A 181 77.482 17.168 -26.935 1.00 63.33 C
-ATOM 1247 CG TYR A 181 78.638 17.366 -27.895 1.00 67.59 C
-ATOM 1248 CD1 TYR A 181 79.604 16.379 -28.041 1.00 70.23 C
-ATOM 1249 CD2 TYR A 181 78.846 18.589 -28.542 1.00 67.60 C
-ATOM 1250 CE1 TYR A 181 80.756 16.601 -28.783 1.00 72.87 C
-ATOM 1251 CE2 TYR A 181 79.998 18.825 -29.285 1.00 68.93 C
-ATOM 1252 CZ TYR A 181 80.954 17.824 -29.394 1.00 72.14 C
-ATOM 1253 OH TYR A 181 82.142 18.028 -30.060 1.00 73.66 O
-ATOM 1254 N GLU A 182 75.768 17.940 -29.700 1.00 61.76 N
-ATOM 1255 CA GLU A 182 75.311 19.022 -30.544 1.00 62.62 C
-ATOM 1256 C GLU A 182 73.807 19.270 -30.346 1.00 61.35 C
-ATOM 1257 O GLU A 182 73.347 20.398 -30.446 1.00 60.73 O
-ATOM 1258 CB GLU A 182 75.619 18.670 -31.998 1.00 67.94 C
-ATOM 1259 CG GLU A 182 75.461 19.786 -33.029 1.00 75.28 C
-ATOM 1260 CD GLU A 182 76.204 19.466 -34.342 1.00 83.01 C
-ATOM 1261 OE1 GLU A 182 77.469 19.423 -34.334 1.00 83.34 O
-ATOM 1262 OE2 GLU A 182 75.526 19.243 -35.380 1.00 86.01 O
-ATOM 1263 N THR A 183 73.035 18.231 -30.045 1.00 61.08 N
-ATOM 1264 CA THR A 183 71.588 18.412 -29.861 1.00 59.74 C
-ATOM 1265 C THR A 183 71.044 17.850 -28.567 1.00 58.29 C
-ATOM 1266 O THR A 183 69.857 18.018 -28.239 1.00 57.54 O
-ATOM 1267 CB THR A 183 70.774 17.745 -30.976 1.00 59.12 C
-ATOM 1268 OG1 THR A 183 71.554 16.702 -31.581 1.00 54.00 O
-ATOM 1269 CG2 THR A 183 70.312 18.780 -31.983 1.00 58.66 C
-ATOM 1270 N ALA A 184 71.902 17.178 -27.825 1.00 54.30 N
-ATOM 1271 CA ALA A 184 71.424 16.591 -26.608 1.00 52.71 C
-ATOM 1272 C ALA A 184 72.282 16.933 -25.433 1.00 50.97 C
-ATOM 1273 O ALA A 184 73.507 16.898 -25.506 1.00 49.86 O
-ATOM 1274 CB ALA A 184 71.334 15.090 -26.771 1.00 54.07 C
-ATOM 1275 N HIS A 185 71.619 17.291 -24.343 1.00 51.73 N
-ATOM 1276 CA HIS A 185 72.318 17.607 -23.119 1.00 52.01 C
-ATOM 1277 C HIS A 185 72.327 16.331 -22.272 1.00 51.68 C
-ATOM 1278 O HIS A 185 71.369 15.557 -22.231 1.00 50.21 O
-ATOM 1279 CB HIS A 185 71.642 18.766 -22.365 1.00 50.96 C
-ATOM 1280 CG HIS A 185 72.140 18.935 -20.959 1.00 54.00 C
-ATOM 1281 ND1 HIS A 185 73.420 19.357 -20.667 1.00 56.01 N
-ATOM 1282 CD2 HIS A 185 71.558 18.653 -19.767 1.00 54.60 C
-ATOM 1283 CE1 HIS A 185 73.608 19.324 -19.358 1.00 55.09 C
-ATOM 1284 NE2 HIS A 185 72.493 18.900 -18.789 1.00 56.57 N
-ATOM 1285 N TYR A 186 73.453 16.096 -21.633 1.00 52.99 N
-ATOM 1286 CA TYR A 186 73.592 14.948 -20.784 1.00 54.07 C
-ATOM 1287 C TYR A 186 73.207 15.413 -19.364 1.00 55.69 C
-ATOM 1288 O TYR A 186 73.826 16.317 -18.799 1.00 56.48 O
-ATOM 1289 CB TYR A 186 75.036 14.468 -20.862 1.00 52.55 C
-ATOM 1290 CG TYR A 186 75.349 13.368 -19.914 1.00 53.59 C
-ATOM 1291 CD1 TYR A 186 76.524 13.384 -19.191 1.00 58.52 C
-ATOM 1292 CD2 TYR A 186 74.455 12.333 -19.697 1.00 53.70 C
-ATOM 1293 CE1 TYR A 186 76.807 12.405 -18.265 1.00 60.85 C
-ATOM 1294 CE2 TYR A 186 74.729 11.340 -18.767 1.00 57.66 C
-ATOM 1295 CZ TYR A 186 75.911 11.387 -18.052 1.00 59.56 C
-ATOM 1296 OH TYR A 186 76.211 10.436 -17.109 1.00 61.72 O
-ATOM 1297 N MET A 187 72.160 14.808 -18.813 1.00 56.35 N
-ATOM 1298 CA MET A 187 71.662 15.131 -17.484 1.00 57.79 C
-ATOM 1299 C MET A 187 72.436 14.375 -16.423 1.00 60.37 C
-ATOM 1300 O MET A 187 72.267 13.166 -16.264 1.00 62.82 O
-ATOM 1301 CB MET A 187 70.202 14.730 -17.368 1.00 59.25 C
-ATOM 1302 CG MET A 187 69.488 15.329 -16.199 1.00 60.96 C
-ATOM 1303 SD MET A 187 69.010 16.991 -16.640 1.00 67.40 S
-ATOM 1304 CE MET A 187 67.412 16.687 -17.423 1.00 57.53 C
-ATOM 1305 N LEU A 188 73.275 15.078 -15.682 1.00 63.26 N
-ATOM 1306 CA LEU A 188 74.041 14.426 -14.643 1.00 66.37 C
-ATOM 1307 C LEU A 188 73.250 14.308 -13.326 1.00 68.79 C
-ATOM 1308 O LEU A 188 72.594 15.258 -12.887 1.00 66.05 O
-ATOM 1309 CB LEU A 188 75.341 15.180 -14.400 1.00 67.54 C
-ATOM 1310 CG LEU A 188 76.344 14.211 -13.795 1.00 69.13 C
-ATOM 1311 CD1 LEU A 188 76.805 13.271 -14.912 1.00 69.44 C
-ATOM 1312 CD2 LEU A 188 77.499 14.949 -13.162 1.00 69.39 C
-ATOM 1313 N GLY A 189 73.321 13.126 -12.710 1.00 72.63 N
-ATOM 1314 CA GLY A 189 72.622 12.879 -11.461 1.00 78.04 C
-ATOM 1315 C GLY A 189 73.494 13.228 -10.267 1.00 82.37 C
-ATOM 1316 O GLY A 189 73.085 13.958 -9.357 1.00 84.42 O
-ATOM 1317 N THR A 190 74.711 12.703 -10.270 1.00 83.56 N
-ATOM 1318 CA THR A 190 75.648 12.953 -9.191 1.00 84.77 C
-ATOM 1319 C THR A 190 76.227 14.360 -9.377 1.00 87.44 C
-ATOM 1320 O THR A 190 75.978 15.015 -10.407 1.00 87.44 O
-ATOM 1321 CB THR A 190 76.796 11.914 -9.232 1.00 84.30 C
-ATOM 1322 OG1 THR A 190 77.643 12.076 -8.086 1.00 86.30 O
-ATOM 1323 CG2 THR A 190 77.628 12.084 -10.511 1.00 81.25 C
-ATOM 1324 N ALA A 191 76.983 14.818 -8.370 1.00 88.36 N
-ATOM 1325 CA ALA A 191 77.657 16.129 -8.386 1.00 86.76 C
-ATOM 1326 C ALA A 191 79.109 15.869 -8.787 1.00 84.87 C
-ATOM 1327 O ALA A 191 79.906 16.799 -8.945 1.00 85.30 O
-ATOM 1328 CB ALA A 191 77.607 16.784 -6.989 1.00 85.03 C
-ATOM 1329 N ALA A 192 79.420 14.584 -8.959 1.00 82.17 N
-ATOM 1330 CA ALA A 192 80.756 14.122 -9.307 1.00 79.59 C
-ATOM 1331 C ALA A 192 80.923 13.820 -10.789 1.00 78.12 C
-ATOM 1332 O ALA A 192 80.730 12.685 -11.233 1.00 79.23 O
-ATOM 1333 CB ALA A 192 81.090 12.880 -8.485 1.00 78.80 C
-ATOM 1334 N GLY A 193 81.293 14.834 -11.557 1.00 75.20 N
-ATOM 1335 CA GLY A 193 81.482 14.620 -12.976 1.00 73.03 C
-ATOM 1336 C GLY A 193 82.513 15.588 -13.491 1.00 72.34 C
-ATOM 1337 O GLY A 193 83.088 16.334 -12.698 1.00 73.64 O
-ATOM 1338 N PRO A 194 82.770 15.616 -14.806 1.00 70.69 N
-ATOM 1339 CA PRO A 194 83.766 16.549 -15.330 1.00 69.29 C
-ATOM 1340 C PRO A 194 83.246 17.981 -15.193 1.00 68.93 C
-ATOM 1341 O PRO A 194 82.037 18.194 -15.035 1.00 69.27 O
-ATOM 1342 CB PRO A 194 83.868 16.137 -16.786 1.00 69.13 C
-ATOM 1343 CG PRO A 194 82.429 15.842 -17.113 1.00 70.38 C
-ATOM 1344 CD PRO A 194 81.997 15.010 -15.906 1.00 70.70 C
-ATOM 1345 N HIS A 195 84.160 18.950 -15.256 1.00 66.98 N
-ATOM 1346 CA HIS A 195 83.816 20.376 -15.188 1.00 62.37 C
-ATOM 1347 C HIS A 195 83.042 20.661 -16.466 1.00 60.95 C
-ATOM 1348 O HIS A 195 83.359 20.118 -17.519 1.00 62.44 O
-ATOM 1349 CB HIS A 195 85.092 21.217 -15.163 1.00 61.15 C
-ATOM 1350 CG HIS A 195 84.867 22.674 -14.911 1.00 62.14 C
-ATOM 1351 ND1 HIS A 195 84.512 23.170 -13.674 1.00 62.84 N
-ATOM 1352 CD2 HIS A 195 84.943 23.744 -15.739 1.00 59.87 C
-ATOM 1353 CE1 HIS A 195 84.378 24.483 -13.753 1.00 62.54 C
-ATOM 1354 NE2 HIS A 195 84.633 24.856 -14.995 1.00 61.18 N
-ATOM 1355 N PRO A 196 82.049 21.546 -16.409 1.00 59.36 N
-ATOM 1356 CA PRO A 196 81.597 22.304 -15.249 1.00 59.97 C
-ATOM 1357 C PRO A 196 80.479 21.666 -14.420 1.00 62.54 C
-ATOM 1358 O PRO A 196 79.829 22.342 -13.629 1.00 65.01 O
-ATOM 1359 CB PRO A 196 81.159 23.603 -15.888 1.00 57.52 C
-ATOM 1360 CG PRO A 196 80.508 23.120 -17.121 1.00 55.99 C
-ATOM 1361 CD PRO A 196 81.477 22.106 -17.645 1.00 57.13 C
-ATOM 1362 N TYR A 197 80.261 20.367 -14.564 1.00 64.32 N
-ATOM 1363 CA TYR A 197 79.169 19.719 -13.831 1.00 63.59 C
-ATOM 1364 C TYR A 197 79.074 19.954 -12.319 1.00 64.13 C
-ATOM 1365 O TYR A 197 78.076 20.495 -11.832 1.00 65.40 O
-ATOM 1366 CB TYR A 197 79.133 18.215 -14.161 1.00 59.66 C
-ATOM 1367 CG TYR A 197 78.413 17.941 -15.477 1.00 58.40 C
-ATOM 1368 CD1 TYR A 197 77.043 18.142 -15.590 1.00 54.21 C
-ATOM 1369 CD2 TYR A 197 79.107 17.552 -16.619 1.00 58.44 C
-ATOM 1370 CE1 TYR A 197 76.381 17.973 -16.783 1.00 52.90 C
-ATOM 1371 CE2 TYR A 197 78.443 17.380 -17.830 1.00 56.94 C
-ATOM 1372 CZ TYR A 197 77.077 17.595 -17.897 1.00 55.86 C
-ATOM 1373 OH TYR A 197 76.395 17.425 -19.085 1.00 59.61 O
-ATOM 1374 N PRO A 198 80.109 19.588 -11.557 1.00 63.85 N
-ATOM 1375 CA PRO A 198 79.971 19.822 -10.122 1.00 62.00 C
-ATOM 1376 C PRO A 198 79.521 21.234 -9.772 1.00 60.79 C
-ATOM 1377 O PRO A 198 78.863 21.431 -8.760 1.00 63.14 O
-ATOM 1378 CB PRO A 198 81.355 19.480 -9.584 1.00 61.53 C
-ATOM 1379 CG PRO A 198 82.233 19.864 -10.693 1.00 64.29 C
-ATOM 1380 CD PRO A 198 81.509 19.303 -11.898 1.00 64.35 C
-ATOM 1381 N THR A 199 79.857 22.223 -10.590 1.00 58.44 N
-ATOM 1382 CA THR A 199 79.422 23.585 -10.278 1.00 57.34 C
-ATOM 1383 C THR A 199 77.933 23.717 -10.508 1.00 57.53 C
-ATOM 1384 O THR A 199 77.179 24.091 -9.616 1.00 57.81 O
-ATOM 1385 CB THR A 199 80.095 24.618 -11.160 1.00 56.32 C
-ATOM 1386 OG1 THR A 199 81.491 24.628 -10.877 1.00 60.82 O
-ATOM 1387 CG2 THR A 199 79.509 26.003 -10.907 1.00 54.86 C
-ATOM 1388 N ILE A 200 77.528 23.429 -11.735 1.00 56.81 N
-ATOM 1389 CA ILE A 200 76.139 23.496 -12.120 1.00 56.09 C
-ATOM 1390 C ILE A 200 75.294 22.747 -11.096 1.00 55.69 C
-ATOM 1391 O ILE A 200 74.279 23.246 -10.592 1.00 52.74 O
-ATOM 1392 CB ILE A 200 75.970 22.871 -13.488 1.00 57.26 C
-ATOM 1393 CG1 ILE A 200 76.795 23.669 -14.501 1.00 59.23 C
-ATOM 1394 CG2 ILE A 200 74.505 22.831 -13.857 1.00 56.22 C
-ATOM 1395 CD1 ILE A 200 76.855 23.046 -15.878 1.00 61.50 C
-ATOM 1396 N VAL A 201 75.731 21.543 -10.771 1.00 55.13 N
-ATOM 1397 CA VAL A 201 75.001 20.758 -9.807 1.00 56.75 C
-ATOM 1398 C VAL A 201 74.963 21.426 -8.441 1.00 57.25 C
-ATOM 1399 O VAL A 201 73.894 21.569 -7.868 1.00 60.48 O
-ATOM 1400 CB VAL A 201 75.588 19.350 -9.691 1.00 57.85 C
-ATOM 1401 CG1 VAL A 201 75.088 18.677 -8.411 1.00 56.40 C
-ATOM 1402 CG2 VAL A 201 75.183 18.534 -10.935 1.00 58.45 C
-ATOM 1403 N ARG A 202 76.111 21.843 -7.915 1.00 57.23 N
-ATOM 1404 CA ARG A 202 76.124 22.491 -6.611 1.00 55.81 C
-ATOM 1405 C ARG A 202 75.229 23.701 -6.674 1.00 54.52 C
-ATOM 1406 O ARG A 202 74.582 24.056 -5.702 1.00 52.80 O
-ATOM 1407 CB ARG A 202 77.536 22.935 -6.219 1.00 58.67 C
-ATOM 1408 CG ARG A 202 78.498 21.790 -5.847 1.00 66.85 C
-ATOM 1409 CD ARG A 202 79.755 22.308 -5.134 1.00 72.33 C
-ATOM 1410 NE ARG A 202 80.670 23.012 -6.032 1.00 77.77 N
-ATOM 1411 CZ ARG A 202 81.717 22.439 -6.626 1.00 80.96 C
-ATOM 1412 NH1 ARG A 202 81.981 21.147 -6.400 1.00 80.96 N
-ATOM 1413 NH2 ARG A 202 82.483 23.146 -7.465 1.00 80.34 N
-ATOM 1414 N GLU A 203 75.166 24.310 -7.848 1.00 53.93 N
-ATOM 1415 CA GLU A 203 74.387 25.511 -8.017 1.00 53.82 C
-ATOM 1416 C GLU A 203 72.906 25.273 -8.009 1.00 54.22 C
-ATOM 1417 O GLU A 203 72.161 26.061 -7.430 1.00 55.27 O
-ATOM 1418 CB GLU A 203 74.789 26.228 -9.305 1.00 56.38 C
-ATOM 1419 CG GLU A 203 74.353 27.696 -9.367 1.00 60.72 C
-ATOM 1420 CD GLU A 203 75.135 28.629 -8.408 1.00 66.53 C
-ATOM 1421 OE1 GLU A 203 74.785 29.831 -8.387 1.00 67.91 O
-ATOM 1422 OE2 GLU A 203 76.082 28.191 -7.680 1.00 66.18 O
-ATOM 1423 N PHE A 204 72.461 24.201 -8.659 1.00 54.42 N
-ATOM 1424 CA PHE A 204 71.022 23.905 -8.700 1.00 52.76 C
-ATOM 1425 C PHE A 204 70.569 23.134 -7.447 1.00 52.71 C
-ATOM 1426 O PHE A 204 69.543 22.481 -7.443 1.00 53.64 O
-ATOM 1427 CB PHE A 204 70.677 23.134 -9.987 1.00 47.68 C
-ATOM 1428 CG PHE A 204 70.899 23.930 -11.257 1.00 46.50 C
-ATOM 1429 CD1 PHE A 204 71.296 23.302 -12.433 1.00 44.87 C
-ATOM 1430 CD2 PHE A 204 70.720 25.309 -11.282 1.00 44.35 C
-ATOM 1431 CE1 PHE A 204 71.511 24.038 -13.601 1.00 40.99 C
-ATOM 1432 CE2 PHE A 204 70.936 26.036 -12.447 1.00 38.75 C
-ATOM 1433 CZ PHE A 204 71.330 25.395 -13.597 1.00 39.58 C
-ATOM 1434 N GLN A 205 71.341 23.243 -6.375 1.00 53.18 N
-ATOM 1435 CA GLN A 205 71.020 22.584 -5.125 1.00 53.11 C
-ATOM 1436 C GLN A 205 71.171 23.536 -3.954 1.00 51.67 C
-ATOM 1437 O GLN A 205 70.814 23.190 -2.838 1.00 50.53 O
-ATOM 1438 CB GLN A 205 71.971 21.431 -4.879 1.00 58.08 C
-ATOM 1439 CG GLN A 205 71.912 20.339 -5.889 1.00 68.69 C
-ATOM 1440 CD GLN A 205 70.778 19.353 -5.631 1.00 75.76 C
-ATOM 1441 OE1 GLN A 205 70.751 18.268 -6.236 1.00 79.54 O
-ATOM 1442 NE2 GLN A 205 69.833 19.717 -4.736 1.00 75.03 N
-ATOM 1443 N ARG A 206 71.694 24.732 -4.207 1.00 51.73 N
-ATOM 1444 CA ARG A 206 71.974 25.690 -3.137 1.00 51.92 C
-ATOM 1445 C ARG A 206 70.805 26.415 -2.480 1.00 51.59 C
-ATOM 1446 O ARG A 206 71.006 27.094 -1.460 1.00 53.65 O
-ATOM 1447 CB ARG A 206 72.988 26.725 -3.621 1.00 49.16 C
-ATOM 1448 CG ARG A 206 72.377 27.662 -4.594 1.00 52.39 C
-ATOM 1449 CD ARG A 206 73.349 28.647 -5.157 1.00 51.47 C
-ATOM 1450 NE ARG A 206 73.973 29.440 -4.117 1.00 52.89 N
-ATOM 1451 CZ ARG A 206 75.216 29.240 -3.719 1.00 54.65 C
-ATOM 1452 NH1 ARG A 206 75.929 28.275 -4.293 1.00 55.02 N
-ATOM 1453 NH2 ARG A 206 75.743 29.996 -2.765 1.00 51.91 N
-ATOM 1454 N MET A 207 69.600 26.267 -3.036 1.00 50.20 N
-ATOM 1455 CA MET A 207 68.412 26.922 -2.481 1.00 47.63 C
-ATOM 1456 C MET A 207 68.103 26.504 -1.056 1.00 45.77 C
-ATOM 1457 O MET A 207 67.522 27.272 -0.302 1.00 45.64 O
-ATOM 1458 CB MET A 207 67.176 26.687 -3.361 1.00 49.67 C
-ATOM 1459 CG MET A 207 66.803 25.226 -3.613 1.00 55.32 C
-ATOM 1460 SD MET A 207 67.832 24.365 -4.871 1.00 64.94 S
-ATOM 1461 CE MET A 207 67.889 25.548 -6.282 1.00 56.83 C
-ATOM 1462 N ILE A 208 68.489 25.295 -0.671 1.00 45.68 N
-ATOM 1463 CA ILE A 208 68.230 24.851 0.698 1.00 46.01 C
-ATOM 1464 C ILE A 208 68.841 25.858 1.667 1.00 48.01 C
-ATOM 1465 O ILE A 208 68.148 26.383 2.553 1.00 46.46 O
-ATOM 1466 CB ILE A 208 68.833 23.461 0.986 1.00 44.72 C
-ATOM 1467 CG1 ILE A 208 68.230 22.424 0.028 1.00 44.66 C
-ATOM 1468 CG2 ILE A 208 68.578 23.087 2.445 1.00 42.57 C
-ATOM 1469 CD1 ILE A 208 68.847 21.028 0.113 1.00 44.11 C
-ATOM 1470 N GLY A 209 70.138 26.127 1.476 1.00 49.75 N
-ATOM 1471 CA GLY A 209 70.851 27.084 2.305 1.00 48.83 C
-ATOM 1472 C GLY A 209 70.343 28.501 2.074 1.00 48.78 C
-ATOM 1473 O GLY A 209 70.218 29.290 3.016 1.00 49.29 O
-ATOM 1474 N GLU A 210 70.046 28.840 0.823 1.00 47.13 N
-ATOM 1475 CA GLU A 210 69.544 30.170 0.526 1.00 46.64 C
-ATOM 1476 C GLU A 210 68.216 30.419 1.247 1.00 47.30 C
-ATOM 1477 O GLU A 210 68.027 31.470 1.881 1.00 47.46 O
-ATOM 1478 CB GLU A 210 69.385 30.334 -0.970 1.00 45.06 C
-ATOM 1479 CG GLU A 210 70.680 30.179 -1.695 1.00 48.34 C
-ATOM 1480 CD GLU A 210 70.508 30.325 -3.178 1.00 52.70 C
-ATOM 1481 OE1 GLU A 210 69.411 29.975 -3.667 1.00 57.34 O
-ATOM 1482 OE2 GLU A 210 71.459 30.768 -3.865 1.00 55.75 O
-ATOM 1483 N GLU A 211 67.301 29.458 1.172 1.00 45.21 N
-ATOM 1484 CA GLU A 211 66.030 29.614 1.861 1.00 46.10 C
-ATOM 1485 C GLU A 211 66.278 29.717 3.353 1.00 48.21 C
-ATOM 1486 O GLU A 211 65.757 30.612 4.018 1.00 48.09 O
-ATOM 1487 CB GLU A 211 65.126 28.432 1.577 1.00 45.18 C
-ATOM 1488 CG GLU A 211 64.746 28.384 0.146 1.00 45.12 C
-ATOM 1489 CD GLU A 211 64.010 27.144 -0.247 1.00 46.14 C
-ATOM 1490 OE1 GLU A 211 63.824 26.973 -1.483 1.00 47.61 O
-ATOM 1491 OE2 GLU A 211 63.624 26.363 0.658 1.00 44.13 O
-ATOM 1492 N THR A 212 67.085 28.798 3.879 1.00 49.04 N
-ATOM 1493 CA THR A 212 67.396 28.798 5.303 1.00 48.89 C
-ATOM 1494 C THR A 212 67.938 30.140 5.726 1.00 48.62 C
-ATOM 1495 O THR A 212 67.511 30.698 6.749 1.00 49.08 O
-ATOM 1496 CB THR A 212 68.456 27.752 5.666 1.00 49.00 C
-ATOM 1497 OG1 THR A 212 67.960 26.448 5.348 1.00 55.12 O
-ATOM 1498 CG2 THR A 212 68.795 27.816 7.149 1.00 47.11 C
-ATOM 1499 N LYS A 213 68.877 30.664 4.941 1.00 45.22 N
-ATOM 1500 CA LYS A 213 69.483 31.927 5.308 1.00 44.73 C
-ATOM 1501 C LYS A 213 68.457 33.038 5.385 1.00 45.02 C
-ATOM 1502 O LYS A 213 68.357 33.733 6.401 1.00 44.20 O
-ATOM 1503 CB LYS A 213 70.606 32.299 4.341 1.00 42.94 C
-ATOM 1504 CG LYS A 213 71.138 33.700 4.566 1.00 39.01 C
-ATOM 1505 CD LYS A 213 72.633 33.730 4.454 1.00 40.05 C
-ATOM 1506 CE LYS A 213 73.097 33.616 3.034 1.00 41.69 C
-ATOM 1507 NZ LYS A 213 74.601 33.653 2.961 1.00 45.07 N
-ATOM 1508 N ALA A 214 67.678 33.183 4.319 1.00 44.48 N
-ATOM 1509 CA ALA A 214 66.658 34.219 4.263 1.00 43.17 C
-ATOM 1510 C ALA A 214 65.583 34.012 5.335 1.00 43.19 C
-ATOM 1511 O ALA A 214 65.130 34.966 5.982 1.00 41.58 O
-ATOM 1512 CB ALA A 214 66.034 34.235 2.891 1.00 39.27 C
-ATOM 1513 N GLN A 215 65.190 32.757 5.527 1.00 43.72 N
-ATOM 1514 CA GLN A 215 64.167 32.426 6.495 1.00 43.83 C
-ATOM 1515 C GLN A 215 64.615 32.743 7.913 1.00 45.92 C
-ATOM 1516 O GLN A 215 63.864 33.307 8.709 1.00 43.19 O
-ATOM 1517 CB GLN A 215 63.797 30.949 6.362 1.00 41.83 C
-ATOM 1518 CG GLN A 215 63.012 30.662 5.117 1.00 45.70 C
-ATOM 1519 CD GLN A 215 62.559 29.223 5.007 1.00 49.79 C
-ATOM 1520 OE1 GLN A 215 63.371 28.311 4.867 1.00 53.91 O
-ATOM 1521 NE2 GLN A 215 61.256 29.011 5.057 1.00 49.95 N
-ATOM 1522 N ILE A 216 65.857 32.388 8.215 1.00 48.72 N
-ATOM 1523 CA ILE A 216 66.405 32.604 9.538 1.00 51.29 C
-ATOM 1524 C ILE A 216 66.571 34.111 9.836 1.00 54.52 C
-ATOM 1525 O ILE A 216 66.352 34.573 10.969 1.00 52.88 O
-ATOM 1526 CB ILE A 216 67.740 31.799 9.675 1.00 50.03 C
-ATOM 1527 CG1 ILE A 216 67.641 30.837 10.852 1.00 49.54 C
-ATOM 1528 CG2 ILE A 216 68.911 32.714 9.864 1.00 54.62 C
-ATOM 1529 CD1 ILE A 216 67.127 31.493 12.086 1.00 48.15 C
-ATOM 1530 N LEU A 217 66.947 34.882 8.819 1.00 56.02 N
-ATOM 1531 CA LEU A 217 67.099 36.313 9.008 1.00 56.74 C
-ATOM 1532 C LEU A 217 65.733 36.913 9.288 1.00 58.84 C
-ATOM 1533 O LEU A 217 65.578 37.676 10.236 1.00 59.64 O
-ATOM 1534 CB LEU A 217 67.710 36.956 7.771 1.00 55.39 C
-ATOM 1535 CG LEU A 217 69.217 36.726 7.689 1.00 59.03 C
-ATOM 1536 CD1 LEU A 217 69.747 37.438 6.481 1.00 53.66 C
-ATOM 1537 CD2 LEU A 217 69.913 37.220 8.976 1.00 56.80 C
-ATOM 1538 N GLU A 218 64.742 36.559 8.471 1.00 60.04 N
-ATOM 1539 CA GLU A 218 63.384 37.062 8.647 1.00 61.13 C
-ATOM 1540 C GLU A 218 62.789 36.796 10.038 1.00 60.39 C
-ATOM 1541 O GLU A 218 62.107 37.641 10.599 1.00 60.70 O
-ATOM 1542 CB GLU A 218 62.469 36.457 7.587 1.00 65.14 C
-ATOM 1543 CG GLU A 218 60.986 36.779 7.767 1.00 75.18 C
-ATOM 1544 CD GLU A 218 60.672 38.288 7.696 1.00 82.91 C
-ATOM 1545 OE1 GLU A 218 59.484 38.670 7.915 1.00 86.33 O
-ATOM 1546 OE2 GLU A 218 61.607 39.092 7.421 1.00 86.53 O
-ATOM 1547 N ARG A 219 63.054 35.635 10.609 1.00 58.46 N
-ATOM 1548 CA ARG A 219 62.486 35.329 11.903 1.00 59.26 C
-ATOM 1549 C ARG A 219 63.366 35.699 13.082 1.00 61.54 C
-ATOM 1550 O ARG A 219 62.853 36.020 14.138 1.00 62.98 O
-ATOM 1551 CB ARG A 219 62.171 33.837 12.004 1.00 59.81 C
-ATOM 1552 CG ARG A 219 61.302 33.265 10.912 1.00 61.32 C
-ATOM 1553 CD ARG A 219 61.563 31.788 10.883 1.00 68.41 C
-ATOM 1554 NE ARG A 219 60.614 30.970 10.120 1.00 74.39 N
-ATOM 1555 CZ ARG A 219 60.409 31.039 8.804 1.00 76.22 C
-ATOM 1556 NH1 ARG A 219 61.076 31.919 8.056 1.00 77.19 N
-ATOM 1557 NH2 ARG A 219 59.575 30.174 8.224 1.00 76.64 N
-ATOM 1558 N GLU A 220 64.685 35.643 12.917 1.00 63.70 N
-ATOM 1559 CA GLU A 220 65.604 35.932 14.025 1.00 63.85 C
-ATOM 1560 C GLU A 220 66.440 37.186 13.836 1.00 64.09 C
-ATOM 1561 O GLU A 220 67.203 37.568 14.715 1.00 64.40 O
-ATOM 1562 CB GLU A 220 66.541 34.745 14.247 1.00 64.72 C
-ATOM 1563 CG GLU A 220 65.843 33.473 14.683 1.00 66.85 C
-ATOM 1564 CD GLU A 220 65.163 33.624 16.018 1.00 69.01 C
-ATOM 1565 OE1 GLU A 220 65.690 34.380 16.860 1.00 70.94 O
-ATOM 1566 OE2 GLU A 220 64.114 32.979 16.241 1.00 72.12 O
-ATOM 1567 N GLY A 221 66.308 37.815 12.679 1.00 64.32 N
-ATOM 1568 CA GLY A 221 67.045 39.030 12.420 1.00 63.89 C
-ATOM 1569 C GLY A 221 68.551 38.883 12.399 1.00 65.72 C
-ATOM 1570 O GLY A 221 69.259 39.891 12.362 1.00 68.61 O
-ATOM 1571 N ARG A 222 69.052 37.651 12.421 1.00 65.10 N
-ATOM 1572 CA ARG A 222 70.501 37.406 12.386 1.00 63.46 C
-ATOM 1573 C ARG A 222 70.739 36.015 11.831 1.00 62.43 C
-ATOM 1574 O ARG A 222 69.796 35.229 11.745 1.00 66.20 O
-ATOM 1575 CB ARG A 222 71.101 37.503 13.793 1.00 61.35 C
-ATOM 1576 CG ARG A 222 70.247 36.868 14.848 1.00 62.26 C
-ATOM 1577 CD ARG A 222 70.979 36.702 16.143 1.00 62.90 C
-ATOM 1578 NE ARG A 222 72.094 35.766 16.024 1.00 66.20 N
-ATOM 1579 CZ ARG A 222 72.390 34.846 16.943 1.00 68.27 C
-ATOM 1580 NH1 ARG A 222 71.648 34.742 18.040 1.00 70.57 N
-ATOM 1581 NH2 ARG A 222 73.421 34.029 16.774 1.00 67.07 N
-ATOM 1582 N LEU A 223 71.976 35.709 11.448 1.00 57.79 N
-ATOM 1583 CA LEU A 223 72.284 34.385 10.923 1.00 55.77 C
-ATOM 1584 C LEU A 223 72.395 33.409 12.075 1.00 56.33 C
-ATOM 1585 O LEU A 223 72.440 33.814 13.232 1.00 58.91 O
-ATOM 1586 CB LEU A 223 73.594 34.403 10.149 1.00 53.92 C
-ATOM 1587 CG LEU A 223 73.629 35.313 8.928 1.00 53.39 C
-ATOM 1588 CD1 LEU A 223 74.860 34.946 8.133 1.00 50.51 C
-ATOM 1589 CD2 LEU A 223 72.358 35.158 8.077 1.00 50.38 C
-ATOM 1590 N PRO A 224 72.449 32.104 11.783 1.00 56.49 N
-ATOM 1591 CA PRO A 224 72.554 31.129 12.871 1.00 56.34 C
-ATOM 1592 C PRO A 224 73.982 31.041 13.379 1.00 57.98 C
-ATOM 1593 O PRO A 224 74.934 31.355 12.660 1.00 57.15 O
-ATOM 1594 CB PRO A 224 72.147 29.813 12.218 1.00 54.19 C
-ATOM 1595 CG PRO A 224 71.883 30.147 10.761 1.00 54.42 C
-ATOM 1596 CD PRO A 224 72.566 31.435 10.485 1.00 55.46 C
-ATOM 1597 N ASP A 225 74.129 30.594 14.617 1.00 59.46 N
-ATOM 1598 CA ASP A 225 75.442 30.427 15.201 1.00 57.72 C
-ATOM 1599 C ASP A 225 76.080 29.245 14.495 1.00 57.10 C
-ATOM 1600 O ASP A 225 77.217 29.331 14.056 1.00 59.16 O
-ATOM 1601 CB ASP A 225 75.299 30.211 16.698 1.00 59.82 C
-ATOM 1602 CG ASP A 225 74.689 31.428 17.384 1.00 65.15 C
-ATOM 1603 OD1 ASP A 225 75.209 32.538 17.144 1.00 67.26 O
-ATOM 1604 OD2 ASP A 225 73.697 31.298 18.142 1.00 65.60 O
-ATOM 1605 N ALA A 226 75.335 28.156 14.344 1.00 56.87 N
-ATOM 1606 CA ALA A 226 75.846 26.983 13.639 1.00 56.16 C
-ATOM 1607 C ALA A 226 74.742 26.324 12.815 1.00 56.44 C
-ATOM 1608 O ALA A 226 73.556 26.462 13.126 1.00 59.31 O
-ATOM 1609 CB ALA A 226 76.408 25.984 14.625 1.00 55.36 C
-ATOM 1610 N VAL A 227 75.135 25.622 11.757 1.00 54.21 N
-ATOM 1611 CA VAL A 227 74.193 24.902 10.909 1.00 52.64 C
-ATOM 1612 C VAL A 227 74.690 23.461 10.923 1.00 53.84 C
-ATOM 1613 O VAL A 227 75.758 23.183 10.401 1.00 55.40 O
-ATOM 1614 CB VAL A 227 74.212 25.412 9.447 1.00 51.05 C
-ATOM 1615 CG1 VAL A 227 73.483 24.425 8.569 1.00 49.85 C
-ATOM 1616 CG2 VAL A 227 73.565 26.790 9.339 1.00 46.48 C
-ATOM 1617 N ILE A 228 73.931 22.557 11.538 1.00 54.35 N
-ATOM 1618 CA ILE A 228 74.300 21.146 11.630 1.00 53.81 C
-ATOM 1619 C ILE A 228 73.641 20.388 10.485 1.00 56.05 C
-ATOM 1620 O ILE A 228 72.471 20.580 10.184 1.00 57.96 O
-ATOM 1621 CB ILE A 228 73.778 20.501 12.924 1.00 54.98 C
-ATOM 1622 CG1 ILE A 228 73.660 21.539 14.034 1.00 55.29 C
-ATOM 1623 CG2 ILE A 228 74.673 19.364 13.337 1.00 54.21 C
-ATOM 1624 CD1 ILE A 228 74.903 22.270 14.286 1.00 59.53 C
-ATOM 1625 N ALA A 229 74.379 19.505 9.851 1.00 56.54 N
-ATOM 1626 CA ALA A 229 73.817 18.753 8.759 1.00 58.70 C
-ATOM 1627 C ALA A 229 74.625 17.484 8.667 1.00 61.50 C
-ATOM 1628 O ALA A 229 75.849 17.528 8.657 1.00 64.94 O
-ATOM 1629 CB ALA A 229 73.923 19.540 7.477 1.00 55.82 C
-ATOM 1630 N CYS A 230 73.942 16.350 8.627 1.00 62.74 N
-ATOM 1631 CA CYS A 230 74.600 15.067 8.540 1.00 63.30 C
-ATOM 1632 C CYS A 230 75.242 14.913 7.160 1.00 63.88 C
-ATOM 1633 O CYS A 230 74.563 14.904 6.138 1.00 63.09 O
-ATOM 1634 CB CYS A 230 73.567 13.974 8.788 1.00 64.41 C
-ATOM 1635 SG CYS A 230 74.168 12.302 8.544 1.00 73.59 S
-ATOM 1636 N VAL A 231 76.562 14.804 7.125 1.00 66.81 N
-ATOM 1637 CA VAL A 231 77.256 14.652 5.851 1.00 70.40 C
-ATOM 1638 C VAL A 231 77.522 13.183 5.555 1.00 73.58 C
-ATOM 1639 O VAL A 231 77.907 12.421 6.431 1.00 75.22 O
-ATOM 1640 CB VAL A 231 78.599 15.420 5.833 1.00 68.50 C
-ATOM 1641 CG1 VAL A 231 79.437 15.041 7.033 1.00 68.64 C
-ATOM 1642 CG2 VAL A 231 79.350 15.105 4.559 1.00 67.95 C
-ATOM 1643 N GLY A 232 77.306 12.784 4.315 1.00 76.79 N
-ATOM 1644 CA GLY A 232 77.538 11.405 3.964 1.00 80.63 C
-ATOM 1645 C GLY A 232 76.770 11.061 2.711 1.00 85.29 C
-ATOM 1646 O GLY A 232 75.944 10.146 2.734 1.00 89.01 O
-ATOM 1647 N GLY A 233 77.023 11.806 1.630 1.00 86.54 N
-ATOM 1648 CA GLY A 233 76.371 11.560 0.348 1.00 85.99 C
-ATOM 1649 C GLY A 233 74.854 11.471 0.336 1.00 85.84 C
-ATOM 1650 O GLY A 233 74.244 10.841 1.205 1.00 86.32 O
-ATOM 1651 N GLY A 234 74.236 12.091 -0.665 1.00 85.24 N
-ATOM 1652 CA GLY A 234 72.790 12.067 -0.749 1.00 84.91 C
-ATOM 1653 C GLY A 234 72.187 12.719 0.484 1.00 85.88 C
-ATOM 1654 O GLY A 234 70.972 12.682 0.705 1.00 87.81 O
-ATOM 1655 N SER A 235 73.047 13.302 1.312 1.00 84.80 N
-ATOM 1656 CA SER A 235 72.591 13.979 2.517 1.00 82.03 C
-ATOM 1657 C SER A 235 72.255 15.377 2.032 1.00 79.72 C
-ATOM 1658 O SER A 235 71.448 16.085 2.623 1.00 78.76 O
-ATOM 1659 CB SER A 235 73.722 14.060 3.551 1.00 82.56 C
-ATOM 1660 OG SER A 235 74.390 12.818 3.699 1.00 84.00 O
-ATOM 1661 N ASN A 236 72.893 15.749 0.926 1.00 78.02 N
-ATOM 1662 CA ASN A 236 72.728 17.064 0.330 1.00 76.52 C
-ATOM 1663 C ASN A 236 73.112 18.122 1.375 1.00 73.04 C
-ATOM 1664 O ASN A 236 72.394 19.098 1.605 1.00 72.14 O
-ATOM 1665 CB ASN A 236 71.284 17.261 -0.156 1.00 79.65 C
-ATOM 1666 CG ASN A 236 71.194 18.220 -1.349 1.00 83.97 C
-ATOM 1667 OD1 ASN A 236 70.104 18.450 -1.901 1.00 85.62 O
-ATOM 1668 ND2 ASN A 236 72.347 18.781 -1.754 1.00 82.85 N
-ATOM 1669 N ALA A 237 74.255 17.902 2.015 1.00 67.79 N
-ATOM 1670 CA ALA A 237 74.747 18.821 3.014 1.00 62.92 C
-ATOM 1671 C ALA A 237 75.274 20.023 2.258 1.00 62.23 C
-ATOM 1672 O ALA A 237 75.058 21.166 2.651 1.00 62.78 O
-ATOM 1673 CB ALA A 237 75.848 18.171 3.801 1.00 62.25 C
-ATOM 1674 N ILE A 238 75.965 19.761 1.156 1.00 59.96 N
-ATOM 1675 CA ILE A 238 76.507 20.835 0.348 1.00 57.44 C
-ATOM 1676 C ILE A 238 75.411 21.800 -0.018 1.00 58.38 C
-ATOM 1677 O ILE A 238 75.673 22.985 -0.176 1.00 60.11 O
-ATOM 1678 CB ILE A 238 77.097 20.320 -0.952 1.00 56.91 C
-ATOM 1679 CG1 ILE A 238 78.110 19.227 -0.648 1.00 60.48 C
-ATOM 1680 CG2 ILE A 238 77.735 21.455 -1.721 1.00 53.25 C
-ATOM 1681 CD1 ILE A 238 79.088 19.602 0.453 1.00 66.38 C
-ATOM 1682 N GLY A 239 74.188 21.281 -0.168 1.00 58.52 N
-ATOM 1683 CA GLY A 239 73.043 22.109 -0.527 1.00 56.61 C
-ATOM 1684 C GLY A 239 72.702 23.072 0.592 1.00 56.45 C
-ATOM 1685 O GLY A 239 72.367 24.248 0.383 1.00 57.99 O
-ATOM 1686 N MET A 240 72.797 22.571 1.809 1.00 54.40 N
-ATOM 1687 CA MET A 240 72.515 23.402 2.946 1.00 53.93 C
-ATOM 1688 C MET A 240 73.709 24.327 3.261 1.00 54.72 C
-ATOM 1689 O MET A 240 73.499 25.492 3.618 1.00 57.21 O
-ATOM 1690 CB MET A 240 72.156 22.521 4.150 1.00 51.71 C
-ATOM 1691 CG MET A 240 72.041 23.270 5.465 1.00 50.79 C
-ATOM 1692 SD MET A 240 70.878 24.637 5.427 1.00 51.24 S
-ATOM 1693 CE MET A 240 69.504 23.931 6.271 1.00 47.93 C
-ATOM 1694 N PHE A 241 74.945 23.838 3.098 1.00 51.81 N
-ATOM 1695 CA PHE A 241 76.135 24.638 3.422 1.00 50.09 C
-ATOM 1696 C PHE A 241 76.584 25.652 2.392 1.00 51.67 C
-ATOM 1697 O PHE A 241 77.180 26.680 2.735 1.00 49.95 O
-ATOM 1698 CB PHE A 241 77.335 23.744 3.698 1.00 47.45 C
-ATOM 1699 CG PHE A 241 77.205 22.915 4.919 1.00 45.65 C
-ATOM 1700 CD1 PHE A 241 76.610 23.422 6.054 1.00 45.09 C
-ATOM 1701 CD2 PHE A 241 77.692 21.620 4.939 1.00 45.67 C
-ATOM 1702 CE1 PHE A 241 76.496 22.649 7.198 1.00 46.46 C
-ATOM 1703 CE2 PHE A 241 77.586 20.836 6.079 1.00 46.41 C
-ATOM 1704 CZ PHE A 241 76.983 21.354 7.213 1.00 46.84 C
-ATOM 1705 N ALA A 242 76.321 25.352 1.126 1.00 52.31 N
-ATOM 1706 CA ALA A 242 76.739 26.223 0.043 1.00 51.22 C
-ATOM 1707 C ALA A 242 76.645 27.697 0.394 1.00 51.57 C
-ATOM 1708 O ALA A 242 77.663 28.359 0.504 1.00 53.36 O
-ATOM 1709 CB ALA A 242 75.934 25.929 -1.194 1.00 51.93 C
-ATOM 1710 N ASP A 243 75.436 28.204 0.606 1.00 50.25 N
-ATOM 1711 CA ASP A 243 75.263 29.625 0.887 1.00 51.00 C
-ATOM 1712 C ASP A 243 75.842 30.164 2.176 1.00 52.29 C
-ATOM 1713 O ASP A 243 75.704 31.363 2.439 1.00 52.50 O
-ATOM 1714 CB ASP A 243 73.788 30.004 0.835 1.00 53.86 C
-ATOM 1715 CG ASP A 243 73.541 31.323 0.125 1.00 54.52 C
-ATOM 1716 OD1 ASP A 243 74.004 31.458 -1.031 1.00 53.47 O
-ATOM 1717 OD2 ASP A 243 72.865 32.205 0.706 1.00 55.23 O
-ATOM 1718 N PHE A 244 76.475 29.314 2.984 1.00 52.17 N
-ATOM 1719 CA PHE A 244 77.080 29.786 4.242 1.00 53.62 C
-ATOM 1720 C PHE A 244 78.629 29.735 4.211 1.00 55.12 C
-ATOM 1721 O PHE A 244 79.298 30.272 5.101 1.00 55.32 O
-ATOM 1722 CB PHE A 244 76.563 28.958 5.429 1.00 52.17 C
-ATOM 1723 CG PHE A 244 75.107 29.176 5.744 1.00 51.63 C
-ATOM 1724 CD1 PHE A 244 74.689 30.308 6.447 1.00 51.79 C
-ATOM 1725 CD2 PHE A 244 74.150 28.254 5.344 1.00 50.48 C
-ATOM 1726 CE1 PHE A 244 73.331 30.521 6.749 1.00 50.24 C
-ATOM 1727 CE2 PHE A 244 72.797 28.459 5.642 1.00 52.13 C
-ATOM 1728 CZ PHE A 244 72.389 29.601 6.348 1.00 49.57 C
-ATOM 1729 N ILE A 245 79.194 29.090 3.191 1.00 54.65 N
-ATOM 1730 CA ILE A 245 80.643 28.991 3.075 1.00 55.20 C
-ATOM 1731 C ILE A 245 81.295 30.368 3.292 1.00 56.73 C
-ATOM 1732 O ILE A 245 82.350 30.467 3.900 1.00 58.60 O
-ATOM 1733 CB ILE A 245 81.085 28.441 1.671 1.00 56.62 C
-ATOM 1734 CG1 ILE A 245 80.578 27.016 1.439 1.00 56.34 C
-ATOM 1735 CG2 ILE A 245 82.585 28.408 1.588 1.00 56.52 C
-ATOM 1736 CD1 ILE A 245 81.127 26.013 2.429 1.00 56.33 C
-ATOM 1737 N ASN A 246 80.691 31.442 2.794 1.00 57.93 N
-ATOM 1738 CA ASN A 246 81.306 32.748 3.004 1.00 56.18 C
-ATOM 1739 C ASN A 246 80.669 33.595 4.086 1.00 57.30 C
-ATOM 1740 O ASN A 246 80.819 34.812 4.095 1.00 56.67 O
-ATOM 1741 CB ASN A 246 81.378 33.528 1.702 1.00 53.49 C
-ATOM 1742 CG ASN A 246 82.375 32.938 0.752 1.00 53.67 C
-ATOM 1743 OD1 ASN A 246 83.202 32.108 1.147 1.00 52.34 O
-ATOM 1744 ND2 ASN A 246 82.319 33.357 -0.507 1.00 54.78 N
-ATOM 1745 N GLU A 247 79.962 32.935 4.997 1.00 59.13 N
-ATOM 1746 CA GLU A 247 79.313 33.590 6.120 1.00 60.70 C
-ATOM 1747 C GLU A 247 80.158 33.128 7.284 1.00 62.69 C
-ATOM 1748 O GLU A 247 79.656 32.562 8.245 1.00 66.03 O
-ATOM 1749 CB GLU A 247 77.880 33.087 6.259 1.00 58.00 C
-ATOM 1750 CG GLU A 247 76.932 33.671 5.238 1.00 60.69 C
-ATOM 1751 CD GLU A 247 76.755 35.175 5.421 1.00 63.03 C
-ATOM 1752 OE1 GLU A 247 76.014 35.817 4.631 1.00 62.46 O
-ATOM 1753 OE2 GLU A 247 77.363 35.715 6.372 1.00 64.52 O
-ATOM 1754 N THR A 248 81.458 33.370 7.169 1.00 64.29 N
-ATOM 1755 CA THR A 248 82.436 32.934 8.162 1.00 65.20 C
-ATOM 1756 C THR A 248 82.064 32.947 9.627 1.00 63.78 C
-ATOM 1757 O THR A 248 82.544 32.120 10.375 1.00 63.82 O
-ATOM 1758 CB THR A 248 83.775 33.672 7.988 1.00 66.12 C
-ATOM 1759 OG1 THR A 248 83.529 35.042 7.644 1.00 69.60 O
-ATOM 1760 CG2 THR A 248 84.603 33.005 6.889 1.00 65.07 C
-ATOM 1761 N ASN A 249 81.211 33.862 10.051 1.00 65.39 N
-ATOM 1762 CA ASN A 249 80.817 33.901 11.460 1.00 66.91 C
-ATOM 1763 C ASN A 249 79.731 32.845 11.776 1.00 65.17 C
-ATOM 1764 O ASN A 249 79.117 32.855 12.846 1.00 65.49 O
-ATOM 1765 CB ASN A 249 80.316 35.307 11.813 1.00 70.86 C
-ATOM 1766 CG ASN A 249 79.251 35.820 10.823 1.00 78.02 C
-ATOM 1767 OD1 ASN A 249 78.488 36.744 11.144 1.00 80.64 O
-ATOM 1768 ND2 ASN A 249 79.208 35.231 9.608 1.00 77.80 N
-ATOM 1769 N VAL A 250 79.499 31.935 10.837 1.00 63.34 N
-ATOM 1770 CA VAL A 250 78.497 30.889 11.003 1.00 59.46 C
-ATOM 1771 C VAL A 250 79.183 29.551 10.894 1.00 58.33 C
-ATOM 1772 O VAL A 250 79.827 29.252 9.883 1.00 55.90 O
-ATOM 1773 CB VAL A 250 77.411 30.938 9.913 1.00 58.90 C
-ATOM 1774 CG1 VAL A 250 76.458 29.778 10.120 1.00 59.30 C
-ATOM 1775 CG2 VAL A 250 76.659 32.272 9.953 1.00 54.81 C
-ATOM 1776 N GLY A 251 79.017 28.745 11.934 1.00 57.26 N
-ATOM 1777 CA GLY A 251 79.651 27.446 11.988 1.00 56.98 C
-ATOM 1778 C GLY A 251 78.990 26.369 11.177 1.00 59.02 C
-ATOM 1779 O GLY A 251 77.768 26.261 11.154 1.00 60.93 O
-ATOM 1780 N LEU A 252 79.806 25.558 10.517 1.00 59.10 N
-ATOM 1781 CA LEU A 252 79.285 24.476 9.706 1.00 60.66 C
-ATOM 1782 C LEU A 252 79.655 23.113 10.298 1.00 62.82 C
-ATOM 1783 O LEU A 252 80.736 22.599 10.050 1.00 66.07 O
-ATOM 1784 CB LEU A 252 79.820 24.601 8.281 1.00 57.34 C
-ATOM 1785 CG LEU A 252 79.230 25.730 7.441 1.00 55.56 C
-ATOM 1786 CD1 LEU A 252 79.157 27.009 8.196 1.00 55.89 C
-ATOM 1787 CD2 LEU A 252 80.087 25.913 6.248 1.00 57.63 C
-ATOM 1788 N ILE A 253 78.751 22.531 11.082 1.00 63.63 N
-ATOM 1789 CA ILE A 253 78.990 21.230 11.701 1.00 61.40 C
-ATOM 1790 C ILE A 253 78.506 20.143 10.757 1.00 61.85 C
-ATOM 1791 O ILE A 253 77.341 20.120 10.393 1.00 61.56 O
-ATOM 1792 CB ILE A 253 78.197 21.049 13.014 1.00 61.36 C
-ATOM 1793 CG1 ILE A 253 78.301 22.293 13.912 1.00 57.61 C
-ATOM 1794 CG2 ILE A 253 78.689 19.800 13.719 1.00 59.17 C
-ATOM 1795 CD1 ILE A 253 79.614 22.460 14.556 1.00 59.01 C
-ATOM 1796 N GLY A 254 79.406 19.256 10.354 1.00 64.24 N
-ATOM 1797 CA GLY A 254 79.040 18.152 9.484 1.00 64.40 C
-ATOM 1798 C GLY A 254 79.041 16.929 10.382 1.00 66.78 C
-ATOM 1799 O GLY A 254 80.064 16.604 10.996 1.00 65.58 O
-ATOM 1800 N VAL A 255 77.898 16.253 10.480 1.00 68.16 N
-ATOM 1801 CA VAL A 255 77.786 15.086 11.345 1.00 67.54 C
-ATOM 1802 C VAL A 255 77.987 13.759 10.640 1.00 69.53 C
-ATOM 1803 O VAL A 255 77.311 13.443 9.667 1.00 66.20 O
-ATOM 1804 CB VAL A 255 76.440 15.071 12.061 1.00 64.96 C
-ATOM 1805 CG1 VAL A 255 76.386 13.929 13.041 1.00 64.12 C
-ATOM 1806 CG2 VAL A 255 76.246 16.376 12.794 1.00 64.82 C
-ATOM 1807 N GLU A 256 78.943 12.992 11.157 1.00 75.08 N
-ATOM 1808 CA GLU A 256 79.275 11.681 10.623 1.00 80.27 C
-ATOM 1809 C GLU A 256 78.822 10.557 11.538 1.00 83.22 C
-ATOM 1810 O GLU A 256 79.184 10.506 12.723 1.00 82.48 O
-ATOM 1811 CB GLU A 256 80.780 11.566 10.379 1.00 80.85 C
-ATOM 1812 CG GLU A 256 81.229 12.418 9.217 1.00 86.00 C
-ATOM 1813 CD GLU A 256 82.650 12.153 8.794 1.00 86.94 C
-ATOM 1814 OE1 GLU A 256 83.559 12.282 9.647 1.00 88.13 O
-ATOM 1815 OE2 GLU A 256 82.850 11.825 7.601 1.00 87.78 O
-ATOM 1816 N PRO A 257 78.009 9.638 10.992 1.00 86.28 N
-ATOM 1817 CA PRO A 257 77.470 8.478 11.719 1.00 88.00 C
-ATOM 1818 C PRO A 257 78.559 7.569 12.323 1.00 88.10 C
-ATOM 1819 O PRO A 257 79.702 7.571 11.859 1.00 89.54 O
-ATOM 1820 CB PRO A 257 76.634 7.771 10.646 1.00 88.24 C
-ATOM 1821 CG PRO A 257 76.120 8.949 9.806 1.00 87.22 C
-ATOM 1822 CD PRO A 257 77.393 9.762 9.655 1.00 85.91 C
-ATOM 1823 N GLY A 258 78.200 6.803 13.355 1.00 87.45 N
-ATOM 1824 CA GLY A 258 79.153 5.898 13.988 1.00 86.29 C
-ATOM 1825 C GLY A 258 79.618 6.342 15.367 1.00 86.20 C
-ATOM 1826 O GLY A 258 80.677 5.932 15.853 1.00 83.23 O
-ATOM 1827 N VAL A 309 88.042 10.267 -1.156 1.00102.35 N
-ATOM 1828 CA VAL A 309 86.843 9.858 -0.439 1.00102.29 C
-ATOM 1829 C VAL A 309 85.572 10.362 -1.137 1.00102.16 C
-ATOM 1830 O VAL A 309 85.629 10.861 -2.267 1.00100.68 O
-ATOM 1831 CB VAL A 309 86.886 10.364 1.030 1.00101.91 C
-ATOM 1832 CG1 VAL A 309 88.082 9.742 1.756 1.00 99.31 C
-ATOM 1833 CG2 VAL A 309 86.975 11.888 1.060 1.00100.01 C
-ATOM 1834 N GLY A 310 84.430 10.212 -0.466 1.00102.84 N
-ATOM 1835 CA GLY A 310 83.160 10.645 -1.032 1.00104.17 C
-ATOM 1836 C GLY A 310 83.231 12.102 -1.433 1.00105.29 C
-ATOM 1837 O GLY A 310 83.782 12.908 -0.680 1.00106.71 O
-ATOM 1838 N PRO A 311 82.695 12.484 -2.608 1.00105.08 N
-ATOM 1839 CA PRO A 311 82.762 13.896 -3.005 1.00103.98 C
-ATOM 1840 C PRO A 311 82.218 14.851 -1.921 1.00102.37 C
-ATOM 1841 O PRO A 311 82.850 15.864 -1.598 1.00102.68 O
-ATOM 1842 CB PRO A 311 81.953 13.930 -4.315 1.00103.96 C
-ATOM 1843 CG PRO A 311 80.996 12.799 -4.177 1.00103.17 C
-ATOM 1844 CD PRO A 311 81.859 11.716 -3.549 1.00104.90 C
-ATOM 1845 N GLN A 312 81.056 14.513 -1.363 1.00 98.54 N
-ATOM 1846 CA GLN A 312 80.433 15.313 -0.319 1.00 94.24 C
-ATOM 1847 C GLN A 312 81.522 15.886 0.595 1.00 91.39 C
-ATOM 1848 O GLN A 312 81.621 17.095 0.789 1.00 89.63 O
-ATOM 1849 CB GLN A 312 79.485 14.420 0.483 1.00 96.05 C
-ATOM 1850 CG GLN A 312 78.623 15.139 1.505 1.00 98.39 C
-ATOM 1851 CD GLN A 312 77.292 15.605 0.934 1.00101.66 C
-ATOM 1852 OE1 GLN A 312 77.240 16.517 0.103 1.00101.59 O
-ATOM 1853 NE2 GLN A 312 76.205 14.970 1.376 1.00102.01 N
-ATOM 1854 N HIS A 313 82.348 14.997 1.137 1.00 89.36 N
-ATOM 1855 CA HIS A 313 83.436 15.378 2.035 1.00 86.97 C
-ATOM 1856 C HIS A 313 84.503 16.113 1.249 1.00 84.64 C
-ATOM 1857 O HIS A 313 84.996 17.159 1.672 1.00 84.90 O
-ATOM 1858 CB HIS A 313 84.054 14.138 2.691 1.00 88.42 C
-ATOM 1859 CG HIS A 313 83.131 13.424 3.629 1.00 89.39 C
-ATOM 1860 ND1 HIS A 313 82.091 12.630 3.193 1.00 90.86 N
-ATOM 1861 CD2 HIS A 313 83.068 13.416 4.982 1.00 89.78 C
-ATOM 1862 CE1 HIS A 313 81.426 12.166 4.237 1.00 91.92 C
-ATOM 1863 NE2 HIS A 313 81.999 12.628 5.335 1.00 90.79 N
-ATOM 1864 N ALA A 314 84.868 15.536 0.111 1.00 80.49 N
-ATOM 1865 CA ALA A 314 85.848 16.121 -0.774 1.00 74.96 C
-ATOM 1866 C ALA A 314 85.614 17.630 -0.829 1.00 73.97 C
-ATOM 1867 O ALA A 314 86.474 18.417 -0.415 1.00 74.47 O
-ATOM 1868 CB ALA A 314 85.697 15.517 -2.151 1.00 75.67 C
-ATOM 1869 N TYR A 315 84.443 18.034 -1.325 1.00 70.75 N
-ATOM 1870 CA TYR A 315 84.118 19.454 -1.421 1.00 66.85 C
-ATOM 1871 C TYR A 315 84.174 20.140 -0.067 1.00 65.75 C
-ATOM 1872 O TYR A 315 84.858 21.143 0.081 1.00 65.27 O
-ATOM 1873 CB TYR A 315 82.741 19.665 -2.059 1.00 65.07 C
-ATOM 1874 CG TYR A 315 82.258 21.104 -2.012 1.00 63.83 C
-ATOM 1875 CD1 TYR A 315 81.495 21.570 -0.934 1.00 64.20 C
-ATOM 1876 CD2 TYR A 315 82.624 22.016 -3.003 1.00 63.84 C
-ATOM 1877 CE1 TYR A 315 81.113 22.899 -0.832 1.00 62.95 C
-ATOM 1878 CE2 TYR A 315 82.253 23.359 -2.917 1.00 66.05 C
-ATOM 1879 CZ TYR A 315 81.498 23.798 -1.822 1.00 67.87 C
-ATOM 1880 OH TYR A 315 81.167 25.141 -1.694 1.00 70.08 O
-ATOM 1881 N LEU A 316 83.464 19.605 0.919 1.00 64.90 N
-ATOM 1882 CA LEU A 316 83.455 20.192 2.263 1.00 66.59 C
-ATOM 1883 C LEU A 316 84.839 20.388 2.917 1.00 67.33 C
-ATOM 1884 O LEU A 316 85.064 21.331 3.702 1.00 65.92 O
-ATOM 1885 CB LEU A 316 82.588 19.342 3.180 1.00 66.90 C
-ATOM 1886 CG LEU A 316 81.128 19.750 3.266 1.00 66.33 C
-ATOM 1887 CD1 LEU A 316 80.318 18.613 3.849 1.00 67.78 C
-ATOM 1888 CD2 LEU A 316 81.017 20.986 4.122 1.00 65.00 C
-ATOM 1889 N ASN A 317 85.767 19.492 2.613 1.00 67.96 N
-ATOM 1890 CA ASN A 317 87.094 19.611 3.186 1.00 67.83 C
-ATOM 1891 C ASN A 317 87.785 20.804 2.561 1.00 67.76 C
-ATOM 1892 O ASN A 317 88.316 21.651 3.270 1.00 67.53 O
-ATOM 1893 CB ASN A 317 87.893 18.337 2.934 1.00 68.49 C
-ATOM 1894 CG ASN A 317 87.237 17.115 3.543 1.00 68.33 C
-ATOM 1895 OD1 ASN A 317 86.897 17.104 4.726 1.00 67.29 O
-ATOM 1896 ND2 ASN A 317 87.058 16.075 2.736 1.00 70.30 N
-ATOM 1897 N SER A 318 87.745 20.874 1.230 1.00 67.54 N
-ATOM 1898 CA SER A 318 88.369 21.962 0.480 1.00 65.51 C
-ATOM 1899 C SER A 318 87.890 23.354 0.843 1.00 64.51 C
-ATOM 1900 O SER A 318 88.661 24.292 0.774 1.00 66.15 O
-ATOM 1901 CB SER A 318 88.178 21.755 -1.019 1.00 65.02 C
-ATOM 1902 OG SER A 318 86.808 21.769 -1.367 1.00 66.34 O
-ATOM 1903 N THR A 319 86.624 23.506 1.216 1.00 65.61 N
-ATOM 1904 CA THR A 319 86.122 24.833 1.576 1.00 66.58 C
-ATOM 1905 C THR A 319 86.832 25.268 2.841 1.00 67.03 C
-ATOM 1906 O THR A 319 86.882 26.451 3.183 1.00 68.39 O
-ATOM 1907 CB THR A 319 84.616 24.843 1.889 1.00 65.60 C
-ATOM 1908 OG1 THR A 319 84.408 24.389 3.234 1.00 65.17 O
-ATOM 1909 CG2 THR A 319 83.863 23.969 0.910 1.00 63.32 C
-ATOM 1910 N GLY A 320 87.373 24.285 3.540 1.00 66.37 N
-ATOM 1911 CA GLY A 320 88.068 24.573 4.767 1.00 65.95 C
-ATOM 1912 C GLY A 320 87.146 25.041 5.876 1.00 66.38 C
-ATOM 1913 O GLY A 320 87.625 25.531 6.898 1.00 67.55 O
-ATOM 1914 N ARG A 321 85.832 24.917 5.728 1.00 66.26 N
-ATOM 1915 CA ARG A 321 85.034 25.386 6.844 1.00 66.45 C
-ATOM 1916 C ARG A 321 84.006 24.498 7.480 1.00 67.64 C
-ATOM 1917 O ARG A 321 83.073 24.992 8.107 1.00 69.11 O
-ATOM 1918 CB ARG A 321 84.406 26.739 6.552 1.00 62.94 C
-ATOM 1919 CG ARG A 321 84.099 27.047 5.152 1.00 59.72 C
-ATOM 1920 CD ARG A 321 83.812 28.536 5.112 1.00 62.37 C
-ATOM 1921 NE ARG A 321 82.594 28.922 5.846 1.00 61.77 N
-ATOM 1922 CZ ARG A 321 82.539 29.209 7.139 1.00 57.44 C
-ATOM 1923 NH1 ARG A 321 81.390 29.541 7.717 1.00 54.55 N
-ATOM 1924 NH2 ARG A 321 83.641 29.175 7.849 1.00 60.85 N
-ATOM 1925 N ALA A 322 84.188 23.191 7.370 1.00 67.68 N
-ATOM 1926 CA ALA A 322 83.251 22.284 7.999 1.00 68.44 C
-ATOM 1927 C ALA A 322 83.905 21.553 9.175 1.00 69.24 C
-ATOM 1928 O ALA A 322 84.937 20.926 9.010 1.00 70.97 O
-ATOM 1929 CB ALA A 322 82.745 21.292 6.980 1.00 68.84 C
-ATOM 1930 N ASP A 323 83.321 21.652 10.363 1.00 69.76 N
-ATOM 1931 CA ASP A 323 83.841 20.940 11.524 1.00 71.31 C
-ATOM 1932 C ASP A 323 83.145 19.599 11.543 1.00 70.90 C
-ATOM 1933 O ASP A 323 81.931 19.541 11.707 1.00 73.45 O
-ATOM 1934 CB ASP A 323 83.466 21.627 12.833 1.00 74.63 C
-ATOM 1935 CG ASP A 323 83.928 23.041 12.894 1.00 79.67 C
-ATOM 1936 OD1 ASP A 323 85.150 23.246 12.754 1.00 83.28 O
-ATOM 1937 OD2 ASP A 323 83.076 23.945 13.080 1.00 82.80 O
-ATOM 1938 N TYR A 324 83.873 18.510 11.386 1.00 68.81 N
-ATOM 1939 CA TYR A 324 83.189 17.234 11.447 1.00 67.45 C
-ATOM 1940 C TYR A 324 83.063 16.770 12.904 1.00 66.32 C
-ATOM 1941 O TYR A 324 83.869 17.147 13.757 1.00 65.08 O
-ATOM 1942 CB TYR A 324 83.932 16.195 10.614 1.00 64.84 C
-ATOM 1943 CG TYR A 324 83.958 16.514 9.138 1.00 64.57 C
-ATOM 1944 CD1 TYR A 324 83.318 15.687 8.214 1.00 62.69 C
-ATOM 1945 CD2 TYR A 324 84.664 17.620 8.658 1.00 64.26 C
-ATOM 1946 CE1 TYR A 324 83.389 15.948 6.855 1.00 63.87 C
-ATOM 1947 CE2 TYR A 324 84.743 17.892 7.297 1.00 62.99 C
-ATOM 1948 CZ TYR A 324 84.107 17.050 6.405 1.00 66.20 C
-ATOM 1949 OH TYR A 324 84.215 17.290 5.056 1.00 70.01 O
-ATOM 1950 N VAL A 325 82.012 16.002 13.186 1.00 65.12 N
-ATOM 1951 CA VAL A 325 81.781 15.433 14.511 1.00 64.03 C
-ATOM 1952 C VAL A 325 81.091 14.090 14.315 1.00 66.05 C
-ATOM 1953 O VAL A 325 80.478 13.835 13.271 1.00 64.44 O
-ATOM 1954 CB VAL A 325 80.890 16.307 15.402 1.00 62.24 C
-ATOM 1955 CG1 VAL A 325 81.432 17.709 15.444 1.00 60.51 C
-ATOM 1956 CG2 VAL A 325 79.438 16.255 14.919 1.00 63.59 C
-ATOM 1957 N SER A 326 81.199 13.225 15.320 1.00 67.83 N
-ATOM 1958 CA SER A 326 80.600 11.907 15.229 1.00 68.59 C
-ATOM 1959 C SER A 326 79.487 11.717 16.220 1.00 68.05 C
-ATOM 1960 O SER A 326 79.502 12.277 17.320 1.00 68.57 O
-ATOM 1961 CB SER A 326 81.648 10.821 15.454 1.00 70.03 C
-ATOM 1962 OG SER A 326 81.123 9.552 15.106 1.00 73.13 O
-ATOM 1963 N ILE A 327 78.515 10.918 15.812 1.00 67.55 N
-ATOM 1964 CA ILE A 327 77.388 10.624 16.655 1.00 70.03 C
-ATOM 1965 C ILE A 327 77.240 9.114 16.636 1.00 71.95 C
-ATOM 1966 O ILE A 327 77.576 8.459 15.650 1.00 71.54 O
-ATOM 1967 CB ILE A 327 76.115 11.355 16.157 1.00 69.76 C
-ATOM 1968 CG1 ILE A 327 75.705 12.419 17.170 1.00 69.06 C
-ATOM 1969 CG2 ILE A 327 74.967 10.402 16.026 1.00 71.55 C
-ATOM 1970 CD1 ILE A 327 76.737 13.480 17.394 1.00 72.83 C
-ATOM 1971 N THR A 328 76.745 8.580 17.748 1.00 74.81 N
-ATOM 1972 CA THR A 328 76.574 7.145 17.959 1.00 75.31 C
-ATOM 1973 C THR A 328 75.129 6.679 17.932 1.00 77.46 C
-ATOM 1974 O THR A 328 74.246 7.329 18.497 1.00 76.88 O
-ATOM 1975 CB THR A 328 77.092 6.768 19.327 1.00 74.40 C
-ATOM 1976 OG1 THR A 328 76.180 7.266 20.319 1.00 71.83 O
-ATOM 1977 CG2 THR A 328 78.454 7.389 19.559 1.00 73.97 C
-ATOM 1978 N ASP A 329 74.910 5.520 17.324 1.00 78.88 N
-ATOM 1979 CA ASP A 329 73.583 4.933 17.230 1.00 81.11 C
-ATOM 1980 C ASP A 329 72.663 5.189 18.410 1.00 80.55 C
-ATOM 1981 O ASP A 329 71.469 5.409 18.223 1.00 81.67 O
-ATOM 1982 CB ASP A 329 73.699 3.438 17.020 1.00 84.87 C
-ATOM 1983 CG ASP A 329 74.340 3.112 15.718 1.00 90.46 C
-ATOM 1984 OD1 ASP A 329 75.537 3.439 15.563 1.00 96.24 O
-ATOM 1985 OD2 ASP A 329 73.649 2.552 14.838 1.00 95.70 O
-ATOM 1986 N ASP A 330 73.184 5.149 19.627 1.00 78.84 N
-ATOM 1987 CA ASP A 330 72.297 5.404 20.748 1.00 79.51 C
-ATOM 1988 C ASP A 330 71.874 6.857 20.748 1.00 77.35 C
-ATOM 1989 O ASP A 330 70.681 7.157 20.852 1.00 78.88 O
-ATOM 1990 CB ASP A 330 72.951 5.021 22.079 1.00 82.59 C
-ATOM 1991 CG ASP A 330 72.948 3.503 22.315 1.00 84.87 C
-ATOM 1992 OD1 ASP A 330 73.495 3.080 23.356 1.00 85.37 O
-ATOM 1993 OD2 ASP A 330 72.398 2.740 21.469 1.00 84.25 O
-ATOM 1994 N GLU A 331 72.844 7.757 20.597 1.00 74.16 N
-ATOM 1995 CA GLU A 331 72.566 9.197 20.551 1.00 68.48 C
-ATOM 1996 C GLU A 331 71.542 9.487 19.460 1.00 65.22 C
-ATOM 1997 O GLU A 331 70.639 10.292 19.646 1.00 63.64 O
-ATOM 1998 CB GLU A 331 73.852 9.958 20.274 1.00 65.96 C
-ATOM 1999 CG GLU A 331 74.908 9.686 21.298 1.00 61.30 C
-ATOM 2000 CD GLU A 331 76.171 10.448 21.033 1.00 63.55 C
-ATOM 2001 OE1 GLU A 331 76.823 10.176 19.994 1.00 61.44 O
-ATOM 2002 OE2 GLU A 331 76.503 11.325 21.867 1.00 61.05 O
-ATOM 2003 N ALA A 332 71.693 8.816 18.325 1.00 61.50 N
-ATOM 2004 CA ALA A 332 70.766 8.981 17.231 1.00 61.37 C
-ATOM 2005 C ALA A 332 69.371 8.610 17.722 1.00 63.02 C
-ATOM 2006 O ALA A 332 68.459 9.447 17.684 1.00 65.16 O
-ATOM 2007 CB ALA A 332 71.163 8.104 16.068 1.00 56.65 C
-ATOM 2008 N LEU A 333 69.209 7.368 18.193 1.00 63.15 N
-ATOM 2009 CA LEU A 333 67.921 6.876 18.692 1.00 60.56 C
-ATOM 2010 C LEU A 333 67.366 7.747 19.796 1.00 58.60 C
-ATOM 2011 O LEU A 333 66.162 7.934 19.891 1.00 58.41 O
-ATOM 2012 CB LEU A 333 68.056 5.452 19.189 1.00 61.86 C
-ATOM 2013 CG LEU A 333 68.122 4.409 18.074 1.00 67.47 C
-ATOM 2014 CD1 LEU A 333 68.575 3.063 18.637 1.00 70.77 C
-ATOM 2015 CD2 LEU A 333 66.762 4.267 17.432 1.00 69.07 C
-ATOM 2016 N GLU A 334 68.249 8.274 20.630 1.00 56.19 N
-ATOM 2017 CA GLU A 334 67.851 9.163 21.714 1.00 57.83 C
-ATOM 2018 C GLU A 334 67.111 10.314 21.027 1.00 59.67 C
-ATOM 2019 O GLU A 334 65.930 10.580 21.288 1.00 58.28 O
-ATOM 2020 CB GLU A 334 69.112 9.704 22.397 1.00 60.54 C
-ATOM 2021 CG GLU A 334 68.966 10.384 23.761 1.00 61.97 C
-ATOM 2022 CD GLU A 334 68.034 11.572 23.764 1.00 65.49 C
-ATOM 2023 OE1 GLU A 334 66.806 11.356 23.882 1.00 66.73 O
-ATOM 2024 OE2 GLU A 334 68.527 12.718 23.648 1.00 64.64 O
-ATOM 2025 N ALA A 335 67.841 10.988 20.138 1.00 60.09 N
-ATOM 2026 CA ALA A 335 67.333 12.116 19.371 1.00 58.77 C
-ATOM 2027 C ALA A 335 66.056 11.727 18.629 1.00 58.27 C
-ATOM 2028 O ALA A 335 65.014 12.376 18.784 1.00 58.79 O
-ATOM 2029 CB ALA A 335 68.395 12.576 18.379 1.00 57.71 C
-ATOM 2030 N PHE A 336 66.149 10.678 17.816 1.00 54.55 N
-ATOM 2031 CA PHE A 336 65.009 10.210 17.061 1.00 53.53 C
-ATOM 2032 C PHE A 336 63.799 10.160 17.980 1.00 55.62 C
-ATOM 2033 O PHE A 336 62.745 10.723 17.690 1.00 56.95 O
-ATOM 2034 CB PHE A 336 65.283 8.813 16.523 1.00 52.07 C
-ATOM 2035 CG PHE A 336 64.101 8.177 15.852 1.00 50.00 C
-ATOM 2036 CD1 PHE A 336 63.907 8.311 14.480 1.00 49.65 C
-ATOM 2037 CD2 PHE A 336 63.178 7.446 16.594 1.00 48.84 C
-ATOM 2038 CE1 PHE A 336 62.807 7.724 13.849 1.00 50.11 C
-ATOM 2039 CE2 PHE A 336 62.074 6.856 15.978 1.00 50.56 C
-ATOM 2040 CZ PHE A 336 61.888 6.995 14.598 1.00 50.51 C
-ATOM 2041 N LYS A 337 63.951 9.481 19.105 1.00 54.95 N
-ATOM 2042 CA LYS A 337 62.843 9.358 20.018 1.00 55.90 C
-ATOM 2043 C LYS A 337 62.391 10.670 20.603 1.00 56.26 C
-ATOM 2044 O LYS A 337 61.198 10.890 20.784 1.00 58.11 O
-ATOM 2045 CB LYS A 337 63.193 8.391 21.133 1.00 57.71 C
-ATOM 2046 CG LYS A 337 63.098 6.944 20.717 1.00 60.50 C
-ATOM 2047 CD LYS A 337 63.545 6.055 21.852 1.00 65.23 C
-ATOM 2048 CE LYS A 337 63.215 4.598 21.595 1.00 66.53 C
-ATOM 2049 NZ LYS A 337 63.655 3.815 22.787 1.00 71.30 N
-ATOM 2050 N THR A 338 63.342 11.541 20.901 1.00 56.82 N
-ATOM 2051 CA THR A 338 63.041 12.846 21.487 1.00 57.56 C
-ATOM 2052 C THR A 338 62.183 13.741 20.581 1.00 58.58 C
-ATOM 2053 O THR A 338 61.194 14.339 21.034 1.00 58.55 O
-ATOM 2054 CB THR A 338 64.347 13.601 21.801 1.00 58.82 C
-ATOM 2055 OG1 THR A 338 65.227 12.727 22.516 1.00 58.64 O
-ATOM 2056 CG2 THR A 338 64.062 14.880 22.624 1.00 55.48 C
-ATOM 2057 N LEU A 339 62.584 13.839 19.311 1.00 56.40 N
-ATOM 2058 CA LEU A 339 61.887 14.664 18.342 1.00 56.24 C
-ATOM 2059 C LEU A 339 60.453 14.185 18.093 1.00 58.40 C
-ATOM 2060 O LEU A 339 59.542 14.991 17.897 1.00 60.54 O
-ATOM 2061 CB LEU A 339 62.668 14.688 17.035 1.00 54.10 C
-ATOM 2062 CG LEU A 339 62.193 15.645 15.947 1.00 52.36 C
-ATOM 2063 CD1 LEU A 339 62.275 17.071 16.438 1.00 49.87 C
-ATOM 2064 CD2 LEU A 339 63.068 15.461 14.733 1.00 53.51 C
-ATOM 2065 N CYS A 340 60.247 12.874 18.092 1.00 58.03 N
-ATOM 2066 CA CYS A 340 58.913 12.335 17.884 1.00 56.55 C
-ATOM 2067 C CYS A 340 58.022 12.792 19.034 1.00 57.40 C
-ATOM 2068 O CYS A 340 56.932 13.328 18.828 1.00 58.12 O
-ATOM 2069 CB CYS A 340 58.957 10.808 17.881 1.00 54.79 C
-ATOM 2070 SG CYS A 340 59.718 10.048 16.455 1.00 58.57 S
-ATOM 2071 N LEU A 341 58.523 12.575 20.245 1.00 56.75 N
-ATOM 2072 CA LEU A 341 57.827 12.874 21.480 1.00 55.18 C
-ATOM 2073 C LEU A 341 57.527 14.325 21.778 1.00 54.07 C
-ATOM 2074 O LEU A 341 56.453 14.644 22.276 1.00 55.79 O
-ATOM 2075 CB LEU A 341 58.609 12.292 22.658 1.00 56.85 C
-ATOM 2076 CG LEU A 341 57.828 11.476 23.694 1.00 55.95 C
-ATOM 2077 CD1 LEU A 341 58.414 11.745 25.062 1.00 52.74 C
-ATOM 2078 CD2 LEU A 341 56.346 11.860 23.671 1.00 57.85 C
-ATOM 2079 N HIS A 342 58.465 15.206 21.484 1.00 54.14 N
-ATOM 2080 CA HIS A 342 58.269 16.615 21.775 1.00 55.42 C
-ATOM 2081 C HIS A 342 57.851 17.487 20.598 1.00 56.04 C
-ATOM 2082 O HIS A 342 57.103 18.450 20.751 1.00 56.17 O
-ATOM 2083 CB HIS A 342 59.546 17.151 22.396 1.00 58.70 C
-ATOM 2084 CG HIS A 342 59.909 16.451 23.667 1.00 65.72 C
-ATOM 2085 ND1 HIS A 342 59.257 16.692 24.860 1.00 65.85 N
-ATOM 2086 CD2 HIS A 342 60.788 15.450 23.915 1.00 65.35 C
-ATOM 2087 CE1 HIS A 342 59.718 15.868 25.783 1.00 64.28 C
-ATOM 2088 NE2 HIS A 342 60.646 15.104 25.236 1.00 64.25 N
-ATOM 2089 N GLU A 343 58.315 17.147 19.410 1.00 55.59 N
-ATOM 2090 CA GLU A 343 57.982 17.944 18.261 1.00 53.54 C
-ATOM 2091 C GLU A 343 56.944 17.314 17.372 1.00 52.87 C
-ATOM 2092 O GLU A 343 56.377 17.976 16.514 1.00 56.05 O
-ATOM 2093 CB GLU A 343 59.251 18.229 17.483 1.00 54.31 C
-ATOM 2094 CG GLU A 343 60.211 19.077 18.268 1.00 56.22 C
-ATOM 2095 CD GLU A 343 59.510 20.262 18.903 1.00 59.44 C
-ATOM 2096 OE1 GLU A 343 58.447 20.664 18.366 1.00 61.55 O
-ATOM 2097 OE2 GLU A 343 60.022 20.796 19.918 1.00 59.71 O
-ATOM 2098 N GLY A 344 56.680 16.038 17.580 1.00 49.29 N
-ATOM 2099 CA GLY A 344 55.705 15.381 16.749 1.00 47.93 C
-ATOM 2100 C GLY A 344 56.245 15.179 15.355 1.00 46.49 C
-ATOM 2101 O GLY A 344 55.481 15.152 14.393 1.00 48.31 O
-ATOM 2102 N ILE A 345 57.561 15.039 15.242 1.00 45.34 N
-ATOM 2103 CA ILE A 345 58.196 14.818 13.953 1.00 47.30 C
-ATOM 2104 C ILE A 345 59.045 13.549 13.988 1.00 49.50 C
-ATOM 2105 O ILE A 345 59.967 13.443 14.799 1.00 49.40 O
-ATOM 2106 CB ILE A 345 59.128 15.996 13.553 1.00 47.11 C
-ATOM 2107 CG1 ILE A 345 58.376 17.317 13.611 1.00 47.04 C
-ATOM 2108 CG2 ILE A 345 59.636 15.809 12.131 1.00 47.54 C
-ATOM 2109 CD1 ILE A 345 59.181 18.480 13.103 1.00 46.48 C
-ATOM 2110 N ILE A 346 58.736 12.604 13.100 1.00 50.70 N
-ATOM 2111 CA ILE A 346 59.472 11.337 12.985 1.00 53.10 C
-ATOM 2112 C ILE A 346 60.687 11.606 12.083 1.00 53.04 C
-ATOM 2113 O ILE A 346 60.555 11.603 10.858 1.00 56.31 O
-ATOM 2114 CB ILE A 346 58.611 10.223 12.269 1.00 55.67 C
-ATOM 2115 CG1 ILE A 346 57.176 10.200 12.796 1.00 54.89 C
-ATOM 2116 CG2 ILE A 346 59.239 8.861 12.472 1.00 54.11 C
-ATOM 2117 CD1 ILE A 346 57.105 9.968 14.262 1.00 59.04 C
-ATOM 2118 N PRO A 347 61.879 11.830 12.654 1.00 51.38 N
-ATOM 2119 CA PRO A 347 63.019 12.088 11.778 1.00 50.67 C
-ATOM 2120 C PRO A 347 63.558 10.811 11.172 1.00 50.96 C
-ATOM 2121 O PRO A 347 63.259 9.727 11.650 1.00 52.34 O
-ATOM 2122 CB PRO A 347 64.028 12.715 12.723 1.00 49.14 C
-ATOM 2123 CG PRO A 347 63.839 11.910 13.922 1.00 50.83 C
-ATOM 2124 CD PRO A 347 62.312 11.843 14.057 1.00 51.65 C
-ATOM 2125 N ALA A 348 64.337 10.956 10.103 1.00 53.00 N
-ATOM 2126 CA ALA A 348 64.999 9.841 9.430 1.00 53.58 C
-ATOM 2127 C ALA A 348 66.275 9.616 10.260 1.00 58.08 C
-ATOM 2128 O ALA A 348 66.650 10.477 11.068 1.00 58.63 O
-ATOM 2129 CB ALA A 348 65.364 10.226 8.022 1.00 48.87 C
-ATOM 2130 N LEU A 349 66.951 8.484 10.089 1.00 60.50 N
-ATOM 2131 CA LEU A 349 68.142 8.264 10.889 1.00 61.93 C
-ATOM 2132 C LEU A 349 69.230 9.268 10.555 1.00 64.17 C
-ATOM 2133 O LEU A 349 69.924 9.733 11.452 1.00 66.19 O
-ATOM 2134 CB LEU A 349 68.640 6.844 10.712 1.00 64.68 C
-ATOM 2135 CG LEU A 349 67.694 5.804 11.311 1.00 66.45 C
-ATOM 2136 CD1 LEU A 349 68.128 4.439 10.845 1.00 67.37 C
-ATOM 2137 CD2 LEU A 349 67.698 5.885 12.832 1.00 66.12 C
-ATOM 2138 N GLU A 350 69.379 9.620 9.276 1.00 65.05 N
-ATOM 2139 CA GLU A 350 70.374 10.621 8.875 1.00 63.92 C
-ATOM 2140 C GLU A 350 70.117 11.953 9.645 1.00 63.05 C
-ATOM 2141 O GLU A 350 71.035 12.508 10.233 1.00 64.47 O
-ATOM 2142 CB GLU A 350 70.291 10.834 7.369 1.00 66.88 C
-ATOM 2143 CG GLU A 350 71.507 11.464 6.717 1.00 77.19 C
-ATOM 2144 CD GLU A 350 71.312 11.681 5.191 1.00 85.71 C
-ATOM 2145 OE1 GLU A 350 70.588 12.641 4.807 1.00 87.95 O
-ATOM 2146 OE2 GLU A 350 71.873 10.887 4.376 1.00 87.38 O
-ATOM 2147 N SER A 351 68.881 12.458 9.669 1.00 60.73 N
-ATOM 2148 CA SER A 351 68.588 13.697 10.407 1.00 58.59 C
-ATOM 2149 C SER A 351 68.845 13.493 11.888 1.00 57.78 C
-ATOM 2150 O SER A 351 69.325 14.386 12.582 1.00 56.87 O
-ATOM 2151 CB SER A 351 67.107 14.123 10.286 1.00 59.68 C
-ATOM 2152 OG SER A 351 66.656 14.320 8.953 1.00 61.53 O
-ATOM 2153 N SER A 352 68.477 12.315 12.375 1.00 58.27 N
-ATOM 2154 CA SER A 352 68.614 11.990 13.788 1.00 59.86 C
-ATOM 2155 C SER A 352 70.001 12.222 14.350 1.00 59.90 C
-ATOM 2156 O SER A 352 70.142 12.681 15.480 1.00 60.83 O
-ATOM 2157 CB SER A 352 68.180 10.550 14.035 1.00 60.42 C
-ATOM 2158 OG SER A 352 66.819 10.400 13.682 1.00 63.22 O
-ATOM 2159 N HIS A 353 71.027 11.894 13.578 1.00 59.11 N
-ATOM 2160 CA HIS A 353 72.381 12.123 14.037 1.00 60.55 C
-ATOM 2161 C HIS A 353 72.620 13.647 14.099 1.00 61.98 C
-ATOM 2162 O HIS A 353 73.180 14.174 15.063 1.00 61.82 O
-ATOM 2163 CB HIS A 353 73.380 11.475 13.076 1.00 62.23 C
-ATOM 2164 CG HIS A 353 73.320 9.978 13.056 1.00 64.82 C
-ATOM 2165 ND1 HIS A 353 72.299 9.281 12.449 1.00 66.83 N
-ATOM 2166 CD2 HIS A 353 74.159 9.044 13.562 1.00 63.15 C
-ATOM 2167 CE1 HIS A 353 72.513 7.984 12.580 1.00 63.45 C
-ATOM 2168 NE2 HIS A 353 73.636 7.815 13.252 1.00 62.73 N
-ATOM 2169 N ALA A 354 72.194 14.364 13.066 1.00 61.52 N
-ATOM 2170 CA ALA A 354 72.395 15.798 13.067 1.00 60.74 C
-ATOM 2171 C ALA A 354 71.647 16.379 14.245 1.00 60.80 C
-ATOM 2172 O ALA A 354 72.159 17.265 14.926 1.00 63.13 O
-ATOM 2173 CB ALA A 354 71.897 16.412 11.770 1.00 60.93 C
-ATOM 2174 N LEU A 355 70.439 15.877 14.492 1.00 59.22 N
-ATOM 2175 CA LEU A 355 69.645 16.376 15.601 1.00 57.42 C
-ATOM 2176 C LEU A 355 70.281 16.016 16.946 1.00 57.00 C
-ATOM 2177 O LEU A 355 70.153 16.744 17.932 1.00 56.76 O
-ATOM 2178 CB LEU A 355 68.226 15.817 15.542 1.00 55.41 C
-ATOM 2179 CG LEU A 355 67.415 16.306 16.760 1.00 56.24 C
-ATOM 2180 CD1 LEU A 355 67.523 17.840 16.854 1.00 50.61 C
-ATOM 2181 CD2 LEU A 355 65.953 15.839 16.668 1.00 52.65 C
-ATOM 2182 N ALA A 356 70.961 14.879 16.975 1.00 55.24 N
-ATOM 2183 CA ALA A 356 71.614 14.430 18.177 1.00 54.34 C
-ATOM 2184 C ALA A 356 72.708 15.417 18.566 1.00 58.03 C
-ATOM 2185 O ALA A 356 72.851 15.768 19.752 1.00 60.05 O
-ATOM 2186 CB ALA A 356 72.203 13.058 17.956 1.00 51.29 C
-ATOM 2187 N HIS A 357 73.481 15.883 17.582 1.00 58.73 N
-ATOM 2188 CA HIS A 357 74.553 16.806 17.896 1.00 58.00 C
-ATOM 2189 C HIS A 357 74.038 18.141 18.387 1.00 58.37 C
-ATOM 2190 O HIS A 357 74.630 18.750 19.278 1.00 57.48 O
-ATOM 2191 CB HIS A 357 75.450 17.043 16.708 1.00 59.51 C
-ATOM 2192 CG HIS A 357 76.653 17.865 17.048 1.00 64.94 C
-ATOM 2193 ND1 HIS A 357 77.817 17.312 17.538 1.00 64.94 N
-ATOM 2194 CD2 HIS A 357 76.845 19.206 17.045 1.00 65.63 C
-ATOM 2195 CE1 HIS A 357 78.673 18.277 17.819 1.00 65.86 C
-ATOM 2196 NE2 HIS A 357 78.108 19.437 17.531 1.00 65.89 N
-ATOM 2197 N ALA A 358 72.942 18.605 17.798 1.00 59.53 N
-ATOM 2198 CA ALA A 358 72.360 19.882 18.208 1.00 62.15 C
-ATOM 2199 C ALA A 358 71.926 19.704 19.640 1.00 62.35 C
-ATOM 2200 O ALA A 358 72.137 20.574 20.483 1.00 62.57 O
-ATOM 2201 CB ALA A 358 71.154 20.233 17.347 1.00 62.48 C
-ATOM 2202 N LEU A 359 71.320 18.549 19.898 1.00 62.12 N
-ATOM 2203 CA LEU A 359 70.840 18.199 21.225 1.00 61.09 C
-ATOM 2204 C LEU A 359 71.993 18.191 22.219 1.00 59.26 C
-ATOM 2205 O LEU A 359 71.850 18.640 23.351 1.00 57.03 O
-ATOM 2206 CB LEU A 359 70.159 16.834 21.173 1.00 60.49 C
-ATOM 2207 CG LEU A 359 68.642 16.775 21.348 1.00 58.96 C
-ATOM 2208 CD1 LEU A 359 67.969 18.046 20.832 1.00 57.43 C
-ATOM 2209 CD2 LEU A 359 68.144 15.533 20.630 1.00 59.17 C
-ATOM 2210 N LYS A 360 73.142 17.688 21.790 1.00 58.41 N
-ATOM 2211 CA LYS A 360 74.300 17.675 22.667 1.00 58.83 C
-ATOM 2212 C LYS A 360 74.777 19.119 22.917 1.00 60.42 C
-ATOM 2213 O LYS A 360 75.038 19.495 24.054 1.00 60.76 O
-ATOM 2214 CB LYS A 360 75.404 16.845 22.042 1.00 55.74 C
-ATOM 2215 CG LYS A 360 76.553 16.567 22.959 1.00 54.90 C
-ATOM 2216 CD LYS A 360 77.518 15.594 22.289 1.00 56.67 C
-ATOM 2217 CE LYS A 360 76.832 14.258 21.939 1.00 55.66 C
-ATOM 2218 NZ LYS A 360 77.720 13.334 21.176 1.00 54.59 N
-ATOM 2219 N MET A 361 74.866 19.934 21.863 1.00 61.12 N
-ATOM 2220 CA MET A 361 75.297 21.325 22.016 1.00 61.31 C
-ATOM 2221 C MET A 361 74.416 22.069 23.026 1.00 63.50 C
-ATOM 2222 O MET A 361 74.909 22.790 23.892 1.00 64.36 O
-ATOM 2223 CB MET A 361 75.261 22.050 20.666 1.00 59.64 C
-ATOM 2224 CG MET A 361 76.297 21.556 19.672 1.00 57.47 C
-ATOM 2225 SD MET A 361 76.282 22.375 18.061 1.00 57.21 S
-ATOM 2226 CE MET A 361 76.170 24.072 18.480 1.00 51.54 C
-ATOM 2227 N MET A 362 73.106 21.892 22.908 1.00 65.54 N
-ATOM 2228 CA MET A 362 72.159 22.533 23.814 1.00 66.13 C
-ATOM 2229 C MET A 362 72.344 21.991 25.251 1.00 66.31 C
-ATOM 2230 O MET A 362 72.582 22.737 26.200 1.00 64.63 O
-ATOM 2231 CB MET A 362 70.729 22.263 23.327 1.00 64.22 C
-ATOM 2232 CG MET A 362 69.636 22.721 24.283 1.00 63.49 C
-ATOM 2233 SD MET A 362 68.011 22.023 23.900 1.00 64.43 S
-ATOM 2234 CE MET A 362 68.467 20.231 23.663 1.00 57.50 C
-ATOM 2235 N ARG A 363 72.241 20.679 25.392 1.00 66.49 N
-ATOM 2236 CA ARG A 363 72.374 20.044 26.683 1.00 65.59 C
-ATOM 2237 C ARG A 363 73.671 20.364 27.401 1.00 68.49 C
-ATOM 2238 O ARG A 363 73.658 20.580 28.618 1.00 68.99 O
-ATOM 2239 CB ARG A 363 72.199 18.546 26.515 1.00 62.46 C
-ATOM 2240 CG ARG A 363 70.749 18.176 26.247 1.00 60.41 C
-ATOM 2241 CD ARG A 363 70.636 16.781 25.690 1.00 57.80 C
-ATOM 2242 NE ARG A 363 69.252 16.375 25.459 1.00 56.60 N
-ATOM 2243 CZ ARG A 363 68.948 15.243 24.843 1.00 55.83 C
-ATOM 2244 NH1 ARG A 363 69.936 14.467 24.433 1.00 54.57 N
-ATOM 2245 NH2 ARG A 363 67.692 14.886 24.631 1.00 52.88 N
-ATOM 2246 N GLU A 364 74.784 20.409 26.667 1.00 70.94 N
-ATOM 2247 CA GLU A 364 76.077 20.728 27.280 1.00 71.36 C
-ATOM 2248 C GLU A 364 76.010 22.085 27.966 1.00 72.35 C
-ATOM 2249 O GLU A 364 76.173 22.156 29.171 1.00 73.94 O
-ATOM 2250 CB GLU A 364 77.198 20.712 26.253 1.00 71.24 C
-ATOM 2251 CG GLU A 364 78.252 19.688 26.578 1.00 72.38 C
-ATOM 2252 CD GLU A 364 78.708 18.909 25.357 1.00 76.40 C
-ATOM 2253 OE1 GLU A 364 79.166 19.546 24.363 1.00 76.70 O
-ATOM 2254 OE2 GLU A 364 78.604 17.656 25.401 1.00 75.38 O
-ATOM 2255 N ASN A 365 75.782 23.170 27.237 1.00 73.26 N
-ATOM 2256 CA ASN A 365 75.661 24.426 27.952 1.00 75.22 C
-ATOM 2257 C ASN A 365 74.267 25.035 27.822 1.00 75.12 C
-ATOM 2258 O ASN A 365 73.988 25.834 26.917 1.00 75.48 O
-ATOM 2259 CB ASN A 365 76.719 25.437 27.531 1.00 79.46 C
-ATOM 2260 CG ASN A 365 76.994 26.463 28.641 1.00 85.51 C
-ATOM 2261 OD1 ASN A 365 76.135 27.296 28.990 1.00 86.30 O
-ATOM 2262 ND2 ASN A 365 78.188 26.383 29.223 1.00 89.33 N
-ATOM 2263 N PRO A 366 73.367 24.656 28.744 1.00 73.45 N
-ATOM 2264 CA PRO A 366 71.978 25.107 28.816 1.00 72.42 C
-ATOM 2265 C PRO A 366 71.822 26.607 28.772 1.00 72.69 C
-ATOM 2266 O PRO A 366 70.741 27.122 28.455 1.00 74.01 O
-ATOM 2267 CB PRO A 366 71.507 24.527 30.137 1.00 70.87 C
-ATOM 2268 CG PRO A 366 72.235 23.232 30.173 1.00 72.57 C
-ATOM 2269 CD PRO A 366 73.626 23.630 29.767 1.00 71.44 C
-ATOM 2270 N ASP A 367 72.898 27.316 29.076 1.00 71.79 N
-ATOM 2271 CA ASP A 367 72.810 28.752 29.088 1.00 72.55 C
-ATOM 2272 C ASP A 367 73.362 29.472 27.908 1.00 70.93 C
-ATOM 2273 O ASP A 367 72.954 30.592 27.637 1.00 70.35 O
-ATOM 2274 CB ASP A 367 73.452 29.304 30.340 1.00 79.86 C
-ATOM 2275 CG ASP A 367 72.555 29.173 31.536 1.00 86.06 C
-ATOM 2276 OD1 ASP A 367 71.365 29.574 31.420 1.00 88.65 O
-ATOM 2277 OD2 ASP A 367 73.034 28.670 32.584 1.00 91.30 O
-ATOM 2278 N LYS A 368 74.300 28.864 27.206 1.00 69.82 N
-ATOM 2279 CA LYS A 368 74.855 29.545 26.052 1.00 69.49 C
-ATOM 2280 C LYS A 368 73.654 29.881 25.208 1.00 71.05 C
-ATOM 2281 O LYS A 368 72.875 28.995 24.856 1.00 73.73 O
-ATOM 2282 CB LYS A 368 75.795 28.626 25.278 1.00 67.73 C
-ATOM 2283 CG LYS A 368 76.589 29.316 24.199 1.00 64.97 C
-ATOM 2284 CD LYS A 368 77.610 28.353 23.654 1.00 66.28 C
-ATOM 2285 CE LYS A 368 78.627 29.020 22.737 1.00 68.89 C
-ATOM 2286 NZ LYS A 368 79.660 28.021 22.277 1.00 69.89 N
-ATOM 2287 N GLU A 369 73.465 31.159 24.927 1.00 70.20 N
-ATOM 2288 CA GLU A 369 72.346 31.565 24.103 1.00 69.31 C
-ATOM 2289 C GLU A 369 72.795 31.287 22.669 1.00 68.85 C
-ATOM 2290 O GLU A 369 73.532 32.065 22.090 1.00 71.14 O
-ATOM 2291 CB GLU A 369 72.075 33.042 24.332 1.00 71.57 C
-ATOM 2292 CG GLU A 369 71.365 33.739 23.196 1.00 83.60 C
-ATOM 2293 CD GLU A 369 71.005 35.193 23.528 1.00 91.80 C
-ATOM 2294 OE1 GLU A 369 70.518 35.920 22.615 1.00 93.56 O
-ATOM 2295 OE2 GLU A 369 71.208 35.607 24.707 1.00 96.29 O
-ATOM 2296 N GLN A 370 72.371 30.161 22.103 1.00 67.85 N
-ATOM 2297 CA GLN A 370 72.760 29.790 20.743 1.00 64.61 C
-ATOM 2298 C GLN A 370 71.586 29.506 19.794 1.00 64.00 C
-ATOM 2299 O GLN A 370 70.559 28.965 20.202 1.00 64.99 O
-ATOM 2300 CB GLN A 370 73.691 28.583 20.803 1.00 63.27 C
-ATOM 2301 CG GLN A 370 73.135 27.414 21.569 1.00 61.33 C
-ATOM 2302 CD GLN A 370 74.199 26.369 21.862 1.00 64.92 C
-ATOM 2303 OE1 GLN A 370 75.280 26.394 21.266 1.00 62.72 O
-ATOM 2304 NE2 GLN A 370 73.896 25.431 22.774 1.00 65.52 N
-ATOM 2305 N LEU A 371 71.765 29.882 18.527 1.00 61.62 N
-ATOM 2306 CA LEU A 371 70.773 29.722 17.459 1.00 58.03 C
-ATOM 2307 C LEU A 371 71.264 28.670 16.476 1.00 57.54 C
-ATOM 2308 O LEU A 371 72.187 28.907 15.695 1.00 57.20 O
-ATOM 2309 CB LEU A 371 70.608 31.047 16.739 1.00 58.07 C
-ATOM 2310 CG LEU A 371 69.699 31.093 15.528 1.00 57.81 C
-ATOM 2311 CD1 LEU A 371 68.366 30.467 15.895 1.00 56.34 C
-ATOM 2312 CD2 LEU A 371 69.533 32.551 15.075 1.00 56.47 C
-ATOM 2313 N LEU A 372 70.621 27.515 16.489 1.00 55.94 N
-ATOM 2314 CA LEU A 372 71.051 26.409 15.644 1.00 53.83 C
-ATOM 2315 C LEU A 372 70.067 26.025 14.569 1.00 51.61 C
-ATOM 2316 O LEU A 372 68.869 26.171 14.748 1.00 54.88 O
-ATOM 2317 CB LEU A 372 71.282 25.181 16.526 1.00 54.39 C
-ATOM 2318 CG LEU A 372 72.143 25.374 17.776 1.00 53.85 C
-ATOM 2319 CD1 LEU A 372 72.100 24.123 18.626 1.00 54.34 C
-ATOM 2320 CD2 LEU A 372 73.561 25.689 17.364 1.00 54.82 C
-ATOM 2321 N VAL A 373 70.559 25.525 13.449 1.00 47.53 N
-ATOM 2322 CA VAL A 373 69.650 25.059 12.422 1.00 46.19 C
-ATOM 2323 C VAL A 373 70.086 23.641 12.056 1.00 47.63 C
-ATOM 2324 O VAL A 373 71.267 23.382 11.849 1.00 46.82 O
-ATOM 2325 CB VAL A 373 69.671 25.957 11.177 1.00 44.31 C
-ATOM 2326 CG1 VAL A 373 68.939 25.284 10.056 1.00 43.67 C
-ATOM 2327 CG2 VAL A 373 69.006 27.283 11.476 1.00 42.42 C
-ATOM 2328 N VAL A 374 69.138 22.714 12.018 1.00 47.67 N
-ATOM 2329 CA VAL A 374 69.453 21.338 11.662 1.00 48.38 C
-ATOM 2330 C VAL A 374 68.794 21.004 10.343 1.00 47.96 C
-ATOM 2331 O VAL A 374 67.596 21.221 10.169 1.00 48.04 O
-ATOM 2332 CB VAL A 374 68.955 20.324 12.734 1.00 49.64 C
-ATOM 2333 CG1 VAL A 374 69.073 18.861 12.226 1.00 44.97 C
-ATOM 2334 CG2 VAL A 374 69.766 20.497 13.983 1.00 51.45 C
-ATOM 2335 N ASN A 375 69.591 20.481 9.418 1.00 47.01 N
-ATOM 2336 CA ASN A 375 69.084 20.099 8.120 1.00 49.22 C
-ATOM 2337 C ASN A 375 68.393 18.750 8.245 1.00 50.82 C
-ATOM 2338 O ASN A 375 69.018 17.776 8.658 1.00 53.28 O
-ATOM 2339 CB ASN A 375 70.223 19.981 7.117 1.00 47.68 C
-ATOM 2340 CG ASN A 375 69.715 19.938 5.702 1.00 49.33 C
-ATOM 2341 OD1 ASN A 375 69.159 20.907 5.223 1.00 53.40 O
-ATOM 2342 ND2 ASN A 375 69.882 18.814 5.030 1.00 52.31 N
-ATOM 2343 N LEU A 376 67.116 18.670 7.893 1.00 50.82 N
-ATOM 2344 CA LEU A 376 66.415 17.398 7.995 1.00 52.07 C
-ATOM 2345 C LEU A 376 66.511 16.596 6.700 1.00 56.59 C
-ATOM 2346 O LEU A 376 66.035 17.046 5.672 1.00 58.32 O
-ATOM 2347 CB LEU A 376 64.965 17.655 8.355 1.00 48.80 C
-ATOM 2348 CG LEU A 376 64.511 17.106 9.709 1.00 49.39 C
-ATOM 2349 CD1 LEU A 376 65.647 17.042 10.696 1.00 48.10 C
-ATOM 2350 CD2 LEU A 376 63.386 17.976 10.232 1.00 48.51 C
-ATOM 2351 N SER A 377 67.137 15.419 6.753 1.00 62.47 N
-ATOM 2352 CA SER A 377 67.300 14.557 5.576 1.00 69.80 C
-ATOM 2353 C SER A 377 65.955 14.115 4.948 1.00 75.80 C
-ATOM 2354 O SER A 377 65.377 14.882 4.178 1.00 79.43 O
-ATOM 2355 CB SER A 377 68.148 13.325 5.918 1.00 70.12 C
-ATOM 2356 OG SER A 377 67.433 12.383 6.707 1.00 72.27 O
-ATOM 2357 N GLY A 378 65.426 12.920 5.229 1.00 78.55 N
-ATOM 2358 CA GLY A 378 64.170 12.638 4.561 1.00 83.95 C
-ATOM 2359 C GLY A 378 63.246 11.444 4.719 1.00 89.08 C
-ATOM 2360 O GLY A 378 62.082 11.624 5.108 1.00 89.15 O
-ATOM 2361 N ARG A 379 63.712 10.239 4.385 1.00 94.01 N
-ATOM 2362 CA ARG A 379 62.842 9.051 4.473 1.00 97.64 C
-ATOM 2363 C ARG A 379 62.382 8.660 5.893 1.00 98.26 C
-ATOM 2364 O ARG A 379 62.442 7.483 6.281 1.00 97.03 O
-ATOM 2365 CB ARG A 379 63.506 7.859 3.751 1.00 98.03 C
-ATOM 2366 CG ARG A 379 65.005 7.772 3.871 1.00 98.17 C
-ATOM 2367 CD ARG A 379 65.539 6.738 2.892 1.00 99.93 C
-ATOM 2368 NE ARG A 379 66.472 5.797 3.523 1.00103.91 N
-ATOM 2369 CZ ARG A 379 67.703 6.099 3.948 1.00104.42 C
-ATOM 2370 NH1 ARG A 379 68.184 7.332 3.811 1.00102.62 N
-ATOM 2371 NH2 ARG A 379 68.452 5.164 4.527 1.00104.51 N
-ATOM 2372 N GLY A 380 61.889 9.671 6.624 1.00 99.37 N
-ATOM 2373 CA GLY A 380 61.414 9.533 7.998 1.00 99.61 C
-ATOM 2374 C GLY A 380 60.500 8.359 8.272 1.00100.44 C
-ATOM 2375 O GLY A 380 60.649 7.670 9.285 1.00 99.86 O
-ATOM 2376 N ASP A 381 59.549 8.134 7.371 1.00101.00 N
-ATOM 2377 CA ASP A 381 58.622 7.023 7.512 1.00101.37 C
-ATOM 2378 C ASP A 381 58.919 5.890 6.524 1.00 99.89 C
-ATOM 2379 O ASP A 381 58.040 5.102 6.164 1.00 99.39 O
-ATOM 2380 CB ASP A 381 57.178 7.516 7.377 1.00102.85 C
-ATOM 2381 CG ASP A 381 56.738 8.341 8.580 1.00104.87 C
-ATOM 2382 OD1 ASP A 381 57.000 7.901 9.724 1.00105.99 O
-ATOM 2383 OD2 ASP A 381 56.132 9.422 8.391 1.00105.43 O
-ATOM 2384 N LYS A 382 60.176 5.815 6.102 1.00 97.20 N
-ATOM 2385 CA LYS A 382 60.616 4.765 5.199 1.00 95.55 C
-ATOM 2386 C LYS A 382 61.586 3.890 6.014 1.00 95.18 C
-ATOM 2387 O LYS A 382 61.481 2.655 6.031 1.00 94.87 O
-ATOM 2388 CB LYS A 382 61.294 5.390 3.981 1.00 95.57 C
-ATOM 2389 CG LYS A 382 60.491 6.557 3.395 1.00 93.08 C
-ATOM 2390 CD LYS A 382 60.924 6.893 1.975 1.00 91.26 C
-ATOM 2391 CE LYS A 382 60.553 5.776 1.009 1.00 89.86 C
-ATOM 2392 NZ LYS A 382 59.084 5.497 0.995 1.00 87.53 N
-ATOM 2393 N ASP A 383 62.517 4.528 6.717 1.00 93.00 N
-ATOM 2394 CA ASP A 383 63.433 3.769 7.554 1.00 89.31 C
-ATOM 2395 C ASP A 383 62.933 3.836 9.015 1.00 86.97 C
-ATOM 2396 O ASP A 383 63.710 3.880 9.969 1.00 85.65 O
-ATOM 2397 CB ASP A 383 64.878 4.283 7.386 1.00 89.71 C
-ATOM 2398 CG ASP A 383 65.086 5.664 7.946 1.00 88.34 C
-ATOM 2399 OD1 ASP A 383 66.169 6.238 7.703 1.00 86.64 O
-ATOM 2400 OD2 ASP A 383 64.176 6.168 8.635 1.00 90.01 O
-ATOM 2401 N ILE A 384 61.604 3.851 9.145 1.00 84.30 N
-ATOM 2402 CA ILE A 384 60.870 3.852 10.417 1.00 79.77 C
-ATOM 2403 C ILE A 384 60.876 2.383 10.838 1.00 79.99 C
-ATOM 2404 O ILE A 384 60.732 2.042 12.012 1.00 80.46 O
-ATOM 2405 CB ILE A 384 59.389 4.278 10.198 1.00 76.95 C
-ATOM 2406 CG1 ILE A 384 58.596 4.233 11.497 1.00 72.75 C
-ATOM 2407 CG2 ILE A 384 58.716 3.329 9.235 1.00 78.19 C
-ATOM 2408 CD1 ILE A 384 58.627 5.507 12.244 1.00 70.37 C
-ATOM 2409 N PHE A 385 61.041 1.526 9.831 1.00 80.37 N
-ATOM 2410 CA PHE A 385 61.075 0.076 9.982 1.00 78.22 C
-ATOM 2411 C PHE A 385 62.377 -0.424 10.608 1.00 76.05 C
-ATOM 2412 O PHE A 385 62.348 -1.213 11.549 1.00 74.70 O
-ATOM 2413 CB PHE A 385 60.851 -0.574 8.619 1.00 78.57 C
-ATOM 2414 CG PHE A 385 59.485 -0.301 8.032 1.00 82.09 C
-ATOM 2415 CD1 PHE A 385 59.265 -0.403 6.658 1.00 84.79 C
-ATOM 2416 CD2 PHE A 385 58.408 0.015 8.849 1.00 82.35 C
-ATOM 2417 CE1 PHE A 385 57.989 -0.198 6.109 1.00 83.74 C
-ATOM 2418 CE2 PHE A 385 57.129 0.221 8.307 1.00 83.10 C
-ATOM 2419 CZ PHE A 385 56.922 0.113 6.936 1.00 81.89 C
-ATOM 2420 N THR A 386 63.521 0.028 10.109 1.00 74.37 N
-ATOM 2421 CA THR A 386 64.766 -0.427 10.709 1.00 74.19 C
-ATOM 2422 C THR A 386 64.897 0.059 12.149 1.00 74.66 C
-ATOM 2423 O THR A 386 65.682 -0.474 12.925 1.00 75.68 O
-ATOM 2424 CB THR A 386 65.996 -0.001 9.894 1.00 71.90 C
-ATOM 2425 OG1 THR A 386 65.930 1.393 9.604 1.00 66.68 O
-ATOM 2426 CG2 THR A 386 66.056 -0.803 8.600 1.00 73.44 C
-ATOM 2427 N VAL A 387 64.120 1.067 12.510 1.00 75.15 N
-ATOM 2428 CA VAL A 387 64.156 1.561 13.866 1.00 75.26 C
-ATOM 2429 C VAL A 387 63.261 0.647 14.686 1.00 77.29 C
-ATOM 2430 O VAL A 387 63.562 0.325 15.832 1.00 77.22 O
-ATOM 2431 CB VAL A 387 63.662 2.998 13.935 1.00 74.73 C
-ATOM 2432 CG1 VAL A 387 63.530 3.437 15.388 1.00 73.32 C
-ATOM 2433 CG2 VAL A 387 64.644 3.893 13.201 1.00 73.69 C
-ATOM 2434 N HIS A 388 62.154 0.217 14.095 1.00 79.70 N
-ATOM 2435 CA HIS A 388 61.255 -0.693 14.791 1.00 81.27 C
-ATOM 2436 C HIS A 388 62.088 -1.913 15.154 1.00 80.71 C
-ATOM 2437 O HIS A 388 61.964 -2.458 16.246 1.00 80.26 O
-ATOM 2438 CB HIS A 388 60.100 -1.097 13.876 1.00 84.39 C
-ATOM 2439 CG HIS A 388 59.046 -1.916 14.555 1.00 88.33 C
-ATOM 2440 ND1 HIS A 388 57.750 -1.998 14.085 1.00 90.24 N
-ATOM 2441 CD2 HIS A 388 59.092 -2.688 15.667 1.00 89.20 C
-ATOM 2442 CE1 HIS A 388 57.044 -2.782 14.880 1.00 91.29 C
-ATOM 2443 NE2 HIS A 388 57.835 -3.214 15.848 1.00 91.37 N
-ATOM 2444 N ASP A 389 62.948 -2.322 14.221 1.00 80.92 N
-ATOM 2445 CA ASP A 389 63.838 -3.465 14.403 1.00 78.68 C
-ATOM 2446 C ASP A 389 64.872 -3.149 15.469 1.00 78.03 C
-ATOM 2447 O ASP A 389 64.890 -3.785 16.508 1.00 77.40 O
-ATOM 2448 CB ASP A 389 64.518 -3.803 13.087 1.00 77.68 C
-ATOM 2449 CG ASP A 389 63.520 -4.085 11.987 1.00 79.17 C
-ATOM 2450 OD1 ASP A 389 62.403 -4.550 12.310 1.00 79.13 O
-ATOM 2451 OD2 ASP A 389 63.850 -3.857 10.803 1.00 79.79 O
-ATOM 2452 N ILE A 390 65.732 -2.169 15.214 1.00 78.47 N
-ATOM 2453 CA ILE A 390 66.729 -1.760 16.201 1.00 80.70 C
-ATOM 2454 C ILE A 390 66.133 -1.868 17.614 1.00 82.21 C
-ATOM 2455 O ILE A 390 66.775 -2.392 18.522 1.00 84.61 O
-ATOM 2456 CB ILE A 390 67.165 -0.281 15.997 1.00 81.53 C
-ATOM 2457 CG1 ILE A 390 67.818 -0.088 14.628 1.00 80.20 C
-ATOM 2458 CG2 ILE A 390 68.115 0.138 17.112 1.00 81.04 C
-ATOM 2459 CD1 ILE A 390 69.267 -0.497 14.560 1.00 82.28 C
-ATOM 2460 N LEU A 391 64.908 -1.368 17.791 1.00 83.11 N
-ATOM 2461 CA LEU A 391 64.223 -1.404 19.089 1.00 83.92 C
-ATOM 2462 C LEU A 391 63.682 -2.786 19.480 1.00 83.95 C
-ATOM 2463 O LEU A 391 63.881 -3.223 20.606 1.00 82.85 O
-ATOM 2464 CB LEU A 391 63.082 -0.377 19.130 1.00 82.02 C
-ATOM 2465 CG LEU A 391 63.459 1.105 19.108 1.00 79.56 C
-ATOM 2466 CD1 LEU A 391 62.210 1.953 19.019 1.00 78.17 C
-ATOM 2467 CD2 LEU A 391 64.232 1.446 20.352 1.00 80.00 C
-ATOM 2468 N LYS A 392 62.989 -3.475 18.577 1.00 85.78 N
-ATOM 2469 CA LYS A 392 62.494 -4.803 18.928 1.00 89.19 C
-ATOM 2470 C LYS A 392 63.715 -5.672 19.240 1.00 91.13 C
-ATOM 2471 O LYS A 392 63.704 -6.475 20.178 1.00 91.51 O
-ATOM 2472 CB LYS A 392 61.657 -5.411 17.791 1.00 89.47 C
-ATOM 2473 CG LYS A 392 61.143 -6.826 18.089 1.00 89.98 C
-ATOM 2474 CD LYS A 392 59.886 -7.202 17.276 1.00 91.20 C
-ATOM 2475 CE LYS A 392 58.592 -6.640 17.907 1.00 91.19 C
-ATOM 2476 NZ LYS A 392 57.362 -7.096 17.188 1.00 86.27 N
-ATOM 2477 N ALA A 393 64.772 -5.483 18.453 1.00 92.28 N
-ATOM 2478 CA ALA A 393 66.028 -6.192 18.650 1.00 92.10 C
-ATOM 2479 C ALA A 393 66.496 -5.874 20.065 1.00 92.84 C
-ATOM 2480 O ALA A 393 66.285 -6.664 20.979 1.00 93.93 O
-ATOM 2481 CB ALA A 393 67.074 -5.716 17.644 1.00 90.79 C
-ATOM 2482 N ARG A 394 67.113 -4.707 20.236 1.00 92.16 N
-ATOM 2483 CA ARG A 394 67.619 -4.268 21.532 1.00 92.07 C
-ATOM 2484 C ARG A 394 66.660 -4.449 22.713 1.00 92.96 C
-ATOM 2485 O ARG A 394 66.934 -3.971 23.813 1.00 93.36 O
-ATOM 2486 CB ARG A 394 68.060 -2.809 21.430 1.00 91.41 C
-ATOM 2487 CG ARG A 394 69.268 -2.652 20.535 1.00 93.49 C
-ATOM 2488 CD ARG A 394 69.403 -1.270 19.908 1.00 94.71 C
-ATOM 2489 NE ARG A 394 69.924 -0.234 20.801 1.00 95.19 N
-ATOM 2490 CZ ARG A 394 69.214 0.372 21.747 1.00 95.47 C
-ATOM 2491 NH1 ARG A 394 67.941 0.043 21.942 1.00 94.25 N
-ATOM 2492 NH2 ARG A 394 69.771 1.333 22.472 1.00 93.95 N
-ATOM 2493 N GLY A 395 65.537 -5.127 22.480 1.00 93.48 N
-ATOM 2494 CA GLY A 395 64.571 -5.386 23.536 1.00 94.79 C
-ATOM 2495 C GLY A 395 63.766 -4.217 24.082 1.00 96.78 C
-ATOM 2496 O GLY A 395 62.786 -4.441 24.796 1.00 95.92 O
-ATOM 2497 N GLU A 396 64.174 -2.984 23.765 1.00 98.11 N
-ATOM 2498 CA GLU A 396 63.469 -1.786 24.230 1.00 99.11 C
-ATOM 2499 C GLU A 396 62.023 -1.784 23.749 1.00 99.15 C
-ATOM 2500 O GLU A 396 61.187 -1.070 24.301 1.00 98.52 O
-ATOM 2501 CB GLU A 396 64.138 -0.499 23.721 1.00 99.80 C
-ATOM 2502 CG GLU A 396 65.607 -0.317 24.082 1.00102.19 C
-ATOM 2503 CD GLU A 396 66.064 1.142 23.965 1.00103.97 C
-ATOM 2504 OE1 GLU A 396 67.278 1.418 24.106 1.00103.57 O
-ATOM 2505 OE2 GLU A 396 65.204 2.021 23.743 1.00105.40 O
-ATOM 2506 N ILE A 397 61.741 -2.572 22.712 1.00 99.58 N
-ATOM 2507 CA ILE A 397 60.397 -2.650 22.149 1.00100.03 C
-ATOM 2508 C ILE A 397 59.417 -3.050 23.232 1.00101.45 C
-ATOM 2509 O ILE A 397 58.751 -2.140 23.767 1.00103.73 O
-ATOM 2510 CB ILE A 397 60.324 -3.682 20.998 1.00100.17 C
-ATOM 2511 CG1 ILE A 397 58.930 -3.659 20.351 1.00 98.26 C
-ATOM 2512 CG2 ILE A 397 60.701 -5.085 21.520 1.00 98.24 C
-ATOM 2513 CD1 ILE A 397 57.906 -4.572 21.001 1.00 96.68 C
-ATOM 2514 OXT ILE A 397 59.338 -4.255 23.550 1.00101.23 O
-TER 2515 ILE A 397
-HETATM 2516 S SO4 801 69.043 7.012 -9.193 1.00 66.31 S
-HETATM 2517 O1 SO4 801 69.648 5.706 -8.897 1.00 68.30 O
-HETATM 2518 O2 SO4 801 68.821 7.147 -10.634 1.00 69.35 O
-HETATM 2519 O3 SO4 801 67.736 7.108 -8.505 1.00 63.38 O
-HETATM 2520 O4 SO4 801 70.013 8.049 -8.788 1.00 67.40 O
-HETATM 2521 S SO4 802 65.764 12.613 -3.024 1.00122.71 S
-HETATM 2522 O1 SO4 802 64.653 13.293 -2.314 1.00122.21 O
-HETATM 2523 O2 SO4 802 65.491 11.162 -3.117 1.00121.98 O
-HETATM 2524 O3 SO4 802 65.883 13.183 -4.375 1.00122.41 O
-HETATM 2525 O4 SO4 802 67.045 12.824 -2.321 1.00119.97 O
-HETATM 2526 S SO4 803 58.623 31.383 4.559 1.00107.36 S
-HETATM 2527 O1 SO4 803 57.430 32.257 4.562 1.00107.44 O
-HETATM 2528 O2 SO4 803 58.210 30.015 4.932 1.00108.48 O
-HETATM 2529 O3 SO4 803 59.264 31.351 3.223 1.00106.54 O
-HETATM 2530 O4 SO4 803 59.588 31.916 5.543 1.00107.97 O
-HETATM 2531 O HOH 1001 66.831 -5.950 -21.554 1.00 43.58 O
-HETATM 2532 O HOH 1002 65.180 -6.209 -19.516 1.00 41.65 O
-HETATM 2533 O HOH 1003 62.688 29.282 -4.030 1.00 34.17 O
-HETATM 2534 O HOH 1004 67.580 31.198 -8.353 1.00 44.19 O
-HETATM 2535 O HOH 1005 75.239 16.003 -1.158 1.00 39.55 O
-HETATM 2536 O HOH 1006 72.167 30.197 -10.130 1.00 61.12 O
-HETATM 2537 O HOH 1007 56.615 -0.232 -19.458 1.00 45.44 O
-HETATM 2538 O HOH 1008 54.711 11.001 10.088 1.00 50.45 O
-HETATM 2539 O HOH 1009 74.094 25.909 -27.795 1.00 51.85 O
-HETATM 2540 O HOH 1010 57.981 28.061 12.982 1.00 43.12 O
-HETATM 2541 O HOH 1011 56.654 12.901 10.569 1.00 59.80 O
-HETATM 2542 O HOH 1012 56.249 17.358 -10.214 1.00 42.97 O
-HETATM 2543 O HOH 1013 58.199 13.864 8.194 1.00 58.34 O
-HETATM 2544 O HOH 1014 84.797 21.480 -8.429 1.00 47.41 O
-HETATM 2545 O HOH 1015 73.057 8.384 -11.162 1.00 37.43 O
-HETATM 2546 O HOH 1016 61.749 32.271 1.216 1.00 32.23 O
-HETATM 2547 O HOH 1017 56.885 27.950 3.803 1.00 38.41 O
-HETATM 2548 O HOH 1018 57.120 18.339 25.504 1.00 42.95 O
-HETATM 2549 O HOH 1019 73.887 30.162 -24.485 1.00 31.25 O
-HETATM 2550 O HOH 1020 63.805 17.814 26.471 1.00 49.84 O
-HETATM 2551 O HOH 1021 80.312 11.302 0.318 1.00 46.36 O
-HETATM 2552 O HOH 1022 57.406 10.099 -0.875 1.00 58.56 O
-HETATM 2553 O HOH 1023 57.120 -1.779 -16.724 1.00 58.40 O
-CONECT 2516 2517 2518 2519 2520
-CONECT 2517 2516
-CONECT 2518 2516
-CONECT 2519 2516
-CONECT 2520 2516
-CONECT 2521 2522 2523 2524 2525
-CONECT 2522 2521
-CONECT 2523 2521
-CONECT 2524 2521
-CONECT 2525 2521
-CONECT 2526 2527 2528 2529 2530
-CONECT 2527 2526
-CONECT 2528 2526
-CONECT 2529 2526
-CONECT 2530 2526
-MASTER 353 0 3 16 10 0 0 6 2552 1 15 31
-END
diff --git a/data/spx.vtk b/data/spx.vtk
deleted file mode 100755
index 7db9582..0000000
--- a/data/spx.vtk
+++ /dev/null
@@ -1,31678 +0,0 @@
-# vtk DataFile Version 3.0
-off file: spx.off
-ASCII
-DATASET UNSTRUCTURED_GRID
-
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diff --git a/data/torus.vtk b/data/torus.vtk
deleted file mode 100755
index 20970ca..0000000
--- a/data/torus.vtk
+++ /dev/null
@@ -1,22046 +0,0 @@
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diff --git a/data/vslice_circ1.bp b/data/vslice_circ1.bp
deleted file mode 100644
index 261fff5..0000000
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-97 337408.437500 289107.937500 1.000000
-98 337550.437500 289237.125000 1.000000
-99 337687.375000 289371.687500 1.000000
-100 337819.031250 289511.375000 1.000000
diff --git a/doc/dist/instructions.txt b/doc/dist/instructions.txt
index 9095b06..f6bb7b3 100644
--- a/doc/dist/instructions.txt
+++ b/doc/dist/instructions.txt
@@ -104,6 +104,7 @@ Make sure the generated users guide is saved to the correct path by
editing the following file:
scripts/build_usersguide.py
By default it is configured for mac
+Make sure the correct branch is used (by default in ~/code/vistrails)
Now run the following:
$ cd dist/mac/
diff --git a/doc/usersguide/conf.py b/doc/usersguide/conf.py
index 935f009..adbbffb 100644
--- a/doc/usersguide/conf.py
+++ b/doc/usersguide/conf.py
@@ -38,7 +38,7 @@ master_doc = 'index'
# General information about the project.
project = u'VisTrails'
-copyright = u'2013, NYU Poly'
+copyright = u'2014, NYU Poly'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@@ -47,7 +47,7 @@ copyright = u'2013, NYU Poly'
# The short X.Y version.
version = '2.1'
# The full version, including alpha/beta/rc tags.
-release = '2.1.1'
+release = '2.1.4'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
diff --git a/doc/usersguide/controlflow.rst b/doc/usersguide/controlflow.rst
index 802e5a0..c2b5260 100644
--- a/doc/usersguide/controlflow.rst
+++ b/doc/usersguide/controlflow.rst
@@ -473,6 +473,8 @@ the previous run.
workflows and that we are twisting it's execution model a little, but this
will demonstrate the functionality should you actually need it.
+ Note that you can find the completed example here: :vtl:`gcd.vt`.
+
The modules we are going to need are:
* ``And``
diff --git a/doc/usersguide/creating.rst b/doc/usersguide/creating.rst
index ff9fa1f..12437e2 100644
--- a/doc/usersguide/creating.rst
+++ b/doc/usersguide/creating.rst
@@ -235,11 +235,9 @@ Configuring Module Ports
pair: ports; adding
pair: ports; deleting
-For convenience, all the inputs and outputs of a module are not always
-shown in the canvas as ports. The ports that are shown by default are
-defined with the method signatures of a package. A full list of ports is available in the ``Module Configuraton`` window, which is accessed by clicking on the ``Configure`` button in the module information tab or pressing 'Ctrl-E' when a module is selected. Alternatively, module ports can be enabled/disabled by clicking in the left margin next to the port name in the ``Inputs`` or ``Outputs`` tabs of the ``Module Information`` tab (see Figure :ref:`Enabling the GetRadius port from the [...]
-
-.. %TODO module_configuration.png should be changed to reflect v2.0. Caption: The module configuration window allows the hidden ports to be displayed.
+For convenience, all the inputs and outputs of a module are not always shown in the canvas as ports. The ports that are shown by default are defined with the method signatures of a package.
+A full list of ports is available in the ``Module Information`` panel on the right side.
+Module ports can be enabled/disabled by clicking in the left margin next to the port name in the ``Inputs`` or ``Outputs`` tabs (see Figure :ref:`Enabling the GetRadius port from the Module Information tab <fig-enabling_ports>`). When enabled, an eye icon will appear to the left of the port name.
.. topic:: Try it now!
diff --git a/doc/usersguide/example_webservices.rst b/doc/usersguide/example_webservices.rst
index 5ff7a57..1250685 100644
--- a/doc/usersguide/example_webservices.rst
+++ b/doc/usersguide/example_webservices.rst
@@ -59,25 +59,24 @@ dialog. (Please refer to Chapter :ref:`chap-packages` for more information on
Adding Web Service Packages
===========================
-Within the ``Module Packages`` tab of the ``Preferences``
-dialog, click the ``Configure`` button to open the configuration
-dialog for this package(``SUDSWebServices``). Select the ``wsdlList`` and click on the ``Value`` field. This is where you will enter the URL(s) of the web service(s) you wish to access. If there is more than one URL, place a semicolon (;) between each URL, but *not* after the final URL. In other words, the URLs must be semicolon-delimited, but not semicolon-terminated.
+Within the ``Module Packages`` tab of the ``Preferences`` dialog, click the ``Configure`` button to open the configuration dialog for this package (``SUDSWebServices``). Select the ``wsdlList`` and click on the ``Value`` field. This is where you will enter the URL(s) of the web service(s) you wish to access. If there is more than one URL, place a semicolon (;) between each URL, but *not* after the final URL. In other words, the URLs must be semicolon-delimited, but not semicolon-terminated.
For our example, we need the following URL:
``http://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl``
-After closing the dialog, you need to reload the ``SUDSWebServices`` package in order to load the changes. Then, close the ``Preferences`` dialog. A new package will be created for each URL provided.
+After closing the dialog, you need to reload the ``SUDSWebServices`` package in order to load the changes. Then, close the ``Preferences`` dialog. A new package will be created for each URL provided.
Alternatively, you may add a web service package by clicking the secondary mouse button on the "SUDS Web Services" package in the module palette and entering the corresponding URL. You may remove a web service by clicking the secondary mouse button on the corresponding package in the module palette and selecting ``Remove this Web Service``.
-.. %.. figure::
-.. % :align: center
-.. % :height=3in,clip=false]{modules_list.png}
-.. %}
-.. % The available modules in the ``webServices`` module are shown in the ``Modules`` panel.}
-.. %.. _fig-webservices_preferences}
-.. %
+.. _fig-webservices_preferences:
+
+.. figure:: figures/example_webservices/modules_list.png
+ :align: center
+ :height: 3in
+
+ The available modules in the ``webServices`` module are shown in the ``Modules`` panel.
+
Creating a new vistrail
=======================
diff --git a/doc/usersguide/figures/creating/module_configuration.png b/doc/usersguide/figures/creating/module_configuration.png
deleted file mode 100644
index 66a7eff..0000000
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diff --git a/doc/usersguide/figures/example_webservices/modules_list.png b/doc/usersguide/figures/example_webservices/modules_list.png
index 09e83aa..10b888c 100644
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diff --git a/doc/usersguide/figures/example_webservices/pythonsource.png b/doc/usersguide/figures/example_webservices/pythonsource.png
deleted file mode 100644
index 577227c..0000000
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diff --git a/doc/usersguide/figures/example_webservices/version_tree_modules.png b/doc/usersguide/figures/example_webservices/version_tree_modules.png
deleted file mode 100644
index d437db2..0000000
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diff --git a/doc/usersguide/figures/example_webservices/ws_preferences.png b/doc/usersguide/figures/example_webservices/ws_preferences.png
deleted file mode 100644
index 201ce1e..0000000
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diff --git a/doc/usersguide/figures/packages/after_enabled_package.png b/doc/usersguide/figures/packages/after_enabled_package.png
deleted file mode 100644
index 7ac6518..0000000
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diff --git a/doc/usersguide/figures/parameter_exploration/fig6_1.png b/doc/usersguide/figures/parameter_exploration/fig6_1.png
deleted file mode 100644
index 0ac90ea..0000000
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diff --git a/doc/usersguide/figures/parameter_exploration/fig6_2.png b/doc/usersguide/figures/parameter_exploration/fig6_2.png
deleted file mode 100644
index c5eafaf..0000000
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diff --git a/doc/usersguide/figures/parameter_exploration/fig6_4.png b/doc/usersguide/figures/parameter_exploration/fig6_4.png
deleted file mode 100644
index cff6d96..0000000
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diff --git a/doc/usersguide/figures/parameter_exploration/fig6_5.png b/doc/usersguide/figures/parameter_exploration/fig6_5.png
deleted file mode 100644
index a2f24fb..0000000
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diff --git a/doc/usersguide/figures/parameter_exploration/inspector.png b/doc/usersguide/figures/parameter_exploration/inspector.png
new file mode 100644
index 0000000..12fec68
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diff --git a/doc/usersguide/figures/querying/query4.png b/doc/usersguide/figures/querying/query4.png
deleted file mode 100644
index 5de29ac..0000000
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diff --git a/doc/usersguide/figures/spreadsheet/spreadsheet_cell_control.png b/doc/usersguide/figures/spreadsheet/spreadsheet_cell_control.png
deleted file mode 100644
index 0f7cb36..0000000
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diff --git a/doc/usersguide/figures/spreadsheet/spreadsheet_editing_mode.png b/doc/usersguide/figures/spreadsheet/spreadsheet_editing_mode.png
deleted file mode 100644
index 269cb91..0000000
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diff --git a/doc/usersguide/figures/spreadsheet/spreadsheet_editing_mode_move.png b/doc/usersguide/figures/spreadsheet/spreadsheet_editing_mode_move.png
deleted file mode 100644
index 1f7bcc8..0000000
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diff --git a/doc/usersguide/figures/version_tree/collapsed.png b/doc/usersguide/figures/version_tree/collapsed.png
deleted file mode 100644
index 8ddf73e..0000000
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diff --git a/doc/usersguide/figures/version_tree/creating_versions.png b/doc/usersguide/figures/version_tree/creating_versions.png
deleted file mode 100644
index a3de7d8..0000000
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diff --git a/doc/usersguide/figures/version_tree/expanded.png b/doc/usersguide/figures/version_tree/expanded.png
deleted file mode 100644
index f6c3cc6..0000000
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diff --git a/doc/usersguide/parameter_exploration.rst b/doc/usersguide/parameter_exploration.rst
index 82b64f0..9059c54 100644
--- a/doc/usersguide/parameter_exploration.rst
+++ b/doc/usersguide/parameter_exploration.rst
@@ -53,15 +53,6 @@ the workflow to be explored and helps resolve ambiguities for parameter
settings, and the ``Spreadsheet Virtual Cell`` aids users in
laying out exploration results in the spreadsheet.
-.. %(shown in Figure :ref:`fig-fig6_1})
-.. %(See Figure :ref:`fig-paramexp-panels` for a close-up view of each of these panels.)
-.. %.. figure::[h]
-.. % :align: center
-.. % :width=0.7\linewidth,clip=false]{fig6_1.png}}
-.. % Parameter Exploration View}
-.. %.. _fig-fig6_1}
-.. %
-
.. index::
pair: parameter exploration; adding parameters
@@ -166,7 +157,7 @@ In our next example, we demonstrate how multiple parameter values can be explore
.. topic:: Try it now!
In the :vtl:`terminator.vt` example vistrail, make sure you're working with the "Isosurface" version of the workflow, then go to the ``Pipeline`` view. Add the module ``vtkImageResample`` to the pipeline, and insert it between ``vtkStructuredPointsReader`` and ``vtkContourFilter``, connecting the output of the reader to input of the resampler and the output of the resampler to the input of the contour filter as shown in Figure :ref:`Inserting a vtkImageResample module... <fig-paramexp [...]
- After modifying the workflow, switch back to the ``Exploration`` view. Inside the ``Set Methods`` panel, select the ``SetValue`` method from the ``vtkContourFilter`` module, and drag it to the center canvas. Also select the ``SetAxisMagnificationFactor`` method from the ``vtkImageResample`` module and drag it to the canvas. Set the values as in the previous example, and set the range of the "Float" parameter of "SetAxisMagnificationFactor" to start at 0.2 and end at 1.0. Also, set t [...]
+ After modifying the workflow, switch back to the ``Exploration`` view. Inside the ``Set Methods`` panel, select the ``SetValue`` method from the ``vtkContourFilter`` module, and drag it to the center canvas. Also select the ``SetAxisMagnificationFactor`` method from the ``vtkImageResample`` module and drag it to the canvas. Set the values as in the previous example, and set the range of the "Float" parameter of "SetAxisMagnificationFactor" to start at 0.2 and end at 1.0. Also, set t [...]
.. _fig-paramexp-vtk_image_resample:
@@ -200,7 +191,7 @@ Our third example shows how to create an animation by exploring parameter values
.. topic:: Try it now!
- To create an animation, we'll use the same :vtl:`terminator <terminator.vt>` example (make sure that you have the "Isosurface" version selected). Follow the same steps as in the first example, but this time, use the range from 30 to 80 and select "time" as the dimension to explore, setting the number of results to generate to 7. See Figure :ref:`Setting up parameter exploration <fig-fig6_11>` to check your settings. After executing, the Spreadsheet will show a *single* cell, but if [...]
+ To create an animation, we'll use the same :vtl:`terminator <terminator.vt>` example (make sure that you have the "Isosurface" version selected). Follow the same steps as in the first example, but this time, use the range from 30 to 80 and select "time" as the dimension to explore, setting the number of results to generate to 7. See Figure :ref:`Setting up parameter exploration <fig-fig6_11>` to check your settings. After executing, the Spreadsheet will show a *single* cell, but if [...]
.. _fig-fig6_11:
@@ -280,6 +271,23 @@ to.
The panels of the Parameter Exploration window. ``Set Methods`` (Top) will appear in the right panel and the others will be on the left. The numbered red circles in the ``Annotated Pipeline`` (Middle) distinguish duplicate modules, and the cells in the ``Spreadsheet Virtual Cell`` (Bottom) determine the layout for spreadsheet results.
+Saving Parameter Explorations
+=============================
+
+.. index::
+ pair: spreadsheet; parameter exploration
+ pair: spreadsheet; saving parameter exploration
+
+New parameter explorations are saved automatically when they are executed. The :ref:`inspector (below) <fig-paramexp-inspector>` has buttons for moving back and forward through the history of parameter explorations. Explorations can be tagged with a name, which will make them visible in the workspace view.
+
+.. _fig-paramexp-inspector:
+
+.. figure:: figures/parameter_exploration/inspector.png
+ :align: center
+ :width: 30%
+
+ The parameter exploration inspector
+
"Virtual Cell" Layout
=====================
diff --git a/doc/usersguide/querying.rst b/doc/usersguide/querying.rst
index bfadc67..53021bf 100644
--- a/doc/usersguide/querying.rst
+++ b/doc/usersguide/querying.rst
@@ -126,14 +126,6 @@ One major difference between the ``Pipeline`` view and the ``Search`` view is th
Textual Queries
===============
-.. %Removing this figure as the addition of the next example makes it redundant.
-.. %\begin{figure}
-.. %\centering
-.. %\includegraphics[width=3in]{query4.png}
-.. %\caption{A query made to find any changes made before February 21.}
-.. %\label{fig:querying:date}
-.. %\end{figure}
-
.. index::
pair: queries; textual
diff --git a/doc/usersguide/vistrails_server.rst b/doc/usersguide/vistrails_server.rst
index 3610c20..3ae0f9e 100644
--- a/doc/usersguide/vistrails_server.rst
+++ b/doc/usersguide/vistrails_server.rst
@@ -104,7 +104,7 @@ Basic Configuration
permitted_addresses = localhost, 127.0.0.1, <crowdlabs-server-address>
-* Add the password for the full permission mysql user created in :ref:`VisTrails Database Setup <mysql-full-perm-user>`::
+* Add the password for the full permission mysql user::
write_user = <write user>
write_password = <write user password>
diff --git a/doc/usersguide/vtl/gcd.vtl b/doc/usersguide/vtl/gcd.vtl
new file mode 100644
index 0000000..eef99ba
--- /dev/null
+++ b/doc/usersguide/vtl/gcd.vtl
@@ -0,0 +1 @@
+<vtlink filename="@examples/gcd.vt"/>
diff --git a/examples/XSLTSample.xsl b/examples-internal/XSLTSample.xsl
similarity index 100%
rename from examples/XSLTSample.xsl
rename to examples-internal/XSLTSample.xsl
diff --git a/examples/afront.xml b/examples-internal/afront.xml
similarity index 100%
rename from examples/afront.xml
rename to examples-internal/afront.xml
diff --git a/examples/corie.xml b/examples-internal/corie.xml
similarity index 100%
rename from examples/corie.xml
rename to examples-internal/corie.xml
diff --git a/examples/mummy.xml b/examples-internal/mummy.xml
similarity index 100%
rename from examples/mummy.xml
rename to examples-internal/mummy.xml
diff --git a/examples/gcd.vt b/examples/gcd.vt
new file mode 100644
index 0000000..1bb521d
Binary files /dev/null and b/examples/gcd.vt differ
diff --git a/examples/gcd.xml b/examples/gcd.xml
deleted file mode 100644
index 2734584..0000000
--- a/examples/gcd.xml
+++ /dev/null
@@ -1,1785 +0,0 @@
-<vistrail id="" name="" version="1.0.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vistrails.org/vistrail.xsd">
- <action date="2013-10-14 15:05:53" id="1" prevId="0" session="0" user="Remi">
- <add id="0" objectId="0" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="0" name="InputPort" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
- </add>
- <add id="1" objectId="0" parentObjId="0" parentObjType="module" what="location">
- <location id="0" x="-127.0" y="52.0" />
- </add>
- </action>
- <action date="2013-10-14 15:05:54" id="2" prevId="1" session="0" user="Remi">
- <add id="2" objectId="1" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="1" name="InputPort" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
- </add>
- <add id="3" objectId="1" parentObjId="1" parentObjType="module" what="location">
- <location id="1" x="110.0" y="42.0" />
- </add>
- </action>
- <action date="2013-10-14 15:05:56" id="3" prevId="2" session="0" user="Remi">
- <add id="4" objectId="0" parentObjId="0" parentObjType="module" what="function">
- <function id="0" name="name" pos="0" />
- </add>
- <add id="5" objectId="0" parentObjId="0" parentObjType="function" what="parameter">
- <parameter alias="" id="0" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:String" val="a" />
- </add>
- </action>
- <action date="2013-10-14 15:05:59" id="4" prevId="3" session="0" user="Remi">
- <add id="6" objectId="1" parentObjId="1" parentObjType="module" what="function">
- <function id="1" name="name" pos="0" />
- </add>
- <add id="7" objectId="1" parentObjId="1" parentObjType="function" what="parameter">
- <parameter alias="" id="1" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:String" val="b" />
- </add>
- </action>
- <action date="2013-10-14 15:06:07" id="5" prevId="4" session="0" user="Remi">
- <change id="8" newObjId="3" oldObjId="0" parentObjId="0" parentObjType="module" what="location">
- <location id="3" x="-111.0" y="218.0" />
- </change>
- <change id="9" newObjId="4" oldObjId="1" parentObjId="1" parentObjType="module" what="location">
- <location id="4" x="110.0" y="222.0" />
- </change>
- </action>
- <action date="2013-10-14 15:06:07" id="6" prevId="5" session="0" user="Remi">
- <add id="10" objectId="2" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="2" name="If" namespace="" package="org.vistrails.vistrails.control_flow" version="0.2.3" />
- </add>
- <add id="11" objectId="2" parentObjId="2" parentObjType="module" what="location">
- <location id="2" x="-9.0" y="-2.0" />
- </add>
- </action>
- <action date="2013-10-14 15:06:10" id="7" prevId="6" session="0" user="Remi">
- <add id="12" objectId="3" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="3" name="OutputPort" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
- </add>
- <add id="13" objectId="5" parentObjId="3" parentObjType="module" what="location">
- <location id="5" x="16.0" y="-102.0" />
- </add>
- </action>
- <action date="2013-10-14 15:06:10" id="8" prevId="7" session="0" user="Remi">
- <add id="14" objectId="0" parentObjId="" parentObjType="" what="connection">
- <connection id="0" />
- </add>
- <add id="15" objectId="0" parentObjId="0" parentObjType="connection" what="port">
- <port id="0" moduleId="2" moduleName="If" name="Result" signature="(org.vistrails.vistrails.basic:Variant)" type="source" />
- </add>
- <add id="16" objectId="1" parentObjId="0" parentObjType="connection" what="port">
- <port id="1" moduleId="3" moduleName="OutputPort" name="InternalPipe" signature="(org.vistrails.vistrails.basic:Variant)" type="destination" />
- </add>
- </action>
- <action date="2013-10-14 15:07:17" id="9" prevId="8" session="0" user="Remi">
- <add id="17" objectId="4" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="4" name="PythonCalc" namespace="" package="org.vistrails.vistrails.pythoncalc" version="0.9.1" />
- </add>
- <add id="18" objectId="6" parentObjId="4" parentObjType="module" what="location">
- <location id="6" x="-217.0" y="86.0" />
- </add>
- </action>
- <action date="2013-10-14 15:07:21" id="10" prevId="9" session="0" user="Remi">
- <add id="19" objectId="5" parentObjId="" parentObjType="" what="module">
- <module cache="1" id="5" name="PythonSource" namespace="" package="org.vistrails.vistrails.basic" version="2.1" />
- </add>
- <add id="20" objectId="7" parentObjId="5" parentObjType="module" what="location">
- <location id="7" x="181.0" y="90.0" />
- </add>
- </action>
- <action date="2013-10-14 15:07:46" id="11" prevId="10" session="0" user="Remi">
- <add id="21" objectId="0" parentObjId="5" parentObjType="module" what="portSpec">
- <portSpec id="0" maxConns="-1" minConns="0" name="a" optional="0" sortKey="0" type="input">
- <portSpecItem default="" entryType="" id="0" label="" module="Integer" namespace="" package="org.vistrails.vistrails.basic" pos="0" values="" />
- </portSpec>
- </add>
- <add id="22" objectId="1" parentObjId="5" parentObjType="module" what="portSpec">
- <portSpec id="1" maxConns="-1" minConns="0" name="b" optional="0" sortKey="1" type="input">
- <portSpecItem default="" entryType="" id="1" label="" module="Integer" namespace="" package="org.vistrails.vistrails.basic" pos="0" values="" />
- </portSpec>
- </add>
- <add id="23" objectId="2" parentObjId="5" parentObjType="module" what="portSpec">
- <portSpec id="2" maxConns="-1" minConns="0" name="o" optional="0" sortKey="0" type="output">
- <portSpecItem default="" entryType="" id="2" label="" module="Boolean" namespace="" package="org.vistrails.vistrails.basic" pos="0" values="" />
- </portSpec>
- </add>
- <add id="24" objectId="2" parentObjId="5" parentObjType="module" what="function">
- <function id="2" name="source" pos="0" />
- </add>
- <add id="25" objectId="2" parentObjId="2" parentObjType="function" what="parameter">
- <parameter alias="" id="2" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:String" val="o%20%3D%20a%20%3C%20b" />
- </add>
- </action>
- <action date="2013-10-14 15:07:51" id="12" prevId="11" session="0" user="Remi">
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diff --git a/examples/primes.vt b/examples/primes.vt
new file mode 100644
index 0000000..da2d945
Binary files /dev/null and b/examples/primes.vt differ
diff --git a/examples/primes.xml b/examples/primes.xml
deleted file mode 100644
index 82ecd79..0000000
--- a/examples/primes.xml
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- </action>
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- </change>
- </action>
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- <location id="73" x="78.1744966443" y="-132.295302013" />
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- </action>
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- <port id="94" moduleId="43" moduleName="Group" name="self" signature="(org.vistrails.vistrails.basic:Group)" type="source" />
- </add>
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- <port id="95" moduleId="46" moduleName="While" name="FunctionPort" signature="(org.vistrails.vistrails.basic:Module)" type="destination" />
- </add>
- </action>
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- <add id="605" objectId="43" parentObjId="46" parentObjType="module" what="function">
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- </add>
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- <parameter alias="" id="56" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:Integer" val="100" />
- </add>
- </action>
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- </add>
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- <parameter alias="" id="57" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:Integer" val="2" />
- </add>
- </action>
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- <add id="609" objectId="45" parentObjId="43" parentObjType="group" what="function">
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- </add>
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- <parameter alias="" id="58" name="<no description>" pos="0" type="org.vistrails.vistrails.basic:List" val="[]" />
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- </add>
- </action>
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- </add>
- </action>
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- </add>
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- </change>
- </action>
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- <actionAnnotation actionId="4" date="2013-09-06 11:28:12" id="6" key="__prune__" user="Remi" value="True" />
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- <actionAnnotation actionId="27" date="2013-09-06 11:32:46" id="10" key="__tag__" user="Remi" value="test_1_1" />
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- <actionAnnotation actionId="29" date="2013-09-06 11:33:03" id="13" key="__tag__" user="Remi" value="test_1_3" />
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- <actionAnnotation actionId="73" date="2013-09-06 11:57:07" id="34" key="__tag__" user="Remi" value="test_5_2" />
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- <actionAnnotation actionId="78" date="2013-09-06 11:58:28" id="37" key="__tag__" user="Remi" value="test_6_1" />
- <actionAnnotation actionId="79" date="2013-09-06 11:58:32" id="38" key="__tag__" user="Remi" value="test_6_2" />
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diff --git a/examples/scripting/combined_script.py b/examples/scripting/combined_script.py
index 073a596..dbc6b1f 100644
--- a/examples/scripting/combined_script.py
+++ b/examples/scripting/combined_script.py
@@ -1,5 +1,13 @@
+import os
import sys
-sys.path.append('/Users/benbu/src/vistrails/vistrails/')
+
+try:
+ import vistrails
+except:
+ #try to append vistrails source dir relative to examples/scripting
+ this_dir = os.path.split(__file__)[0]
+ sys.path.append(os.path.join(this_dir, '../..'))
+ import vistrails
import vistrails.core.application
import vistrails.core.db.action
@@ -9,6 +17,7 @@ import vistrails.core.modules.module_registry
#init vistrails
vt_app = vistrails.core.application.init()
+vt_app.new_vistrail()
controller = vt_app.get_controller()
registry = vistrails.core.modules.module_registry.get_module_registry()
diff --git a/examples/scripting/vtk_book_3rd_p189_script.py b/examples/scripting/vtk_book_3rd_p189_script.py
index b6ca03a..bc835f0 100644
--- a/examples/scripting/vtk_book_3rd_p189_script.py
+++ b/examples/scripting/vtk_book_3rd_p189_script.py
@@ -1,5 +1,13 @@
+import os
import sys
-sys.path.append('/Users/benbu/src/vistrails/vistrails/')
+
+try:
+ import vistrails
+except:
+ #try to append vistrails source dir relative to examples/scripting
+ this_dir = os.path.split(__file__)[0]
+ sys.path.append(os.path.join(this_dir, '../..'))
+ import vistrails
import vistrails.core.application
import vistrails.core.db.action
@@ -9,6 +17,7 @@ import vistrails.core.modules.module_registry
#init vistrails
vt_app = vistrails.core.application.init()
+vt_app.new_vistrail()
controller = vt_app.get_controller()
registry = vistrails.core.modules.module_registry.get_module_registry()
diff --git a/scripts/create_release_wiki_table.py b/scripts/create_release_wiki_table.py
index 6d83867..1ec8d3d 100644
--- a/scripts/create_release_wiki_table.py
+++ b/scripts/create_release_wiki_table.py
@@ -6,8 +6,8 @@ wiki page
"""
from datetime import date
#Release version
-VT_VERSION = "2.1.1"
-VT_REVISION = "90975fc00211"
+VT_VERSION = "2.1.4"
+VT_REVISION = "8262f078ed3b"
#Sourceforge information
SF_ROOT_URL = "http://downloads.sourceforge.net/project/vistrails/vistrails/"
diff --git a/scripts/release_notes.py b/scripts/release_notes.py
index 35ce651..61c4ec4 100755
--- a/scripts/release_notes.py
+++ b/scripts/release_notes.py
@@ -49,14 +49,15 @@ import subprocess
import shutil
#### configuration ####
-commit_start = "90975fc00211" # hash of version used on last release notes
+commit_start = "8262f078ed3b" # hash of version used on last release notes
commit_end = "HEAD" # current hash
branch = "v2.1" # git branch to be used
-release_name = "2.1.1"
-clonepath = None # set this to the complete path of a vistrails clone to be used
- # if None, the remote repository will be cloned to a temporary
- # folder and removed at the end of the script
-#clonepath = '/Users/tommy/git/vistrails'
+release_name = "2.1.4"
+clonepath = None # set this to the complete path of a vistrails clone to be
+ # used
+ # if None, the remote repository will be cloned to a
+ # temporary folder and removed at the end of the script
+clonepath = '/Users/tommy/git/vistrails'
cloneremote = 'git://www.vistrails.org/vistrails.git'
#### end configuration #####
@@ -90,8 +91,7 @@ def clone_vistrails_git_repository(path_to):
process = subprocess.Popen(cmdlist, shell=False,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
- stderr=subprocess.STDOUT,
- close_fds=True)
+ stderr=subprocess.STDOUT)
process.wait()
if process.returncode == 0:
print "repository is cloned."
@@ -142,8 +142,7 @@ def init_branch(path_to, branch):
process = subprocess.Popen(cmdlist, shell=False,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
- stderr=subprocess.STDOUT,
- close_fds=True)
+ stderr=subprocess.STDOUT)
process.wait()
lines = process.stdout.readlines()
for line in lines:
@@ -163,8 +162,7 @@ def pull_changes(path_to):
process = subprocess.Popen(cmdlist, shell=False,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
- stderr=subprocess.STDOUT,
- close_fds=True)
+ stderr=subprocess.STDOUT)
process.wait()
lines = process.stdout.readlines()
for line in lines:
@@ -197,6 +195,7 @@ def build_release_notes(repo, branch):
re_ticket_old = re.compile(r'<ticket>(.*?)</ticket>', re.M | re.S)
re_ticket = re.compile(r'^Ticket: (.*?)$', re.M | re.S)
+ re_ticket2 = re.compile(r'^Fixes: (.*?)$', re.M | re.S)
re_bugfix_old = re.compile(r'<bugfix>(.*?)</bugfix>', re.M | re.S)
re_bugfix = re.compile(r'^Bugfix: (.*?)$', re.M | re.S)
re_feature_old = re.compile(r'<feature>(.*?)</feature>', re.M | re.S)
@@ -223,9 +222,10 @@ def build_release_notes(repo, branch):
lf = re_feature.findall(log.message)
lf.extend(re_feature_old.findall(log.message))
lt = re_ticket.findall(log.message)
+ lt.extend(re_ticket2.findall(log.message))
lt.extend(re_ticket_old.findall(log.message))
lb = re_bugfix.findall(log.message)
- lb.extend(re_ticket_old.findall(log.message))
+ lb.extend(re_bugfix_old.findall(log.message))
for s in ls:
changes[s.strip()] = log.hexsha
for f in lf:
@@ -257,13 +257,13 @@ def build_release_notes(repo, branch):
password)
server = xmlrpclib.ServerProxy(url)
print "downloading tickets.",
- for (tid,r) in tickets.iteritems():
+ for (tid,r) in tickets.items():
print ".",
sys.stdout.flush()
try:
ticket_info[tid] = server.ticket.get(tid)
except Exception, e:
- tickets.remove(tid)
+ del tickets[tid]
print "commit %s: Could not get info for ticket %s"%(r,tid)
print "done."
diff --git a/scripts/update_db.py b/scripts/update_db.py
index 81c7acb..cd8daa1 100644
--- a/scripts/update_db.py
+++ b/scripts/update_db.py
@@ -78,10 +78,15 @@ def update_db(config, new_version=None, tmp_dir=None, restore=False):
print 'getting', obj_type, 'id', obj_id
local_tmp_dir = os.path.join(tmp_dir, str(obj_id))
vt_name = os.path.join(tmp_dir, str(obj_id) + '.vt')
- filenames.append(vt_name)
- os.mkdir(local_tmp_dir)
- res = obj_types[obj_type](obj_type, db_connection, obj_id,
+ try:
+ res = obj_types[obj_type](obj_type, db_connection, obj_id,
thumbnail_dir)
+ filenames.append(vt_name)
+ os.mkdir(local_tmp_dir)
+ except:
+ import traceback
+ print "Could not read:", traceback.format_exc()
+ continue
io.save_vistrail_bundle_to_zip_xml(res, vt_name, local_tmp_dir)
# drop the old database
diff --git a/scripts/update_hash.py b/scripts/update_hash.py
index f3616f3..370ae49 100755
--- a/scripts/update_hash.py
+++ b/scripts/update_hash.py
@@ -10,15 +10,12 @@ if len(sys.argv)<3:
files = ["release_notes.py",
"create_release_wiki_table.py",
"../vistrails/core/system/__init__.py",
- "../dist/mac/Input/README",
- "../dist/windows/Input/releaseNotes.txt",
"../dist/source/make-vistrails-src-release.py",
"../doc/usersguide/conf.py"]
for path in files:
for f in glob.glob(path):
print "Updating", f
-
file = open(f)
text = file.read()
file.close()
@@ -28,3 +25,7 @@ for path in files:
file = open(f, "w")
file.write(text)
file.close()
+
+print "These files need to be updated manually:"
+print " ../dist/mac/Input/README"
+print " ../dist/windows/Input/releaseNotes.txt"
diff --git a/vistrails/core/application.py b/vistrails/core/application.py
index 9dd3d01..5fd6b44 100644
--- a/vistrails/core/application.py
+++ b/vistrails/core/application.py
@@ -739,6 +739,7 @@ after self.init()"""
return False
old_locator = controller.locator
+ controller.flush_delayed_actions()
try:
controller.write_vistrail(locator, export=export)
except Exception, e:
diff --git a/vistrails/core/collection/__init__.py b/vistrails/core/collection/__init__.py
index 191d745..f270187 100644
--- a/vistrails/core/collection/__init__.py
+++ b/vistrails/core/collection/__init__.py
@@ -188,7 +188,7 @@ class Collection(object):
def load_entity(self, *args):
if args[1] in Collection.entity_types:
- entity = Collection.entity_types[args[1]].load(*args)
+ entity = Collection.entity_types[args[1]].create(*args)
return entity
else:
debug.critical("Cannot find entity type '%s'" % args[1])
diff --git a/vistrails/core/collection/entity.py b/vistrails/core/collection/entity.py
index 4daf1e0..1e52bbb 100644
--- a/vistrails/core/collection/entity.py
+++ b/vistrails/core/collection/entity.py
@@ -33,8 +33,11 @@
##
###############################################################################
from vistrails.core.db.locator import BaseLocator
+from datetime import datetime
class Entity(object):
+ DATE_FORMAT = '%Y-%m-%d %H:%M:%S.%f'
+
def __init__(self):
self.parent = None
self.children = []
@@ -45,21 +48,24 @@ class Entity(object):
def load(self, *args):
(self.id,
_,
- self.name,
+ self.name,
self.user,
- self.mod_time,
+ self.mod_time,
self.create_time,
self.size,
self.description,
self.url) = args
+ self.mod_time = self.timeval(self.mod_time)
+ self.create_time = self.timeval(self.create_time)
+
def save(self):
return (self.id,
self.type_id,
self.name,
self.user,
- self.mod_time,
- self.create_time,
+ self.mod_time.strftime(self.DATE_FORMAT),
+ self.create_time.strftime(self.DATE_FORMAT),
self.size,
self.description,
self.url)
@@ -72,6 +78,20 @@ class Entity(object):
return self.mod_time
end_date = property(_get_end_date)
+ def now(self):
+ return datetime.now()
+
+ def timeval(self, time):
+ try:
+ return datetime.strptime(time, self.DATE_FORMAT)
+ except ValueError:
+ # try old format
+ try:
+ return datetime.strptime(time, '%d %b %Y %H:%M:%S')
+ except ValueError:
+ # locale or other error
+ return self.now()
+
# # returns string
# def get_name(self):
# return self.name
diff --git a/vistrails/core/collection/mashup.py b/vistrails/core/collection/mashup.py
index 2f88e90..55d58b2 100644
--- a/vistrails/core/collection/mashup.py
+++ b/vistrails/core/collection/mashup.py
@@ -44,9 +44,9 @@ class MashupEntity(Entity):
self.update(mashup)
@staticmethod
- def load(*args):
+ def create(*args):
entity = MashupEntity()
- Entity.load(entity, *args)
+ entity.load(*args)
return entity
def update(self, mashup):
@@ -55,55 +55,13 @@ class MashupEntity(Entity):
self.name = mashup.name \
if mashup.name else "Version #" + str(mashup.id)
self.user = 'testing'
- self.mod_time = 'test'
- self.create_time = 'test'
+ self.mod_time = self.now()
+ self.create_time = self.now()
self.size = len(self.mashup.alias_list)
self.description = ""
self.url = 'test'
self.was_updated = True
-# self.name = self.workflow.name
-# self.user = self.workflow.user
-# self.mod_time = self.workflow.py_date
-# self.create_time = self.workflow.py_date
-# self.size = len(self.workflow.modules)
-# self.description = self.workflow.notes
-# self.was_updated = True
-
-# # returns string
-# def get_name(self):
-# raise RuntimeError("Method is abstract")
-
-# # returns datetime
-# def get_mod_time(self):
-# raise RuntimeError("Method is abstract")
-
-# # returns datetime
-# def get_create_time(self):
-# raise RuntimeError("Method is abstract")
-
-# # returns string
-# # FIXME: perhaps this should be a User object at some point
-# def get_user(self):
-# raise RuntimeError("Method is abstract")
-
-# # returns tuple (<entity_type>, <entity_id>)
-# def get_id(self):
-# raise RuntimeError("Method is abstract")
-
-# # returns integer
-# def get_size(self):
-# raise RuntimeError("Method is abstract")
-
-# # returns possibly empty list of Entity objects
-# def get_children(self):
-# raise RuntimeError("Method is abstract")
-
-# # returns list of strings representing paths
-# # FIXME: should this be uris for database access?
-# def get_image_fnames(self):
-# raise RuntimeError("Method is abstract")
-
# returns boolean, True if search input is satisfied else False
def match(self, search):
raise RuntimeError("Not implemented")
\ No newline at end of file
diff --git a/vistrails/core/collection/parameter_exploration.py b/vistrails/core/collection/parameter_exploration.py
index 942cf87..124c93b 100644
--- a/vistrails/core/collection/parameter_exploration.py
+++ b/vistrails/core/collection/parameter_exploration.py
@@ -44,9 +44,9 @@ class ParameterExplorationEntity(Entity):
self.update(pe)
@staticmethod
- def load(*args):
+ def create(*args):
entity = ParameterExplorationEntity()
- Entity.load(entity, *args)
+ entity.load(*args)
return entity
def update(self, pe):
@@ -54,8 +54,8 @@ class ParameterExplorationEntity(Entity):
if self.pe is not None:
self.name = pe.name
self.user = pe.user
- self.mod_time = pe.date
- self.create_time = pe.date
+ self.mod_time = pe.date if pe.date else self.now()
+ self.create_time = pe.date if pe.date else self.now()
self.size = len(pe.functions)
self.description = ""
self.url = 'test'
diff --git a/vistrails/core/collection/search.py b/vistrails/core/collection/search.py
index 8628cb2..119c96e 100644
--- a/vistrails/core/collection/search.py
+++ b/vistrails/core/collection/search.py
@@ -41,7 +41,6 @@ from vistrails.core.query import extract_text
import unittest
import datetime
-import vistrails.core
################################################################################
@@ -398,14 +397,14 @@ class BeforeSearchStmt(TimeSearchStmt):
def match(self, entity):
if not entity.mod_time:
return False
- t = time.mktime(time.strptime(entity.mod_time, "%d %b %Y %H:%M:%S"))
+ t = time.mktime(entity.mod_time)
return t <= self.date
class AfterSearchStmt(TimeSearchStmt):
def match(self, entity):
if not entity.mod_time:
return False
- t = time.mktime(time.strptime(entity.mod_time, "%d %b %Y %H:%M:%S"))
+ t = time.mktime(entity.mod_time)
return t >= self.date
class UserSearchStmt(SearchStmt):
diff --git a/vistrails/core/collection/thumbnail.py b/vistrails/core/collection/thumbnail.py
index 4134dc8..a54ae7c 100644
--- a/vistrails/core/collection/thumbnail.py
+++ b/vistrails/core/collection/thumbnail.py
@@ -49,9 +49,9 @@ class ThumbnailEntity(Entity):
self.update(thumbnail)
@staticmethod
- def load(*args):
+ def create(*args):
entity = ThumbnailEntity()
- Entity.load(entity, *args)
+ entity.load(*args)
return entity
def update(self, thumbnail):
@@ -64,8 +64,8 @@ class ThumbnailEntity(Entity):
statinfo = os.stat(self.thumbnail)
self.user = statinfo[stat.ST_UID]
self.size = statinfo[stat.ST_SIZE]
- time = datetime(*localtime(statinfo[stat.ST_MTIME])[:6]).strftime('%d %b %Y %H:%M:%S')
- self.mod_time = ''
+ time = datetime(*localtime(statinfo[stat.ST_MTIME])[:6])
+ self.mod_time = time
self.create_time = time
self.description = ""
self.url = 'test'
diff --git a/vistrails/core/collection/vistrail.py b/vistrails/core/collection/vistrail.py
index 38c48a7..1525398 100644
--- a/vistrails/core/collection/vistrail.py
+++ b/vistrails/core/collection/vistrail.py
@@ -65,9 +65,9 @@ class VistrailEntity(Entity):
self.reload(vistrail)
@staticmethod
- def load(*args):
+ def create(*args):
entity = VistrailEntity()
- Entity.load(entity, *args)
+ entity.load(*args)
return entity
def create_workflow_entity(self, workflow, action):
@@ -80,8 +80,8 @@ class VistrailEntity(Entity):
else:
entity.description = ''
entity.user = action.user
- entity.mod_time = action.date
- entity.create_time = action.date
+ entity.mod_time = action.db_date
+ entity.create_time = action.db_date
locator = BaseLocator.from_url(self.url)
locator.kwargs['version_node'] = action.id
entity.url = locator.to_url()
@@ -98,8 +98,8 @@ class VistrailEntity(Entity):
else:
entity.description = ''
entity.user = action.user
- entity.mod_time = action.date
- entity.create_time = action.date
+ entity.mod_time = action.db_date
+ entity.create_time = action.db_date
locator = BaseLocator.from_url(self.url)
locator.kwargs['mashuptrail'] = trail_id
locator.kwargs['mashup'] = action.id
@@ -153,11 +153,11 @@ class VistrailEntity(Entity):
latestVersionId = vistrail.get_latest_version()
latestVersion = vistrail.actionMap[latestVersionId]
user = latestVersion.user
- mod_time = latestVersion.date
+ mod_time = latestVersion.db_date
# FIXME: relies on 1 being the first version...
firstVersion = vistrail.actionMap[1] \
if 1 in vistrail.actionMap else latestVersion
- create_time = firstVersion.date
+ create_time = firstVersion.db_date
url = vistrail.locator.to_url() if vistrail.locator else "untitled:"
return (name, size, user, mod_time, create_time, url)
diff --git a/vistrails/core/collection/workflow.py b/vistrails/core/collection/workflow.py
index a5c339f..44346ff 100644
--- a/vistrails/core/collection/workflow.py
+++ b/vistrails/core/collection/workflow.py
@@ -43,9 +43,9 @@ class WorkflowEntity(Entity):
self.update(workflow)
@staticmethod
- def load(*args):
+ def create(*args):
entity = WorkflowEntity()
- Entity.load(entity, *args)
+ entity.load(*args)
return entity
def update(self, workflow):
@@ -54,8 +54,8 @@ class WorkflowEntity(Entity):
self.name = workflow.name \
if workflow.name else "Version #" + str(workflow.id)
self.user = 'testing'
- self.mod_time = 'test'
- self.create_time = 'test'
+ self.mod_time = self.now()
+ self.create_time = self.now()
self.size = len(self.workflow.modules)
self.description = ""
self.url = 'test'
diff --git a/vistrails/core/collection/workflow_exec.py b/vistrails/core/collection/workflow_exec.py
index f3fef3e..1f21778 100644
--- a/vistrails/core/collection/workflow_exec.py
+++ b/vistrails/core/collection/workflow_exec.py
@@ -43,9 +43,9 @@ class WorkflowExecEntity(Entity):
self.update(workflow_exec)
@staticmethod
- def load(*args):
+ def create(*args):
entity = WorkflowExecEntity()
- Entity.load(entity, *args)
+ entity.load(*args)
return entity
def update(self, workflow_exec):
@@ -53,12 +53,10 @@ class WorkflowExecEntity(Entity):
if self.workflow_exec is not None:
self.name = "%s" % self.workflow_exec.db_ts_start
self.user = self.workflow_exec.user
- self.mod_time = \
- self.workflow_exec.ts_end.strftime('%d %b %Y %H:%M:%S') \
- if self.workflow_exec.ts_end else '1 Jan 0000 00:00:00'
- self.create_time = \
- self.workflow_exec.ts_start.strftime('%d %b %Y %H:%M:%S') \
- if self.workflow_exec.ts_start else '1 Jan 0000 00:00:00'
+ self.mod_time = self.workflow_exec.ts_end \
+ if self.workflow_exec.ts_end else self.now()
+ self.create_time = self.workflow_exec.ts_start \
+ if self.workflow_exec.ts_start else self.now()
self.size = len(self.workflow_exec.item_execs)
self.description = ""
self.url = 'test'
diff --git a/vistrails/core/console_mode.py b/vistrails/core/console_mode.py
index 196218d..bcc4314 100644
--- a/vistrails/core/console_mode.py
+++ b/vistrails/core/console_mode.py
@@ -67,6 +67,7 @@ def run_and_get_results(w_list, parameters='', workflow_info=None,
"""
elements = parameters.split("$&$")
aliases = {}
+ params = []
result = []
for locator, workflow in w_list:
(v, abstractions , thumbnails, mashups) = load_vistrail(locator)
@@ -91,7 +92,14 @@ def run_and_get_results(w_list, parameters='', workflow_info=None,
if controller.current_pipeline.has_alias(key):
aliases[key] = value
-
+ elif 'mashup_id' in extra_info:
+ # new-style mashups can have aliases not existing in pipeline
+ for mashuptrail in mashups:
+ if mashuptrail.vtVersion == version:
+ mashup = mashuptrail.getMashup(extra_info['mashup_id'])
+ c = mashup.getAliasByName(key).component
+ params.append((c.vttype, c.vtid, value))
+
if workflow_info is not None and controller.current_pipeline is not None:
# FIXME DAK: why is this always done?!? there is a flag for it...
if is_running_gui():
@@ -112,6 +120,7 @@ def run_and_get_results(w_list, parameters='', workflow_info=None,
(results, _) = \
controller.execute_current_workflow(custom_aliases=aliases,
+ custom_params=params,
extra_info=extra_info,
reason=reason)
new_version = controller.current_version
diff --git a/vistrails/core/data_structures/graph.py b/vistrails/core/data_structures/graph.py
index 68d99c3..3dae82b 100644
--- a/vistrails/core/data_structures/graph.py
+++ b/vistrails/core/data_structures/graph.py
@@ -91,7 +91,7 @@ class Graph(object):
"""
result = Graph()
if vertex_map is None:
- vertex_map = dict((v, v) for v in self.vertices)
+ vertex_map = dict((v, v) for v in graph.vertices)
if edge_map is None:
edge_map = {}
for vfrom, lto in graph.adjacency_list.iteritems():
@@ -682,7 +682,7 @@ class Graph(object):
for i in [map(lambda (t, i): (f, t, i), l)
for (f, l) in self.adjacency_list.items()]:
al.extend(i)
- al.sort(edge_cmp)
+ al.sort()
return "digraph G { " \
+ ";".join([str(s) for s in vs]) + ";" \
+ ";".join(["%s -> %s [label=\"%s\"]" % s for s in al]) + "}"
@@ -722,53 +722,6 @@ class Graph(object):
def __ne__(self, other):
return not (self == other)
- ##########################################################################
- # Etc
-
- @staticmethod
- def from_random(size):
- """ from_random(size:int) -> Graph
- Create a DAG with approximately size/e vertices and 3*|vertex| edges
- and return a Graph
-
- Keyword arguments:
- size -- the estimated size of the graph to generate
-
- """
- result = Graph()
- verts = filter(lambda x: x>0, peckcheck.a_list(peckcheck.an_int)(size))
- for v in verts:
- result.add_vertex(v)
- k = size / math.e
- p = (6*k) / ((k+1)*(k+2))
- eid = 0
- for v in verts:
- for k in verts:
- if v < k and random.random() > p:
- result.add_edge(v, k, eid)
- eid = eid + 1
- return result
-
-def edge_cmp(v1, v2):
- """ edge_cmp(v1: id type, v2:id type) -> int
- Defines how the comparison must be done between edges and return a boolean
-
- Keyword arguments:
- v1 -- 'sequence' edge information
- v2 -- 'sequence' other edge information
-
- """
- (from1, to1, id1) = v1
- (from2, to2, id2) = v2
- c1 = cmp(from1, from2)
- if c1:
- return c1
- c2 = cmp(to1, to2)
- if c2:
- return c2
- else:
- return cmp(id1, id2)
-
################################################################################
# Unit testing
diff --git a/vistrails/core/mashup/controller.py b/vistrails/core/mashup/controller.py
index 97b1ab7..14b378e 100644
--- a/vistrails/core/mashup/controller.py
+++ b/vistrails/core/mashup/controller.py
@@ -127,7 +127,9 @@ class MashupController(object):
new_aliases = []
pos = 0
for old_pos in new_order:
- alias = copy.copy(self.currentMashup.alias_list[old_pos])
+ alias = self.currentMashup.alias_list[old_pos].do_copy(
+ new_ids=True, id_scope=self.mshptrail.id_scope,
+ id_remap={})
alias.component.pos = pos
new_aliases.append(alias)
pos += 1
@@ -145,10 +147,14 @@ class MashupController(object):
if self.currentMashup:
for a in self.currentMashup.alias_list:
if a.id != alias.id:
- calias = copy.copy(a)
+ calias = a.do_copy(new_ids=True,
+ id_scope=self.mshptrail.id_scope,
+ id_remap={})
else:
#print "found alias: ", a
- calias = copy.copy(alias)
+ calias = alias.do_copy(new_ids=True,
+ id_scope=self.mshptrail.id_scope,
+ id_remap={})
new_aliases.append(calias)
return self.createMashupVersion(new_aliases, quiet=False)
@@ -158,7 +164,9 @@ class MashupController(object):
pos = 0
for alias in self.currentMashup.alias_list:
if alias.component.vtid != param.id:
- calias = copy.copy(alias)
+ calias = alias.do_copy(new_ids=True,
+ id_scope=self.mshptrail.id_scope,
+ id_remap={})
calias.component.pos = pos
new_aliases.append(calias)
pos += 1
@@ -166,14 +174,16 @@ class MashupController(object):
#print "found alias: ", alias
add_alias = False
if param.alias != '':
- new_alias = copy.copy(alias)
+ new_alias = alias.do_copy(new_ids=True,
+ id_scope=self.mshptrail.id_scope,
+ id_remap={})
new_alias.name = param.alias
new_aliases.append(new_alias)
pos += 1
if add_alias:
parameter = self.vtPipeline.db_get_object(param.dbtype, param.id)
- cid = self.id_scope.getNewId('component')
- aid = self.id_scope.getNewId('alias')
+ cid = self.id_scope.getNewId('mashup_component')
+ aid = self.id_scope.getNewId('mashup_alias')
component = Component(cid, parameter.vtType,
parameter.real_id, param.parent_dbtype,
param.parent_id,
@@ -209,7 +219,9 @@ class MashupController(object):
new_a = None
for a in self.currentMashup.alias_list:
if a.name not in pip_aliases:
- old_a = copy.copy(a)
+ old_a = a.do_copy(new_ids=True,
+ id_scope=self.mshptrail.id_scope,
+ id_remap={})
new_aliases.append(old_a)
else:
new_aliases.append(a)
@@ -234,7 +246,9 @@ class MashupController(object):
pos = 0
for a in self.currentMashup.alias_list:
if a.name in pip_aliases:
- alias = copy.copy(a)
+ alias = a.do_copy(new_ids=True,
+ id_scope=self.mshptrail.id_scope,
+ id_remap={})
alias.component.pos = pos
new_aliases.append(alias)
pos += 1
@@ -246,8 +260,8 @@ class MashupController(object):
if a not in mashup_aliases:
info = pipeline.aliases[a]
parameter = pipeline.db_get_object(info[0],info[1])
- cid = self.id_scope.getNewId('component')
- aid = self.id_scope.getNewId('alias')
+ cid = self.id_scope.getNewId('mashup_component')
+ aid = self.id_scope.getNewId('mashup_alias')
component = Component(cid, parameter.vtType,
parameter.real_id, info[2], info[3],
info[4], parameter.type,
@@ -322,7 +336,9 @@ class MashupController(object):
pos = 0
for alias in self.currentMashup.alias_list:
if alias.name != name:
- calias = copy.copy(alias)
+ calias = alias.do_copy(new_ids=True,
+ id_scope=self.mshptrail.id_scope,
+ id_remap={})
calias.component.pos = pos
new_aliases.append(calias)
pos += 1
diff --git a/vistrails/core/mashup/mashup.py b/vistrails/core/mashup/mashup.py
index fd83b10..ca77ffc 100644
--- a/vistrails/core/mashup/mashup.py
+++ b/vistrails/core/mashup/mashup.py
@@ -290,12 +290,12 @@ layout='%s' geometry='%s' alias_list='%s')@%X" %
class TestMashup(unittest.TestCase):
def create_mashup(self, id_scope=IdScope()):
- c1 = Component(id=id_scope.getNewId('component'),
+ c1 = Component(id=id_scope.getNewId('mashup_component'),
vttype='parameter', param_id=15L,
parent_vttype='function', parent_id=3L, mid=4L,
type='String', value='test', p_pos=0, pos=1,
strvaluelist='test1,test2', widget="text")
- a1 = Alias(id=id_scope.getNewId('alias'), name='alias1', component=c1)
+ a1 = Alias(id=id_scope.getNewId('mashup_alias'), name='alias1', component=c1)
m = Mashup(id=id_scope.getNewId('mashup'), name='mashup1', vtid='empty.vt',
version=15L, alias_list=[a1])
@@ -321,4 +321,4 @@ class TestMashup(unittest.TestCase):
def test_str(self):
m1 = self.create_mashup()
str(m1)
-
\ No newline at end of file
+
diff --git a/vistrails/core/modules/basic_modules.py b/vistrails/core/modules/basic_modules.py
index 2a17b6d..cacd6dd 100644
--- a/vistrails/core/modules/basic_modules.py
+++ b/vistrails/core/modules/basic_modules.py
@@ -410,24 +410,23 @@ Directory.default_value = Directory()
def path_parameter_hasher(p):
def get_mtime(path):
- v_list = [int(os.path.getmtime(path))]
+ t = int(os.path.getmtime(path))
if os.path.isdir(path):
for subpath in os.listdir(path):
subpath = os.path.join(path, subpath)
if os.path.isdir(subpath):
- v_list.extend(get_mtime(subpath))
- return v_list
+ t = max(t, get_mtime(subpath))
+ return t
h = vistrails.core.cache.hasher.Hasher.parameter_signature(p)
try:
# FIXME: This will break with aliases - I don't really care that much
- v_list = get_mtime(p.strValue)
+ t = get_mtime(p.strValue)
except OSError:
return h
hasher = sha_hash()
hasher.update(h)
- for v in v_list:
- hasher.update(str(v))
+ hasher.update(str(t))
return hasher.digest()
##############################################################################
@@ -1131,6 +1130,53 @@ class AssertEqual(Module):
##############################################################################
+class StringFormat(Module):
+ """
+ Builds a string from objects using Python's str.format().
+ """
+ @staticmethod
+ def list_placeholders(fmt):
+ placeholders = set()
+ nb = 0
+ i = 0
+ n = len(fmt)
+ while i < n:
+ if fmt[i] == '{':
+ i += 1
+ if fmt[i] == '{': # KeyError:
+ i += 1
+ continue
+ e = fmt.index('}', i) # KeyError
+ f = e
+ for c in (':', '!', '[', '.'):
+ c = fmt.find(c, i)
+ if c != -1:
+ f = min(f, c)
+ if i == f:
+ nb += 1
+ else:
+ arg = fmt[i:f]
+ try:
+ arg = int(arg)
+ except ValueError:
+ placeholders.add(arg)
+ else:
+ nb = max(nb, arg + 1)
+ i = e
+ i += 1
+ return nb, placeholders
+
+ def compute(self):
+ fmt = self.getInputFromPort('format')
+ args, kwargs = StringFormat.list_placeholders(fmt)
+ f_args = [self.getInputFromPort('_%d' % n)
+ for n in xrange(args)]
+ f_kwargs = dict((n, self.getInputFromPort(n))
+ for n in kwargs)
+ self.setResult('value', fmt.format(*f_args, **f_kwargs))
+
+##############################################################################
+
def init_constant(m):
reg = get_module_registry()
@@ -1282,6 +1328,13 @@ def initialize(*args, **kwargs):
reg.add_input_port(TupleToList, 'in_value', Variant)
reg.add_output_port(TupleToList, 'out_value', List)
+ reg.add_module(StringFormat,
+ configureWidgetType=(
+ "vistrails.gui.modules.stringformat_configuration",
+ "StringFormatConfigurationWidget"))
+ reg.add_input_port(StringFormat, 'format', String)
+ reg.add_output_port(StringFormat, 'value', String)
+
# initialize the sub_module modules, too
import vistrails.core.modules.sub_module
vistrails.core.modules.sub_module.initialize(*args, **kwargs)
@@ -1338,6 +1391,8 @@ def handle_module_upgrade_request(controller, module_id, pipeline):
{'dst_port_remap': {'old_name': None}})],
'PythonSource':
[(None, '1.6', None, {})],
+ 'Tuple':
+ [(None, '2.1', None, {})],
}
return UpgradeWorkflowHandler.remap_module(controller, module_id, pipeline,
@@ -1346,6 +1401,7 @@ def handle_module_upgrade_request(controller, module_id, pipeline):
###############################################################################
+import sys
import unittest
class TestConcatenateString(unittest.TestCase):
@@ -1708,3 +1764,45 @@ class TestTypechecking(unittest.TestCase):
(1, 'output', 'r',
'org.vistrails.vistrails.basic:String'),
])
+
+
+class TestStringFormat(unittest.TestCase):
+ def test_list_placeholders(self):
+ fmt = 'a {} b}} {c!s} {{d e}} {}f'
+ self.assertEqual(StringFormat.list_placeholders(fmt),
+ (2, set(['c'])))
+
+ def run_format(self, fmt, expected, **kwargs):
+ from vistrails.tests.utils import execute, intercept_result
+ functions = [('format', [('String', fmt)])]
+ functions.extend((n, [(t, v)])
+ for n, (t, v) in kwargs.iteritems())
+ with intercept_result(StringFormat, 'value') as results:
+ self.assertFalse(execute([
+ ('StringFormat', 'org.vistrails.vistrails.basic',
+ functions),
+ ],
+ add_port_specs=[
+ (0, 'input', n, t)
+ for n, (t, v) in kwargs.iteritems()
+ ]))
+ self.assertEqual(results, [expected])
+
+ def test_format(self):
+ self.run_format('{{ {a} }} b {c!s}', '{ 42 } b 12',
+ a=('Integer', '42'),
+ c=('Integer', '12'))
+
+ def test_format_27(self):
+ # Python 2.6 doesn't support {}
+ if (sys.version_info < (2, 7)):
+ raise unittest.SkipTest("No {} support on 2.6")
+ self.run_format('{} {}', 'a b',
+ _0=('String', 'a'), _1=('String', 'b'))
+ self.run_format('{{ {a} {} {b!s}', '{ 42 b 12',
+ a=('Integer', '42'), _0=('String', 'b'),
+ b=('Integer', '12'))
+ self.run_format('{} {} {!r}{ponc} {:.2f}', "hello dear 'world'! 1.33",
+ _0=('String', 'hello'), _1=('String', 'dear'),
+ _2=('String', 'world'), _3=('Float', '1.333333333'),
+ ponc=('String', '!'))
diff --git a/vistrails/core/modules/package.py b/vistrails/core/modules/package.py
index 0bb64f3..348fb9e 100644
--- a/vistrails/core/modules/package.py
+++ b/vistrails/core/modules/package.py
@@ -251,9 +251,9 @@ class Package(DBPackage):
##########################################################################
# Methods
- _python_lib_regex = re.compile(r'python[0-9.]+[a-z]?/lib/',
+ _python_lib_regex = re.compile(r'python[0-9.]+[a-z]?/lib/(?!vistrails)',
re.IGNORECASE)
- _lib_python_regex = re.compile(r'lib/python[0-9.]+[a-z]?/',
+ _lib_python_regex = re.compile(r'lib/python[0-9.]+[a-z]?/(?!vistrails)',
re.IGNORECASE)
def import_override(self, orig_import,
name, globals, locals, fromlist, level,
@@ -734,7 +734,7 @@ class Package(DBPackage):
(dom, element) = self.find_own_dom_element()
configuration = enter_named_element(element, 'configuration')
- if configuration:
+ if configuration and self.configuration is not None:
self.configuration.set_from_dom_node(configuration)
dom.unlink()
diff --git a/vistrails/core/modules/paramexplore.py b/vistrails/core/modules/paramexplore.py
index 6b8214a..d95d612 100644
--- a/vistrails/core/modules/paramexplore.py
+++ b/vistrails/core/modules/paramexplore.py
@@ -202,9 +202,12 @@ class TestLinearInterpolator(unittest.TestCase):
# test the property that differences in value must be linearly
# proportional to differences in index for a linear interpolation
import random
- s = random.randint(4, 10000)
+ s = random.randint(40, 1000)
v1 = random.random()
v2 = random.random()
+ # avoid very small differences
+ while abs(v2 - v1) < 0.01:
+ v2 = random.random()
mn = min(v1, v2)
mx = max(v1, v2)
x = BaseLinearInterpolator(float, mn, mx, s).get_values()
@@ -218,8 +221,8 @@ class TestLinearInterpolator(unittest.TestCase):
v4 = random.randint(0, s-1)
r1 = (v2 - v1) / (x[v2] - x[v1])
r2 = (v4 - v3) / (x[v4] - x[v3])
- assert abs(r1 - r2) < 1e-6
+ self.assertTrue(abs(r1 - r2) < 1e-6, "r1=%.20f\nr2=%.20f"%(r1,r2))
class TestColorInterpolation(unittest.TestCase):
def test_rgb_interpolation(self):
diff --git a/vistrails/core/paramexplore/paramexplore.py b/vistrails/core/paramexplore/paramexplore.py
index df468c9..8a1de5d 100644
--- a/vistrails/core/paramexplore/paramexplore.py
+++ b/vistrails/core/paramexplore/paramexplore.py
@@ -236,7 +236,7 @@ class ParameterExploration(DBParameterExploration):
new_param = ModuleParam(id=tmp_p_id,
pos=old_param.pos,
name=old_param.name,
- alias=pe_function.is_alias,
+ alias=old_param.alias,
val=str_value,
type=old_param.type)
tmp_p_id -= 1
@@ -264,10 +264,13 @@ class ParameterExploration(DBParameterExploration):
if len(self.functions) != len(other.functions):
return False
for p,q in zip(self.functions, other.functions):
- if p.real_id != q.real_id or p != q:
+ if p != q:
return False
return True
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
# Testing
@@ -303,21 +306,12 @@ class TestParameterExploration(unittest.TestCase):
q.action_id = 8
self.assertNotEqual(p, q)
q.action_id = 6
- q.user = 'bobo'
- self.assertNotEqual(p, q)
- q.user = 'tommy'
- q.date = '2008-11-23 12:48'
- self.assertNotEqual(p, q)
- q.date = p.date
q._dims = '[1,4]'
self.assertNotEqual(p, q)
q._dims = '[1,2]'
q._layout = '{1:"different"}'
self.assertNotEqual(p, q)
q._layout = p._layout
- q.name = 'test-pe2'
- self.assertNotEqual(p, q)
- q.name = p.name
q.functions = [1]
self.assertNotEqual(p, q)
diff --git a/vistrails/core/system/__init__.py b/vistrails/core/system/__init__.py
index 6ab99e9..7099165 100644
--- a/vistrails/core/system/__init__.py
+++ b/vistrails/core/system/__init__.py
@@ -278,7 +278,7 @@ def vistrails_version():
# 0.3 was the plugin/vtk version
# 0.4 is cleaned up version with new GUI
# 1.0 is version with new schema
- return '2.1.1'
+ return '2.1.4'
def get_latest_vistrails_version():
"""get_latest_vistrails_version() -> string - Returns latest vistrails
@@ -324,7 +324,7 @@ def vistrails_revision():
"""
git_dir = os.path.join(vistrails_root_directory(), '..')
with Chdir(git_dir):
- release = "97362185cfd1"
+ release = "269e4808eca3"
import vistrails.core.requirements
if vistrails.core.requirements.executable_file_exists('git'):
lines = []
diff --git a/vistrails/core/vistrail/controller.py b/vistrails/core/vistrail/controller.py
index 03a4bd4..47a3852 100644
--- a/vistrails/core/vistrail/controller.py
+++ b/vistrails/core/vistrail/controller.py
@@ -299,7 +299,12 @@ class VistrailController(object):
if self.vistrail:
return self.vistrail.get_vistrail_var(name)
return None
-
+
+ def has_vistrail_variable_with_uuid(self, uuid):
+ if self.vistrail:
+ return self.vistrail.db_has_vistrailVariable_with_uuid(uuid)
+ return None
+
def get_vistrail_variable_by_uuid(self, uuid):
if self.vistrail:
return self.vistrail.db_get_vistrailVariable_by_uuid(uuid)
@@ -312,12 +317,6 @@ class VistrailController(object):
return self.vistrail.vistrail_vars
return []
- def get_vistrail_variable_name_by_uuid(self, uuid):
- """def get_vistrail_variable_name_by_uuid(uuid: str) -> dict
- Returns the var name for vistrail variable with uuid """
- if self.vistrail and self.vistrail.db_has_vistrailVariable_with_uuid(uuid):
- return self.vistrail.db_get_vistrailVariable_by_uuid(uuid).name
-
def find_vistrail_var_module(self, var_uuid):
for m in self.current_pipeline.modules.itervalues():
if m.is_vistrail_var() and m.get_vistrail_var() == var_uuid:
@@ -424,6 +423,35 @@ class VistrailController(object):
# action.id)
return (to_delete_modules, to_delete_conns)
+ def get_connected_vistrail_vars(self, module_ids, to_delete=False):
+ """get_connected_vistrail_vars(module_ids: list, to_delete: bool)->list
+
+ Returns the vistrail variables connected to the specified module_id:s
+ If to_delete is true we exclude modules that have connections to
+ modules not in the module_ids list
+
+ """
+ vv_modules = {}
+ connections = self.get_connections_to(self.current_pipeline,
+ module_ids)
+ pipeline = self.current_pipeline
+ final_connections = []
+ for connection in connections:
+ m = pipeline.modules[connection.source.moduleId]
+ if m.is_vistrail_var():
+ if m.id not in vv_modules:
+ vv_modules[m.id] = []
+ vv_modules[m.id].append(connection)
+ final_connections.append(connection.id)
+ if to_delete:
+ for module_id, connections in vv_modules.items():
+ total_conns = self.get_connections_from(self.current_pipeline,
+ [module_id])
+ if len(total_conns) != len(connections):
+ # there are connections to other modules so don't delete
+ del vv_modules[module_id]
+ return vv_modules.keys(), final_connections
+
def getParameterExplorationById(self, id):
""" getParameterExplorationById(self, id) -> ParameterExploration
Returns a ParameterExploration given its id
@@ -540,8 +568,8 @@ class VistrailController(object):
self.current_session)
if description is not None:
self.vistrail.change_description(description, action.id)
- self.set_changed(True)
self.current_version = action.db_id
+ self.set_changed(True)
self.recompute_terse_graph()
def create_module_from_descriptor(self, *args, **kwargs):
@@ -686,7 +714,7 @@ class VistrailController(object):
query_methods=[]):
params = []
for i in xrange(len(port_spec.descriptors())):
- if i < len(values):
+ if i < len(values) and values[i] is not None:
value = str(values[i])
else:
value = None
@@ -711,7 +739,8 @@ class VistrailController(object):
def create_function_static(id_scope, module, function_name,
param_values=[], aliases=[], query_methods=[]):
port_spec = module.get_port_spec(function_name, 'input')
- if len(param_values) <= 0 and port_spec.defaults is not None:
+ if (len(param_values) <= 0 and port_spec.defaults is not None and
+ any(d is not None for d in port_spec.defaults)):
param_values = port_spec.defaults
f_id = id_scope.getNewId(ModuleFunction.vtType)
@@ -2574,23 +2603,25 @@ class VistrailController(object):
if 'compare_thumbnails' in extra_info:
# check thumbnail difference
prev = None
- if self.vistrail.has_thumbnail(version):
- prev = thumb_cache.get_abs_name_entry(self.vistrail.get_thumbnail(version))
- elif version in self.vistrail.actionMap and \
- int(self.vistrail.get_upgrade(self.vistrail.actionMap[version].parent)) == version and \
- self.vistrail.has_thumbnail(self.vistrail.actionMap[version].parent):
- prev = thumb_cache.get_abs_name_entry(self.vistrail.get_thumbnail(self.vistrail.actionMap[version].parent))
+ thumb_version = version
+ # the thumb can be in a previous upgrade
+ while not self.vistrail.has_thumbnail(thumb_version) and \
+ thumb_version in self.vistrail.actionMap and \
+ self.vistrail.has_upgrade(self.vistrail.actionMap[thumb_version].parent):
+ thumb_version = self.vistrail.actionMap[thumb_version].parent
+ if self.vistrail.has_thumbnail(thumb_version):
+ prev = thumb_cache.get_abs_name_entry(self.vistrail.get_thumbnail(thumb_version))
else:
- error = CompareThumbnailsError("No thumbnail exist for version %s" % version)
+ error = CompareThumbnailsError("No thumbnail exist for version %s" % thumb_version)
if prev:
if not prev:
- error = CompareThumbnailsError("No thumbnail file exist for version %s" % version)
+ error = CompareThumbnailsError("No thumbnail file exist for version %s" % thumb_version)
elif not fname:
raise CompareThumbnailsError("No thumbnail generated")
else:
next = thumb_cache.get_abs_name_entry(fname)
if not next:
- raise CompareThumbnailsError("No thumbnail file generated for version %s" % version)
+ raise CompareThumbnailsError("No thumbnail file generated for version %s" % thumb_version)
else:
min_err = extra_info['compare_thumbnails'](prev, next)
treshold = 0.1
@@ -3197,9 +3228,9 @@ class VistrailController(object):
pe.action_id = new_version
self.vistrail.db_add_parameter_exploration(pe)
for mashup in new_mashups:
- mashup.vtVersion = self.current_version
+ mashup.vtVersion = new_version
for action in mashup.actions:
- action.mashup.version = self.current_version
+ action.mashup.version = new_version
self._mashups.append(mashup)
self.set_changed(True)
diff --git a/vistrails/db/services/io.py b/vistrails/db/services/io.py
index d155cec..a1ef3bf 100644
--- a/vistrails/db/services/io.py
+++ b/vistrails/db/services/io.py
@@ -162,6 +162,9 @@ class SaveBundle(object):
for t in self.thumbnails:
cp.thumbnails.append(t)
+
+ for m in self.mashups:
+ cp.mashups.append(m)
return cp
@@ -954,6 +957,7 @@ def save_vistrail_bundle_to_zip_xml(save_bundle, filename, vt_save_dir=None, ver
raise VistrailsDBException('save_vistrail_bundle_to_zip_xml failed, '
'thumbnail list entry must be a filename')
# Save Mashups
+ saved_mashups = []
#print " mashups:"
if len(save_bundle.mashups) > 0 and not os.path.exists(mashup_dir):
os.mkdir(mashup_dir)
@@ -962,6 +966,7 @@ def save_vistrail_bundle_to_zip_xml(save_bundle, filename, vt_save_dir=None, ver
try:
xml_fname = os.path.join(mashup_dir, str(obj.id))
save_mashuptrail_to_xml(obj, xml_fname)
+ saved_mashups.append(obj)
except Exception, e:
raise VistrailsDBException('save_vistrail_bundle_to_zip_xml failed, '
'when saving mashup: %s'%str(e))
@@ -1002,7 +1007,10 @@ def save_vistrail_bundle_to_zip_xml(save_bundle, filename, vt_save_dir=None, ver
finally:
os.unlink(tmp_zip_file)
os.rmdir(tmp_zip_dir)
- save_bundle = SaveBundle(save_bundle.bundle_type, save_bundle.vistrail, save_bundle.log, thumbnails=saved_thumbnails, abstractions=saved_abstractions)
+ save_bundle = SaveBundle(save_bundle.bundle_type, save_bundle.vistrail,
+ save_bundle.log, thumbnails=saved_thumbnails,
+ abstractions=saved_abstractions,
+ mashups=saved_mashups)
return (save_bundle, vt_save_dir)
def save_vistrail_bundle_to_db(save_bundle, db_connection, do_copy=False, version=None):
@@ -1026,7 +1034,10 @@ def save_vistrail_bundle_to_db(save_bundle, db_connection, do_copy=False, versio
save_abstractions_to_db(save_bundle.abstractions, vistrail.db_id, db_connection, do_copy)
save_mashuptrails_to_db(save_bundle.mashups, vistrail.db_id, db_connection, do_copy)
save_thumbnails_to_db(save_bundle.thumbnails, db_connection)
- return SaveBundle(DBVistrail.vtType, vistrail, log, abstractions=list(save_bundle.abstractions), thumbnails=list(save_bundle.thumbnails))
+ return SaveBundle(DBVistrail.vtType, vistrail, log,
+ abstractions=list(save_bundle.abstractions),
+ thumbnails=list(save_bundle.thumbnails),
+ mashups=list(save_bundle.mashups))
def save_vistrail_to_db(vistrail, db_connection, do_copy=False, version=None):
if db_connection is None:
@@ -1582,7 +1593,7 @@ def open_thumbnails_from_db(db_connection, obj_type, obj_id, tmp_dir=None):
prepared_statement = format_prepared_statement(
"""
SELECT a.value
- FROM annotation a
+ FROM action_annotation a
WHERE a.akey = '__thumb__' AND a.entity_id = ? AND a.entity_type = ?
""")
try:
@@ -1594,7 +1605,6 @@ def open_thumbnails_from_db(db_connection, obj_type, obj_id, tmp_dir=None):
msg = "Couldn't get thumbnails list from db (%d : %s)" % \
(e.args[0], e.args[1])
raise VistrailsDBException(msg)
-
# Next get all thumbnails from the db that aren't already in tmp_dir
get_db_file_names = [fname for fname in file_names if fname not in os.listdir(tmp_dir)]
for file_name in get_db_file_names:
@@ -1753,7 +1763,10 @@ def save_mashuptrails_to_db(mashuptrails, vt_id, db_connection, do_copy=False):
msg = "Need to call open_db_connection() before reading"
raise VistrailsDBException(msg)
- old_ids = get_db_mashuptrail_ids_from_vistrail(db_connection, vt_id)
+ # for now we replace all mashups
+ for old_id in get_db_mashuptrail_ids_from_vistrail(db_connection, vt_id):
+ delete_entity_from_db(db_connection, Mashuptrail.vtType, old_id)
+
for mashuptrail in mashuptrails:
try:
id_key = '__mashuptrail_vistrail_id__'
@@ -1766,9 +1779,6 @@ def save_mashuptrails_to_db(mashuptrails, vt_id, db_connection, do_copy=False):
id_key, id_value)
mashuptrail.db_add_annotation(annotation)
- if mashuptrail.db_id in old_ids:
- delete_entity_from_db(db_connection, mashuptrail.vtType, mashuptrail.db_id)
-
# add vt_id to mashups
for action in mashuptrail.db_actions:
action.db_mashup.db_vtid = vt_id
diff --git a/vistrails/db/services/locator.py b/vistrails/db/services/locator.py
index ab9ac51..65fee95 100644
--- a/vistrails/db/services/locator.py
+++ b/vistrails/db/services/locator.py
@@ -477,7 +477,7 @@ class UntitledLocator(SaveTemporariesMixin, BaseLocator):
locators[my_uuid] = cls(my_uuid)
return locators.values()
-class XMLFileLocator(BaseLocator, SaveTemporariesMixin):
+class XMLFileLocator(SaveTemporariesMixin, BaseLocator):
def __init__(self, filename, **kwargs):
self._name = filename
self._vnode = kwargs.get('version_node', None)
diff --git a/vistrails/db/services/vistrail.py b/vistrails/db/services/vistrail.py
index d3caef8..2e093c7 100644
--- a/vistrails/db/services/vistrail.py
+++ b/vistrails/db/services/vistrail.py
@@ -208,6 +208,10 @@ def merge(sb, next_sb, app='', interactive = False, tmp_dir = '', next_tmp_dir =
MergeGUI = merge_gui.MergeGUI if merge_gui else False
skip = 0
+ # right now we just replace mashups and subworkflows
+ sb.mashups = list(next_sb.mashups)
+ sb.abstractions = list(next_sb.abstractions)
+
id_remap = {}
checkout_key = "__checkout_version_"
diff --git a/vistrails/db/specs/all.xml b/vistrails/db/specs/all.xml
index ab07b76..40df0ef 100644
--- a/vistrails/db/specs/all.xml
+++ b/vistrails/db/specs/all.xml
@@ -2365,6 +2365,7 @@
</property>
<property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
<sql type="datetime"/>
</property>
diff --git a/vistrails/db/versions/v1_0_3/persistence/xml/auto_gen.py b/vistrails/db/versions/v1_0_3/persistence/xml/auto_gen.py
index d1b6ebf..d09cce4 100644
--- a/vistrails/db/versions/v1_0_3/persistence/xml/auto_gen.py
+++ b/vistrails/db/versions/v1_0_3/persistence/xml/auto_gen.py
@@ -4580,6 +4580,8 @@ class DBParameterExplorationXMLDAOBase(XMLDAO):
action_id = self.convertFromStr(data, 'long')
data = node.get('name', None)
name = self.convertFromStr(data, 'str')
+ data = node.get('date', None)
+ date = self.convertFromStr(data, 'datetime')
data = node.get('user', None)
user = self.convertFromStr(data, 'str')
data = node.get('dims', None)
@@ -4606,6 +4608,7 @@ class DBParameterExplorationXMLDAOBase(XMLDAO):
obj = DBParameterExploration(id=id,
action_id=action_id,
name=name,
+ date=date,
user=user,
dims=dims,
layout=layout,
@@ -4621,6 +4624,7 @@ class DBParameterExplorationXMLDAOBase(XMLDAO):
node.set('id',self.convertToStr(parameter_exploration.db_id, 'long'))
node.set('actionId',self.convertToStr(parameter_exploration.db_action_id, 'long'))
node.set('name',self.convertToStr(parameter_exploration.db_name, 'str'))
+ node.set('date',self.convertToStr(parameter_exploration.db_date, 'datetime'))
node.set('user',self.convertToStr(parameter_exploration.db_user, 'str'))
node.set('dims',self.convertToStr(parameter_exploration.db_dims, 'str'))
node.set('layout',self.convertToStr(parameter_exploration.db_layout, 'str'))
diff --git a/vistrails/db/versions/v1_0_3/schemas/xml/vistrail.xsd b/vistrails/db/versions/v1_0_3/schemas/xml/vistrail.xsd
index 29a043d..06a88d4 100644
--- a/vistrails/db/versions/v1_0_3/schemas/xml/vistrail.xsd
+++ b/vistrails/db/versions/v1_0_3/schemas/xml/vistrail.xsd
@@ -99,6 +99,7 @@
<xs:attribute name="id" type="xs:int"/>
<xs:attribute name="actionId" type="xs:int"/>
<xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="date" type="xs:dateTime"/>
<xs:attribute name="user" type="xs:string"/>
<xs:attribute name="dims" type="xs:string"/>
<xs:attribute name="layout" type="xs:string"/>
diff --git a/vistrails/db/versions/v1_0_3/specs/all.xml b/vistrails/db/versions/v1_0_3/specs/all.xml
index ab07b76..40df0ef 100644
--- a/vistrails/db/versions/v1_0_3/specs/all.xml
+++ b/vistrails/db/versions/v1_0_3/specs/all.xml
@@ -2365,6 +2365,7 @@
</property>
<property name="date" type="datetime">
+ <xml nodeType="xs:attribute" type="xs:dateTime"/>
<sql type="datetime"/>
</property>
diff --git a/vistrails/gui/application.py b/vistrails/gui/application.py
index 48a71d8..005b964 100644
--- a/vistrails/gui/application.py
+++ b/vistrails/gui/application.py
@@ -230,6 +230,8 @@ class VistrailsApplicationSingleton(VistrailsApplicationInterface,
return APP_SUCCESS
def ask_update_default_application(self, dont_ask_checkbox=True):
+ if hasattr(self, 'splashScreen') and self.splashScreen:
+ self.splashScreen.hide()
dialog = QtGui.QDialog()
dialog.setWindowTitle(u"Install .vt .vtl handler")
layout = QtGui.QVBoxLayout()
diff --git a/vistrails/gui/application_server.py b/vistrails/gui/application_server.py
index 6acb922..241d771 100644
--- a/vistrails/gui/application_server.py
+++ b/vistrails/gui/application_server.py
@@ -73,6 +73,7 @@ from vistrails.core import system
from vistrails.core.modules.module_registry import get_module_registry as module_registry
from vistrails.core import interpreter
from vistrails.core.packagemanager import get_package_manager
+from vistrails.core.thumbnails import ThumbnailCache
import vistrails.core.system
import vistrails.db.services.io
import gc
@@ -238,6 +239,51 @@ class RequestHandler(object):
self.server_logger.error(traceback.format_exc())
return (result, 0)
+ def get_wf_mashups(self, host, port, db_name, vt_id, version):
+ """get_wf_mashups(host:str, port:int, db_name:str, vt_id:int,
+ version:int) -> (return_status, list of dict)
+ Returns a list of mashups in a workflow
+ in a list of dictionaries. The dictionary has the following keys:
+ name, package, documentation.
+ """
+ self.server_logger.info("Request: get_wf_mashups(%s,%s,%s,%s,%s)" % \
+ (host, port, db_name, vt_id, version))
+ result = []
+ try:
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+ (vistrail, abstractions, thumbnails, mashups) = \
+ io.load_vistrail(locator)
+ for mashuptrail in mashups:
+ # Find tagged mashups for this version
+ if mashuptrail.vtVersion == version:
+ for name, mashup_id in mashuptrail.getTagMap().iteritems():
+ if name != 'ROOT':
+ mashup = MedleySimpleGUI.from_mashup(
+ mashuptrail.getMashup(mashup_id))
+ result.append([name, ElementTree.tostring(mashup.to_xml())])
+ return (result, 1)
+ except xmlrpclib.ProtocolError, err:
+ err_msg = ("A protocol error occurred\n"
+ "URL: %s\n"
+ "HTTP/HTTPS headers: %s\n"
+ "Error code: %d\n"
+ "Error message: %s\n") % (err.url, err.headers,
+ err.errcode, err.errmsg)
+ self.server_logger.error(err_msg)
+ return (str(err), 0)
+ except Exception, e:
+ result = str(e)
+ self.server_logger.error(result)
+ self.server_logger.error(traceback.format_exc())
+ return (result, 0)
+
def get_packages(self):
"""get_packages()-> dict
This returns a dictionary with all the packages available in the
@@ -280,8 +326,10 @@ class RequestHandler(object):
def get_server_packages(self, codepath=None, status=None):
"""get_server_packages()-> dict
- This returns a dictionary with all the packages to vistrails with status indicating wether it is loaded.
- It is also possible to enable/disable a package by passing a package codepath and the desired status on/off
+ This returns a dictionary with all the packages to vistrails with
+ status indicating wether it is loaded.
+ It is also possible to enable/disable a package by passing a package
+ codepath and the desired status on/off
The keys are the package identifier.
"""
self.server_logger.info("Request: get_server_packages()")
@@ -312,11 +360,12 @@ class RequestHandler(object):
"Error message: %s\n") % (err.url, err.headers,
err.errcode, err.errmsg)
self.server_logger.error(err_msg)
+ finally:
+ self.proxies_queue.put(proxy)
if s == 0:
messages.append('An error occurred: %s' % result)
else:
messages.append(result[1])
- self.proxies_queue.put(proxy)
try:
pkg_manager = get_package_manager()
@@ -390,7 +439,7 @@ class RequestHandler(object):
"""
try:
if is_local:
- locator = ZIPFileLocator(vt_filepath).load()
+ bundle = ZIPFileLocator(vt_filepath).load()
else:
# vt_filepath contains vt file datastream
# write to tmp file, read into FileLocator
@@ -402,19 +451,19 @@ class RequestHandler(object):
vt_file = open(fname, "wb")
vt_file.write(vt_filepath.data)
vt_file.close()
- locator = ZIPFileLocator(fname).load()
+ bundle = ZIPFileLocator(fname).load()
finally:
os.unlink(fname)
# set some crowdlabs id info
if repository_vt_id != -1:
- vistrail = locator.vistrail
+ vistrail = bundle.vistrail
vistrail.set_annotation('repository_vt_id', repository_vt_id)
vistrail.set_annotation('repository_creator', repository_creator)
db_locator = DBLocator(host=host, port=int(port), database=db_name,
name=filename, user=db_write_user, passwd=db_write_pass)
- db_locator.save_as(locator)
+ db_locator.save_as(bundle)
return (db_locator.obj_id, 1)
except xmlrpclib.ProtocolError, err:
@@ -459,6 +508,8 @@ class RequestHandler(object):
new_locator = ZIPFileLocator(tmp_file)
new_bundle = new_locator.load()
+ # add thumbnails to cache
+ ThumbnailCache.getInstance()._copy_thumbnails(new_bundle.thumbnails)
new_locator.save(new_bundle)
old_db_locator = DBLocator(host=host, port=int(port), database=db_name,
obj_id=int(old_db_vt_id), user=db_write_user, passwd=db_write_pass)
@@ -577,6 +628,91 @@ class RequestHandler(object):
self.server_logger.error(str(e))
return (str(e), 0)
+ #webgl
+ def run_from_db_webgl(self, host, port, db_name, vt_id, path_to_figures,
+ version=None, pdf=False, vt_tag='', build_always=False,
+ parameters='', is_local=True):
+ # get vistrail
+ locator = DBLocator(host=host,
+ port=int(port),
+ database=db_name,
+ user=db_read_user,
+ passwd=db_read_pass,
+ obj_id=int(vt_id),
+ obj_type=None,
+ connection_id=None)
+ (vistrail, abstractions , thumbnails, mashups) = io.load_vistrail(locator)
+ from core.vistrail.controller import VistrailController as BaseController
+ c = BaseController()
+ c.set_vistrail(vistrail, locator, abstractions, thumbnails, mashups)
+
+ # get server packages
+ local_packages = [x.identifier for x in module_registry().package_list]
+ version_id = 0
+ version_tag = 0
+
+ from db.domain import IdScope
+ from core.vistrail.connection import Connection
+ from core.vistrail.module import Module
+ from core.vistrail.port import Port
+
+ # get last pipeline
+ workflow = False
+ if (vt_tag == ''):
+ version = vistrail.get_latest_version()#-1;
+ else:
+ version = int(vt_tag)
+
+ c.change_selected_version(version)
+ workflow = c.current_pipeline.__copy__()
+
+ #id_scope = IdScope(version)
+ id_scope = vistrail.idScope
+ if workflow:
+ # if doesnt have VTKWebView and vtkRenderer
+ if ("vtkRenderer" not in [x.name for x in workflow.module_list]):
+ return (str("Doesn't have vtkRenderer"), 1)
+
+ # if already have VTKWebView, execute it
+ if ("VTKWebView" not in [x.name for x in workflow.module_list]):
+ # else, add VTKWebView to vtkRenderer and execute it
+ renderer = workflow.module_list[[x.name for x in workflow.module_list].index('vtkRenderer')]
+
+ action_list = []
+
+ mWeb = Module(id=id_scope.getNewId(Module.vtType),
+ name='VTKWebView',
+ package='edu.utah.sci.vistrails.vtWebGL',
+ functions=[])
+ mWeb.version = '0.0.2'
+ workflow.add_module(mWeb);
+ # create connection from render to web
+ source = Port(id=id_scope.getNewId(Port.vtType),
+ type='source',
+ moduleId=renderer.id,
+ moduleName='vtkRenderer',
+ name='self',
+ signature='(edu.utah.sci.vistrails.vtk:vtkRenderer)')
+ destination = Port(id=id_scope.getNewId(Port.vtType),
+ type='destination',
+ moduleId=mWeb.id,
+ moduleName='VTKWebView',
+ name='vtkrenderer',
+ signature='(edu.utah.sci.vistrails.vtk:vtkRenderer)')
+ c1 = Connection(id=id_scope.getNewId(Connection.vtType), ports=[source, destination])
+ # add connection to action list.
+ workflow.add_connection(c1)
+ workflow.validate()
+
+ c.current_pipeline = workflow;
+ (results, x) = c.execute_current_workflow()
+ if len(results[0].errors.values()) > 0:
+ print "> ERROR: ", results[0].errors
+ return (-1, str(results[0].errors.values()[0]))
+ else: return (1, 1)
+
+ return ("Doesnt have working workflow.", 1)
+
#medleys
def executeMedley(self, xml_medley, extra_info=None):
@@ -637,6 +773,7 @@ class RequestHandler(object):
obj_type=None,
connection_id=None)
+ extra_info['mashup_id'] = medley._id
workflow = medley._version
sequence = False
for (k,v) in medley._alias_list.iteritems():
@@ -665,6 +802,7 @@ class RequestHandler(object):
vistrails.core.console_mode.run_and_get_results( \
[(locator,int(workflow))],
s_alias,
+ update_vistrail=False,
extra_info=extra_info)
self.server_logger.info("Memory usage: %s"% self.memory_usage())
interpreter.cached.CachedInterpreter.flush()
@@ -758,7 +896,8 @@ class RequestHandler(object):
for f in file_names:
sub.append(os.path.join(root[root.find(subdir):],
f))
- s.append(";".join(sub))
+ if len(sub):
+ s.append(";".join(sub))
result = ":::".join(s)
# FIXME: copy images to extra_path
self.server_logger.info("returning %s" % result)
@@ -793,7 +932,7 @@ class RequestHandler(object):
# use same hashing as on crowdlabs webserver
dest_version = "%s_%s_%d_%d_%d" % (host, db_name, int(port), int(vt_id), int(version))
dest_version = hashlib.sha1(dest_version).hexdigest()
- path_to_figures = os.path.join(media_dir, "wf_execution", dest_version)
+ path_to_figures = os.path.join(media_dir, "photos", "wf_execution", dest_version)
if ((not self.path_exists_and_not_empty(path_to_figures) or
build_always) and self.proxies_queue is not None):
@@ -833,7 +972,7 @@ class RequestHandler(object):
if os.path.exists(extra_info['pathDumpCells']):
shutil.rmtree(extra_info['pathDumpCells'])
os.mkdir(extra_info['pathDumpCells'])
-
+
result = ''
if vt_tag !='':
version = vt_tag;
@@ -847,6 +986,8 @@ class RequestHandler(object):
obj_type=None,
connection_id=None)
results = []
+ self.server_logger.info("run_and_get_results(%s,%s,%s,%s,%s)" % \
+ (locator, version, parameters, True, extra_info))
try:
results = \
vistrails.core.console_mode.run_and_get_results([(locator,
@@ -856,6 +997,7 @@ class RequestHandler(object):
extra_info=extra_info,
reason="Server Pipeline Execution")
except Exception, e:
+ self.server_logger.error("workflow execution failed:")
self.server_logger.error(str(e))
self.server_logger.error(traceback.format_exc())
return (str(e), 0)
@@ -1668,6 +1810,17 @@ class XMLObject(object):
return str(value)
return ''
+ @staticmethod
+ def type_name(type):
+ d = {'Integer':'int',
+ 'String':'str',
+ 'Long':'long',
+ 'Float':'float',
+ 'Boolean':'bool',
+ 'Date':'date',
+ 'DateTime':'datetime',
+ }
+ return d.get(type, 'str')
################################################################################
class MedleySimpleGUI(XMLObject):
@@ -1734,6 +1887,21 @@ class MedleySimpleGUI(XMLObject):
alias_list[alias._name] = alias
return MedleySimpleGUI(id=id, name=name, vtid=vtid, version=version,
alias_list=alias_list, t=type, has_seq=seq)
+
+ @staticmethod
+ def from_mashup(mashup):
+ #read attributes
+ alias_list = {}
+ for child in mashup.aliases:
+ alias = AliasSimpleGUI.from_alias(child)
+ alias_list[alias._name] = alias
+ return MedleySimpleGUI(id=mashup.id,
+ name=mashup.name,
+ vtid=mashup.vtid,
+ version=mashup.version,
+ alias_list=alias_list,
+ t=mashup.type,
+ has_seq=mashup.has_seq)
################################################################################
@@ -1774,6 +1942,12 @@ class AliasSimpleGUI(XMLObject):
alias = AliasSimpleGUI(id,name,component)
return alias
+ @staticmethod
+ def from_alias(alias):
+ component = ComponentSimpleGUI.from_component(alias.component)
+ alias = AliasSimpleGUI(alias.id, alias.name, component)
+ return alias
+
################################################################################
class ComponentSimpleGUI(XMLObject):
@@ -1882,6 +2056,22 @@ class ComponentSimpleGUI(XMLObject):
seq=seq,
widget=widget)
return component
+
+ @staticmethod
+ def from_component(c):
+ component = ComponentSimpleGUI(id=c.id,
+ pos=c.pos,
+ ctype='Parameter',
+ spec=ComponentSimpleGUI.type_name(c.type),
+ val=c.val,
+ minVal=c.minVal,
+ maxVal=c.maxVal,
+ stepSize=c.stepSize,
+ strvalueList=c.strvaluelist,
+ parent=c.parent,
+ seq=c.seq,
+ widget=c.widget)
+ return component
################################################################################
################################################################################
diff --git a/vistrails/gui/bundles/installbundle.py b/vistrails/gui/bundles/installbundle.py
index a0e52de..021bf7a 100644
--- a/vistrails/gui/bundles/installbundle.py
+++ b/vistrails/gui/bundles/installbundle.py
@@ -42,18 +42,13 @@ from vistrails.core.system import get_executable_path
from vistrails.core.system import vistrails_root_directory, systemType
from vistrails.gui.bundles.utils import guess_system, guess_graphical_sudo
import vistrails.gui.bundles.installbundle # this is on purpose
+from vistrails.gui.requirements import qt_available
+import os
import subprocess
import sys
##############################################################################
-def has_qt():
- try:
- import PyQt4.QtGui
- return True
- except ImportError:
- return False
-
pip_installed = True
try:
import pip
@@ -72,7 +67,7 @@ def shell_escape(arg):
return '"%s"' % arg.replace('\\', '\\\\').replace('"', '\\"')
-def run_install_command_as_root(graphical, cmd, args):
+def run_install_command(graphical, cmd, args, as_root=True):
if isinstance(args, str):
cmd += ' %s' % shell_escape(args)
elif isinstance(args, list):
@@ -83,27 +78,29 @@ def run_install_command_as_root(graphical, cmd, args):
else:
raise TypeError("Expected string or list of strings")
- if graphical:
- sucmd, escape = guess_graphical_sudo()
- else:
- debug.warning("VisTrails wants to install package(s) %r" %
- args)
- if get_executable_path('sudo'):
- sucmd, escape = "sudo %s", False
- elif systemType not in ['Darwin', 'Windows']:
- sucmd, escape = "su -c %s", True
+ debug.warning("VisTrails wants to install package(s) %r" %
+ args)
+
+ if as_root and systemType != 'Windows':
+ if graphical:
+ sucmd, escape = guess_graphical_sudo()
else:
- sucmd, escape = '%s', False
+ if get_executable_path('sudo'):
+ sucmd, escape = "sudo %s", False
+ elif systemType != 'Darwin':
+ sucmd, escape = "su -c %s", True
+ else:
+ sucmd, escape = '%s', False
- if escape:
- sucmd = sucmd % shell_escape(cmd)
- else:
- sucmd = sucmd % cmd
+ if escape:
+ cmd = sucmd % shell_escape(cmd)
+ else:
+ cmd = sucmd % cmd
- print "about to run: %s" % sucmd
- p = subprocess.Popen(sucmd, stdout=subprocess.PIPE,
- stderr=subprocess.STDOUT,
- shell=True)
+ print "about to run: %s" % cmd
+ p = subprocess.Popen(cmd, stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT,
+ shell=True)
lines = []
try:
for line in iter(p.stdout.readline, ''):
@@ -120,7 +117,7 @@ def run_install_command_as_root(graphical, cmd, args):
def linux_debian_install(package_name):
- qt = has_qt()
+ qt = qt_available()
try:
import apt
import apt_pkg
@@ -136,13 +133,13 @@ def linux_debian_install(package_name):
if get_executable_path('aptitude')
else 'apt-get')
- return run_install_command_as_root(qt, cmd, package_name)
+ return run_install_command(qt, cmd, package_name)
linux_ubuntu_install = linux_debian_install
def linux_fedora_install(package_name):
- qt = has_qt()
+ qt = qt_available()
hide_splash_if_necessary()
if qt:
@@ -151,7 +148,7 @@ def linux_fedora_install(package_name):
else:
cmd = 'yum -y install'
- return run_install_command_as_root(qt, cmd, package_name)
+ return run_install_command(qt, cmd, package_name)
def pip_install(package_name):
@@ -161,13 +158,25 @@ def pip_install(package_name):
cmd = '%s install' % shell_escape(get_executable_path('pip'))
else:
cmd = shell_escape(sys.executable) + ' -m pip install'
- return run_install_command_as_root(has_qt(), cmd, package_name)
+
+ if systemType != 'Windows':
+ use_root = True
+ try:
+ from distutils.sysconfig import get_python_lib
+ f = get_python_lib()
+ except Exception:
+ f = sys.executable
+ use_root = os.stat(f).st_uid == 0
+ else:
+ use_root = False
+
+ return run_install_command(qt_available(), cmd, package_name, use_root)
def show_question(which_files, has_distro_pkg, has_pip):
- if has_qt():
+ if isinstance(which_files, str):
+ which_files = [which_files]
+ if qt_available():
from PyQt4 import QtCore, QtGui
- if isinstance(which_files, str):
- which_files = [which_files]
dialog = QtGui.QDialog()
dialog.setWindowTitle("Required packages missing")
layout = QtGui.QVBoxLayout()
@@ -223,11 +232,11 @@ def show_question(which_files, has_distro_pkg, has_pip):
return 'pip'
return 'distro'
else:
- print "\nRequired package missing"
- print ("A required package is missing, but VisTrails can " +
- "automatically install it. " +
- "If you say Yes, VisTrails will need "+
- "administrator privileges, and you" +
+ print "\nRequired package(s) missing: %s" % (" ".join(which_files))
+ print ("A required package is missing, but VisTrails can "
+ "automatically install it. "
+ "If you say Yes, VisTrails will need "
+ "administrator privileges, and you "
"might be asked for the administrator password.")
if has_distro_pkg:
print "(VisTrails will use your distribution's package manager)"
diff --git a/vistrails/gui/bundles/linux_debian_install.py b/vistrails/gui/bundles/linux_debian_install.py
index 3bfc8b9..12edef9 100755
--- a/vistrails/gui/bundles/linux_debian_install.py
+++ b/vistrails/gui/bundles/linux_debian_install.py
@@ -37,6 +37,7 @@
# Installs a package through APT, showing progress.
import apt
import apt_pkg
+import locale
import sys
import time
@@ -54,6 +55,12 @@ package_name = sys.argv[1]
##############################################################################
+def smart_decode(msg):
+ if isinstance(msg, bytes):
+ encoding = locale.getpreferredencoding() or 'utf-8'
+ msg = msg.decode(encoding, 'replace').replace(u'\xFFFD', '?')
+ return msg
+
class GuiOpProgress(OpProgress):
def __init__(self, pbar):
OpProgress.__init__(self)
@@ -80,12 +87,12 @@ class GUIAcquireProgress(AcquireProgress):
current_item = self.total_items
if self.current_cps > 0:
text = (_("Downloading file %(current)li of %(total)li with "
- "%(speed)s/s") % \
+ "%(speed)s/s") %
{"current": current_item,
"total": self.total_items,
"speed": apt_pkg.size_to_str(self.current_cps)})
else:
- text = (_("Downloading file %(current)li of %(total)li") % \
+ text = (_("Downloading file %(current)li of %(total)li") %
{"current": current_item,
"total": self.total_items})
self.status_label.setText(text)
@@ -130,7 +137,7 @@ class GUIInstallProgress(InstallProgress):
def status_change(self, pkg, percent, status):
if self.last >= percent:
return
- self.status_label.setText(status)
+ self.status_label.setText(smart_decode(status))
self.pbar.setValue(int(percent))
self.last = percent
QtGui.qApp.processEvents()
diff --git a/vistrails/gui/collection/workspace.py b/vistrails/gui/collection/workspace.py
index 538d647..97b0896 100644
--- a/vistrails/gui/collection/workspace.py
+++ b/vistrails/gui/collection/workspace.py
@@ -43,10 +43,8 @@ from vistrails.core.thumbnails import ThumbnailCache
from vistrails.core import debug
from vistrails.core.collection import Collection, MashupEntity, ThumbnailEntity, \
VistrailEntity, WorkflowEntity, WorkflowExecEntity, ParameterExplorationEntity
-from vistrails.core.collection.search import SearchCompiler, SearchParseError
from vistrails.core.db.locator import FileLocator
from vistrails.db.services.locator import UntitledLocator
-from vistrails.gui.common_widgets import QToolWindowInterface, QToolWindow, QSearchBox
from vistrails.gui.vistrails_palette import QVistrailsPaletteInterface
from vistrails.gui.theme import CurrentTheme
from vistrails.gui.module_palette import QModuleTreeWidgetItemDelegate
@@ -103,13 +101,8 @@ class QCollectionWidget(QtGui.QTreeWidget):
for i in xrange(item.childCount())])
def item_selected(self, widget_item, column):
- #print 'item_selected'
locator = widget_item.entity.locator()
- #print "locator", locator
import vistrails.gui.application
-# if not locator.is_valid():
-# debug.critical("Locator is not valid:" % locator.to_url())
-# return
app = vistrails.gui.application.get_vistrails_application()
open_vistrail = app.builderWindow.open_vistrail_without_prompt
args = {}
@@ -118,24 +111,16 @@ class QCollectionWidget(QtGui.QTreeWidget):
if args['version']:
# set vistrail name
locator = widget_item.entity.parent.locator()
- pass
- #locator._name = widget_item.entity.parent.name
workflow_exec = locator.kwargs.get('workflow_exec', None)
if workflow_exec:
args['workflow_exec'] = workflow_exec
locator = widget_item.entity.parent.parent.locator()
locator.update_from_gui(self)
- # set vistrail name
- #locator._name = widget_item.entity.parent.parent.name
-
+
locator.update_from_gui(self)
-# print '*** opening'
-# print locator.to_url()
-# print locator.name
-# print '***'
open_vistrail(locator, **args)
-
+
def contextMenuEvent(self, event):
item = self.itemAt(event.pos())
menu = QtGui.QMenu(self)
@@ -293,7 +278,6 @@ class QWorkspaceWidget(QCollectionWidget):
for entity in self.collection.workspaces[self.collection.currentWorkspace]:
item = QBrowserWidgetItem(entity, self)
self.addTopLevelItem(item)
-# if self.collection.currentWorkspace != 'Default':
self.setSortingEnabled(True)
self.sortItems(0, QtCore.Qt.AscendingOrder)
@@ -325,16 +309,7 @@ class QBrowserWidgetItem(QtGui.QTreeWidgetItem):
self.addChild(self.paramExplorationsItem)
self.setIcon(0, CurrentTheme.HISTORY_ICON)
return
-
- # # old, esoteric code
- #
- # l = list(str(x) for x in entity.save())
- # l.pop(0) # remove identifier
- # type = l.pop(0)
- # desc = l[5]
- # if len(desc) > 20:
- # l[5] = desc[:20] + '...'
- klass = self.__class__
+
self.entity = entity
QtGui.QTreeWidgetItem.__init__(self, parent, [entity.name])
if entity.type_id == VistrailEntity.type_id:
@@ -360,7 +335,6 @@ class QBrowserWidgetItem(QtGui.QTreeWidgetItem):
tooltip = '<html>%s' % entity.url
for child in entity.children:
- # l = child.save()
if child.type_id == ThumbnailEntity.type_id:
# is a thumbnail
# add to parent workflow item
@@ -408,14 +382,6 @@ class QBrowserWidgetItem(QtGui.QTreeWidgetItem):
tooltip += '</html>'
self.setToolTip(0, tooltip)
- #def __lt__(self, other):
- # sort_col = self.treeWidget().sortColumn()
- # if sort_col in set([4]):
- # return int(self.text(sort_col)) < int(other.text(sort_col))
- # elif sort_col in set([2,3]):
- # return datetime(*strptime(str(self.text(sort_col)), '%d %b %Y %H:%M:%S')[0:6]) < datetime(*strptime(str(other.text(sort_col)), '%d %b %Y %H:%M:%S')[0:6])
- # return QtGui.QTreeWidgetItem.__lt__(self, other)
-
def refresh_object(self):
Collection.getInstance().updateVistrail(self.entity.url)
Collection.getInstance().commit()
@@ -473,7 +439,6 @@ class QExplorerWidget(QCollectionWidget):
for entity in self.collection.workspaces[self.collection.currentWorkspace]:
item = QExplorerWidgetItem(entity)
self.addTopLevelItem(item)
-# if self.collection.currentWorkspace != 'Default':
self.setSortingEnabled(True)
self.sortItems(0, QtCore.Qt.AscendingOrder)
@@ -483,9 +448,6 @@ class QExplorerWidgetItem(QtGui.QTreeWidgetItem):
l.pop(0) # remove identifier
type = l.pop(0)
desc = l.pop(5)
-# l.pop(7)
-# if len(desc) > 20:
-# l[5] = desc[:20] + '...'
QtGui.QTreeWidgetItem.__init__(self, parent, l)
self.entity = entity
if type == '1':
@@ -528,47 +490,19 @@ class QWorkspaceWindow(QtGui.QWidget, QVistrailsPaletteInterface):
def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
-# self.workspace_list = QtGui.QComboBox()
-# self.titleWidget = QtGui.QWidget()
-# self.titleLayout = QtGui.QHBoxLayout()
-# self.titleLayout.setMargin(0)
-# self.titleLayout.setSpacing(5)
-# self.titleLayout.addWidget(QtGui.QLabel('Project:'), 0)
-# self.titleLayout.addWidget(self.workspace_list, 1)
-# self.titleWidget.setLayout(self.titleLayout)
-# self.setTitleBarWidget(self.titleWidget)
self.setWindowTitle('Workspace')
# make it possible to ignore updates during updating of workspace list
self.updatingWorkspaceList = False
-# self.connect(self.workspace_list,
-# QtCore.SIGNAL("currentIndexChanged(QString)"),
-# self.workspace_changed)
layout = QtGui.QVBoxLayout()
layout.setMargin(0)
layout.setSpacing(5)
-# self.search_box = QSearchBox(True, False, self)
-# layout.addWidget(self.search_box)
self.collection = Collection.getInstance()
self.open_list = QVistrailList()
self.open_list.collection = self.collection
layout.addWidget(self.open_list)
-# layout.addWidget(self.titleWidget)
-
-# self.browser = QWorkspaceWidget(self.collection)
-# layout.addWidget(self.browser)
-# self.browser.setup_widget('Default')
-# self.connect(self.search_box, QtCore.SIGNAL('resetSearch()'),
-# self.reset_search)
-# self.connect(self.search_box, QtCore.SIGNAL('executeSearch(QString)'),
-# self.execute_search)
-# self.connect(self.search_box, QtCore.SIGNAL('refineMode(bool)'),
-# self.refine_mode)
-# self.connect(self.browser, QtCore.SIGNAL('workspaceListUpdated()'),
-# self.update_workspace_list)
self.setLayout(layout)
-# self.update_workspace_list()
self.addButtonsToToolbar()
@@ -612,16 +546,15 @@ class QWorkspaceWindow(QtGui.QWidget, QVistrailsPaletteInterface):
self.open_list.state_changed(view)
def gotoSearch(self):
+ from vistrails.gui.vistrails_window import _app
if self.searchAction.searchMode:
self.open_list.hide_search_results()
self.searchAction.searchMode = False
self.open_list.searchMode = False
self.searchAction.setText("Search")
- from vistrails.gui.vistrails_window import _app
_app.notify('query_changed', None)
else:
- from vistrails.gui.vistrails_window import _app
_app.qactions['search'].trigger()
def updateSearchResults(self, search=None, result_list=None):
@@ -687,16 +620,6 @@ class QWorkspaceWindow(QtGui.QWidget, QVistrailsPaletteInterface):
def set_results(self, results):
pass
- def execute_search(self, text):
- s = str(text)
- try:
- search = SearchCompiler(s).searchStmt
- except SearchParseError, e:
- debug.warning("Search Parse Error", str(e))
- search = None
-
- self.browser.run_search(search)
-
def refine_mode(self, on):
pass
@@ -709,82 +632,6 @@ class QWorkspaceWindow(QtGui.QWidget, QVistrailsPaletteInterface):
def remove_vt_window(self, vistrail_window):
self.open_list.remove_vt_window(vistrail_window)
-class QExplorerDialog(QToolWindow, QToolWindowInterface):
- def __init__(self, parent=None):
- QToolWindow.__init__(self, parent=parent)
-
- self.widget = QtGui.QWidget()
- self.setWidget(self.widget)
- self.workspace_list = QtGui.QComboBox()
- self.setTitleBarWidget(self.workspace_list)
- # make it possible to ignore updates during updating of workspace list
- self.updatingWorkspaceList = False
- self.connect(self.workspace_list,
- QtCore.SIGNAL("currentIndexChanged(QString)"),
- self.workspace_changed)
- layout = QtGui.QVBoxLayout()
-# layout.setMargin(0)
-# layout.setSpacing(5)
- self.search_box = QSearchBox(True, False, self)
- layout.addWidget(self.search_box)
-
- self.collection = Collection.getInstance()
- self.browser = QExplorerWidget(self.collection, self)
- layout.addWidget(self.browser)
- self.browser.setup_widget('Recent files')
- self.connect(self.search_box, QtCore.SIGNAL('resetSearch()'),
- self.reset_search)
- self.connect(self.search_box, QtCore.SIGNAL('executeSearch(QString)'),
- self.execute_search)
- self.connect(self.search_box, QtCore.SIGNAL('refineMode(bool)'),
- self.refine_mode)
- self.connect(self.browser, QtCore.SIGNAL('workspaceListUpdated()'),
- self.update_workspace_list)
- self.widget.setLayout(layout)
- self.update_workspace_list()
-
- def update_workspace_list(self):
- """ Updates workspace list and highlights currentWorkspace
- Keeps 'Default' on top
- """
- self.updatingWorkspaceList = True
- self.workspace_list.clear()
- self.workspace_list.addItem('Default')
- if 'Default' == self.browser.collection.currentWorkspace:
- self.workspace_list.setCurrentIndex(self.workspace_list.count()-1)
- sorted_workspaces = self.browser.collection.workspaces.keys()
- if 'Default' in sorted_workspaces:
- sorted_workspaces.remove('Default')
- sorted_workspaces.sort()
- for p in sorted_workspaces:
- self.workspace_list.addItem(p)
- if p == self.browser.collection.currentWorkspace:
- self.workspace_list.setCurrentIndex(self.workspace_list.count()-1)
- self.updatingWorkspaceList = False
-
- def workspace_changed(self, workspace):
- if not self.updatingWorkspaceList:
- self.browser.setup_widget(str(workspace))
-
- def reset_search(self):
- self.browser.reset_search()
-
- def set_results(self, results):
- pass
-
- def execute_search(self, text):
- s = str(text)
- try:
- search = SearchCompiler(s).searchStmt
- except SearchParseError, e:
- debug.warning("Search Parse Error", str(e))
- search = None
-
- self.browser.run_search(search)
-
- def refine_mode(self, on):
- pass
-
class QVistrailEntityItem(QBrowserWidgetItem):
def __init__(self, entity, window=None):
QBrowserWidgetItem.__init__(self, entity)
@@ -796,7 +643,6 @@ class QVistrailEntityItem(QBrowserWidgetItem):
# make them draggable
self.setFlags(self.flags() | QtCore.Qt.ItemIsDragEnabled
| QtCore.Qt.ItemIsDropEnabled
-# | QtCore.Qt.ItemIsSelectable
)
def open_in_new_window(self):
@@ -1018,7 +864,6 @@ class QVistrailList(QtGui.QTreeWidget):
if self.searchMode:
self.search_result_selected(view, version)
else:
- # _app.view_changed(view)
_app.change_view(view)
if version:
view.version_selected(version, True, double_click=True)
@@ -1057,9 +902,7 @@ class QVistrailList(QtGui.QTreeWidget):
vistrail_entity = entity.parent.parent
locator = vistrail_entity.locator()
locator.update_from_gui(self)
- # set vistrail name
- #locator._name = widget_item.entity.parent.parent.name
-
+
if isinstance(widget_item, QVistrailListLatestItem):
# find the latest item (max action id)
vistrail = widget_item.parent().parent().window.controller.vistrail
@@ -1234,7 +1077,7 @@ class QVistrailList(QtGui.QTreeWidget):
self.setSortingEnabled(False)
if not (hasattr(item, 'tag_to_item') or hasattr(item, 'mshp_to_item')):
return
- for tag, wf in item.tag_to_item.iteritems():
+ for wf in item.tag_to_item.itervalues():
index = wf.parent().indexOfChild(wf)
wf = wf.parent().takeChild(index)
item.workflowsItem.addChild(wf)
@@ -1285,11 +1128,6 @@ class QVistrailList(QtGui.QTreeWidget):
(new_entity, was_updated) = \
entity.update_vistrail(view.controller.vistrail)
- #if new_entity:
- # Collection.getInstance().create_vistrail_entity(
- # view.controller.vistrail)
- # self.add_vt_window(view)
- # return
if was_updated:
item.setText(0, entity.name)
(added_wfs, deleted_wfs) = entity.update_workflows()
@@ -1397,7 +1235,7 @@ class QVistrailList(QtGui.QTreeWidget):
recent.entity.url == entity.url:
self.setSelected(None)
index = self.closedFilesItem.indexOfChild(recent)
- item = self.closedFilesItem.takeChild(index)
+ self.closedFilesItem.takeChild(index)
item = QVistrailEntityItem(entity, vistrail_window)
item.current_item = QVistrailListLatestItem()
item.workflowsItem.addChild(item.current_item)
@@ -1452,7 +1290,7 @@ class QVistrailList(QtGui.QTreeWidget):
item.paramExplorationsItem.setHidden(
not item.paramExplorationsItem.childCount())
self.make_tree(item) if self.isTreeView else self.make_list(item)
- self.setSelected(vistrail_window)
+ self.item_changed(item, None)
self.updateHideExecutions()
def remove_vt_window(self, vistrail_window):
@@ -1500,7 +1338,7 @@ class QVistrailList(QtGui.QTreeWidget):
item = parent_item.child(i)
font = item.font(0)
window = item.window if hasattr(item, 'window') else None
- font.setBold(view == window if window and view else False)
+ font.setBold(bool(window and view and view == window))
item.setFont(0, font)
if window:
item.setText(0, window.get_name())
@@ -1520,7 +1358,6 @@ class QVistrailList(QtGui.QTreeWidget):
# parent node
return
vistrail = vistrail.parent()
- #print "*** item clicked", id(vistrail.window)
self.setSelected(vistrail.window)
self.parent().emit(QtCore.SIGNAL("vistrailChanged(PyQt_PyObject)"),
@@ -1571,7 +1408,7 @@ class QVistrailList(QtGui.QTreeWidget):
menu.addAction(act)
menu.exec_(event.globalPos())
elif (isinstance(item, QWorkflowEntityItem) or
- isinstance(item, QVistrailListLatestItem)):
+ isinstance(item, QVistrailListLatestItem)):
if item and self.openFilesItem.indexOfChild(item.get_vistrail()) == -1:
# vistrail is not open
return
@@ -1590,7 +1427,7 @@ class QVistrailList(QtGui.QTreeWidget):
act.setStatusTip("Open specified workflow in a new window")
menu.addAction(act)
menu.exec_(event.globalPos())
- elif isinstance(item,QMashupEntityItem):
+ elif isinstance(item, QMashupEntityItem):
if item and self.openFilesItem.indexOfChild(item.parent().parent()) == -1:
# vistrail is not open
return
@@ -1605,27 +1442,3 @@ class QVistrailList(QtGui.QTreeWidget):
act.setStatusTip("Execute the mashup")
menu.addAction(act)
menu.exec_(event.globalPos())
-
-if __name__ == '__main__':
- import sys
- sys.path.append('/vistrails/src/query/vistrails')
- from vistrails.core.collection import Collection
-
-# vt_1 = load_vistrail(ZIPFileLocator('/vistrails/examples/spx.vt'))[0]
-# vt_2 = load_vistrail(DBLocator('vistrails.sci.utah.edu', 3306,
-# 'vistrails', 'vistrails', '8edLj4',
-# obj_id=9, obj_type='vistrail'))[0]
-
- c = Collection('test.db')
- # c.clear()
- # e_1 = c.create_vistrail_entity(vt_1)
- # e_2 = c.create_vistrail_entity(vt_2)
-
- c.entities = {}
- c.load_entities()
-
- app = QtGui.QApplication(sys.argv)
- widget = QBrowserWidget(c)
- widget.setup_widget('Recent items')
- widget.show()
- sys.exit(app.exec_())
diff --git a/vistrails/gui/common_widgets.py b/vistrails/gui/common_widgets.py
index 228e489..d49c8cd 100644
--- a/vistrails/gui/common_widgets.py
+++ b/vistrails/gui/common_widgets.py
@@ -89,6 +89,10 @@ class QToolWindow(QtGui.QDockWidget):
self.mwindow.addToolBar(self.toolbar)
def setDefaultPinStatus(self, topLevel):
+ # Fixes QTBUG-30276
+ if self.acceptDrops():
+ self.setAcceptDrops(False)
+ self.setAcceptDrops(True)
if topLevel:
self.setPinStatus(False)
self.pinButton.setEnabled(False)
diff --git a/vistrails/gui/graphics_view.py b/vistrails/gui/graphics_view.py
index 5ea2abc..39171f3 100644
--- a/vistrails/gui/graphics_view.py
+++ b/vistrails/gui/graphics_view.py
@@ -123,10 +123,10 @@ class QInteractiveGraphicsScene(QtGui.QGraphicsScene):
else:
self.sceneBoundingRect.adjust(0, -diff/2, 0, diff/2)
panRect = self.sceneBoundingRect.adjusted(
- -self.sceneBoundingRect.width()*100,
- -self.sceneBoundingRect.height()*100,
- self.sceneBoundingRect.width()*100,
- self.sceneBoundingRect.height()*100)
+ -self.sceneBoundingRect.width()*2,
+ -self.sceneBoundingRect.height()*2,
+ self.sceneBoundingRect.width()*2,
+ self.sceneBoundingRect.height()*2)
if panRect.width()<1e-6 and panRect.height()<1e-6:
panRect = QtCore.QRectF(-1000,-1000,2000,2000)
self.setSceneRect(panRect)
@@ -234,8 +234,8 @@ class QInteractiveGraphicsView(QtGui.QGraphicsView):
self.setRenderHints (QtGui.QPainter.Antialiasing |
QtGui.QPainter.TextAntialiasing |
QtGui.QPainter.SmoothPixmapTransform)
- self.scaleMax = 2000
- self.scaleRatio = self.scaleMax/10
+ self.scaleMax = 1000
+ self.scaleRatio = self.scaleMax/5
self.currentScale = self.scaleMax/2
self.startScroll = (0,0)
self.lastPos = QtCore.QPoint(0,0)
@@ -274,8 +274,8 @@ class QInteractiveGraphicsView(QtGui.QGraphicsView):
if changeFlags & QtGui.QPinchGesture.ScaleFactorChanged:
if self.gestureStartScale is None:
self.gestureStartScale = self.currentScale
- newScale = self.gestureStartScale * \
- pinch.property("scaleFactor").toReal()[0]
+ newScale = self.gestureStartScale + self.scaleMax * \
+ math.log(pinch.property("scaleFactor"))/2
# Clamp the scale
if newScale<0: newScale = 0
if newScale>self.scaleMax: newScale = self.scaleMax
diff --git a/vistrails/gui/mashups/mashup_app.py b/vistrails/gui/mashups/mashup_app.py
index 6f8bf17..0678354 100644
--- a/vistrails/gui/mashups/mashup_app.py
+++ b/vistrails/gui/mashups/mashup_app.py
@@ -481,13 +481,13 @@ class QMashupAppMainWindow(QtGui.QMainWindow):
cellWidget = event.cellType(self.centralWidget())
if event.cellType.__name__ == 'QVTKWidget':
vtkCells.append(cellWidget)
- cellWidget.updateContents(event.inputPorts)
cellWidget.show()
cellWidget.setSizePolicy(QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
cellWidget.setMinimumSize(300, 100)
cellLayout.addWidget(cellWidget)
self.cellWidgets.append(cellWidget)
+ cellWidget.updateContents(event.inputPorts)
def getSelectedCellWidgets():
return vtkCells
for cellWidget in self.vtkCells:
@@ -619,6 +619,8 @@ class TestMashupApp(TestVisTrailsGUI):
view = vistrails.api.open_vistrail_from_file(filename)
id = "d5026457-de6c-11e2-b074-3c07543dba07"
mashup = view.get_mashup_from_mashuptrail_id(id, "loop")
+ self.assert_(mashup)
view.open_mashup(mashup)
mashup = view.get_mashup_from_mashuptrail_id(id, "no loop")
+ self.assert_(mashup)
view.open_mashup(mashup)
diff --git a/vistrails/gui/modules/constant_configuration.py b/vistrails/gui/modules/constant_configuration.py
index 88d517a..8042f0c 100644
--- a/vistrails/gui/modules/constant_configuration.py
+++ b/vistrails/gui/modules/constant_configuration.py
@@ -45,6 +45,8 @@ from vistrails.core.utils import any, expression, versions_increasing
from vistrails.core import system
from vistrails.gui.theme import CurrentTheme
+import os
+
############################################################################
def setPlaceholderTextCompat(self, value):
@@ -503,12 +505,18 @@ class PathChooserToolButton(QtGui.QToolButton):
def openChooser(self):
text = self.lineEdit.text() or system.vistrails_data_directory()
- return QtGui.QFileDialog.getOpenFileName(self,
- 'Use Filename '
- 'as Value...',
- text,
- 'All files '
- '(*.*)')
+ fileName = QtGui.QFileDialog.getOpenFileName(self,
+ 'Use Filename '
+ 'as Value...',
+ text,
+ 'All files '
+ '(*.*)')
+ if not fileName:
+ return None
+ filename = os.path.abspath(str(QtCore.QFile.encodeName(fileName)))
+ dirName = os.path.dirname(filename)
+ system.set_vistrails_data_directory(dirName)
+ return filename
def runDialog(self):
path = self.openChooser()
@@ -583,12 +591,19 @@ class FileChooserToolButton(PathChooserToolButton):
def openChooser(self):
text = self.lineEdit.text() or system.vistrails_data_directory()
- return QtGui.QFileDialog.getOpenFileName(self,
- 'Use Filename '
- 'as Value...',
- text,
- 'All files '
- '(*.*)')
+ fileName = QtGui.QFileDialog.getOpenFileName(self,
+ 'Use Filename '
+ 'as Value...',
+ text,
+ 'All files '
+ '(*.*)')
+ if not fileName:
+ return None
+ filename = os.path.abspath(str(QtCore.QFile.encodeName(fileName)))
+ dirName = os.path.dirname(filename)
+ system.set_vistrails_data_directory(dirName)
+ return filename
+
class FileChooserWidget(PathChooserWidget):
def create_browse_button(self):
@@ -602,10 +617,17 @@ class DirectoryChooserToolButton(PathChooserToolButton):
def openChooser(self):
text = self.lineEdit.text() or system.vistrails_data_directory()
- return QtGui.QFileDialog.getExistingDirectory(self,
- 'Use Directory '
- 'as Value...',
- text)
+ fileName = QtGui.QFileDialog.getExistingDirectory(self,
+ 'Use Directory '
+ 'as Value...',
+ text)
+ if not fileName:
+ return None
+ filename = os.path.abspath(str(QtCore.QFile.encodeName(fileName)))
+ dirName = os.path.dirname(filename)
+ system.set_vistrails_data_directory(dirName)
+ return filename
+
class DirectoryChooserWidget(PathChooserWidget):
def create_browse_button(self):
@@ -618,10 +640,16 @@ class OutputPathChooserToolButton(PathChooserToolButton):
def openChooser(self):
text = self.lineEdit.text() or system.vistrails_data_directory()
- return QtGui.QFileDialog.getSaveFileName(self,
- 'Save Path',
- text,
- 'All files (*.*)')
+ fileName = QtGui.QFileDialog.getSaveFileName(self,
+ 'Save Path',
+ text,
+ 'All files (*.*)')
+ if not fileName:
+ return None
+ filename = os.path.abspath(str(QtCore.QFile.encodeName(fileName)))
+ dirName = os.path.dirname(filename)
+ system.set_vistrails_data_directory(dirName)
+ return filename
class OutputPathChooserWidget(PathChooserWidget):
def create_browse_button(self):
diff --git a/vistrails/gui/modules/python_source_configure.py b/vistrails/gui/modules/python_source_configure.py
index 45546af..6991781 100644
--- a/vistrails/gui/modules/python_source_configure.py
+++ b/vistrails/gui/modules/python_source_configure.py
@@ -142,7 +142,6 @@ def NewPythonEditor(parent):
# conventionally, margin 0 is for line numbers
self.setMarginWidth(0, fm.width( "0000" ) + 4)
self.setMarginLineNumbers(0, True)
-
self.setAutoIndent(True)
## Edge Mode shows a red vetical bar at 80 chars
@@ -198,7 +197,8 @@ def NewPythonEditor(parent):
redirect to self.text()
"""
- return self.text()
+ text = self.text()
+ return text.replace('\r\n', '\n').replace('\r', '\n')
# def focusOutEvent(self, event):
# if self.parent():
diff --git a/vistrails/gui/modules/string_configure.py b/vistrails/gui/modules/string_configure.py
index 059ef5e..2757fe7 100644
--- a/vistrails/gui/modules/string_configure.py
+++ b/vistrails/gui/modules/string_configure.py
@@ -114,8 +114,7 @@ def NewTextEditor(parent):
"""
text = self.text()
- return text.replace('\r', '\n')
-
+ return text.replace('\r\n', '\n').replace('\r', '\n')
# def focusOutEvent(self, event):
# if self.parent():
# QtCore.QCoreApplication.sendEvent(self.parent(), event)
diff --git a/vistrails/gui/modules/stringformat_configuration.py b/vistrails/gui/modules/stringformat_configuration.py
new file mode 100644
index 0000000..934d24c
--- /dev/null
+++ b/vistrails/gui/modules/stringformat_configuration.py
@@ -0,0 +1,86 @@
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core.system import get_vistrails_basic_pkg_id
+from vistrails.gui.modules.module_configure import StandardModuleConfigurationWidget
+
+
+class StringFormatConfigurationWidget(StandardModuleConfigurationWidget):
+ """
+ Configuration widget creating the ports corresponding to the format.
+
+ """
+ def __init__(self, module, controller, parent=None):
+ """ StringFormatConfigurationWidget(
+ module: Module,
+ controller: VistrailController,
+ parent: QWidget)
+ -> TupleConfigurationWidget
+
+ Let StandardModuleConfigurationWidget constructor store the
+ controller/module object from the builder and set up the
+ configuration widget.
+ After StandardModuleConfigurationWidget constructor, all of
+ these will be available:
+ self.module : the Module object int the pipeline
+ self.controller: the current vistrail controller
+
+ """
+ StandardModuleConfigurationWidget.__init__(self, module,
+ controller, parent)
+
+ # Give it a nice window title
+ self.setWindowTitle("StringFormat Configuration")
+
+ # Add an empty vertical layout
+ centralLayout = QtGui.QVBoxLayout()
+ centralLayout.setMargin(0)
+ centralLayout.setSpacing(0)
+ self.setLayout(centralLayout)
+
+ # Add the configuration button
+ self.button = QtGui.QPushButton("Sync ports")
+ self.connect(self.button, QtCore.SIGNAL('clicked()'),
+ self.saveTriggered)
+ centralLayout.addWidget(self.button)
+
+ def activate(self):
+ self.button.focusWidget(QtCore.Qt.ActiveWindowFocusReason)
+
+ def saveTriggered(self, checked = False):
+ """ saveTriggered(checked: bool) -> None
+ Update vistrail controller and module when the user click Ok
+
+ """
+ if self.updateVistrail():
+ self.emit(QtCore.SIGNAL('stateChanged'))
+ self.emit(QtCore.SIGNAL('doneConfigure'), self.module.id)
+
+ def get_format(self):
+ for i in xrange(self.module.getNumFunctions()):
+ func = self.module.functions[i]
+ if func.name == 'format':
+ return func.params[0].strValue
+ else:
+ return ''
+
+ def updateVistrail(self):
+ """ updateVistrail() -> None
+ Update Vistrail to contain changes in the port table
+
+ """
+ from vistrails.core.modules.basic_modules import StringFormat
+ args, kwargs = StringFormat.list_placeholders(self.get_format())
+ wanted_ports = set('_%d' % n for n in xrange(args)) | kwargs
+
+ current_ports = set(port_spec.name
+ for port_spec in self.module.input_port_specs)
+
+ sigstring = '(org.vistrails.vistrails.basic:Variant)'
+ add_ports = [('input', n, sigstring, -1)
+ for n in (wanted_ports - current_ports)]
+ delete_ports = [('input', n)
+ for n in (current_ports - wanted_ports)]
+
+ self.controller.update_ports(self.module.id, delete_ports, add_ports)
+
+ return True
diff --git a/vistrails/gui/paramexplore/param_view.py b/vistrails/gui/paramexplore/param_view.py
index 2f51b34..bf7b290 100644
--- a/vistrails/gui/paramexplore/param_view.py
+++ b/vistrails/gui/paramexplore/param_view.py
@@ -202,9 +202,13 @@ class QParameterTreeWidget(QSearchTreeWidget):
continue
port_spec_items = port_spec.port_spec_items
+ if not controller.has_vistrail_variable_with_uuid(
+ module.get_vistrail_var()):
+ continue
vv = controller.get_vistrail_variable_by_uuid(
module.get_vistrail_var())
+
label = ['%s = %s' % (vv.name, vv.value)]
pList = [ParameterInfo(module_id=mId,
name=port_spec.name,
diff --git a/vistrails/gui/paramexplore/pe_inspector.py b/vistrails/gui/paramexplore/pe_inspector.py
index c2e4c3a..692c3c4 100644
--- a/vistrails/gui/paramexplore/pe_inspector.py
+++ b/vistrails/gui/paramexplore/pe_inspector.py
@@ -225,7 +225,8 @@ class QParamExpProperties(QtGui.QWidget):
self.tagReset.setEnabled(True)
self.tagEdit.setText(self.pe.name or "")
self.userEdit.setText(self.pe.user or "")
- self.dateEdit.setText(self.pe.date or "")
+ self.dateEdit.setText(self.pe.date.strftime('%Y-%m-%d %H:%M:%S')
+ if self.pe.date else "")
else:
self.versionsLabel.setText('Exploration: 0/0')
self.backAction.setEnabled(False)
diff --git a/vistrails/gui/paramexplore/pe_table.py b/vistrails/gui/paramexplore/pe_table.py
index 786778e..895b981 100644
--- a/vistrails/gui/paramexplore/pe_table.py
+++ b/vistrails/gui/paramexplore/pe_table.py
@@ -211,7 +211,7 @@ class QParameterExplorationWidget(QtGui.QScrollArea):
functions.append(function)
pe = ParameterExploration(dims=str(self.table.label.getCounts()),
layout=repr(palette.virtual_cell.getConfiguration()[2]),
- date=current_time().strftime('%Y-%m-%d %H:%M:%S'),
+ date=current_time(),
user=getuser(),
functions=functions)
return pe
diff --git a/vistrails/gui/pipeline_view.py b/vistrails/gui/pipeline_view.py
index 53e1214..a3f85af 100644
--- a/vistrails/gui/pipeline_view.py
+++ b/vistrails/gui/pipeline_view.py
@@ -227,8 +227,12 @@ class QAbstractGraphicsPortItem(QtGui.QAbstractGraphicsShapeItem):
painter.setBrush(self.brush())
self.draw(painter, option, widget)
- def addVistrailVar(self, vistrail_var):
- self.vistrail_vars[vistrail_var.uuid] = vistrail_var
+ def addVistrailVar(self, uuid, name=None):
+ if name is None:
+ name = self.getVistrailVarName(uuid)
+ self.vistrail_vars[uuid] = name
+ if not self.controller.has_vistrail_variable_with_uuid(uuid):
+ self.setInvalid(True)
self.updateActions()
self.updateToolTip()
@@ -242,13 +246,18 @@ class QAbstractGraphicsPortItem(QtGui.QAbstractGraphicsShapeItem):
self.updateActions()
self.updateToolTip()
+ def getVistrailVarName(self, uuid):
+ if self.controller.has_vistrail_variable_with_uuid(uuid):
+ return self.controller.get_vistrail_variable_by_uuid(uuid).name
+ return '<missing>'
+
def updateToolTip(self):
tooltip = ""
if (self.port is not None and self.port.is_valid and
hasattr(self.port, 'toolTip')):
tooltip = self.port.toolTip()
for vistrail_var in self.vistrail_vars.itervalues():
- tooltip += '\nConnected to vistrail var "%s"' % vistrail_var.name
+ tooltip += '\nConnected to vistrail var "%s"' % vistrail_var
self.setToolTip(tooltip)
def contextMenuEvent(self, event):
@@ -277,14 +286,16 @@ class QAbstractGraphicsPortItem(QtGui.QAbstractGraphicsShapeItem):
QtCore.QObject.connect(removeAllVarsAct,
QtCore.SIGNAL("triggered()"),
self.removeAllVars)
- self.removeVarActions.append((removeAllVarsAct, self.removeAllVars))
- for vistrail_var in sorted(self.vistrail_vars.itervalues(),
- key=lambda x: x.name):
+ self.removeVarActions.append((removeAllVarsAct,
+ self.removeAllVars))
+ for vistrail_var_uuid in sorted(self.vistrail_vars,
+ key=lambda x: self.getVistrailVarName(x)):
+ vistrail_var_name = self.getVistrailVarName(vistrail_var_uuid)
removeVarAction = QtGui.QAction('Disconnect vistrail var "%s"' % \
- vistrail_var.name, self.scene())
+ vistrail_var_name, self.scene())
removeVarAction.setStatusTip('Disconnects vistrail variable "%s"'
- ' from the port' % vistrail_var.name)
- callback = gen_action(vistrail_var.uuid)
+ ' from the port' % vistrail_var_name)
+ callback = gen_action(vistrail_var_uuid)
QtCore.QObject.connect(removeVarAction,
QtCore.SIGNAL("triggered()"),
callback)
@@ -301,6 +312,7 @@ class QAbstractGraphicsPortItem(QtGui.QAbstractGraphicsShapeItem):
self.deleteVistrailVar(var_uuid)
self.controller.disconnect_vistrail_vars(to_delete_modules,
to_delete_conns)
+ self.setInvalid(False)
def removeAllVars(self):
@@ -1714,6 +1726,11 @@ class QGraphicsModuleItem(QGraphicsItemInterface, QtGui.QGraphicsItem):
else:
yield (item, True)
+ def mouseReleaseEvent(self, event):
+ super(QGraphicsModuleItem, self).mouseReleaseEvent(event)
+ if not self.controller.changed and self.controller.has_move_actions():
+ self.controller.set_changed(True)
+
def itemChange(self, change, value):
""" itemChange(change: GraphicsItemChange, value: value) -> value
Capture move event to also move the connections. Also unselect any
@@ -1929,8 +1946,7 @@ class QPipelineScene(QInteractiveGraphicsScene):
if srcModule.module.is_vistrail_var():
connectionItem.hide()
var_uuid = srcModule.module.get_vistrail_var()
- dstPortItem.addVistrailVar(
- self.controller.get_vistrail_variable_by_uuid(var_uuid))
+ dstPortItem.addVistrailVar(var_uuid)
return connectionItem
def selected_subgraph(self):
@@ -2603,6 +2619,16 @@ class QPipelineScene(QInteractiveGraphicsScene):
elif isinstance(it, QGraphicsConnectionItem):
connection_ids.append(it.id)
if len(modules)>0:
+ # add connected vistrail variables
+ vvms, vvcs = \
+ self.controller.get_connected_vistrail_vars(module_ids, True)
+ for vvm in vvms:
+ if vvm not in module_ids:
+ modules.append(self.modules[vvm])
+ module_ids.append(vvm)
+ for vvc in vvcs:
+ if vvc not in connection_ids:
+ connection_ids.append(vvc)
self.noUpdate = True
dep_connection_ids = set()
for m in modules:
@@ -2677,6 +2703,13 @@ class QPipelineScene(QInteractiveGraphicsScene):
for item in selectedItems:
if isinstance(item, QGraphicsModuleItem):
module_ids[item.module.id] = 1
+ # Add connected vistrail variables
+ vvms, vvcs = \
+ self.controller.get_connected_vistrail_vars(module_ids)
+ for vvm in vvms:
+ module_ids[vvm] = 1
+ for vvc in vvcs:
+ connection_ids[vvc] = 1
for item in selectedItems:
if isinstance(item, QGraphicsModuleItem):
for connItem in item.dependingConnectionItems().itervalues():
diff --git a/vistrails/gui/preferences.py b/vistrails/gui/preferences.py
index ed08003..7e7a437 100644
--- a/vistrails/gui/preferences.py
+++ b/vistrails/gui/preferences.py
@@ -311,6 +311,10 @@ class QPackagesWidget(QtGui.QWidget):
except Package.MissingDependency, e:
debug.critical("Missing dependencies", str(e))
else:
+ # Deselects available list to prevent another package from getting
+ # selected once the current item leaves the list
+ self._available_packages_list.setCurrentItem(None)
+
palette = QModulePalette.instance()
palette.setUpdatesEnabled(False)
try:
@@ -318,6 +322,8 @@ class QPackagesWidget(QtGui.QWidget):
except Package.InitializationFailed, e:
debug.critical("Initialization of package '%s' failed" %
codepath, str(e))
+ # Loading failed: reselect the item
+ self._available_packages_list.setCurrentItem(item)
raise
finally:
palette.setUpdatesEnabled(True)
diff --git a/vistrails/gui/repository.py b/vistrails/gui/repository.py
index a7f1419..0a26544 100644
--- a/vistrails/gui/repository.py
+++ b/vistrails/gui/repository.py
@@ -424,13 +424,10 @@ class QRepositoryPushWidget(QtGui.QWidget):
(fd, filename) = tempfile.mkstemp(suffix='.vt', prefix='vt_tmp')
os.close(fd)
- # writing tmp vt and switching back to orginal vt
+ # writing tmp vt and switching back to original vt
locator = ZIPFileLocator(filename)
controller = vistrails.api.get_current_controller()
- tmp_controller = VistrailController(controller.vistrail.do_copy(),
- locator)
- tmp_controller.changed = True
- tmp_controller.write_vistrail(locator)
+ controller.write_vistrail(locator, export=True)
# check if this vt is from the repository
if controller.vistrail.get_annotation('repository_vt_id'):
@@ -515,10 +512,11 @@ class QRepositoryPushWidget(QtGui.QWidget):
load_vistrail(updated_locator)
# FIXME need to figure out what to do with this !!!
+ current_version = controller.current_version
controller.set_vistrail(up_vistrail,
controller.vistrail.locator,
abstractions, thumbnails, mashups)
-
+ controller.change_selected_version(current_version)
# update version tree drawing
controller.recompute_terse_graph()
controller.invalidate_version_tree()
diff --git a/vistrails/gui/requirements.py b/vistrails/gui/requirements.py
index 3b59180..6b7adf8 100644
--- a/vistrails/gui/requirements.py
+++ b/vistrails/gui/requirements.py
@@ -33,8 +33,10 @@
##
###############################################################################
+import os
+import sys
+
from vistrails.core.requirements import MissingRequirement, require_python_module
-import vistrails.gui.bundles.installbundle
def setNewPyQtAPI():
@@ -44,18 +46,33 @@ def setNewPyQtAPI():
sip.setapi('QVariant', 2)
-def require_pyqt4_api2():
+def qt_available():
try:
require_python_module('sip')
setNewPyQtAPI()
require_python_module('PyQt4.QtGui')
require_python_module('PyQt4.QtOpenGL')
except MissingRequirement:
- r = vistrails.gui.bundles.installbundle.install({
+ return False
+ else:
+ return True
+
+
+def require_pyqt4_api2():
+ # Forces the use of PyQt4 (avoid PySide even if installed)
+ # This is necessary at least for IPython
+ if os.environ.get('QT_API', None) not in (None, 'pyqt'):
+ sys.stderr.write("Warning: QT_API was set to %r, changing to 'pyqt'\n" %
+ os.environ['QT_API'])
+ os.environ['QT_API'] = 'pyqt'
+
+ if not qt_available():
+ from vistrails.gui.bundles.installbundle import install
+ r = install({
'linux-debian': ['python-qt4', 'python-qt4-gl', 'python-qt4-sql'],
'linux-ubuntu': ['python-qt4', 'python-qt4-gl', 'python-qt4-sql'],
'linux-fedora': ['PyQt4'],
'pip': ['PyQt<5.0']})
if not r:
- raise
+ raise MissingRequirement('PyQt4')
setNewPyQtAPI()
diff --git a/vistrails/gui/resources/images/vistrails_splash.png b/vistrails/gui/resources/images/vistrails_splash.png
index 87d44e6..c53e406 100644
Binary files a/vistrails/gui/resources/images/vistrails_splash.png and b/vistrails/gui/resources/images/vistrails_splash.png differ
diff --git a/vistrails/gui/shell.py b/vistrails/gui/shell.py
index 27587c5..bff7c37 100644
--- a/vistrails/gui/shell.py
+++ b/vistrails/gui/shell.py
@@ -854,6 +854,7 @@ def getIPythonDialog():
VisTrails environment"""
def __init__(self, parent=None):
RichIPythonWidget.__init__(self, parent)
+ self.running_workflow = False
self.kernel_manager = km
self.kernel_client = kernel_client
self.exit_requested.connect(stop)
@@ -937,7 +938,25 @@ def getIPythonDialog():
Simulate stdin, stdout, and stderr.
"""
+ self.input_buffer = ''
+ if not self.running_workflow:
+ self.running_workflow = True
+ # make text blue
+ self._append_plain_text("\n\x1b[34m<STANDARD OUTPUT>\x1b[0m\n", True)
self._append_plain_text(text, True)
+ self._prompt_pos = self._get_end_cursor().position()
+ self._control.ensureCursorVisible()
+ self._control.moveCursor(QtGui.QTextCursor.End)
+
+
+ def eventFilter(self, obj, event):
+ """ Reimplemented to ensure a console-like behavior in the underlying
+ text widgets.
+ """
+ etype = event.type()
+ if etype == QtCore.QEvent.KeyPress:
+ self.running_workflow = False
+ return RichIPythonWidget.eventFilter(self, obj, event)
return IPythonDialog
diff --git a/vistrails/gui/theme.py b/vistrails/gui/theme.py
index 9d7b878..b65e0cf 100644
--- a/vistrails/gui/theme.py
+++ b/vistrails/gui/theme.py
@@ -72,6 +72,9 @@ class DefaultTheme(DefaultCoreTheme):
######################
#### MEASUREMENTS ####
+ # pipeline view bounding rect
+ self.BOUNDING_RECT_MINIMUM = 512
+
# Port shape
self.PORT_RECT = QtCore.QRectF(0, 0, self.PORT_WIDTH, self.PORT_HEIGHT)
diff --git a/vistrails/gui/view_manager.py b/vistrails/gui/view_manager.py
index 105488d..55abd54 100644
--- a/vistrails/gui/view_manager.py
+++ b/vistrails/gui/view_manager.py
@@ -492,6 +492,7 @@ class QViewManager(QtGui.QTabWidget):
if not locator:
return False
# update collection
+ vistrailView.controller.flush_delayed_actions()
try:
vistrailView.controller.write_vistrail(locator)
except Exception, e:
diff --git a/vistrails/gui/vistrail_view.py b/vistrails/gui/vistrail_view.py
index b5cb0f3..0f6fcfb 100644
--- a/vistrails/gui/vistrail_view.py
+++ b/vistrails/gui/vistrail_view.py
@@ -597,12 +597,12 @@ class QVistrailView(QtGui.QWidget):
def view_changed(self):
from vistrails.gui.vistrails_window import _app
- _app.closeNotPinPalettes()
#view = self.stack.currentWidget()
view = self.get_current_outer_tab()
#print "changing tab from: ",self.current_tab, " to ", view
#print self.tab_to_stack_idx
if view != self.current_tab:
+ _app.closeNotPinPalettes()
#print "!!unset_action_links of ", self.current_tab
_app.unset_action_links(self.current_tab)
self.current_tab = view
@@ -616,10 +616,10 @@ class QVistrailView(QtGui.QWidget):
#print "\n!!set_action_links of ", self.current_tab
_app.set_action_links(self.current_tab.action_links, self.current_tab,
self)
+ self.showCurrentViewPalettes()
#else:
# print "tabs the same. do nothing"
- self.showCurrentViewPalettes()
if isinstance(view, QQueryView):
_app.notify("controller_changed", view.p_controller)
_app.notify("entry_klass_changed", QueryEntry)
@@ -889,6 +889,7 @@ class QVistrailView(QtGui.QWidget):
#print "CALLED SAVE VISTRAIL", locator_class
self.flush_changes()
+ self.controller.flush_delayed_actions()
gui_get = locator_class.save_from_gui
# get a locator to write to
if not locator or locator.is_untitled():
diff --git a/vistrails/gui/vistrails_window.py b/vistrails/gui/vistrails_window.py
index 1ad99ce..4cf8e4b 100644
--- a/vistrails/gui/vistrails_window.py
+++ b/vistrails/gui/vistrails_window.py
@@ -62,6 +62,7 @@ from vistrails.core import debug
from vistrails.gui.application import get_vistrails_application
from vistrails.gui.preferences import QPreferencesDialog
from vistrails.gui.base_view import BaseView
+from vistrails.gui.common_widgets import QToolWindow
from vistrails.gui.pipeline_view import QPipelineView
from vistrails.gui.repository import QRepositoryDialog
from vistrails.gui.theme import initializeCurrentTheme, CurrentTheme
@@ -1375,11 +1376,11 @@ class QVistrailsWindow(QVistrailViewWindow):
def change_view(self, view):
#print 'changing view', id(view), view
if isinstance(view, QVistrailView) or view is None:
+ self.view_changed(view)
if view and view not in self.windows:
if self.stack.currentWidget() != view:
self.stack.setCurrentWidget(view)
view.reset_tab_state()
- self.view_changed(view)
if view and get_vistrails_configuration().detachHistoryView:
self.history_view.stack.setCurrentIndex(view.version_index)
self.history_view.view = view.controller
@@ -2623,7 +2624,8 @@ class QVistrailsWindow(QVistrailViewWindow):
QAliasInspector,
QCellWidget,
QMashupViewTab,
- QVistrailsPaletteInterface]
+ QVistrailsPaletteInterface,
+ QToolWindow]
old_view = self.get_current_view()
view = None
if self.isAncestorOf(current):
diff --git a/vistrails/index/__core.py b/vistrails/index/__core.py
deleted file mode 100644
index dffedde..0000000
--- a/vistrails/index/__core.py
+++ /dev/null
@@ -1,143 +0,0 @@
-###############################################################################
-##
-## Copyright (C) 2011-2014, NYU-Poly.
-## Copyright (C) 2006-2011, University of Utah.
-## All rights reserved.
-## Contact: contact at vistrails.org
-##
-## This file is part of VisTrails.
-##
-## "Redistribution and use in source and binary forms, with or without
-## modification, are permitted provided that the following conditions are met:
-##
-## - Redistributions of source code must retain the above copyright notice,
-## this list of conditions and the following disclaimer.
-## - Redistributions in binary form must reproduce the above copyright
-## notice, this list of conditions and the following disclaimer in the
-## documentation and/or other materials provided with the distribution.
-## - Neither the name of the University of Utah nor the names of its
-## contributors may be used to endorse or promote products derived from
-## this software without specific prior written permission.
-##
-## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
-## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
-## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
-##
-###############################################################################
-""" This is the core classes for the general workflow model
-
-The structures can hold a description of a workflow and lists of operations.
-
-This file implements:
- Annotation
- Parameter
- Module
- Connection
- Pipeline
- Port
- Operation
- Service
-"""
-
-class Annotation:
- """
- annotation
- """
- def __init__(self, key='', value=''):
- self.key = key
- self.value = value
- self.annotations = [] # list of annotations
- def __eq__(self, other):
- """ equal if keys are equal """
- return self.key == other.key
-
-class Parameter:
- """
- module parameter
- """
- def __init__(self, name, value='', type=''):
- self.name = name # parameter name
- self.value = value # value
- self.type = type # value type type/class (actually redundant)
- self.annotations = [] # list of annotations
-
-class Module:
- """
- workflow module
- """
- def __init__(self, name = 'New', package = '',
- version = '', type = 'Module'):
- self.name = name # module name
- self.package = package # package that the 'type' is in
- self.version = version # version of the package
- self.type = type # module type
- self.annotations = [] # list of annotations
- self.parameters = [] # list of parameters
- self.up = [] # input modules (redundant)
- self.down = [] # output modules (redundant)
-
-class Connection:
- """
- A connection between modules
- """
- def __init__(self, startModule=None, endModule=None, \
- startPort='', endPort=''):
- self.startModule = startModule # reference to startmodule
- self.endModule = endModule # reference to endmodule
- self.startPort = startPort
- self.endPort = endPort
- self.annotations = [] # list of annotations
-
-class Pipeline:
- """
- A representation of a pipeline
- """
- def __init__(self, name='', type='', version='', source=''):
- self.name = name # textual representation of pipeline
- self.source = source # location of source
- self.type = type # source format
- self.version = version # version of source format
- self.modules = [] # list of modules
- self.connections = [] # list of connections
- self.annotations = [] # list of annotations
-
-outPort = False
-inPort = True
-class Port:
- """
- module port
- """
- def __init__(self, name, type=None, kind=inPort):
- self.name = name # port name
- self.type = type # port type/class
- self.kind = kind # inPort/outPort
- self.annotations = [] # list of annotations
-
-class Operation:
- """
- An operation
- """
- def __init__(self, name):
- self.name = name # operation name
- self.ports = [] # list of ports
- self.annotations = [] # list of annotations
-
-class Service:
- """
- A service representation
- """
- def __init__(self, name='', source='', type='', version=''):
- self.name = name # textual representation of pipeline
- self.source = source # location of source
- self.type = type # source format (namespace)
- self.version = version # version of source format
- self.operations = [] # list of operations
- self.annotations = [] # list of annotations
diff --git a/vistrails/index/__init__.py b/vistrails/index/__init__.py
deleted file mode 100644
index fac3164..0000000
--- a/vistrails/index/__init__.py
+++ /dev/null
@@ -1,35 +0,0 @@
-###############################################################################
-##
-## Copyright (C) 2011-2014, NYU-Poly.
-## Copyright (C) 2006-2011, University of Utah.
-## All rights reserved.
-## Contact: contact at vistrails.org
-##
-## This file is part of VisTrails.
-##
-## "Redistribution and use in source and binary forms, with or without
-## modification, are permitted provided that the following conditions are met:
-##
-## - Redistributions of source code must retain the above copyright notice,
-## this list of conditions and the following disclaimer.
-## - Redistributions in binary form must reproduce the above copyright
-## notice, this list of conditions and the following disclaimer in the
-## documentation and/or other materials provided with the distribution.
-## - Neither the name of the University of Utah nor the names of its
-## contributors may be used to endorse or promote products derived from
-## this software without specific prior written permission.
-##
-## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
-## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
-## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
-##
-###############################################################################
-
diff --git a/vistrails/index/indexworkflow.py b/vistrails/index/indexworkflow.py
deleted file mode 100755
index 00df65b..0000000
--- a/vistrails/index/indexworkflow.py
+++ /dev/null
@@ -1,226 +0,0 @@
-#!/usr/bin/python
-###############################################################################
-##
-## Copyright (C) 2011-2014, NYU-Poly.
-## Copyright (C) 2006-2011, University of Utah.
-## All rights reserved.
-## Contact: contact at vistrails.org
-##
-## This file is part of VisTrails.
-##
-## "Redistribution and use in source and binary forms, with or without
-## modification, are permitted provided that the following conditions are met:
-##
-## - Redistributions of source code must retain the above copyright notice,
-## this list of conditions and the following disclaimer.
-## - Redistributions in binary form must reproduce the above copyright
-## notice, this list of conditions and the following disclaimer in the
-## documentation and/or other materials provided with the distribution.
-## - Neither the name of the University of Utah nor the names of its
-## contributors may be used to endorse or promote products derived from
-## this software without specific prior written permission.
-##
-## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
-## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
-## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
-##
-###############################################################################
-import os
-import sys
-import urllib
-import hashlib
-import shutil
-import subprocess
-
-from lucene import FSDirectory, IndexWriter, StandardAnalyzer, initVM, CLASSPATH, Field, Document, Term, File
-
-from vistrailanalyzer import vistrailAnalyzer
-from __core import *
-from spec_io import spec
-
-lvm = initVM(CLASSPATH, maxheap='512m')
-
-location = "/server/index"
-
-class WorkflowIndexer:
- store = None
- writer = None
- def __init__(self):
- self.save = Field.Store.YES
- self.ddict = dict()
-
- lvm.attachCurrentThread()
-
- if not WorkflowIndexer.store and not WorkflowIndexer.writer:
- try:
- # open lucene index
- WorkflowIndexer.store = FSDirectory.open(File(location))
- # if the index directory does not exist, create it.
- WorkflowIndexer.writer = IndexWriter( WorkflowIndexer.store,
- vistrailAnalyzer(), not len(WorkflowIndexer.store.list()))
- except Exception, e:
- print "EXCEPTION", e
- self.close()
- raise
-
- def close(self):
- if WorkflowIndexer.writer:
- WorkflowIndexer.writer.commit()
-
- def remove(self, id):
- print "removing index for", id
- spec.remove(id)
- # Delete old versions
- WorkflowIndexer.writer.deleteDocuments(
- [Term('workflow_id', id)] )
- print "done removing", id
-
- def index_vt_wf(self, wf_info, pipeline):
- # convert to general workflow model
- wf = self.convert_vt_wf(pipeline)
- wf.id = str(wf_info['crowdlabs_wf_id'])
- # add meta information
- wf.name = wf_info['name']
- wf.annotations.append(Annotation("title", wf_info['name']))
- wf.annotations.append(Annotation("user", wf_info['user']))
-#value.strftime('%Y-%m-%d %H:%M:%S')
- wf.annotations.append(Annotation("date", wf_info['date']))
- wf.annotations.append(Annotation("note", wf_info['description']))
- if wf_info['thumbnail'] != '':
- wf.annotations.append(Annotation("__thumb__", wf_info['thumbnail']))
- return self.index_wf(wf)
-
- def index_wf(self, wf):
- # upload to database
- print "uploading", wf.name
- spec.add(wf)
- # index workflow using lucene
- print "indexing", wf.name
- self.write_index(wf)
- print "done indexing", wf.name
-
- #
- # Creates pickle workflow object from vistrails pipeline
- #
- def convert_vt_wf(self, wf):
- pipeline = Pipeline("", "vistrail", wf.db_version, "")
-
- # process modules
- mdict = {}
- for module in wf.db_modules:
- name = module.db_name
- for annotation in module.db_annotations:
- if annotation.db_key == "__desc__":
- name = annotation.db_value
- m = Module(name, module.db_package, module.db_version, module.db_name)
- m.id = module.db_id
- mdict[m.id] = m
- pipeline.modules.append(m)
-
- # location x/y
- m.annotations.append(Annotation('loc_x', str(module.db_location.db_x)))
- m.annotations.append(Annotation('loc_y', str(module.db_location.db_y)))
-
- # add functions
- for function in module.db_functions:
- name = function.db_name
- for parameter in function.db_parameters:
- value = urllib.unquote(parameter.db_val) # decode pythonsources
- pos = str(parameter.db_pos)
- name += ((':' + pos) if len(function.db_parameters)>1 else '')
- m.parameters.append(Parameter(name, value, parameter.db_type))
- # empty parameter
- if len(function.db_parameters) == 0:
- m.parameters.append(Parameter(name, '', ''))
-
- for connection in wf.db_connections:
- start = connection.db_get_port_by_type('source')
- startModuleId = start.db_moduleId
- end = connection.db_get_port_by_type('destination')
- endModuleId = end.db_moduleId
-
- # get the references
- startModule = mdict[startModuleId] if startModuleId in mdict else None
- endModule = mdict[endModuleId] if endModuleId in mdict else None
-
- if startModule and endModule:
- # redundant attribute: add a module chain for fast traversal
- if startModule not in endModule.up:
- endModule.up.append(startModule)
- if endModule not in startModule.down:
- startModule.down.append(endModule)
- pipeline.connections.append(Connection(startModule, endModule,
- start.db_name, end.db_name))
- else:
- print "A broken connection was found"
- return pipeline
-
- def adddd(self, k, v):
- self.ddict[k] = self.ddict[k] + " " + v if self.ddict.has_key(k) else v
-
- def write_index(self, workflow, property = False):
- """
- adds all keywords in workflow to the index at the specified location
- types of the keywords can be preserved by setting (Property = True)
- """
- self.ddict = dict()
- # name is used as id in this case
- self.adddd("workflow_id", str(workflow.id))
-
- self.adddd("text", workflow.id)
- self.adddd("text", workflow.name)
- # this is a key for the workflow
- #adddd("workflow_source", workflow.source)
- #self.adddd("text", workflow.source)
- #adddd("workflow_type", workflow.type)
- self.adddd("text", workflow.type)
- # not very interesting
- #d.add( Field("workflow_version", workflow.version, save, Field.Index.UN_TOKENIZED))
- self.indexAnnotations(workflow.annotations, property)
-
- for module in workflow.modules:
- self.adddd("module_name" if property else "text", module.name)
- self.adddd("package" if property else "text", module.package)
- # not very interesting
- #d.add( Field("package_version", module.version, save, Field.Index.UN_TOKENIZED))
- self.adddd("module_type" if property else "text", module.type)
- self.indexAnnotations(module.annotations, property)
- for p in module.parameters:
- self.adddd("parameter_name" if property else "text", p.name)
- self.adddd("parameter_value" if property else "text", p.value)
- self.adddd("parameter_type" if property else "text", p.type)
- self.indexAnnotations(p.annotations, property)
-
- for c in workflow.connections:
- self.adddd("port_name" if property else "text", c.startPort)
- self.adddd("port_name" if property else "text", c.endPort)
- self.indexAnnotations(c.annotations, property)
-
- d = Document()
- for (k, v) in self.ddict.iteritems():
- d.add(Field(k, v, self.save, Field.Index.TOKENIZED))
-
- # Delete old versions
- WorkflowIndexer.writer.deleteDocuments(
- [Term('workflow_id', str(workflow.id))] )
- # add new
- WorkflowIndexer.writer.addDocument(d)
-
- def indexAnnotations(self, annotations, p):
- """
- design choice: key and values are indexed separately,
- it would be possible to index them as the same type
- """
- for annotation in annotations:
- self.adddd("annotation_key" if p else "text", annotation.key)
- self.adddd("annotation_value" if p else "text", annotation.value)
- # annotations can be recursive
- self.indexAnnotations(annotation.annotations, p)
diff --git a/vistrails/index/spec_io.py b/vistrails/index/spec_io.py
deleted file mode 100644
index 6f8d450..0000000
--- a/vistrails/index/spec_io.py
+++ /dev/null
@@ -1,137 +0,0 @@
-###############################################################################
-##
-## Copyright (C) 2011-2014, NYU-Poly.
-## Copyright (C) 2006-2011, University of Utah.
-## All rights reserved.
-## Contact: contact at vistrails.org
-##
-## This file is part of VisTrails.
-##
-## "Redistribution and use in source and binary forms, with or without
-## modification, are permitted provided that the following conditions are met:
-##
-## - Redistributions of source code must retain the above copyright notice,
-## this list of conditions and the following disclaimer.
-## - Redistributions in binary form must reproduce the above copyright
-## notice, this list of conditions and the following disclaimer in the
-## documentation and/or other materials provided with the distribution.
-## - Neither the name of the University of Utah nor the names of its
-## contributors may be used to endorse or promote products derived from
-## this software without specific prior written permission.
-##
-## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
-## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
-## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
-##
-###############################################################################
-import sys
-import cPickle
-import MySQLdb
-from __core import Pipeline
-
-DBHOST = 'localhost'
-DBUSER = 'specuser'
-DBPASS = 'specpass'
-DBDB = 'wfspec'
-
-class Spec:
- def __init__(self):
- try:
- self.db = MySQLdb.connect(DBHOST, DBUSER, DBPASS, DBDB)
- except MySQLdb.Error, e:
- print "1Database Connection Error %d: %s" % (e.args[0], e.args[1])
- sys.exit(1)
- self.cursor = MySQLdb.cursors.DictCursor(self.db)
-
- def _exec(self, command):
- try:
- self.cursor.execute(command)
- except MySQLdb.Error, e:
- try:
- self.db = MySQLdb.connect(DBHOST, DBUSER, DBPASS, DBDB)
- self.cursor = MySQLdb.cursors.DictCursor(self.db)
- self.cursor.execute(command)
- except MySQLdb.Error, e:
- print "3Database Connection Error %d: %s"%(e.args[0],e.args[1])
- sys.exit(1)
- return self.cursor.fetchall()
-
- def get(self, name):
- """ Given a name - returns the specification as a pickle object """
- command = "SELECT wf FROM single_spec WHERE name='%s'" % name
- for r in self._exec(command):
- wf = r['wf']
- # change class of pickle object (core module not allowed)-UGLY hack
- if wf[0:14] == '(iindex.__core':
- wf = wf.replace('(iindex.__core\n', '(i__core\n')
- return cPickle.loads(wf)
- return None
-
- def names(self):
- """ returns all names in db """
- command = "SELECT name FROM single_spec"
- return [name['name'] for name in self._exec(command)]
-
- def getIndex(self, name):
- command = "SELECT paths FROM spec_index WHERE name='%s'" % name
- for r in self._exec(command):
- return cPickle.loads(r['paths'])
-
- def add(self, wf):
- """ Inserts name, wf to single_spec """
- dump = cPickle.dumps(wf)
- dump = MySQLdb.escape_string(dump)
- command = "REPLACE INTO single_spec VALUES ('%s', '%s')"%(wf.id, dump)
- self._exec(command)
-
- def __del__(self):
- self.cursor.close()
- self.db.close()
-
-spec = Spec()
-
-idf = False
-def get_idf(module):
- global idf
- if not idf:
- idf = cPickle.load(open("/server/crowdlabs/apps/vistrails/index/module.idf"))
- return idf.get(module.type, 9.0)
-def getIDF(type):
- global idf
- if not idf:
- idf = cPickle.load(open("/server/crowdlabs/apps/vistrails/index/module.idf"))
- return idf.get(type, 9.0)
-
-idf2 = False
-def get2IDF(type):
- global idf2
- if not idf2:
- idf2 = cPickle.load(open("2grams.idf"))
- return idf2.get(type, 9.0)
-
-# right now actually just DF
-path_idf = False
-def getPathIDF(path):
- global path_idf
- if not path_idf:
- path_idf = cPickle.load(open("idf.pi"))
- return path_idf.get(path, 0)
-
-# right now actually just DF
-coIndex = False
-def getCoIndex(pair):
- global coIndex
- if not coIndex:
- coIndex = cPickle.load(open("coindex.pi"))
- return coIndex.get(pair, 1)
-
-
-
diff --git a/vistrails/index/vistrailanalyzer.py b/vistrails/index/vistrailanalyzer.py
deleted file mode 100644
index 303e92b..0000000
--- a/vistrails/index/vistrailanalyzer.py
+++ /dev/null
@@ -1,116 +0,0 @@
-###############################################################################
-##
-## Copyright (C) 2011-2014, NYU-Poly.
-## Copyright (C) 2006-2011, University of Utah.
-## All rights reserved.
-## Contact: contact at vistrails.org
-##
-## This file is part of VisTrails.
-##
-## "Redistribution and use in source and binary forms, with or without
-## modification, are permitted provided that the following conditions are met:
-##
-## - Redistributions of source code must retain the above copyright notice,
-## this list of conditions and the following disclaimer.
-## - Redistributions in binary form must reproduce the above copyright
-## notice, this list of conditions and the following disclaimer in the
-## documentation and/or other materials provided with the distribution.
-## - Neither the name of the University of Utah nor the names of its
-## contributors may be used to endorse or promote products derived from
-## this software without specific prior written permission.
-##
-## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
-## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
-## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
-##
-###############################################################################
-import re
-
-from lucene import *
-import lucene
-dir(lucene)
-
-class vistrailAnalyzer(PythonAnalyzer):
-
- def tokenStream(self, fieldName, reader):
-
- result = StandardTokenizer(reader)
- result = StandardFilter(result)
- result = vistrailFilter(result)
- result = LowerCaseFilter(result)
- result = PorterStemFilter(result)
- result = StopFilter(result, StopAnalyzer.ENGLISH_STOP_WORDS)
-
- return result
-
-class stemmingAnalyzer(PythonAnalyzer):
-
- def tokenStream(self, fieldName, reader):
-
- result = StandardTokenizer(reader)
- result = StandardFilter(result)
- result = LowerCaseFilter(result)
- result = PorterStemFilter(result)
- result = StopFilter(result, StopAnalyzer.ENGLISH_STOP_WORDS)
-
- return result
-
-# patterns for splitting words into substrings
-patterns = [
- # 32 char md5 sums
- "[a-f0-9]{32}",
- # '2D', '3D'
- "2D", "3D",
- # words beginning with capital letters
- "[A-Z][a-z]+",
- # capital letter sequence ending with a word that begins with a capital letter
- "[A-Z]*(?=[A-Z][a-z])",
- # capital letter sequence
- "[A-Z]{2,}",
- # non-capital letter sequence
- "[a-z]{2,}" ]
-
-splitPattern = re.compile("|".join(patterns))
-
-class vistrailFilter(PythonTokenFilter):
-
- TOKEN_TYPE_PART = "text"
-
-
- def __init__(self, input):
- super(vistrailFilter, self).__init__(input)
- self.input = input
- self.parts = [] # parts found for the current token
- self.current = None
-
- def next(self):
- if self.parts:
- # continue adding parts
- part = self.parts.pop()
- t = Token(part, self.current.startOffset(),
- self.current.endOffset(), self.TOKEN_TYPE_PART)
- t.setPositionIncrement(0)
- return t
- else:
- # find parts
- self.current = self.input.next()
- if self.current is None:
- return None
- text = str(self.current.termText())
- pattern = splitPattern.findall(text)
- # remove single characters and duplicates
- pattern = set([p for p in pattern if len(p)>1 and p != text])
-# if len(pattern) > 0:
-# print "vistrailFilter", text, "-->",','.join(pattern)
- self.parts = pattern
- return self.current
-
-
diff --git a/vistrails/packages/CLTools/init.py b/vistrails/packages/CLTools/init.py
index 4e23521..5c66aa2 100644
--- a/vistrails/packages/CLTools/init.py
+++ b/vistrails/packages/CLTools/init.py
@@ -171,8 +171,8 @@ def add_tool(path):
try:
shutil.copyfile(value.name, outfile.name)
except IOError, e:
- raise ModuleError("Error copying file '%s': %s" %
- (value.name, e))
+ raise ModuleError(self, "Error copying file '%s': %s" % (
+ value.name, e))
value = '%s%s' % (options.get('prefix', ''), outfile.name)
# check for flag and append file name
if 'flag' in options:
@@ -242,10 +242,7 @@ def add_tool(path):
else:
kwargs['stderr'] = subprocess.PIPE
- if "return_code" in self.conf:
- return_code = self.forceGetInputFromPort(name)
- else:
- return_code = None
+ return_code = self.conf.get('return_code', None)
env = {}
# 0. add defaults
@@ -261,7 +258,8 @@ def add_tool(path):
if key:
env[key] = value
except Exception, e:
- raise ModuleError('Error parsing configuration env: %s' % e)
+ raise ModuleError(self,
+ "Error parsing configuration env: %s" % e)
if 'options' in self.conf and 'env' in self.conf['options']:
try:
@@ -272,7 +270,8 @@ def add_tool(path):
if key:
env[key] = value
except Exception, e:
- raise ModuleError('Error parsing module env: %s' % e)
+ raise ModuleError(self,
+ "Error parsing module env: %s" % e)
if 'options' in self.conf and 'env_port' in self.conf['options']:
for e in self.forceGetInputListFromPort('env'):
@@ -286,7 +285,8 @@ def add_tool(path):
if key:
env[key] = value
except Exception, e:
- raise ModuleError('Error parsing env port: %s' % e)
+ raise ModuleError(self,
+ "Error parsing env port: %s" % e)
if env:
kwargs['env'] = dict(os.environ)
@@ -313,7 +313,7 @@ def add_tool(path):
if return_code is not None:
if process.returncode != return_code:
- raise ModuleError("Command returned %d (!= %d)" % (
+ raise ModuleError(self, "Command returned %d (!= %d)" % (
process.returncode, return_code))
self.setResult('return_code', process.returncode)
diff --git a/vistrails/packages/CLTools/wizard.py b/vistrails/packages/CLTools/wizard.py
index 41bc170..51a0895 100644
--- a/vistrails/packages/CLTools/wizard.py
+++ b/vistrails/packages/CLTools/wizard.py
@@ -1008,15 +1008,17 @@ class QArgWidget(QtGui.QWidget):
def fromList(self, arg):
if self.argtype not in self.stdTypes:
- self.argtype, self.name, self.klass, self.options = arg
+ self.argtype, self.name, klass, self.options = arg
else:
- self.name, self.klass, self.options = arg
+ self.name, klass, self.options = arg
+ self.klass = klass.lower()
self.setValues()
def klassChanged(self, index=None):
if self.argtype in self.stdTypes:
return
klass = self.klassList.itemData(self.klassList.currentIndex())
+ type = self.typeList.itemData(self.typeList.currentIndex())
self.listLabel.setVisible(klass == "list" and type == 'input')
self.subtype.setVisible(klass == "list" and type == 'input')
diff --git a/vistrails/packages/HTTP/init.py b/vistrails/packages/HTTP/init.py
index bd89b7a..41279b4 100644
--- a/vistrails/packages/HTTP/init.py
+++ b/vistrails/packages/HTTP/init.py
@@ -151,7 +151,7 @@ class HTTPFile(Module):
if not size_header:
raise ValueError
size_header = int(size_header)
- except ValueError:
+ except (KeyError, ValueError):
size_header = None
result = vistrails.core.modules.basic_modules.File()
diff --git a/vistrails/packages/SUDSWebServices/init.py b/vistrails/packages/SUDSWebServices/init.py
index 3851e99..90e7e7c 100644
--- a/vistrails/packages/SUDSWebServices/init.py
+++ b/vistrails/packages/SUDSWebServices/init.py
@@ -851,9 +851,10 @@ def callContextMenu(signature):
s = Service(wsdl)
if s.service:
webServicesDict[wsdl] = s
- wsdlList = configuration.wsdlList.split(";")
- wsdlList.append(wsdl)
- configuration.wsdlList = ';'.join(wsdlList)
+ if configuration.wsdlList:
+ configuration.wsdlList += ';' + wsdl
+ else:
+ configuration.wsdlList = wsdl
elif signature.startswith('SUDS#'):
address = toAddress(signature)
from PyQt4 import QtGui
diff --git a/vistrails/packages/controlflow/__init__.py b/vistrails/packages/controlflow/__init__.py
index 2211a9b..5121f7e 100644
--- a/vistrails/packages/controlflow/__init__.py
+++ b/vistrails/packages/controlflow/__init__.py
@@ -35,5 +35,5 @@
identifier="org.vistrails.vistrails.control_flow"
name="Control Flow"
-version="0.2.3"
+version="0.2.4"
old_identifiers = ["edu.utah.sci.vistrails.control_flow"]
diff --git a/vistrails/packages/controlflow/init.py b/vistrails/packages/controlflow/init.py
index 9055d59..20a22ef 100644
--- a/vistrails/packages/controlflow/init.py
+++ b/vistrails/packages/controlflow/init.py
@@ -87,6 +87,10 @@ def initialize(*args,**keywords):
reg.add_input_port(FoldWithModule, 'InputPort', (List, ""))
reg.add_input_port(FoldWithModule, 'OutputPort', (String, ""))
+ reg.add_output_port(Map, 'Result', (List, ""))
+
+ reg.add_output_port(Filter, 'Result', (List, ""))
+
reg.add_input_port(If, 'Condition', (Boolean, ""))
reg.add_input_port(If, 'TruePort', (Module, ""))
reg.add_input_port(If, 'FalsePort', (Module, ""))
diff --git a/vistrails/packages/dialogs/__init__.py b/vistrails/packages/dialogs/__init__.py
index 16057bd..cb4d4e6 100644
--- a/vistrails/packages/dialogs/__init__.py
+++ b/vistrails/packages/dialogs/__init__.py
@@ -35,7 +35,18 @@
"""dialogs provides modules for user-based interaction on execution.
Users can then enter file names, numbers, strings, etc."""
+from vistrails.core.packagemanager import get_package_manager
+
+
identifier = 'org.vistrails.vistrails.dialogs'
name = 'Dialogs'
-version = '0.9.1'
+version = '0.9.2'
old_identifiers = ['edu.utah.sci.vistrails.dialogs']
+
+
+def package_dependencies():
+ pm = get_package_manager()
+ if pm.has_package('org.vistrails.vistrails.spreadsheet'):
+ return ['org.vistrails.vistrails.spreadsheet']
+ else:
+ return []
diff --git a/vistrails/packages/dialogs/continue_prompt.py b/vistrails/packages/dialogs/continue_prompt.py
new file mode 100644
index 0000000..7cbd285
--- /dev/null
+++ b/vistrails/packages/dialogs/continue_prompt.py
@@ -0,0 +1,63 @@
+from PyQt4 import QtCore, QtGui
+
+from vistrails.core.configuration import get_vistrails_configuration
+from vistrails.core.modules import basic_modules
+from vistrails.core.modules.vistrails_module import Module, ModuleError
+
+from vistrails.packages.spreadsheet.basic_widgets import SpreadsheetCell
+from vistrails.packages.spreadsheet.spreadsheet_cell import QCellContainer
+
+
+class PromptWindow(QtGui.QDialog):
+ def __init__(self, widget, label=None):
+ QtGui.QDialog.__init__(self)
+ self.setWindowTitle("Check intermediate results")
+ self.setLayout(QtGui.QVBoxLayout())
+ self.layout().addWidget(widget)
+ if label is not None:
+ self.layout().addWidget(QtGui.QLabel(label))
+ buttons = QtGui.QDialogButtonBox(
+ QtGui.QDialogButtonBox.Yes | QtGui.QDialogButtonBox.No)
+ self.connect(buttons, QtCore.SIGNAL('accepted()'),
+ self, QtCore.SLOT('accept()'))
+ self.connect(buttons, QtCore.SIGNAL('rejected()'),
+ self, QtCore.SLOT('reject()'))
+ self.layout().addWidget(buttons)
+
+
+class PromptIsOkay(Module):
+ _input_ports = [('label', basic_modules.String,
+ {'optional': True}),
+ ('carry_on', basic_modules.Boolean,
+ {'optional': True, 'defaults': "['False']"}),
+ ('cell', SpreadsheetCell)]
+ _output_ports = [('result', basic_modules.Boolean)]
+
+ def compute(self):
+ vt_configuration = get_vistrails_configuration()
+ if not getattr(vt_configuration, 'interactiveMode', False):
+ self.setResult('result', True)
+ return
+
+ cell = self.getInputFromPort('cell')
+ label = self.forceGetInputFromPort('label', None)
+
+ # FIXME : This should be done via the spreadsheet, removing it properly
+ # and then sending a new DisplayCellEvent
+ # However, there is currently no facility to remove the widget from
+ # wherever it is
+ oldparent = cell.parent()
+ assert isinstance(oldparent, QCellContainer)
+ ncell = oldparent.takeWidget()
+ assert ncell == cell
+ dialog = PromptWindow(cell, label)
+ result = dialog.exec_() == QtGui.QDialog.Accepted
+ oldparent.setWidget(cell)
+
+ self.setResult('result', result)
+
+ if not result and not self.getInputFromPort('carry_on'):
+ raise ModuleError(self, "Execution aborted")
+
+
+_modules = [PromptIsOkay]
diff --git a/vistrails/packages/dialogs/init.py b/vistrails/packages/dialogs/init.py
index 53c4e9d..6291ecf 100644
--- a/vistrails/packages/dialogs/init.py
+++ b/vistrails/packages/dialogs/init.py
@@ -32,50 +32,46 @@
## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
##
###############################################################################
+
+from vistrails.core.modules import basic_modules
from vistrails.core.modules.vistrails_module import Module, ModuleError
-import vistrails.core.modules
-import vistrails.core.modules.basic_modules
-import vistrails.core.modules.module_registry
-import vistrails.core.system
-import vistrails.gui.application
-from PyQt4 import QtCore, QtGui
+from vistrails.core.packagemanager import get_package_manager
+from PyQt4 import QtGui
-##############################################################################
class Dialog(Module):
- pass
-
-class TextDialog(Dialog):
- password = False
+ _input_ports = [('title', basic_modules.String,
+ {'optional': True}),
+ ('cacheable', basic_modules.Boolean,
+ {'optional': True, 'defaults': "['False']"})]
def __init__(self, *args, **kwargs):
- super(TextDialog,self).__init__(*args, **kwargs)
+ super(Dialog,self).__init__(*args, **kwargs)
self.cacheable_dialog = False
def is_cacheable(self):
return self.cacheable_dialog
+
+class TextDialog(Dialog):
+ _input_ports = [('label', basic_modules.String,
+ {'optional': True, 'defaults': "['']"}),
+ ('default', basic_modules.String,
+ {'optional': True, 'defaults': "['']"})]
+ _output_ports = [('result', basic_modules.String)]
+
+ password = False
+
def compute(self):
if self.hasInputFromPort('title'):
title = self.getInputFromPort('title')
else:
title = 'VisTrails Dialog'
- if self.hasInputFromPort('label'):
- label = self.getInputFromPort('label')
- else:
- label = ''
- if self.password:
- label = 'Password'
+ label = self.getInputFromPort('label')
- if self.hasInputFromPort('default'):
- default = self.getInputFromPort('default')
- else:
- default = ''
-
- if self.hasInputFromPort('cacheable') and self.getInputFromPort('cacheable'):
- self.cacheable_dialog = True
- else:
- self.cacheable_dialog = False
+ default = self.getInputFromPort('default')
+
+ self.cacheable_dialog = self.getInputFromPort('cacheable')
mode = QtGui.QLineEdit.Normal
if self.password:
@@ -90,21 +86,41 @@ class TextDialog(Dialog):
class PasswordDialog(TextDialog):
+ _input_ports = [('label', basic_modules.String,
+ {'optional': True, 'defaults': "['Password']"})]
+
password = True
-##############################################################################
+class YesNoDialog(Dialog):
+ _input_ports = [('label', basic_modules.String,
+ {'optional': True, 'defaults': "['Yes/No?']"})]
+ _output_ports = [('result', basic_modules.Boolean)]
+
+ def compute(self):
+ if self.hasInputFromPort('title'):
+ title = self.getInputFromPort('title')
+ else:
+ title = 'VisTrails Dialog'
+ label = self.getInputFromPort('label')
+
+ self.cacheable_dialog = self.getInputFromPort('cacheable')
+
+ result = QtGui.QMessageBox.question(
+ None,
+ title, label,
+ QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
+ result = result == QtGui.QMessageBox.Yes
+
+ self.setResult('result', result)
+
-def initialize(*args, **keywords):
- reg = vistrails.core.modules.module_registry.get_module_registry()
- basic = vistrails.core.modules.basic_modules
- reg.add_module(Dialog, abstract=True)
- reg.add_module(TextDialog)
+_modules = [(Dialog, {'abstract': True}),
+ TextDialog, PasswordDialog,
+ YesNoDialog]
- reg.add_input_port(TextDialog, "title", basic.String)
- reg.add_input_port(TextDialog, "label", basic.String)
- reg.add_input_port(TextDialog, "default", basic.String)
- reg.add_input_port(TextDialog, "cacheable", basic.Boolean)
- reg.add_output_port(TextDialog, "result", basic.String)
- reg.add_module(PasswordDialog)
+pm = get_package_manager()
+if pm.has_package('org.vistrails.vistrails.spreadsheet'):
+ from .continue_prompt import _modules as continue_modules
+ _modules.extend(continue_modules)
diff --git a/vistrails/packages/matplotlib/bases.py b/vistrails/packages/matplotlib/bases.py
index 92b7ea5..428505d 100644
--- a/vistrails/packages/matplotlib/bases.py
+++ b/vistrails/packages/matplotlib/bases.py
@@ -123,19 +123,12 @@ class MplSource(CodeRunnerMixin, MplPlot):
self.run_code(s, use_input=True, use_output=True)
class MplFigure(Module):
- # _input_ports = [("addPlot", "(MplPlot)"),
- # ("numSubfigRows", "(edu.utah.sci.vistrails.basic:Integer)",
- # {"defaults": ["1"]}),
- # ("numSubfigCols", "(edu.utah.sci.vistrails.basic:Integer)",
- # {"defaults": ["1"]}),
- # ]
_input_ports = [("addPlot", "(MplPlot)"),
("axesProperties", "(MplAxesProperties)"),
("figureProperties", "(MplFigureProperties)"),
("setLegend", "(MplLegend)")]
- _output_ports = [("file", "(basic:File)"),
- ("self", "(MplFigure)")]
+ _output_ports = [("self", "(MplFigure)")]
def __init__(self):
Module.__init__(self)
@@ -149,17 +142,6 @@ class MplFigure(Module):
def compute(self):
plots = self.getInputListFromPort("addPlot")
- # num_rows = self.getInputFromPort("numSubfigRows")
- # if num_rows < 1:
- # raise ModuleError(self, "numSubfigRows must be at least 1.")
- # num_cols = self.getInputFromPort("numSubfigCols")
- # if num_cols < 1:
- # raise ModuleError(self, "numSubfigCols must be at least 1.")
- # if len(plots) < 1:
- # raise ModuleError(self, "Must add at least one plot to figure.")
-
- # FIXME just take the fig instance from the first plot
- # self.figInstance = plots[0].figInstance
if self.hasInputFromPort("figureProperties"):
figure_props = self.getInputFromPort("figureProperties")
@@ -171,107 +153,6 @@ class MplFigure(Module):
legend = self.getInputFromPort("setLegend")
self.figInstance.gca().legend()
- #FIXME write file out if File port is attached!
-
- # if num_rows > 1 or num_cols > 1:
- # # need to reconstruct plot...
- # self.figInstance = pylab.figure()
- # else:
- # self.figInstance = plots[0].figInstance
-
- # for plot in plots:
- # p_axes = plot.get_fig().gca()
- # print "DPI:", plot.get_fig().dpi
- # for c in p_axes.collections:
- # print "TRANSFORM:", c._transform
- # print "DATALIM:", c.get_datalim(p_axes.transData)
- # print "PREPARE POINTS:", c._prepare_points()
-
- # self.figInstance = pylab.figure()
- # axes = self.figInstance.gca()
- # x0 = None
- # x1 = None
- # y0 = None
- # y1 = None
- # dataLim = None
- # for plot in plots:
- # p_axes = plot.get_fig().gca()
- # dataLim = p_axes.dataLim.frozen()
- # p_x0, p_x1 = p_axes.get_xlim()
- # if x0 is None or p_x0 < x0:
- # x0 = p_x0
- # if x1 is None or p_x1 > x1:
- # x1 = p_x1
- # p_y0, p_y1 = p_axes.get_ylim()
- # if y0 is None or p_y0 < y0:
- # y0 = p_y0
- # if y1 is None or p_y1 > y1:
- # y1 = p_y1
-
- # print x0, x1, y0, y1
- # axes.set_xlim(x0, x1, emit=False, auto=None)
- # axes.set_ylim(y0, y1, emit=False, auto=None)
-
- # # axes.dataLim = dataLim
- # # axes.ignore_existing_data_limits = False
- # # axes.autoscale_view()
-
- # for plot in plots:
- # p_axes = plot.get_fig().gca()
- # # axes.lines.extend(p_axes.lines)
- # for line in p_axes.lines:
- # print "adding line!"
- # line = copy.copy(line)
- # line._transformSet = False
- # axes.add_line(line)
- # # axes.patches.extend(p_axes.patches)
- # for patch in p_axes.patches:
- # print "adding patch!"
- # patch = copy.copy(patch)
- # patch._transformSet = False
- # axes.add_patch(patch)
- # axes.texts.extend(p_axes.texts)
- # # axes.tables.extend(p_axes.tables)
- # for table in p_axes.tables:
- # table = copy.copy(table)
- # table._transformSet = False
- # axes.add_table(table)
- # # axes.artists.extend(p_axes.artists)
- # for artist in p_axes.artists:
- # artist = copy.copy(artist)
- # artist._transformSet = False
- # axes.add_artist(artist)
- # axes.images.extend(p_axes.images)
- # # axes.collections.extend(p_axes.collections)
- # for collection in p_axes.collections:
- # print "adding collection!"
- # # print "collection:", collection.__class__.__name__
- # # print "datalim:", p_axes.dataLim
- # # transOffset = axes.transData
- # collection = copy.copy(collection)
- # # collection._transformSet = False
- # # print dir(mtransforms)
- # collection.set_transform(mtransforms.IdentityTransform())
- # collection._transOffset = axes.transData
- # # collection._transformSet = False
- # collection._label = None
- # collection._clippath = None
- # axes.add_collection(collection)
- # # collection.set_transform(mtransforms.IdentityTransform())
- # # axes.collections.append(collection)
- # # axes.containers.extend(p_axes.containers)
- # print "transFigure start:", self.figInstance.transFigure
- # # axes.dataLim = dataLim
- # # axes.ignore_existing_data_limits = False
- # # print "datalim after:", axes.dataLim
-
-
- # # print "DPI:", self.figInstance.dpi
- # # for c in axes.collections:
- # # print "TRANSFORM:", c._transform
- # # print "DATALIM:", c.get_datalim(p_axes.transData)
- # # print "PREPARE POINTS:", c._prepare_points()
-
self.setResult("self", self)
diff --git a/vistrails/packages/spreadsheet/basic_widgets.py b/vistrails/packages/spreadsheet/basic_widgets.py
index 1228529..f651d26 100644
--- a/vistrails/packages/spreadsheet/basic_widgets.py
+++ b/vistrails/packages/spreadsheet/basic_widgets.py
@@ -80,6 +80,7 @@ def registerWidget(reg, basicModules, basicWidgets):
reg.add_module(SpreadsheetCell)
reg.add_input_port(SpreadsheetCell, "Location", CellLocation)
+ reg.add_output_port(SpreadsheetCell, "Widget", SpreadsheetCell)
reg.add_module(SingleCellSheetReference)
reg.add_input_port(SingleCellSheetReference, "SheetName",
@@ -216,21 +217,6 @@ class SpreadsheetCell(NotCacheable, Module):
e.cellType = cellType
e.inputPorts = inputPorts
return e
-
- def display(self, cellType, inputPorts):
- """ display(cellType: python type, iputPorts: tuple) -> None
- Dispatch the cellType to the spreadsheet with appropriate input data
- to display it
-
- Keyword arguments:
- cellType --- widget type, this is truely a python type
- inputPorts --- a tuple of input data that cellType() will understand
-
- """
- if spreadsheetController.echoMode():
- return self.displayAndWait(cellType, inputPorts)
- e = self.createDisplayEvent(cellType, inputPorts)
- spreadsheetController.postEventToSpreadsheet(e)
def displayAndWait(self, cellType, inputPorts):
""" displayAndWait(cellType: python type, iputPorts: tuple)
@@ -247,7 +233,11 @@ class SpreadsheetCell(NotCacheable, Module):
spreadsheetWindow = spreadsheetController.findSpreadsheetWindow()
if spreadsheetWindow.echoMode == False:
spreadsheetWindow.configShow(show=True)
- return spreadsheetWindow.displayCellEvent(e)
+ self.cellWidget = spreadsheetWindow.displayCellEvent(e)
+ self.setResult('Widget', self.cellWidget)
+ return self.cellWidget
+
+ display = displayAndWait
class SingleCellSheetReference(SheetReference):
"""
diff --git a/vistrails/packages/spreadsheet/spreadsheet_cell.py b/vistrails/packages/spreadsheet/spreadsheet_cell.py
index 31f39ad..a2b8bef 100644
--- a/vistrails/packages/spreadsheet/spreadsheet_cell.py
+++ b/vistrails/packages/spreadsheet/spreadsheet_cell.py
@@ -1090,7 +1090,7 @@ class QCellManipulator(QtGui.QFrame):
self.cellInfo[2])
if info:
info = info[0]
- view = builderWindow.ensureController(info['controller'])
+ view = builderWindow.ensureVistrail(info['locator'])
if view:
controller = view.controller
controller.change_selected_version(info['version'])
@@ -1109,7 +1109,7 @@ class QCellManipulator(QtGui.QFrame):
self.cellInfo[2])
if info:
info = info[0]
- view = builderWindow.ensureController(info['controller'])
+ view = builderWindow.ensureVistrail(info['locator'])
if view:
view.version_selected(info['version'], True)
view.version_view.select_current_version()
diff --git a/vistrails/packages/spreadsheet/widgets/iebrowser/iecell.py b/vistrails/packages/spreadsheet/widgets/iebrowser/iecell.py
index 28feaa5..0a41462 100644
--- a/vistrails/packages/spreadsheet/widgets/iebrowser/iecell.py
+++ b/vistrails/packages/spreadsheet/widgets/iebrowser/iecell.py
@@ -61,7 +61,7 @@ class IECell(SpreadsheetCell):
else:
fileValue = None
urlValue = None
- self.display(IECellWidget, (urlValue, fileValue))
+ self.displayAndWait(IECellWidget, (urlValue, fileValue))
class IECellWidget(QCellWidget):
"""
diff --git a/vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer.py b/vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer.py
index 53e7e3a..7e927a1 100644
--- a/vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer.py
+++ b/vistrails/packages/spreadsheet/widgets/imageviewer/imageviewer.py
@@ -60,7 +60,7 @@ class ImageViewerCell(SpreadsheetCell):
fileValue = window.file_pool.make_local_copy(file_to_display.name)
else:
fileValue = None
- self.cellWidget = self.displayAndWait(ImageViewerCellWidget, (fileValue, ))
+ self.displayAndWait(ImageViewerCellWidget, (fileValue, ))
class ImageViewerCellWidget(QCellWidget):
"""
@@ -99,7 +99,7 @@ class ImageViewerCellWidget(QCellWidget):
img = QtGui.QImage()
if img.load(fileValue.name):
self.originalPix = QtGui.QPixmap.fromImage(img)
- self.label.setPixmap(self.originalPix.scaled(len(self.label),
+ self.label.setPixmap(self.originalPix.scaled(self.label.size(),
QtCore.Qt.KeepAspectRatio,
QtCore.Qt.SmoothTransformation))
else:
diff --git a/vistrails/packages/spreadsheet/widgets/richtext/richtext.py b/vistrails/packages/spreadsheet/widgets/richtext/richtext.py
index 11849ce..b26b7b5 100644
--- a/vistrails/packages/spreadsheet/widgets/richtext/richtext.py
+++ b/vistrails/packages/spreadsheet/widgets/richtext/richtext.py
@@ -36,7 +36,7 @@
# Richtext widgets implementation
################################################################################
import os
-from PyQt4 import QtGui
+from PyQt4 import QtCore, QtGui
from PyQt4.QtCore import QUrl
from PyQt4.QtXmlPatterns import QXmlQuery
@@ -60,7 +60,7 @@ class RichTextCell(SpreadsheetCell):
text_format = self.getInputFromPort("Format")
with open(filename, 'rb') as fp:
if text_format == 'html':
- html = fp.read()
+ html = fp.read() # reads bytes
elif text_format == 'rtf':
try:
py_import('pyth', {'pip': 'pyth'})
@@ -71,11 +71,11 @@ class RichTextCell(SpreadsheetCell):
from pyth.plugins.rtf15.reader import Rtf15Reader
from pyth.plugins.xhtml.writer import XHTMLWriter
doc = Rtf15Reader.read(fp)
- html = XHTMLWriter.write(doc).read().decode('utf-8')
+ html = XHTMLWriter.write(doc).read() # gets bytes
else:
raise ModuleError(self, "'%s' format is unknown" % text_format)
- self.cellWidget = self.displayAndWait(RichTextCellWidget, (html,))
+ self.displayAndWait(RichTextCellWidget, (html,))
class XSLCell(SpreadsheetCell):
@@ -93,9 +93,11 @@ class XSLCell(SpreadsheetCell):
query = QXmlQuery(QXmlQuery.XSLT20)
query.setFocus(QUrl.fromLocalFile(os.path.join(os.getcwd(), xml)))
query.setQuery(QUrl.fromLocalFile(os.path.join(os.getcwd(), xsl)))
- html = query.evaluateToString()
+ html = query.evaluateToString() # gets a unicode object
+ if html is None:
+ raise ModuleError(self, "Error applying XSL")
- self.cellWidget = self.displayAndWait(RichTextCellWidget, (html,))
+ self.displayAndWait(RichTextCellWidget, (html,))
class RichTextCellWidget(QCellWidget):
@@ -122,7 +124,12 @@ class RichTextCellWidget(QCellWidget):
"""
(self.html,) = inputPorts
- self.browser.setHtml(self.html)
+ if isinstance(self.html, unicode):
+ html = self.html
+ else:
+ codec = QtCore.QTextCodec.codecForHtml(self.html)
+ html = codec.toUnicode(self.html)
+ self.browser.setHtml(html)
def dumpToFile(self, filename):
""" dumpToFile(filename) -> None
@@ -133,7 +140,13 @@ class RichTextCellWidget(QCellWidget):
if self.html is not None:
basename, ext = os.path.splitext(filename)
with open(basename + '.html', 'wb') as fp:
- fp.write(self.html.encode('utf-8'))
+ if isinstance(self.html, bytes):
+ fp.write(self.html)
+ else:
+ codec = QtCore.QTextCodec.codecForHtml(
+ self.html.encode('utf-8'),
+ QtCore.QTextCodec.codecForName('UTF-8'))
+ fp.write(codec.fromUnicode(self.html))
QCellWidget.dumpToFile(self,filename)
def saveToPDF(self, filename):
diff --git a/vistrails/packages/spreadsheet/widgets/svg/svg.py b/vistrails/packages/spreadsheet/widgets/svg/svg.py
index f431983..e231f42 100644
--- a/vistrails/packages/spreadsheet/widgets/svg/svg.py
+++ b/vistrails/packages/spreadsheet/widgets/svg/svg.py
@@ -62,7 +62,7 @@ class SVGCell(SpreadsheetCell):
fileValue = window.file_pool.make_local_copy(file_to_display.name)
else:
fileValue = None
- self.display(SVGCellWidget, (fileValue,))
+ self.displayAndWait(SVGCellWidget, (fileValue,))
### SVG Cell widget type
class SVGCellWidget(QCellWidget):
diff --git a/vistrails/packages/spreadsheet/widgets/webview/webview.py b/vistrails/packages/spreadsheet/widgets/webview/webview.py
index 58418ff..da77d24 100644
--- a/vistrails/packages/spreadsheet/widgets/webview/webview.py
+++ b/vistrails/packages/spreadsheet/widgets/webview/webview.py
@@ -61,7 +61,7 @@ class WebViewCell(SpreadsheetCell):
else:
fileValue = None
urlValue = None
- self.display(WebViewCellWidget, (urlValue, fileValue))
+ self.displayAndWait(WebViewCellWidget, (urlValue, fileValue))
class WebViewCellWidget(QCellWidget):
"""
diff --git a/vistrails/packages/tabledata/convert/convert_dates.py b/vistrails/packages/tabledata/convert/convert_dates.py
index 6e4e6af..25161ae 100644
--- a/vistrails/packages/tabledata/convert/convert_dates.py
+++ b/vistrails/packages/tabledata/convert/convert_dates.py
@@ -76,45 +76,45 @@ _decimal_fmt = re.compile(
'([0-9][0-9])?$') # minutes
def make_timezone(s):
- if s == 'local':
- return LocalTimezone()
-
- match = _decimal_fmt.match(s)
- if match is not None:
- sign, hours, minutes = match.groups('')
- sign = -1 if sign == '-' else 1
- hours = int(hours)
- minutes = int(minutes) if minutes else 0
- offset = datetime.timedelta(
- minutes=sign * (hours*60 + minutes))
- name = '%s%02d%02d' % (
- '-' if sign == -1 else '+',
- hours,
- minutes)
- return FixedOffset(offset, name)
-
+ if s == 'local':
+ return LocalTimezone()
+
+ match = _decimal_fmt.match(s)
+ if match is not None:
+ sign, hours, minutes = match.groups('')
+ sign = -1 if sign == '-' else 1
+ hours = int(hours)
+ minutes = int(minutes) if minutes else 0
+ offset = datetime.timedelta(
+ minutes=sign * (hours*60 + minutes))
+ name = '%s%02d%02d' % (
+ '-' if sign == -1 else '+',
+ hours,
+ minutes)
+ return FixedOffset(offset, name)
+
+ try:
+ pytz = py_import('pytz', {
+ 'pip': 'pytz',
+ 'linux-debian': 'python-tz',
+ 'linux-ubuntu': 'python-tz',
+ 'linux-fedora': 'pytz'})
+ except ImportError:
+ raise ValueError("can't understand timezone %r (maybe you should "
+ "install pytz?)" % s)
+ else:
+ ver = LooseVersion(pytz.__version__)
+ if ver < LooseVersion('2012'):
+ warnings.warn(
+ "You are using an old version of pytz (%s). You might "
+ "run into some issues with daylight saving handling." %
+ pytz.__version__,
+ category=UserWarning)
try:
- pytz = py_import('pytz', {
- 'pip': 'pytz',
- 'linux-debian': 'python-tz',
- 'linux-ubuntu': 'python-tz',
- 'linux-fedora': 'pytz'})
- except ImportError:
- raise ValueError("can't understand timezone %r (maybe you should "
- "install pytz?)" % s)
- else:
- ver = LooseVersion(pytz.__version__)
- if ver < LooseVersion('2012'):
- warnings.warn(
- "You are using an old version of pytz (%s). You might "
- "run into some issues with daylight saving handling." %
- pytz.__version__,
- category=UserWarning)
- try:
- return pytz.timezone(s)
- except KeyError:
- raise ValueError("can't understand timezone %r (defaulted to "
- "pytz, which gave no answer)" % s)
+ return pytz.timezone(s)
+ except KeyError:
+ raise ValueError("can't understand timezone %r (defaulted to "
+ "pytz, which gave no answer)" % s)
class TimestampsToDates(Module):
@@ -194,7 +194,11 @@ class StringsToDates(Module):
else:
result = [datetime.datetime.strptime(s, fmt) for s in strings]
- if tz:
+ if tz is None:
+ result = [dt.replace(tzinfo=None) for dt in result]
+ elif hasattr(tz, 'localize'):
+ result = [tz.localize(dt) for dt in result]
+ else:
# Compute the time without daylight saving
result = [dt.replace(tzinfo=tz) for dt in result]
@@ -215,8 +219,6 @@ class StringsToDates(Module):
# For dst -> standard (fall): the time will be in dst,
# although it could also have been standard (there is
# noway to know which one was meant)
- else:
- result = [dt.replace(tzinfo=None) for dt in result]
return result
diff --git a/vistrails/packages/tabledata/read/read_csv.py b/vistrails/packages/tabledata/read/read_csv.py
index 65f8ddc..c69859d 100644
--- a/vistrails/packages/tabledata/read/read_csv.py
+++ b/vistrails/packages/tabledata/read/read_csv.py
@@ -13,6 +13,10 @@ def count_lines(fp):
return lines
+class ReadError(Exception):
+ pass
+
+
class CSVFile(Table):
_input_ports = [
('file', '(org.vistrails.vistrails.basic:File)'),
@@ -43,8 +47,7 @@ class CSVFile(Table):
izip(CSVFile._STANDARD_DELIMITERS, counts),
key=lambda (delim, count): count)
if count == 0:
- raise ModuleError(self,
- "Couldn't guess the field delimiter")
+ raise ReadError("Couldn't guess the field delimiter")
else:
delimiter = read_delimiter
else:
@@ -59,7 +62,7 @@ class CSVFile(Table):
else:
column_names = None
except IOError:
- raise ModuleError(self, "File does not exist")
+ raise ReadError("File does not exist")
return column_count, column_names, delimiter
@@ -74,8 +77,13 @@ class CSVFile(Table):
self.filename = csv_file
- self.columns, self.names, self.delimiter = \
- self.read_file(csv_file, self.delimiter, self.header_present)
+ try:
+ self.columns, self.names, self.delimiter = self.read_file(
+ csv_file,
+ self.delimiter,
+ self.header_present)
+ except ReadError, e:
+ raise ModuleError(self, *e.args)
self.column_cache = {}
diff --git a/vistrails/packages/tabledata/viewer.py b/vistrails/packages/tabledata/viewer.py
index 7b39b09..fbc67b3 100644
--- a/vistrails/packages/tabledata/viewer.py
+++ b/vistrails/packages/tabledata/viewer.py
@@ -11,7 +11,7 @@ class TableCell(SpreadsheetCell):
def compute(self):
table = self.getInputFromPort('table')
- self.cellWidget = self.displayAndWait(TableCellWidget, (table,))
+ self.displayAndWait(TableCellWidget, (table,))
class TableCellWidget(QCellWidget):
diff --git a/vistrails/packages/vtk/vtkcell.py b/vistrails/packages/vtk/vtkcell.py
index 0b87922..10f4dbf 100644
--- a/vistrails/packages/vtk/vtkcell.py
+++ b/vistrails/packages/vtk/vtkcell.py
@@ -89,7 +89,7 @@ class VTKCell(SpreadsheetCell):
iHandlers = self.forceGetInputListFromPort('InteractionHandler')
iStyle = self.forceGetInputFromPort('InteractorStyle')
picker = self.forceGetInputFromPort('AddPicker')
- self.cellWidget = self.displayAndWait(QVTKWidget, (renderers, renderView, iHandlers, iStyle, picker))
+ self.displayAndWait(QVTKWidget, (renderers, renderView, iHandlers, iStyle, picker))
AsciiToKeySymTable = ( None, None, None, None, None, None, None,
None, None,
diff --git a/vistrails/packages/vtk/vtkviewcell.py b/vistrails/packages/vtk/vtkviewcell.py
index b06eacc..1eed757 100644
--- a/vistrails/packages/vtk/vtkviewcell.py
+++ b/vistrails/packages/vtk/vtkviewcell.py
@@ -79,7 +79,7 @@ class VTKViewCell(SpreadsheetCell):
renderView = self.forceGetInputFromPort('SetRenderView')
if renderView==None:
raise ModuleError(self, 'A vtkRenderView input is required.')
- self.cellWidget = self.displayAndWait(QVTKViewWidget, (renderView,))
+ self.displayAndWait(QVTKViewWidget, (renderView,))
AsciiToKeySymTable = ( None, None, None, None, None, None, None,
None, None,
diff --git a/vistrails/run.py b/vistrails/run.py
index 681d63a..a5034de 100644
--- a/vistrails/run.py
+++ b/vistrails/run.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
###############################################################################
##
## Copyright (C) 2011-2014, NYU-Poly.
diff --git a/vistrails/tests/resources/spx_loop.vt b/vistrails/tests/resources/spx_loop.vt
index d1680bd..6bbf39b 100644
Binary files a/vistrails/tests/resources/spx_loop.vt and b/vistrails/tests/resources/spx_loop.vt differ
diff --git a/vistrails/tests/utils.py b/vistrails/tests/utils.py
index dfbaa55..bae8836 100644
--- a/vistrails/tests/utils.py
+++ b/vistrails/tests/utils.py
@@ -104,8 +104,9 @@ def execute(modules, connections=[], add_port_specs=[], enable_pkg=True):
for func_name, params in functions:
param_list = []
- for param_type, param_val in params:
- param_list.append(ModuleParam(type=param_type,
+ for j, (param_type, param_val) in enumerate(params):
+ param_list.append(ModuleParam(pos=j,
+ type=param_type,
val=param_val))
function_list.append(ModuleFunction(name=func_name,
parameters=param_list))
diff --git a/vistrails/vistrails_server.py b/vistrails/vistrails_server.py
index b285641..76554d4 100644
--- a/vistrails/vistrails_server.py
+++ b/vistrails/vistrails_server.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
###############################################################################
##
## Copyright (C) 2011-2014, NYU-Poly.
@@ -35,33 +36,46 @@
"""Main file for running VisTrails in server mode"""
import os
import sys
-if __name__ == '__main__':
+
+def fix_paths():
+ import site
+ if not hasattr(site, "USER_BASE"): return # We are running py2app
+
# Fix import path: add parent directory(so that we can
# import vistrails.[gui|...] and remove other paths below it (we might have
# been started from a subdir)
-
- # DAK: the deletes screw things up in the binary (definitely for
- # Mac) and since subdir is unlikely, I'm commenting them out. A
- # better solution is probably to move run.py up a
- # directory in the repo
+ # A better solution is probably to move run.py up a
+ # directory in the repo
+ old_dir = os.path.realpath(os.path.dirname(__file__))
vistrails_dir = os.path.realpath(os.path.join(os.path.dirname(__file__), '..'))
- # i = 0
- # print "vistrails_dir:", vistrails_dir
- # while i < len(sys.path):
- # rpath = os.path.realpath(sys.path[i])
- # if rpath.startswith(vistrails_dir):
- # print " deleting", rpath, sys.path[i]
- # del sys.path[i]
- # else:
- # i += 1
- sys.path.insert(0, vistrails_dir)
+ i = 0
+ while i < len(sys.path):
+ rpath = os.path.realpath(sys.path[i])
+ if rpath.startswith(old_dir):
+ del sys.path[i]
+ else:
+ i += 1
+ if vistrails_dir not in sys.path:
+ sys.path.insert(0, vistrails_dir)
+
+if __name__ == '__main__':
+ fix_paths()
+
+ # Set locale to English
+ import locale
+ locale.setlocale(locale.LC_ALL, 'C')
import vistrails.gui.requirements
vistrails.gui.requirements.require_pyqt4_api2()
import vistrails.gui.application_server
try:
- v = vistrails.gui.application_server.start_server()
+ optionsDict = {
+ 'interactiveMode': False,
+ 'enablePackagesSilently': False,
+ 'handlerDontAsk': True,
+ }
+ v = vistrails.gui.application_server.start_server(optionsDict)
app = vistrails.gui.application_server.VistrailsServer()
except SystemExit, e:
print str(e)
--
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