[med-svn] [plastimatch] branch upstream updated (2c241e2 -> daaa737)
Greg Sharp
gregsharp-guest at moszumanska.debian.org
Thu Jun 30 19:38:31 UTC 2016
This is an automated email from the git hooks/post-receive script.
gregsharp-guest pushed a change to branch upstream
in repository plastimatch.
from 2c241e2 Imported Upstream version 1.6.2+dfsg
adds daaa737 Imported Upstream version 1.6.3+dfsg
No new revisions were added by this update.
Summary of changes:
CMakeLists.txt | 250 +-
Testing/CMakeLists.txt | 415 +-
Testing/CTestCustom.cmake.in | 16 +-
Testing/Data/plm-bsp-regularize-numeric.txt | 11 +-
Testing/Data/plm-reg-itk-similarity.txt | 33 +
Testing/Data/plm-reg-multi-b.txt | 15 +
Testing/Data/proton-dose-1.txt | 49 +-
Testing/Data/proton-dose-2.txt | 6 +-
Testing/Data/proton-dose-3.txt | 72 +-
Testing/Data/proton-dose-4.txt | 46 +-
Testing/Data/proton-dose-5a.txt | 18 +
Testing/Data/proton-dose-5g.txt | 18 +
Testing/Data/proton-dose-6a.txt | 18 +
.../Data/{plm-bsp-mse-c.txt => speedtest-a.txt} | 34 +-
Testing/Data/wed-a.txt | 19 +
Testing/Data/wed-b.txt | 19 +
Testing/Data/wed-c.txt | 18 +
Testing/PlmSpeedTest.cmake | 17 +
cmake/CheckEpsilon.cmake | 1 -
cmake/CheckQt.cmake | 19 +
cmake/FindCUDA_wrap.cmake | 6 +
cmake/PlmMacros.cmake | 14 +-
cmake/test_qt.cxx | 17 +
doc/NOTES.TXT | 1447 ++
doc/README.TXT | 7 +
doc/ROADMAP.TXT | 52 +
doc/STYLE_GUIDE_1.TXT | 172 +
doc/STYLE_GUIDE_2.TXT | 174 +
src/CMakeLists.txt | 10 +-
src/plastimatch/CHANGELOG.TXT | 17 +
src/plastimatch/CMakeLists.txt | 193 +-
src/plastimatch/base/CMakeLists.txt | 229 +-
src/plastimatch/base/aperture.cxx | 127 +-
src/plastimatch/base/aperture.h | 6 +-
src/plastimatch/base/bspline_macros.h | 22 +-
src/plastimatch/base/bspline_xform.cxx | 296 +-
src/plastimatch/base/bspline_xform.h | 32 +-
src/plastimatch/base/cxt_extract.cxx | 6 +-
src/plastimatch/base/dcmtk_file.cxx | 13 +
src/plastimatch/base/dcmtk_file.h | 2 +
src/plastimatch/base/dcmtk_image.cxx | 284 +-
src/plastimatch/base/dcmtk_rt_study.cxx | 7 +-
src/plastimatch/base/dcmtk_rtdose.cxx | 35 +-
src/plastimatch/base/dcmtk_rtss.cxx | 5 +-
src/plastimatch/base/dcmtk_sro.cxx | 94 +-
src/plastimatch/base/direction_cosines.cxx | 4 -
src/plastimatch/{util => base}/float_pair_list.cxx | 0
src/plastimatch/{util => base}/float_pair_list.h | 4 +-
src/plastimatch/base/gdcm1_dose.cxx | 27 +-
src/plastimatch/base/hnd_io.cxx | 2 +-
src/plastimatch/base/itk_dicom_save.h | 1 -
src/plastimatch/base/itk_image.cxx | 19 +-
src/plastimatch/base/itk_image.h | 11 +-
src/plastimatch/base/itk_image_create.cxx | 21 +-
src/plastimatch/base/itk_image_load.txx | 1 +
src/plastimatch/base/itk_image_load_char.cxx | 2 -
src/plastimatch/base/itk_image_load_double.cxx | 2 -
src/plastimatch/base/itk_image_load_float.cxx | 2 -
src/plastimatch/base/itk_image_load_int32.cxx | 2 -
src/plastimatch/base/itk_image_load_short.cxx | 2 -
src/plastimatch/base/itk_image_load_uchar.cxx | 2 -
src/plastimatch/base/itk_image_load_uint32.cxx | 2 -
src/plastimatch/base/itk_image_load_ushort.cxx | 2 -
src/plastimatch/base/itk_image_origin.cxx | 53 +
.../base/{dcmtk_rtss.h => itk_image_origin.h} | 10 +-
src/plastimatch/base/itk_image_region.cxx | 55 +
.../base/{dcmtk_rtss.h => itk_image_region.h} | 10 +-
src/plastimatch/base/itk_image_save.cxx | 7 -
src/plastimatch/base/itk_image_save.h | 11 +-
src/plastimatch/base/itk_image_type.h | 3 -
src/plastimatch/base/itk_resample.cxx | 35 +-
src/plastimatch/base/itk_volume_header.cxx | 25 +-
src/plastimatch/base/itk_volume_header.h | 2 +-
src/plastimatch/base/metadata.cxx | 17 +
src/plastimatch/base/metadata.h | 14 +-
src/plastimatch/base/nki_io.cxx | 6 +-
src/plastimatch/base/plm_image.cxx | 38 +-
src/plastimatch/base/plm_image.h | 3 +-
src/plastimatch/base/plm_image_convert.cxx | 6 +
src/plastimatch/base/plm_image_header.cxx | 381 +-
src/plastimatch/base/plm_image_header.h | 142 +-
src/plastimatch/base/plm_image_p.h | 1 +
src/plastimatch/base/plm_image_type.cxx | 44 +-
src/plastimatch/base/plm_image_type.h | 3 +-
.../{script/lua_tty_preview.h => base/plm_itk.h} | 15 +-
src/plastimatch/base/pointset.cxx | 10 +
src/plastimatch/base/pointset.h | 4 +
src/plastimatch/base/proj_image.cxx | 35 +-
src/plastimatch/base/proj_image.h | 25 +-
src/plastimatch/base/proj_matrix.cxx | 110 +-
src/plastimatch/base/proj_matrix.h | 31 +-
src/plastimatch/base/proj_volume.cxx | 222 +-
src/plastimatch/base/proj_volume.h | 15 +-
src/plastimatch/base/pwlut.cxx | 90 +
src/plastimatch/base/pwlut.h | 38 +
src/plastimatch/base/ray_data.h | 24 +-
src/plastimatch/base/ray_trace.h | 3 +-
src/plastimatch/base/ray_trace_exact.cxx | 26 +-
src/plastimatch/base/ray_trace_uniform.cxx | 21 +-
src/plastimatch/base/rpl_volume.cxx | 1260 +-
src/plastimatch/base/rpl_volume.h | 54 +-
src/plastimatch/base/rt_study.cxx | 99 +-
src/plastimatch/base/rt_study.h | 24 +-
src/plastimatch/base/rt_study_metadata.cxx | 83 +-
src/plastimatch/base/rt_study_metadata.h | 19 +-
src/plastimatch/base/rtog_io.cxx | 12 +-
src/plastimatch/base/rtss.cxx | 43 +-
src/plastimatch/base/rtss_contour.h | 2 +-
src/plastimatch/base/rtss_roi.cxx | 13 +
src/plastimatch/base/rtss_roi.h | 1 +
src/plastimatch/base/segmentation.cxx | 238 +-
src/plastimatch/base/segmentation.h | 4 +-
src/plastimatch/base/slice_list.cxx | 6 +-
src/plastimatch/base/volume.cxx | 19 +-
src/plastimatch/base/volume.h | 16 +-
src/plastimatch/base/volume_fill.cxx | 23 +
.../base/{plm_image_p.h => volume_fill.h} | 33 +-
src/plastimatch/base/volume_macros.h | 16 +
src/plastimatch/base/xform.cxx | 297 +-
src/plastimatch/base/xform.h | 14 +-
src/plastimatch/base/xio_ct.h | 1 -
src/plastimatch/base/xio_ct_transform.cxx | 16 +-
src/plastimatch/base/xio_demographic.cxx | 11 +-
src/plastimatch/base/xio_demographic.h | 1 +
src/plastimatch/base/xio_studyset.cxx | 297 +-
src/plastimatch/base/xio_studyset.h | 3 +
src/plastimatch/cli/pcmd_dice.cxx | 17 -
src/plastimatch/cli/pcmd_filter.cxx | 11 +-
src/plastimatch/cli/pcmd_filter.h | 1 +
src/plastimatch/cli/pcmd_gamma.cxx | 22 +-
src/plastimatch/cli/pcmd_gamma.h | 4 +-
src/plastimatch/cli/pcmd_mabs.cxx | 19 +-
src/plastimatch/cli/pcmd_resample.cxx | 21 +-
src/plastimatch/cli/pcmd_stats.cxx | 4 +-
src/plastimatch/cli/pcmd_synth.cxx | 12 +-
src/plastimatch/cli/pcmd_warp.cxx | 72 +-
src/plastimatch/cli/pcmd_warp_dij.cxx | 448 +-
src/plastimatch/cli/pcmd_xf_convert.cxx | 49 +-
src/plastimatch/cli/plastimatch_main.cxx | 2 +-
....cmake.in => PlastimatchConfig-Legacy.cmake.in} | 0
src/plastimatch/cmake/PlastimatchConfig.cmake.in | 18 +-
src/plastimatch/cuda/CMakeLists.txt | 1 +
src/plastimatch/dose/CMakeLists.txt | 5 +-
src/plastimatch/dose/bragg_curve.cxx | 14 +-
src/plastimatch/dose/bragg_curve.h | 7 -
src/plastimatch/dose/dose_volume_functions.cxx | 103 +-
src/plastimatch/dose/dose_volume_functions.h | 6 +-
src/plastimatch/dose/particle_type.cxx | 5 +
src/plastimatch/dose/particle_type.h | 5 +-
src/plastimatch/dose/rt_beam.cxx | 638 +-
src/plastimatch/dose/rt_beam.h | 146 +-
src/plastimatch/dose/rt_depth_dose.cxx | 138 +-
src/plastimatch/dose/rt_depth_dose.h | 18 +-
src/plastimatch/dose/rt_dose.cxx | 1142 +-
src/plastimatch/dose/rt_dose.h | 70 +-
src/plastimatch/dose/rt_lut.cxx | 848 +-
src/plastimatch/dose/rt_lut.h | 39 +-
src/plastimatch/dose/rt_mebs.cxx | 1693 +++
src/plastimatch/dose/rt_mebs.h | 152 +
src/plastimatch/dose/rt_parms.cxx | 216 +-
src/plastimatch/dose/rt_parms.h | 1 -
src/plastimatch/dose/rt_plan.cxx | 1343 +-
src/plastimatch/dose/rt_plan.h | 35 +-
src/plastimatch/dose/rt_sigma.cxx | 371 +-
src/plastimatch/dose/rt_sigma.h | 19 +-
src/plastimatch/dose/rt_sobp.cxx | 780 -
src/plastimatch/dose/rt_sobp.h | 143 -
src/plastimatch/dose/rt_sobp_optimize.cxx | 429 -
src/plastimatch/dose/rt_sobp_p.cxx | 131 -
src/plastimatch/dose/rt_sobp_p.h | 65 -
src/plastimatch/dose/wed_parms.cxx | 211 +-
src/plastimatch/dose/wed_parms.h | 36 +-
src/plastimatch/opencl/CMakeLists.txt | 1 +
src/plastimatch/plastimatch_version.txt | 2 +-
src/plastimatch/reconstruct/CMakeLists.txt | 1 +
src/plastimatch/reconstruct/cuda/CMakeLists.txt | 1 +
src/plastimatch/reconstruct/drr.h | 22 +-
src/plastimatch/register/CMakeLists.txt | 6 +-
src/plastimatch/register/bspline.cxx | 216 +-
src/plastimatch/register/bspline.h | 15 +-
src/plastimatch/register/bspline_gm.cxx | 12 -
src/plastimatch/register/bspline_gm.txx | 2 +-
src/plastimatch/register/bspline_landmarks.cxx | 2 +-
src/plastimatch/register/bspline_loop.txx | 12 +-
src/plastimatch/register/bspline_mi.cxx | 115 +-
src/plastimatch/register/bspline_mi.txx | 4 +-
src/plastimatch/register/bspline_mse.cxx | 167 +-
src/plastimatch/register/bspline_mse.txx | 2 +-
.../register/bspline_optimize_lbfgsb.cxx | 2 +-
.../register/bspline_optimize_liblbfgs.cxx | 2 +-
.../register/bspline_optimize_nlopt.cxx | 2 +-
.../register/bspline_optimize_steepest.cxx | 32 +-
src/plastimatch/register/bspline_parms.cxx | 16 +-
src/plastimatch/register/bspline_parms.h | 4 +-
src/plastimatch/register/bspline_regularize.cxx | 6 +-
src/plastimatch/register/bspline_regularize.h | 20 +-
.../register/bspline_regularize_analytic.cxx | 22 +-
.../register/bspline_regularize_numeric.cxx | 44 +-
.../register/bspline_regularize_semi_analytic.cxx | 15 +-
src/plastimatch/register/bspline_score.cxx | 136 +-
src/plastimatch/register/bspline_score.h | 59 +-
src/plastimatch/register/bspline_stage.cxx | 5 +
src/plastimatch/register/bspline_state.cxx | 14 +-
src/plastimatch/register/bspline_state.h | 11 +-
src/plastimatch/register/cuda/CMakeLists.txt | 1 +
src/plastimatch/register/cuda/bspline_cuda.cu | 5 +-
src/plastimatch/register/cuda/bspline_cuda.cxx | 70 +-
src/plastimatch/register/cuda/bspline_cuda.h | 1 +
src/plastimatch/register/itk_optimizer.cxx | 39 +-
src/plastimatch/register/itk_registration.cxx | 20 +
src/plastimatch/register/registration.cxx | 37 +-
src/plastimatch/register/registration.h | 2 +
.../register/registration_metric_type.cxx | 28 +
.../register/registration_metric_type.h | 2 +
src/plastimatch/register/registration_parms.cxx | 42 +-
src/plastimatch/register/registration_resample.cxx | 6 +
src/plastimatch/register/shared_parms.h | 1 +
src/plastimatch/register/stage_parms.cxx | 14 +
src/plastimatch/register/stage_parms.h | 5 +
.../register/translation_grid_search.cxx | 3 +
src/plastimatch/segment/CMakeLists.txt | 1 +
src/plastimatch/segment/autolabel.cxx | 12 +-
src/plastimatch/segment/mabs.cxx | 334 +-
src/plastimatch/segment/mabs.h | 9 +-
src/plastimatch/segment/mabs_atlas_selection.cxx | 6 +-
src/plastimatch/segment/mabs_parms.cxx | 10 +-
src/plastimatch/segment/mabs_parms.h | 1 +
src/plastimatch/segment/plmsegment_config.h.in | 4 -
src/plastimatch/segment/segment_body.cxx | 227 +-
src/plastimatch/segment/segment_body.h | 6 +-
src/plastimatch/standalone/CMakeLists.txt | 101 +-
src/plastimatch/standalone/DlgGammaView.cxx | 24 +
src/plastimatch/standalone/DlgGammaView.h | 33 +
src/plastimatch/standalone/DlgGammaView.ui | 1980 +++
src/plastimatch/standalone/Launch_cmd_prompt.bat | 24 +
src/plastimatch/standalone/YK16GrayImage.cxx | 2761 ++++
src/plastimatch/standalone/YK16GrayImage.h | 299 +
src/plastimatch/standalone/YKThreadRegi.cpp | 93 +
src/plastimatch/standalone/YKThreadRegi.h | 28 +
src/plastimatch/standalone/bspline_main.cxx | 5 +-
src/plastimatch/standalone/bspline_opts.cxx | 3 +-
src/plastimatch/standalone/check_grad.cxx | 51 +-
src/plastimatch/standalone/cmd_prompt_launcher.cxx | 40 +-
.../standalone/colormap_customgamma.txt | 100 +
src/plastimatch/standalone/colormap_jet.txt | 64 +
src/plastimatch/standalone/create_wed_volumes.cxx | 107 -
src/plastimatch/standalone/drr_main.cxx | 17 +-
src/plastimatch/standalone/drr_opts.cxx | 35 +-
src/plastimatch/standalone/extract_contour.cxx | 114 -
src/plastimatch/standalone/gamma_gui.cpp | 3353 +++++
src/plastimatch/standalone/gamma_gui.h | 200 +
src/plastimatch/standalone/gamma_gui.ui | 1628 ++
...i2mha_converter_main.cpp => gamma_gui_main.cpp} | 20 +-
src/plastimatch/standalone/hnd_to_pfm.cxx | 2 +-
src/plastimatch/standalone/nki2mha_converter.cpp | 22 +-
src/plastimatch/standalone/nki2mha_converter.h | 114 +-
src/plastimatch/standalone/nki2mha_converter.ui | 363 +-
.../standalone/nki2mha_converter_main.cpp | 20 +-
src/plastimatch/standalone/qcustomplot.cpp | 15034 +++++++++++++++++++
src/plastimatch/standalone/qcustomplot.h | 2171 +++
src/plastimatch/standalone/qt_util.cxx | 1436 ++
src/plastimatch/standalone/qt_util.h | 74 +
src/plastimatch/standalone/qyklabel.cpp | 459 +
src/plastimatch/standalone/qyklabel.h | 91 +
src/plastimatch/standalone/register_gui.cpp | 2357 +++
src/plastimatch/standalone/register_gui.h | 201 +
src/plastimatch/standalone/register_gui.ui | 1209 ++
...ha_converter_main.cpp => register_gui_main.cpp} | 20 +-
src/plastimatch/standalone/shuffle_mha_main.cxx | 2 +-
src/plastimatch/standalone/sobp_main.cxx | 188 +-
src/plastimatch/standalone/wed_main.cxx | 556 +-
src/plastimatch/standalone/xf_to_empirefmt.cxx | 262 +-
src/plastimatch/standalone/xvi_archive.cxx | 350 +-
src/plastimatch/standalone/yk_config.h | 149 +
src/plastimatch/sys/CMakeLists.txt | 7 +-
src/plastimatch/sys/file_util.cxx | 46 +-
src/plastimatch/sys/file_util.h | 7 +-
src/plastimatch/sys/path_util.cxx | 10 +
src/plastimatch/sys/path_util.h | 2 +
src/plastimatch/sys/plm_config.h.in | 46 +-
src/plastimatch/sys/plm_math.h | 6 +
src/plastimatch/sys/print_and_exit.cxx | 2 +-
src/plastimatch/sys/string_util.cxx | 54 +-
src/plastimatch/sys/string_util.h | 6 +
src/plastimatch/test/itk_test.cxx | 9 +-
src/plastimatch/test/itk_test_directions.cxx | 1 +
src/plastimatch/util/CMakeLists.txt | 5 +-
src/plastimatch/util/dice_statistics.cxx | 11 +-
src/plastimatch/util/dvh.cxx | 22 -
src/plastimatch/util/gamma_dose_comparison.cxx | 153 +-
src/plastimatch/util/gamma_dose_comparison.h | 38 +-
src/plastimatch/util/geometry_chooser.cxx | 3 +
src/plastimatch/util/hausdorff_distance.cxx | 10 +-
src/plastimatch/util/image_boundary.cxx | 5 +-
src/plastimatch/util/image_center.cxx | 99 +
src/plastimatch/util/image_center.h | 45 +
src/plastimatch/util/itk_adjust.cxx | 11 +
src/plastimatch/util/itk_mask.cxx | 2 +
src/plastimatch/util/rt_study_warp.cxx | 29 +-
src/plastimatch/util/synthetic_mha.cxx | 10 +-
src/plastimatch/util/warp_parms.h | 10 +-
301 files changed, 47228 insertions(+), 9554 deletions(-)
create mode 100755 Testing/Data/plm-reg-itk-similarity.txt
create mode 100755 Testing/Data/plm-reg-multi-b.txt
create mode 100644 Testing/Data/proton-dose-5a.txt
create mode 100644 Testing/Data/proton-dose-5g.txt
create mode 100644 Testing/Data/proton-dose-6a.txt
copy Testing/Data/{plm-bsp-mse-c.txt => speedtest-a.txt} (60%)
create mode 100755 Testing/Data/wed-a.txt
create mode 100755 Testing/Data/wed-b.txt
create mode 100755 Testing/Data/wed-c.txt
create mode 100755 Testing/PlmSpeedTest.cmake
create mode 100644 cmake/CheckQt.cmake
create mode 100644 cmake/test_qt.cxx
create mode 100644 doc/NOTES.TXT
create mode 100755 doc/README.TXT
create mode 100644 doc/ROADMAP.TXT
create mode 100644 doc/STYLE_GUIDE_1.TXT
create mode 100644 doc/STYLE_GUIDE_2.TXT
rename src/plastimatch/{util => base}/float_pair_list.cxx (100%)
rename src/plastimatch/{util => base}/float_pair_list.h (82%)
create mode 100644 src/plastimatch/base/itk_image_origin.cxx
copy src/plastimatch/base/{dcmtk_rtss.h => itk_image_origin.h} (54%)
mode change 100755 => 100644
create mode 100644 src/plastimatch/base/itk_image_region.cxx
copy src/plastimatch/base/{dcmtk_rtss.h => itk_image_region.h} (54%)
mode change 100755 => 100644
copy src/plastimatch/{script/lua_tty_preview.h => base/plm_itk.h} (61%)
create mode 100755 src/plastimatch/base/pwlut.cxx
create mode 100755 src/plastimatch/base/pwlut.h
create mode 100755 src/plastimatch/base/volume_fill.cxx
copy src/plastimatch/base/{plm_image_p.h => volume_fill.h} (66%)
mode change 100644 => 100755
copy src/plastimatch/cmake/{PlastimatchConfig.cmake.in => PlastimatchConfig-Legacy.cmake.in} (100%)
create mode 100644 src/plastimatch/dose/rt_mebs.cxx
create mode 100644 src/plastimatch/dose/rt_mebs.h
delete mode 100644 src/plastimatch/dose/rt_sobp.cxx
delete mode 100644 src/plastimatch/dose/rt_sobp.h
delete mode 100644 src/plastimatch/dose/rt_sobp_optimize.cxx
delete mode 100644 src/plastimatch/dose/rt_sobp_p.cxx
delete mode 100644 src/plastimatch/dose/rt_sobp_p.h
create mode 100644 src/plastimatch/register/registration_metric_type.cxx
create mode 100644 src/plastimatch/standalone/DlgGammaView.cxx
create mode 100644 src/plastimatch/standalone/DlgGammaView.h
create mode 100644 src/plastimatch/standalone/DlgGammaView.ui
create mode 100644 src/plastimatch/standalone/Launch_cmd_prompt.bat
create mode 100644 src/plastimatch/standalone/YK16GrayImage.cxx
create mode 100644 src/plastimatch/standalone/YK16GrayImage.h
create mode 100644 src/plastimatch/standalone/YKThreadRegi.cpp
create mode 100644 src/plastimatch/standalone/YKThreadRegi.h
create mode 100644 src/plastimatch/standalone/colormap_customgamma.txt
create mode 100644 src/plastimatch/standalone/colormap_jet.txt
delete mode 100644 src/plastimatch/standalone/create_wed_volumes.cxx
delete mode 100644 src/plastimatch/standalone/extract_contour.cxx
create mode 100644 src/plastimatch/standalone/gamma_gui.cpp
create mode 100644 src/plastimatch/standalone/gamma_gui.h
create mode 100644 src/plastimatch/standalone/gamma_gui.ui
copy src/plastimatch/standalone/{nki2mha_converter_main.cpp => gamma_gui_main.cpp} (66%)
create mode 100644 src/plastimatch/standalone/qcustomplot.cpp
create mode 100644 src/plastimatch/standalone/qcustomplot.h
create mode 100644 src/plastimatch/standalone/qt_util.cxx
create mode 100644 src/plastimatch/standalone/qt_util.h
create mode 100644 src/plastimatch/standalone/qyklabel.cpp
create mode 100644 src/plastimatch/standalone/qyklabel.h
create mode 100644 src/plastimatch/standalone/register_gui.cpp
create mode 100644 src/plastimatch/standalone/register_gui.h
create mode 100644 src/plastimatch/standalone/register_gui.ui
copy src/plastimatch/standalone/{nki2mha_converter_main.cpp => register_gui_main.cpp} (66%)
create mode 100644 src/plastimatch/standalone/yk_config.h
create mode 100755 src/plastimatch/util/image_center.cxx
create mode 100755 src/plastimatch/util/image_center.h
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