[med-svn] [plastimatch] branch master updated (eebf60d -> 4497def)
Greg Sharp
gregsharp-guest at moszumanska.debian.org
Thu Jun 30 19:37:23 UTC 2016
This is an automated email from the git hooks/post-receive script.
gregsharp-guest pushed a change to branch master
in repository plastimatch.
from eebf60d cme fix dpkg-control
new daaa737 Imported Upstream version 1.6.3+dfsg
new f32c3ed Merge tag 'upstream/1.6.3+dfsg'
new 4497def Update changelog
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
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 +
debian/changelog | 6 +
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 +-
302 files changed, 47234 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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