[med-svn] [plastimatch] branch upstream updated (e1533f5 -> 9a47d41)
Greg Sharp
gregsharp-guest at moszumanska.debian.org
Wed Oct 11 17:25:33 UTC 2017
This is an automated email from the git hooks/post-receive script.
gregsharp-guest pushed a change to branch upstream
in repository plastimatch.
from e1533f5 New upstream version 1.6.5+dfsg.1
adds 9a47d41 New upstream version 1.6.6+dfsg.1
No new revisions were added by this update.
Summary of changes:
CMakeLists.txt | 20 +-
INSTALL.TXT | 0
LICENSE.TXT | 0
README.TXT | 37 +-
Testing/CMakeLists.txt | 180 ++--
...{plm-reg-stiffness-a.txt => plm-bsp-dmap-k.txt} | 13 +-
Testing/Data/plm-bsp-sm-multi-a.txt | 12 +-
Testing/Data/plm-reg-align-center.txt | 9 +-
Testing/Data/plm-reg-gw-a.txt | 8 +
Testing/Data/plm-reg-multi-a.txt | 1 -
Testing/Data/proton-dose-1.txt | 0
.../{proton-dose-5g.txt => proton-dose-5d.txt} | 36 +-
.../{proton-dose-5a.txt => proton-dose-7a.txt} | 36 +-
cmake/FindCUDA_wrap.cmake | 9 +
cmake/FindKaze.cmake | 35 +
cmake/FindPaxscan.cmake | 2 +-
doc/NOTES.TXT | 396 +++++++-
doc/STYLE_GUIDE_2.TXT | 35 +
doc/man/drr.1 | 2 +-
doc/man/fdk.1 | 6 +-
doc/man/landmark_warp.1 | 2 +-
doc/man/plastimatch.1 | 32 +-
run_lcov.sh | 7 -
src/CMakeLists.txt | 5 +
src/plastimatch/CHANGELOG.TXT | 10 +
src/plastimatch/CMakeLists.txt | 5 +-
src/plastimatch/COPYRIGHT.TXT | 0
src/plastimatch/Doxyfile.in | 0
src/plastimatch/base/CMakeLists.txt | 3 +
src/plastimatch/base/aperture.cxx | 82 +-
src/plastimatch/base/aperture.h | 11 +-
src/plastimatch/base/bspline_xform.cxx | 33 +-
src/plastimatch/base/bspline_xform.h | 10 +
src/plastimatch/base/dcmtk_config.h | 0
src/plastimatch/base/dcmtk_file.cxx | 8 +-
src/plastimatch/base/dcmtk_file.h | 0
src/plastimatch/base/dcmtk_image.cxx | 11 +-
src/plastimatch/base/dcmtk_metadata.cxx | 0
src/plastimatch/base/dcmtk_metadata.h | 0
src/plastimatch/base/dcmtk_module.cxx | 13 +-
src/plastimatch/base/dcmtk_rdd.cxx | 0
src/plastimatch/base/dcmtk_rdd.h | 0
src/plastimatch/base/dcmtk_rt_study.cxx | 0
src/plastimatch/base/dcmtk_rt_study.h | 1 +
src/plastimatch/base/dcmtk_rtdose.cxx | 5 +-
src/plastimatch/base/dcmtk_rtplan.cxx | 152 ++-
src/plastimatch/base/dcmtk_rtss.cxx | 7 +-
src/plastimatch/base/dcmtk_rtss.h | 0
src/plastimatch/base/dcmtk_series.cxx | 0
src/plastimatch/base/dcmtk_series.h | 2 +-
src/plastimatch/base/dcmtk_slice_data.h | 0
src/plastimatch/base/dcmtk_uid.cxx | 0
src/plastimatch/base/dcmtk_uid.h | 0
src/plastimatch/base/dcmtk_util.cxx | 6 +
src/plastimatch/base/dcmtk_util.h | 2 +
src/plastimatch/base/dicom.dic | 0
src/plastimatch/base/dicom_util.cxx | 0
src/plastimatch/base/dicom_util.h | 0
src/plastimatch/base/direction_cosines.cxx | 0
src/plastimatch/base/direction_cosines.h | 0
src/plastimatch/base/direction_matrices.cxx | 0
src/plastimatch/base/direction_matrices.h | 0
src/plastimatch/base/float_pair_list.cxx | 0
src/plastimatch/base/float_pair_list.h | 0
src/plastimatch/base/gaussian.cxx | 1 -
src/plastimatch/base/gaussian.h | 0
src/plastimatch/base/gdcm1_dose.cxx | 0
src/plastimatch/base/gdcm1_dose.h | 0
src/plastimatch/base/gdcm1_file.cxx | 0
src/plastimatch/base/gdcm1_file.h | 0
src/plastimatch/base/gdcm1_rdd.cxx | 0
src/plastimatch/base/gdcm1_rdd.h | 0
src/plastimatch/base/gdcm1_rtss.cxx | 0
src/plastimatch/base/gdcm1_rtss.h | 0
src/plastimatch/base/gdcm1_series.cxx | 0
src/plastimatch/base/gdcm1_series.h | 0
src/plastimatch/base/gdcm1_series_helper_2.cxx | 0
src/plastimatch/base/gdcm1_series_helper_2.h | 0
src/plastimatch/base/gdcm1_util.cxx | 0
src/plastimatch/base/gdcm1_util.h | 0
src/plastimatch/base/gdcm2_util.cxx | 0
src/plastimatch/base/gdcm2_util.h | 0
src/plastimatch/base/hnd_io.cxx | 2 +-
src/plastimatch/base/interpolate.cxx | 76 +-
src/plastimatch/base/interpolate.h | 23 +-
src/plastimatch/base/itkClampCastImageFilter.h | 0
src/plastimatch/base/itkClampCastImageFilter.txx | 0
src/plastimatch/base/itk_bbox.cxx | 50 +
.../base/{dcmtk_rtdose.h => itk_bbox.h} | 9 +-
src/plastimatch/base/itk_dicom_load.cxx | 0
src/plastimatch/base/itk_dicom_load.h | 0
src/plastimatch/base/itk_dicom_save.cxx | 0
src/plastimatch/base/itk_dicom_save.h | 0
src/plastimatch/base/itk_directions.cxx | 0
src/plastimatch/base/itk_directions.h | 0
src/plastimatch/base/itk_image_clone.cxx | 22 +-
src/plastimatch/base/itk_image_clone.h | 2 +
src/plastimatch/base/itk_image_load_char.cxx | 0
src/plastimatch/base/itk_image_load_double.cxx | 0
src/plastimatch/base/itk_image_type.h | 0
src/plastimatch/base/itk_metadata.cxx | 0
src/plastimatch/base/itk_metadata.h | 0
src/plastimatch/base/itk_pointset.cxx | 0
src/plastimatch/base/itk_pointset.h | 0
src/plastimatch/base/parameter_parser.cxx | 42 +-
src/plastimatch/base/parameter_parser.h | 12 +
src/plastimatch/base/plm_file_format.cxx | 0
src/plastimatch/base/plm_file_format.h | 0
src/plastimatch/base/plm_image_header.cxx | 13 +
src/plastimatch/base/plm_image_header.h | 2 +
src/plastimatch/base/plm_image_type.cxx | 0
src/plastimatch/base/proj_image.cxx | 6 +-
src/plastimatch/base/proj_matrix.cxx | 21 +-
src/plastimatch/base/proj_matrix.h | 14 +-
src/plastimatch/base/proj_volume.cxx | 51 +-
src/plastimatch/base/proj_volume.h | 23 +-
src/plastimatch/base/pwlut.cxx | 0
src/plastimatch/base/pwlut.h | 0
src/plastimatch/base/ray_trace.h | 7 +-
src/plastimatch/base/ray_trace_uniform.cxx | 6 -
src/plastimatch/base/rpl_volume.cxx | 1051 ++++++--------------
src/plastimatch/base/rpl_volume.h | 58 +-
src/plastimatch/base/rpl_volume_lut.cxx | 163 +++
src/plastimatch/base/rpl_volume_lut.h | 37 +
src/plastimatch/base/rt_study_metadata.cxx | 109 +-
src/plastimatch/base/rt_study_metadata.h | 24 +-
src/plastimatch/base/rt_study_p.h | 0
src/plastimatch/base/rtplan.cxx | 11 +
src/plastimatch/base/rtplan.h | 16 +
src/plastimatch/base/rtplan_beam.cxx | 43 +-
src/plastimatch/base/rtplan_beam.h | 30 +-
src/plastimatch/base/rtplan_control_pt.h | 0
src/plastimatch/base/rtss.cxx | 16 +-
src/plastimatch/base/slice_list.cxx | 0
src/plastimatch/base/slice_list.h | 0
src/plastimatch/base/thumbnail.cxx | 0
src/plastimatch/base/thumbnail.h | 0
src/plastimatch/base/vf.cxx | 0
src/plastimatch/base/vf_convolve.cxx | 0
src/plastimatch/base/volume.cxx | 2 +-
src/plastimatch/base/volume.h | 24 +-
src/plastimatch/base/volume_boundary_behavior.h | 24 +
src/plastimatch/base/volume_fill.cxx | 0
src/plastimatch/base/volume_fill.h | 0
src/plastimatch/base/volume_grad.cxx | 8 +-
src/plastimatch/base/volume_grad.h | 4 +-
src/plastimatch/base/volume_header.cxx | 11 +
src/plastimatch/base/volume_header.h | 2 +
src/plastimatch/base/volume_limit.h | 0
src/plastimatch/base/volume_macros.h | 0
src/plastimatch/base/volume_resample.cxx | 0
src/plastimatch/base/volume_stats.cxx | 0
src/plastimatch/base/volume_stats.h | 0
src/plastimatch/base/xform_convert.cxx | 0
src/plastimatch/base/xform_convert.h | 0
src/plastimatch/base/xform_legacy.cxx | 0
src/plastimatch/base/xform_legacy.h | 0
src/plastimatch/base/xio_ct.cxx | 0
src/plastimatch/base/xio_ct_transform.cxx | 0
src/plastimatch/base/xio_ct_transform.h | 0
src/plastimatch/base/xio_demographic.cxx | 0
src/plastimatch/base/xio_demographic.h | 0
src/plastimatch/base/xio_dir.cxx | 0
src/plastimatch/base/xio_patient.cxx | 0
src/plastimatch/base/xio_patient.h | 0
src/plastimatch/base/xio_structures.cxx | 0
src/plastimatch/cli/CMakeLists.txt | 5 +-
src/plastimatch/cli/pcmd_add.h | 0
src/plastimatch/cli/pcmd_adjust.cxx | 0
src/plastimatch/cli/pcmd_adjust.h | 0
src/plastimatch/cli/pcmd_autolabel.cxx | 0
src/plastimatch/cli/pcmd_autolabel.h | 0
src/plastimatch/cli/pcmd_autolabel_train.cxx | 0
src/plastimatch/cli/pcmd_autolabel_train.h | 0
src/plastimatch/cli/pcmd_bbox.cxx | 130 +++
src/plastimatch/cli/{pcmd_drr.h => pcmd_bbox.h} | 6 +-
src/plastimatch/cli/pcmd_benchmark.cxx | 0
src/plastimatch/cli/pcmd_benchmark.h | 0
src/plastimatch/cli/pcmd_boundary.cxx | 0
src/plastimatch/cli/pcmd_boundary.h | 0
src/plastimatch/cli/pcmd_compare.cxx | 0
src/plastimatch/cli/pcmd_compare.h | 0
src/plastimatch/cli/pcmd_compose.cxx | 0
src/plastimatch/cli/pcmd_compose.h | 0
src/plastimatch/cli/pcmd_crop.cxx | 0
src/plastimatch/cli/pcmd_crop.h | 0
src/plastimatch/cli/pcmd_dice.cxx | 0
src/plastimatch/cli/pcmd_dice.h | 0
src/plastimatch/cli/pcmd_diff.cxx | 0
src/plastimatch/cli/pcmd_diff.h | 0
src/plastimatch/cli/pcmd_dmap.cxx | 0
src/plastimatch/cli/pcmd_dmap.h | 0
src/plastimatch/cli/pcmd_dose.cxx | 33 +
src/plastimatch/cli/{pcmd_add.h => pcmd_dose.h} | 6 +-
src/plastimatch/cli/pcmd_drr.cxx | 0
src/plastimatch/cli/pcmd_drr.h | 0
src/plastimatch/cli/pcmd_dvh.cxx | 0
src/plastimatch/cli/pcmd_dvh.h | 0
src/plastimatch/cli/pcmd_filter.cxx | 0
src/plastimatch/cli/pcmd_filter.h | 0
src/plastimatch/cli/pcmd_gamma.cxx | 0
src/plastimatch/cli/pcmd_gamma.h | 0
src/plastimatch/cli/pcmd_header.cxx | 0
src/plastimatch/cli/pcmd_header.h | 0
src/plastimatch/cli/pcmd_mabs.cxx | 0
src/plastimatch/cli/pcmd_mabs.h | 0
src/plastimatch/cli/pcmd_mask.cxx | 0
src/plastimatch/cli/pcmd_mask.h | 0
src/plastimatch/cli/pcmd_probe.h | 0
src/plastimatch/cli/pcmd_register.cxx | 9 +-
src/plastimatch/cli/pcmd_scale.h | 0
src/plastimatch/cli/pcmd_segment.cxx | 0
src/plastimatch/cli/pcmd_segment.h | 0
src/plastimatch/cli/pcmd_sift.h | 0
src/plastimatch/cli/pcmd_stats.cxx | 0
src/plastimatch/cli/pcmd_stats.h | 0
src/plastimatch/cli/pcmd_synth.cxx | 0
src/plastimatch/cli/pcmd_synth.h | 0
src/plastimatch/cli/pcmd_synth_vf.cxx | 0
src/plastimatch/cli/pcmd_synth_vf.h | 0
src/plastimatch/cli/pcmd_threshold.cxx | 0
src/plastimatch/cli/pcmd_threshold.h | 0
src/plastimatch/cli/pcmd_thumbnail.cxx | 0
src/plastimatch/cli/pcmd_thumbnail.h | 0
src/plastimatch/cli/pcmd_union.h | 0
.../vf_invert_main.cxx => cli/pcmd_vf_invert.cxx} | 51 +-
.../cli/{pcmd_benchmark.h => pcmd_vf_invert.h} | 6 +-
src/plastimatch/cli/pcmd_warp.cxx | 0
src/plastimatch/cli/pcmd_warp.h | 0
src/plastimatch/cli/pcmd_warp_pointset.cxx | 0
src/plastimatch/cli/pcmd_xf_convert.cxx | 0
src/plastimatch/cli/pcmd_xf_convert.h | 0
src/plastimatch/cli/pcmd_xio_dvh.cxx | 0
src/plastimatch/cli/pcmd_xio_dvh.h | 0
src/plastimatch/cli/plastimatch_main.cxx | 30 +-
src/plastimatch/clp/CMakeLists.txt | 0
src/plastimatch/clp/plm_clp.cxx | 0
src/plastimatch/clp/plm_clp.h | 0
src/plastimatch/cuda/cuda_probe.h | 0
src/plastimatch/dose/CMakeLists.txt | 27 +-
src/plastimatch/dose/dose_volume_functions.cxx | 115 ++-
src/plastimatch/dose/dose_volume_functions.h | 4 +-
src/plastimatch/dose/rt_beam.cxx | 1006 +++++++++++++++----
src/plastimatch/dose/rt_beam.h | 114 ++-
.../dose/{bragg_curve.h => rt_beam_model.cxx} | 26 +-
src/plastimatch/dose/rt_beam_model.h | 21 +
src/plastimatch/dose/rt_depth_dose.cxx | 180 ++--
src/plastimatch/dose/rt_depth_dose.h | 24 +-
src/plastimatch/dose/rt_dij.cxx | 57 ++
src/plastimatch/dose/rt_dij.h | 48 +
src/plastimatch/dose/rt_dose.cxx | 1033 ++++++++-----------
src/plastimatch/dose/rt_dose.h | 28 +-
src/plastimatch/dose/rt_dose_timing.h | 39 +
src/plastimatch/dose/rt_lut.cxx | 36 +-
src/plastimatch/dose/rt_mebs.cxx | 308 +++---
src/plastimatch/dose/rt_mebs.h | 49 +-
src/plastimatch/dose/rt_parms.cxx | 80 +-
src/plastimatch/dose/rt_parms.h | 3 +
src/plastimatch/dose/rt_plan.cxx | 848 ++++++----------
src/plastimatch/dose/rt_plan.h | 24 +-
src/plastimatch/dose/rt_sigma.cxx | 264 ++---
src/plastimatch/dose/rt_sigma.h | 12 +-
src/plastimatch/dose/rt_spot_map.cxx | 55 +
src/plastimatch/dose/rt_spot_map.h | 43 +
src/plastimatch/dose/wed_parms.h | 7 +-
src/plastimatch/opencl/CMakeLists.txt | 0
src/plastimatch/opencl/autotune_opencl.cxx | 0
src/plastimatch/opencl/autotune_opencl.h | 0
src/plastimatch/reconstruct/drr.cxx | 7 +-
src/plastimatch/reconstruct/drr_opencl.cxx | 5 -
src/plastimatch/reconstruct/fdk.cxx | 2 +-
src/plastimatch/register/CMakeLists.txt | 76 +-
src/plastimatch/register/bspline.cxx | 149 +--
src/plastimatch/register/bspline.h | 3 +-
src/plastimatch/register/bspline_gm.h | 0
src/plastimatch/register/bspline_gm.txx | 6 +-
src/plastimatch/register/bspline_loop.txx | 34 +-
src/plastimatch/register/bspline_mi.cxx | 365 ++-----
src/plastimatch/register/bspline_mi.h | 0
src/plastimatch/register/bspline_mi.txx | 16 +-
src/plastimatch/register/bspline_mi_hist.h | 77 --
src/plastimatch/register/bspline_mse.cxx | 55 +-
src/plastimatch/register/bspline_mse.h | 0
src/plastimatch/register/bspline_mse.txx | 13 +-
src/plastimatch/register/bspline_optimize.cxx | 84 +-
src/plastimatch/register/bspline_optimize.h | 10 +-
.../register/bspline_optimize_lbfgsb.cxx | 14 +-
.../register/bspline_optimize_liblbfgs.cxx | 2 +-
.../register/bspline_optimize_nlopt.cxx | 2 +-
.../register/bspline_optimize_steepest.cxx | 47 +-
src/plastimatch/register/bspline_parms.cxx | 18 +-
src/plastimatch/register/bspline_parms.h | 58 +-
src/plastimatch/register/bspline_regularize.cxx | 2 -
src/plastimatch/register/bspline_regularize.h | 2 -
src/plastimatch/register/bspline_score.cxx | 43 +-
src/plastimatch/register/bspline_score.h | 40 +-
src/plastimatch/register/bspline_stage.cxx | 277 +++---
src/plastimatch/register/bspline_stage.h | 2 -
src/plastimatch/register/bspline_state.cxx | 218 ++--
src/plastimatch/register/bspline_state.h | 35 +-
src/plastimatch/register/cuda/CMakeLists.txt | 3 -
src/plastimatch/register/cuda/bspline_cuda.cu | 19 +-
src/plastimatch/register/cuda/bspline_cuda.cxx | 60 +-
src/plastimatch/register/cuda/bspline_cuda.h | 10 +-
src/plastimatch/register/gpuit_demons.cxx | 6 +-
.../register/{viscous.h => groupwise_parms.cxx} | 14 +-
.../register/{bspline_gm.h => groupwise_parms.h} | 12 +-
src/plastimatch/register/histogram.cxx | 33 +
src/plastimatch/register/histogram.h | 38 +
src/plastimatch/register/itk_align_center.cxx | 23 +-
src/plastimatch/register/itk_demons.cxx | 81 +-
src/plastimatch/register/itk_registration.cxx | 71 +-
.../register/itk_registration_observer.cxx | 25 +-
.../{bspline_mi_hist.cxx => joint_histogram.cxx} | 260 ++++-
src/plastimatch/register/joint_histogram.h | 50 +
src/plastimatch/register/landmark_warp.cxx | 2 +-
src/plastimatch/register/metric_parms.cxx | 54 +
src/plastimatch/register/metric_parms.h | 28 +
...spline_optimize_steepest.h => metric_state.cxx} | 32 +-
src/plastimatch/register/metric_state.h | 39 +
src/plastimatch/register/process_parms.cxx | 12 +-
src/plastimatch/register/rbf_gauss.cxx | 19 +-
src/plastimatch/register/registration.cxx | 65 +-
src/plastimatch/register/registration.h | 4 +-
src/plastimatch/register/registration_data.cxx | 282 +++++-
src/plastimatch/register/registration_data.h | 55 +-
.../register/registration_metric_type.h | 18 -
src/plastimatch/register/registration_parms.cxx | 230 +----
src/plastimatch/register/registration_parms.h | 16 +-
src/plastimatch/register/registration_resample.cxx | 0
src/plastimatch/register/registration_resample.h | 0
.../register/registration_similarity_data.h | 24 +
src/plastimatch/register/registration_util.cxx | 44 +
.../register/{itk_demons.h => registration_util.h} | 17 +-
src/plastimatch/register/shared_parms.cxx | 17 +
src/plastimatch/register/shared_parms.h | 8 +-
..._metric_type.cxx => similarity_metric_type.cxx} | 18 +-
src/plastimatch/register/similarity_metric_type.h | 19 +
src/plastimatch/register/stage_parms.cxx | 4 -
src/plastimatch/register/stage_parms.h | 9 +-
.../register/translation_grid_search.cxx | 180 ++--
src/plastimatch/register/translation_mi.cxx | 21 +-
src/plastimatch/register/translation_mi.h | 3 +-
src/plastimatch/register/translation_mse.cxx | 8 +-
src/plastimatch/register/translation_mse.h | 3 +-
src/plastimatch/segment/autolabel_parms.cxx | 4 +-
src/plastimatch/segment/autolabel_parms.h | 1 +
src/plastimatch/segment/mabs.cxx | 12 +-
src/plastimatch/segment/mabs.h | 0
src/plastimatch/segment/mabs_atlas_selection.cxx | 4 +-
src/plastimatch/segment/mabs_parms.cxx | 2 +
src/plastimatch/segment/mabs_stats.cxx | 0
src/plastimatch/segment/mabs_stats.h | 0
src/plastimatch/standalone/CMakeLists.txt | 6 -
src/plastimatch/standalone/YKThreadRegi.cpp | 4 -
src/plastimatch/standalone/bspline_main.cxx | 49 +-
src/plastimatch/standalone/bspline_opts.cxx | 5 +-
src/plastimatch/standalone/bspline_opts.h | 3 +
src/plastimatch/standalone/check_grad.cxx | 37 +-
src/plastimatch/standalone/dlib_train.cxx | 0
src/plastimatch/standalone/drr_main.cxx | 6 +-
src/plastimatch/standalone/gamma_gui.cpp | 317 ++++++
src/plastimatch/standalone/gamma_gui.h | 3 +
src/plastimatch/standalone/gamma_gui.ui | 23 +
src/plastimatch/standalone/hnd_to_pfm.cxx | 0
src/plastimatch/standalone/opencl_probe.cxx | 0
src/plastimatch/standalone/opencl_probe.h | 0
src/plastimatch/standalone/qt_util.cxx | 2 +-
src/plastimatch/standalone/qt_util.h | 2 +-
src/plastimatch/standalone/shuffle_mha_main.cxx | 0
src/plastimatch/standalone/sobp_main.cxx | 18 +-
src/plastimatch/standalone/vf_invert_main.cxx | 0
src/plastimatch/sys/CMakeLists.txt | 5 +-
src/plastimatch/sys/compiler_warnings.h | 0
src/plastimatch/sys/dlib_threads.cxx | 0
src/plastimatch/sys/dlib_threads.h | 0
src/plastimatch/sys/logfile.cxx | 0
src/plastimatch/sys/plm_endian.cxx | 0
src/plastimatch/sys/plm_macros.h | 0
src/plastimatch/sys/plm_math.h | 29 +-
src/plastimatch/sys/plm_return_code.h | 0
src/plastimatch/sys/plm_sleep.cxx | 0
src/plastimatch/sys/plm_sleep.h | 0
src/plastimatch/sys/plm_timer.cxx | 7 +
src/plastimatch/sys/plm_timer.h | 1 +
src/plastimatch/sys/smart_pointer.h | 0
src/plastimatch/sys/string_util.cxx | 37 +-
src/plastimatch/sys/string_util.h | 6 +-
src/plastimatch/test/api_test.cxx | 0
src/plastimatch/test/cpp_eps_test.cxx | 0
src/plastimatch/test/cpp_limits_test.cxx | 0
src/plastimatch/test/cpp_overflow_test.cxx | 0
src/plastimatch/test/cpp_sizeof_test.cxx | 0
src/plastimatch/test/cpp_template_test.cxx | 17 +-
src/plastimatch/test/cuda/cuda_test.cu | 19 +-
src/plastimatch/test/dcmtk_test.cxx | 0
src/plastimatch/test/dlib_test.cxx | 0
src/plastimatch/test/dlib_thread_test.cxx | 0
src/plastimatch/test/gabor_test.cxx | 0
src/plastimatch/test/itk_test.cxx | 0
src/plastimatch/test/itk_test_directions.cxx | 0
src/plastimatch/test/itk_thread_test.cxx | 0
src/plastimatch/test/libyaml_test.cxx | 0
src/plastimatch/test/plm_restart_test.cxx | 0
src/plastimatch/test/rapidjson_test.cxx | 0
src/plastimatch/test/rtplan_test.cxx | 0
src/plastimatch/test/smartp_test_i.cxx | 0
src/plastimatch/test/smartp_test_ii.cxx | 0
src/plastimatch/test/yamlcpp_test.cxx | 0
src/plastimatch/util/CMakeLists.txt | 5 +-
src/plastimatch/util/dicom_sro_save.cxx | 0
src/plastimatch/util/dicom_sro_save.h | 0
src/plastimatch/util/distance_map.cxx | 26 +-
src/plastimatch/util/distance_map.h | 7 +
src/plastimatch/util/gabor.cxx | 0
src/plastimatch/util/gabor.h | 0
src/plastimatch/util/hausdorff_distance.cxx | 13 +-
src/plastimatch/util/hausdorff_distance.h | 4 +
src/plastimatch/util/image_boundary.cxx | 45 +-
src/plastimatch/util/image_boundary.h | 15 +-
src/plastimatch/util/image_center.cxx | 0
src/plastimatch/util/image_center.h | 0
src/plastimatch/util/itk_adjust.cxx | 73 --
src/plastimatch/util/itk_distance_map.cxx | 0
src/plastimatch/util/itk_threshold.cxx | 0
src/plastimatch/util/itk_threshold.h | 0
src/plastimatch/util/vf_invert.cxx | 0
src/plastimatch/util/vf_invert.h | 0
src/plastimatch/util/volume_adjust.cxx | 40 +
src/plastimatch/util/volume_adjust.h | 15 +
430 files changed, 7497 insertions(+), 4949 deletions(-)
mode change 100755 => 100644 INSTALL.TXT
mode change 100755 => 100644 LICENSE.TXT
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copy Testing/Data/{plm-reg-stiffness-a.txt => plm-bsp-dmap-k.txt} (54%)
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rename Testing/Data/{proton-dose-5g.txt => proton-dose-5d.txt} (92%)
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copy Testing/Data/{proton-dose-5a.txt => proton-dose-7a.txt} (67%)
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mode change 100755 => 100644 src/plastimatch/COPYRIGHT.TXT
mode change 100755 => 100644 src/plastimatch/Doxyfile.in
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mode change 100755 => 100644 src/plastimatch/base/dcmtk_config.h
mode change 100755 => 100644 src/plastimatch/base/dcmtk_file.cxx
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mode change 100755 => 100644 src/plastimatch/base/dcmtk_metadata.h
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mode change 100755 => 100644 src/plastimatch/base/dcmtk_rt_study.cxx
mode change 100755 => 100644 src/plastimatch/base/dcmtk_rt_study.h
mode change 100755 => 100644 src/plastimatch/base/dcmtk_rtdose.cxx
mode change 100755 => 100644 src/plastimatch/base/dcmtk_rtplan.cxx
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mode change 100755 => 100644 src/plastimatch/base/direction_matrices.cxx
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mode change 100755 => 100644 src/plastimatch/base/gdcm1_dose.cxx
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mode change 100755 => 100644 src/plastimatch/base/gdcm1_series_helper_2.cxx
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mode change 100755 => 100644 src/plastimatch/base/gdcm2_util.h
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mode change 100644 => 100755 src/plastimatch/base/interpolate.h
mode change 100755 => 100644 src/plastimatch/base/itkClampCastImageFilter.h
mode change 100755 => 100644 src/plastimatch/base/itkClampCastImageFilter.txx
create mode 100644 src/plastimatch/base/itk_bbox.cxx
copy src/plastimatch/base/{dcmtk_rtdose.h => itk_bbox.h} (64%)
mode change 100755 => 100644 src/plastimatch/base/itk_dicom_load.cxx
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mode change 100755 => 100644 src/plastimatch/base/itk_directions.cxx
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mode change 100755 => 100644 src/plastimatch/base/itk_image_load_char.cxx
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mode change 100755 => 100644 src/plastimatch/base/itk_image_type.h
mode change 100755 => 100644 src/plastimatch/base/itk_metadata.cxx
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mode change 100644 => 100755 src/plastimatch/base/rpl_volume.cxx
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create mode 100755 src/plastimatch/base/rpl_volume_lut.h
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mode change 100755 => 100644 src/plastimatch/base/xio_structures.cxx
mode change 100755 => 100644 src/plastimatch/cli/pcmd_add.h
mode change 100755 => 100644 src/plastimatch/cli/pcmd_adjust.cxx
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_autolabel.cxx
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_autolabel_train.cxx
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create mode 100644 src/plastimatch/cli/pcmd_bbox.cxx
copy src/plastimatch/cli/{pcmd_drr.h => pcmd_bbox.h} (73%)
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_benchmark.h
mode change 100755 => 100644 src/plastimatch/cli/pcmd_boundary.cxx
mode change 100755 => 100644 src/plastimatch/cli/pcmd_boundary.h
mode change 100755 => 100644 src/plastimatch/cli/pcmd_compare.cxx
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_compose.cxx
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_crop.cxx
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_dmap.cxx
mode change 100755 => 100644 src/plastimatch/cli/pcmd_dmap.h
create mode 100644 src/plastimatch/cli/pcmd_dose.cxx
copy src/plastimatch/cli/{pcmd_add.h => pcmd_dose.h} (74%)
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_filter.cxx
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_gamma.cxx
mode change 100755 => 100644 src/plastimatch/cli/pcmd_gamma.h
mode change 100755 => 100644 src/plastimatch/cli/pcmd_header.cxx
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_mabs.cxx
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_mask.cxx
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_probe.h
mode change 100755 => 100644 src/plastimatch/cli/pcmd_scale.h
mode change 100755 => 100644 src/plastimatch/cli/pcmd_segment.cxx
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mode change 100755 => 100644 src/plastimatch/cli/pcmd_sift.h
mode change 100755 => 100644 src/plastimatch/cli/pcmd_stats.cxx
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copy src/plastimatch/cli/{pcmd_benchmark.h => pcmd_vf_invert.h} (71%)
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mode change 100755 => 100644 src/plastimatch/clp/CMakeLists.txt
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mode change 100644 => 100755 src/plastimatch/dose/CMakeLists.txt
mode change 100644 => 100755 src/plastimatch/dose/dose_volume_functions.cxx
mode change 100644 => 100755 src/plastimatch/dose/dose_volume_functions.h
mode change 100644 => 100755 src/plastimatch/dose/rt_beam.cxx
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copy src/plastimatch/dose/{bragg_curve.h => rt_beam_model.cxx} (55%)
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create mode 100755 src/plastimatch/dose/rt_beam_model.h
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mode change 100755 => 100644 src/plastimatch/register/bspline_gm.h
mode change 100755 => 100644 src/plastimatch/register/bspline_mi.h
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copy src/plastimatch/register/{bspline_gm.h => groupwise_parms.h} (62%)
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create mode 100644 src/plastimatch/register/histogram.cxx
create mode 100644 src/plastimatch/register/histogram.h
rename src/plastimatch/register/{bspline_mi_hist.cxx => joint_histogram.cxx} (67%)
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create mode 100644 src/plastimatch/register/joint_histogram.h
create mode 100644 src/plastimatch/register/metric_parms.cxx
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copy src/plastimatch/register/{bspline_optimize_steepest.h => metric_state.cxx} (51%)
create mode 100644 src/plastimatch/register/metric_state.h
delete mode 100755 src/plastimatch/register/registration_metric_type.h
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create mode 100644 src/plastimatch/register/registration_similarity_data.h
create mode 100644 src/plastimatch/register/registration_util.cxx
copy src/plastimatch/register/{itk_demons.h => registration_util.h} (55%)
mode change 100755 => 100644 src/plastimatch/register/shared_parms.cxx
mode change 100755 => 100644 src/plastimatch/register/shared_parms.h
rename src/plastimatch/register/{registration_metric_type.cxx => similarity_metric_type.cxx} (59%)
create mode 100644 src/plastimatch/register/similarity_metric_type.h
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mode change 100755 => 100644 src/plastimatch/standalone/dlib_train.cxx
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mode change 100755 => 100644 src/plastimatch/standalone/hnd_to_pfm.cxx
mode change 100755 => 100644 src/plastimatch/standalone/opencl_probe.cxx
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mode change 100755 => 100644 src/plastimatch/sys/compiler_warnings.h
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mode change 100755 => 100644 src/plastimatch/sys/logfile.cxx
mode change 100755 => 100644 src/plastimatch/sys/plm_endian.cxx
mode change 100755 => 100644 src/plastimatch/sys/plm_macros.h
mode change 100644 => 100755 src/plastimatch/sys/plm_math.h
mode change 100755 => 100644 src/plastimatch/sys/plm_return_code.h
mode change 100755 => 100644 src/plastimatch/sys/plm_sleep.cxx
mode change 100755 => 100644 src/plastimatch/sys/plm_sleep.h
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mode change 100755 => 100644 src/plastimatch/test/dcmtk_test.cxx
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mode change 100755 => 100644 src/plastimatch/test/dlib_thread_test.cxx
mode change 100755 => 100644 src/plastimatch/test/gabor_test.cxx
mode change 100755 => 100644 src/plastimatch/test/itk_test.cxx
mode change 100755 => 100644 src/plastimatch/test/itk_test_directions.cxx
mode change 100755 => 100644 src/plastimatch/test/itk_thread_test.cxx
mode change 100755 => 100644 src/plastimatch/test/libyaml_test.cxx
mode change 100755 => 100644 src/plastimatch/test/plm_restart_test.cxx
mode change 100755 => 100644 src/plastimatch/test/rapidjson_test.cxx
mode change 100755 => 100644 src/plastimatch/test/rtplan_test.cxx
mode change 100755 => 100644 src/plastimatch/test/smartp_test_i.cxx
mode change 100755 => 100644 src/plastimatch/test/smartp_test_ii.cxx
mode change 100755 => 100644 src/plastimatch/test/yamlcpp_test.cxx
mode change 100755 => 100644 src/plastimatch/util/dicom_sro_save.cxx
mode change 100755 => 100644 src/plastimatch/util/dicom_sro_save.h
mode change 100755 => 100644 src/plastimatch/util/distance_map.cxx
mode change 100755 => 100644 src/plastimatch/util/distance_map.h
mode change 100755 => 100644 src/plastimatch/util/gabor.cxx
mode change 100755 => 100644 src/plastimatch/util/gabor.h
mode change 100755 => 100644 src/plastimatch/util/image_boundary.cxx
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mode change 100755 => 100644 src/plastimatch/util/image_center.cxx
mode change 100755 => 100644 src/plastimatch/util/image_center.h
mode change 100755 => 100644 src/plastimatch/util/itk_adjust.cxx
mode change 100755 => 100644 src/plastimatch/util/itk_distance_map.cxx
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mode change 100755 => 100644 src/plastimatch/util/itk_threshold.h
mode change 100755 => 100644 src/plastimatch/util/vf_invert.cxx
mode change 100755 => 100644 src/plastimatch/util/vf_invert.h
create mode 100644 src/plastimatch/util/volume_adjust.cxx
create mode 100644 src/plastimatch/util/volume_adjust.h
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