├── .clang-format ├── .compile_replit ├── .github ├── copilot-instructions.md └── workflows │ ├── main.yml │ └── pull_requests.yml ├── .gitignore ├── .gitlab-ci.yml ├── .gitlab └── .gitlab-webide.yml ├── .lgtm.yml ├── .replit ├── .setup_replit ├── CMakeLists.txt ├── LICENSE.txt ├── PKGBUILD ├── README.md ├── artifacts ├── dcma_guides │ └── tutorials │ │ └── introduction.txt ├── dcma_scripts │ ├── QA │ │ ├── de-EQD2.dscr │ │ └── point-dose_EQD2.dscr │ ├── debugging │ │ ├── script_comments.dscr │ │ ├── script_functions.dscr │ │ ├── script_functions_disallowed_names.dscr │ │ ├── script_quotes.dscr │ │ ├── script_variables.dscr │ │ └── script_variables_disallowed_names.dscr │ ├── examples │ │ ├── CleanContours.dscr │ │ ├── GenerateMeshes.dscr │ │ ├── ModelIVIM.dscr │ │ ├── ROIImageHistogramStatistics.dscr │ │ ├── TransferContours.dscr │ │ ├── TransferContours2.dscr │ │ └── ValidateRTPlan.dscr │ ├── images │ │ ├── DICOM_image_partition.dscr │ │ ├── assign_time_in_seconds.dscr │ │ ├── isolate_most_numerous_array.dscr │ │ ├── make_new_image_array.dscr │ │ ├── reorder_images_via_instance_number.dscr │ │ └── reorder_images_via_position.dscr │ ├── plumbing │ │ ├── copy_existing_contours.dscr │ │ ├── dilate_erode_margin.dscr │ │ ├── export_contours_DICOM_RTSTRUCT.dscr │ │ ├── export_images_DICOM_CT.dscr │ │ ├── export_images_DICOM_MR.dscr │ │ ├── export_images_DICOM_RTDOSE.dscr │ │ ├── export_original_images.dscr │ │ ├── extract_contours_from_mask.dscr │ │ └── iterate_polyominoes.dscr │ ├── tables │ │ └── make_new_table.dscr │ ├── tutorials │ │ ├── tutorial_1_scripting_basics.dscr │ │ └── tutorial_2_Boolean_operations.dscr │ └── usage │ │ ├── ConvertParametersToTable.dscr │ │ ├── Isolate.dscr │ │ ├── MapTableToParameters.dscr │ │ └── Polyominoes.dscr ├── logos │ ├── DCMA.ico │ ├── DCMA2.ico │ ├── DCMA3.ico │ ├── DCMA4.ico │ ├── DCMA_cycle_opti.svg │ ├── DCMA_cycle_opti.txt │ └── DCMA_logo_4_variations.svg ├── reports │ ├── 20180318_include-what-you-use │ │ ├── iwyu_how-to.txt │ │ └── iwyu_report.txt │ ├── 20200131_Fuzz_Testing │ │ └── Explicator.txt │ ├── 20200207_Fuzz_Testing │ │ └── DICOMautomaton_Dispatcher.txt │ ├── 20200707_include-what-you-use │ │ ├── implement_iwyu_suggestions.sh │ │ ├── iwyu_how-to.txt │ │ └── iwyu_report.txt │ ├── 20200708_clang_check │ │ └── how_to_run_clang-tidy.txt │ └── 20200716_mxe_compilation_attempt │ │ ├── explicator_mxe_errors.txt │ │ └── ygor_mxe_errors.txt └── test_files │ ├── 1x1x1_random_negative.3ddose │ ├── 1x1x1_random_positive.3ddose │ ├── 20200212_Aria_v13.6.5.10_registered_explicit.txz │ ├── 20200212_Aria_v13.6.5.10_registered_implicit.txz │ ├── 2x2x2_random_negative.3ddose │ ├── 2x2x2_random_positive.3ddose │ ├── 320_face_sphere.obj │ ├── 3x3x3_random_negative.3ddose │ ├── 3x3x3_random_positive.3ddose │ ├── 500_vert_heart.stl.xz │ ├── 500_vert_heart_binary.stl │ ├── 5_nested_spheres.obj │ ├── 80_face_sphere.obj │ ├── M6x20_screw_nonmanifold_binary.ply.tgz │ ├── MR_continents.dcm │ ├── MR_distorted_grid.dcm │ ├── MR_distributed_squares.dcm │ ├── MR_fuzzy_noise.dcm │ ├── MR_kaleidoscope.dcm │ ├── MR_mosaic.dcm │ ├── MR_overlapping_circles.dcm │ ├── MR_rectangular_anisovoxelvol_DCMA_logo.tgz │ ├── MR_rectilinear_grid.dcm │ ├── MR_sobel_edges.dcm │ ├── MR_sobel_edges_x2.dcm │ ├── MR_tileable_continents.dcm │ ├── cube_with_flat_faces.ply │ ├── dodecahedron.obj │ ├── flat_faces.ply │ ├── icosahedron.obj │ ├── icosahedron.stl │ ├── icosahedron_binary.stl │ ├── line_sample_cumulative_dvh_absolute_volume.dat │ ├── line_sample_cumulative_dvh_relative_volume.dat │ ├── mesh_cube_with_normals.ply │ ├── mesh_cube_with_normals_binary.ply │ ├── meshing_phantom_dalek.obj.tgz │ ├── opposing_short_cylinders_with_outlier.xyz │ ├── pcloud_cube_with_normals.ply │ ├── pcloud_cube_with_normals_binary.ply │ ├── perturbed_cylinder.obj.xz │ ├── short_cylinder_with_outlier.xyz │ ├── square.obj │ ├── table.csv │ ├── table.tsv │ ├── tabular_dvh_plan_uncertainty.tgz │ ├── tabular_dvh_purely_absolute.tgz │ ├── tabular_dvh_purely_relative.tgz │ ├── torus.obj.tgz │ ├── twisted_rhombus.obj │ ├── twisted_rhombus.xyz │ └── unwrapped_cylinder_phantom_dose.snc.tgz ├── check_syntax.sh ├── compile_and_install.sh ├── compile_on.sh ├── config-files ├── CMakeLists.txt ├── webserver.conf └── webserver_styles │ └── Forms.css ├── development_log.md ├── docker ├── build_all_containers.sh ├── build_bases │ ├── alpine │ │ ├── Dockerfile_aarch64 │ │ ├── Dockerfile_armv7 │ │ ├── Dockerfile_x86_64 │ │ ├── build_aarch64.sh │ │ ├── build_armv7.sh │ │ ├── build_install_customized_system_dependencies.sh │ │ ├── build_install_dcma.sh │ │ ├── build_install_other_dependencies.sh │ │ ├── build_x86_64.sh │ │ ├── implementation_alpine.sh │ │ ├── run_aarch64.sh │ │ ├── run_armv7.sh │ │ ├── run_x86_64.sh │ │ ├── set_environment.sh │ │ └── setup_host.sh │ ├── arch │ │ ├── Dockerfile │ │ ├── build.sh │ │ ├── implementation_arch.sh │ │ └── xpra-xorg.conf │ ├── debian_bookworm │ │ ├── Dockerfile │ │ ├── build.sh │ │ ├── create_foreign_chroot.sh │ │ ├── implementation_debian_bookworm.sh │ │ ├── libwt-dev.phony │ │ ├── libwt-dev_10.0_all.deb │ │ ├── libwthttp-dev.phony │ │ ├── libwthttp-dev_10.0_all.deb │ │ ├── make_phony_Debian_packages.sh │ │ └── xpra-xorg.conf │ ├── debian_bullseye │ │ ├── Dockerfile │ │ ├── build.sh │ │ ├── create_foreign_chroot.sh │ │ ├── implementation_debian_bullseye.sh │ │ ├── libwt-dev.phony │ │ ├── libwt-dev_10.0_all.deb │ │ ├── libwthttp-dev.phony │ │ ├── libwthttp-dev_10.0_all.deb │ │ ├── make_phony_Debian_packages.sh │ │ └── xpra-xorg.conf │ ├── debian_buster │ │ ├── Dockerfile │ │ ├── build.sh │ │ ├── create_foreign_chroot.sh │ │ ├── implementation_debian_buster.sh │ │ ├── libwt-dev.phony │ │ ├── libwt-dev_10.0_all.deb │ │ ├── libwthttp-dev.phony │ │ ├── libwthttp-dev_10.0_all.deb │ │ ├── make_phony_Debian_packages.sh │ │ └── xpra-xorg.conf │ ├── debian_stretch │ │ ├── Dockerfile │ │ ├── build.sh │ │ ├── implementation_debian_stretch.sh │ │ ├── libwt-dev.phony │ │ ├── libwt-dev_10.0_all.deb │ │ ├── libwthttp-dev.phony │ │ ├── libwthttp-dev_10.0_all.deb │ │ ├── make_phony_Debian_packages.sh │ │ └── xpra-xorg.conf │ ├── macos │ │ └── implementation_macos.sh │ ├── mxe │ │ ├── Dockerfile │ │ ├── build.sh │ │ └── implementation_mxe.sh │ ├── ubuntu │ │ ├── Dockerfile │ │ ├── build.sh │ │ └── implementation_ubuntu.sh │ └── void │ │ ├── Dockerfile │ │ ├── build.sh │ │ ├── implementation_void.sh │ │ └── xpra-xorg.conf ├── builders │ ├── alpine │ │ ├── Dockerfile_aarch64 │ │ ├── Dockerfile_armv7 │ │ ├── Dockerfile_x86_64 │ │ ├── build_aarch64.sh │ │ ├── build_armv7.sh │ │ ├── build_x86_64.sh │ │ └── implementation_alpine.sh │ ├── arch │ │ ├── Dockerfile │ │ ├── Run_WebServer.sh │ │ ├── build.sh │ │ └── implementation_arch.sh │ ├── ci │ │ ├── Dockerfile │ │ ├── build.sh │ │ ├── implementation_ci_arch.sh │ │ ├── implementation_ci_debian_buster.sh │ │ ├── libwt-dev.phony │ │ ├── libwt-dev_10.0_all.deb │ │ ├── libwthttp-dev.phony │ │ ├── libwthttp-dev_10.0_all.deb │ │ ├── make_phony_Debian_packages.sh │ │ └── xpra-xorg.conf │ ├── debian_bookworm │ │ ├── Dockerfile │ │ ├── build.sh │ │ └── implementation_debian_bookworm.sh │ ├── debian_bullseye │ │ ├── Dockerfile │ │ ├── build.sh │ │ └── implementation_debian_bullseye.sh │ ├── debian_buster │ │ ├── Dockerfile │ │ ├── build.sh │ │ └── implementation_debian_buster.sh │ ├── macos │ │ └── implementation_macos.sh │ ├── mxe │ │ ├── Dockerfile │ │ ├── build.sh │ │ └── implementation_mxe.sh │ └── void │ │ ├── Dockerfile │ │ ├── Run_WebServer.sh │ │ ├── build.sh │ │ └── implementation_void.sh ├── devel │ └── arch_sycl │ │ ├── Dockerfile │ │ ├── build.sh │ │ ├── implementation_arch_sycl.sh │ │ ├── test_program │ │ ├── compile.sh │ │ └── test.cpp │ │ └── xpra-xorg.conf ├── fuzz_testing │ ├── Dockerfile │ ├── build.sh │ ├── libwt-dev.phony │ ├── libwt-dev_10.0_all.deb │ ├── libwthttp-dev.phony │ ├── libwthttp-dev_10.0_all.deb │ ├── make_phony_Debian_packages.sh │ └── xpra-xorg.conf └── scripts │ ├── arch │ ├── Compile_to_Webassembly.sh │ ├── Run_Container.sh │ └── Run_Container_Interactively.sh │ ├── ci │ ├── Extract_AppImage.sh │ └── Run_Container.sh │ ├── debian_buster │ ├── Download_Sources.sh │ ├── Extract_AppImage.sh │ ├── Run_Container.sh │ ├── Run_Container_Interactively.sh │ └── Run_Container_Interactively_X_Passthrough.sh │ ├── fuzz_testing │ └── Run_Container_Interactively.sh │ ├── mxe │ ├── Extract_Executables.sh │ └── Run_Container_Interactively.sh │ └── void │ ├── Run_Container.sh │ └── Run_Container_Interactively.sh ├── documentation ├── compile_documentation.sh ├── compiling_on_termux.md ├── fuzz_testing.md ├── reference_guide.md ├── thin_plate_splines.pdf ├── view_manpage.sh └── wip_zeromq_network_protocol.md ├── fonts ├── README.txt ├── dcma_minimal.otf ├── dcma_minimal.sfd └── dcma_minimal.ttf ├── functionality_tests ├── IVIM_csv_test.ipynb ├── ivim_signal_full.csv ├── ivim_signal_gaussian_SNR10.csv ├── ivim_signal_gaussian_SNR20.csv ├── ivim_signal_gaussian_SNR40.csv ├── ivim_signal_high.csv ├── ivim_signal_low.csv ├── ivim_signal_minimal.csv ├── ivim_signal_noise_uniform.csv └── ivim_signal_whitepaper.csv ├── img_registration ├── CMakeLists.txt ├── GUIDE.md ├── compile_and_install.sh └── src │ ├── Alignment_ABC.cc │ ├── Alignment_ABC.h │ ├── CMakeLists.txt │ └── Run_Def_Reg.cc ├── integration_tests ├── Run.sh └── tests │ ├── BEDConvert.sh │ ├── CellularAutomata.sh │ ├── ContourViaThreshold.sh │ ├── DICOMExportImagesAsDose.sh │ ├── DeleteContours.sh │ ├── Example_MachineScrew.sh │ ├── ExportSurfaceMeshesOBJ.sh │ ├── ExportSurfaceMeshesOFF.sh │ ├── ExportSurfaceMeshesPLY.sh │ ├── ExportSurfaceMeshesSTL.sh │ ├── ForEachDistinct.sh │ ├── Fuzzy_Operations.sh │ ├── GroupImages.sh │ ├── HighlightROIs.sh │ ├── Load_DAT_files.sh │ ├── Load_OBJ_Files.sh │ ├── Load_PLY_Files.sh │ ├── Load_STL_Files.sh │ ├── Load_TAR_Files.sh │ ├── Load_XYZ_Files.sh │ ├── MeldDose.sh │ ├── NoOp.sh │ ├── PurgeContours.sh │ ├── ReduceNeighbourhood.sh │ ├── Repeat.sh │ ├── RigidWarpImages.sh │ ├── dicomautomaton_dispatcher_help.sh │ └── dicomautomaton_dispatcher_usage.sh ├── linux └── Run.sh ├── nix ├── NOTES ├── compile_natively.sh ├── compile_with_docker.sh ├── config.nix ├── dicomautomaton_derivation.nix ├── explicator_derivation.nix ├── nixpkgs.nix ├── overlays.nix ├── ygor_derivation.nix └── ygorclustering_derivation.nix ├── pc_registration ├── CMakeLists.txt ├── GUIDE.md ├── README.md ├── compile_and_install.sh ├── src │ ├── CMakeLists.txt │ ├── CPD_Affine.cc │ ├── CPD_Affine.h │ ├── CPD_Nonrigid.cc │ ├── CPD_Nonrigid.h │ ├── CPD_Rigid.cc │ ├── CPD_Rigid.h │ ├── CPD_Shared.cc │ ├── CPD_Shared.h │ ├── IFGT.cc │ ├── IFGT.h │ └── Run_Def_Reg.cc └── unit_tests │ ├── CPD_Tests.cc │ ├── Main.cc │ └── compile_and_run.sh ├── py ├── .gitignore ├── README.md ├── dicomautomaton │ └── __init__.py └── pyproject.toml ├── scripts ├── CMakeLists.txt ├── bash_completion.sh ├── check_markdown_document_url_reachability.sh ├── check_url_reachability.sh ├── compute_sloccount.sh ├── convert_colour_map.sh ├── cross_compile_minimal_musl_static.sh ├── dump_portable_dcma_bundle.sh ├── edit_operations_with_tags.sh ├── enable_swapfile.sh ├── extract_dcma_version.sh ├── extract_system_appimage.sh ├── gather_macos_dylibs.sh ├── generate_standard_guides.sh ├── generate_standard_scripts.sh ├── install_AppImage_runtime_dependencies.sh ├── list_operation_tags.sh ├── perform_static_checks.sh ├── purge_irrelevant_headers.sh ├── select_files.ps1 ├── validate_scripts.sh └── verbatim_replace.cc ├── src ├── 3ddose_File_Loader.cc ├── 3ddose_File_Loader.h ├── Alignment_Field.cc ├── Alignment_Field.h ├── Alignment_Rigid.cc ├── Alignment_Rigid.h ├── Alignment_TPSRPM.cc ├── Alignment_TPSRPM.h ├── BED_Conversion.cc ├── BED_Conversion.h ├── Boost_Serialization_Archive_Converter.cc ├── Boost_Serialization_File_Loader.cc ├── Boost_Serialization_File_Loader.h ├── CMakeLists.txt ├── CSG_SDF.cc ├── CSG_SDF.h ├── CSV_File_Loader.cc ├── CSV_File_Loader.h ├── Colour_Maps.cc ├── Colour_Maps.h ├── Common_Boost_Serialization.cc ├── Common_Boost_Serialization.h ├── Common_Image_File_Loader.cc ├── Common_Image_File_Loader.h ├── Common_Plotting.cc ├── Common_Plotting.h ├── Contour_Boolean_Operations.cc ├── Contour_Boolean_Operations.h ├── Contour_Collection_Estimates.cc ├── Contour_Collection_Estimates.h ├── Contour_Collection_File_Loader.cc ├── Contour_Collection_File_Loader.h ├── DCMA_DICOM.cc ├── DCMA_DICOM.h ├── DCMA_Definitions.h.in ├── DCMA_Version.cc ├── DCMA_Version.h ├── DICOM_File_Loader.cc ├── DICOM_File_Loader.h ├── DICOMautomaton_Dispatcher.cc ├── DICOMautomaton_Dump.cc ├── DICOMautomaton_WebServer.cc ├── DVH_File_Loader.cc ├── DVH_File_Loader.h ├── Dialogs.cc ├── Dialogs.h ├── Dialogs │ ├── Selectors.cc │ ├── Selectors.h │ ├── Text_Query.cc │ ├── Text_Query.h │ ├── Tray_Notification.cc │ └── Tray_Notification.h ├── Documentation.cc ├── Documentation.h ├── Dose_Meld.cc ├── Dose_Meld.h ├── FITS_File_Loader.cc ├── FITS_File_Loader.h ├── File_Loader.cc ├── File_Loader.h ├── Font_DCMA_Minimal.cc ├── Font_DCMA_Minimal.h ├── GIS.cc ├── GIS.h ├── Imebra_Shim.cc ├── Imebra_Shim.h ├── Insert_Contours.cc ├── Insert_Contours.h ├── KineticModel_1Compartment2Input_5Param_Chebyshev_Common.cc ├── KineticModel_1Compartment2Input_5Param_Chebyshev_Common.h ├── KineticModel_1Compartment2Input_5Param_Chebyshev_FreeformOptimization.cc ├── KineticModel_1Compartment2Input_5Param_Chebyshev_FreeformOptimization.h ├── KineticModel_1Compartment2Input_5Param_Chebyshev_LevenbergMarquardt.cc ├── KineticModel_1Compartment2Input_5Param_Chebyshev_LevenbergMarquardt.h ├── KineticModel_1Compartment2Input_5Param_LinearInterp_Common.cc ├── KineticModel_1Compartment2Input_5Param_LinearInterp_Common.h ├── KineticModel_1Compartment2Input_5Param_LinearInterp_LevenbergMarquardt.cc ├── KineticModel_1Compartment2Input_5Param_LinearInterp_LevenbergMarquardt.h ├── KineticModel_1Compartment2Input_Reduced3Param_Chebyshev_Common.cc ├── KineticModel_1Compartment2Input_Reduced3Param_Chebyshev_Common.h ├── KineticModel_1Compartment2Input_Reduced3Param_Chebyshev_FreeformOptimization.cc ├── KineticModel_1Compartment2Input_Reduced3Param_Chebyshev_FreeformOptimization.h ├── KineticModel_1Compartment2Input_Reduced3Param_Chebyshev_FreeformOptimization_NLOpt.cc ├── KineticModel_1Compartment2Input_Reduced3Param_Chebyshev_FreeformOptimization_NLOpt.h ├── Lexicon_Loader.cc ├── Lexicon_Loader.h ├── Line_Sample_File_Loader.cc ├── Line_Sample_File_Loader.h ├── Metadata.cc ├── Metadata.h ├── OBJ_File_Loader.cc ├── OBJ_File_Loader.h ├── OFF_File_Loader.cc ├── OFF_File_Loader.h ├── Operation_Dispatcher.cc ├── Operation_Dispatcher.h ├── Operations │ ├── AccumulateRowsColumns.cc │ ├── AccumulateRowsColumns.h │ ├── AnalyzeHistograms.cc │ ├── AnalyzeHistograms.h │ ├── AnalyzeLightRadFieldCoincidence.cc │ ├── AnalyzeLightRadFieldCoincidence.h │ ├── AnalyzePicketFence.cc │ ├── AnalyzePicketFence.h │ ├── AnalyzeRTPlan.cc │ ├── AnalyzeRTPlan.h │ ├── And.cc │ ├── And.h │ ├── AnyOf.cc │ ├── AnyOf.h │ ├── ApplyCalibrationCurve.cc │ ├── ApplyCalibrationCurve.h │ ├── AutoCropImages.cc │ ├── AutoCropImages.h │ ├── Average.cc │ ├── Average.h │ ├── BCCAExtractRadiomicFeatures.cc │ ├── BCCAExtractRadiomicFeatures.h │ ├── BEDConvert.cc │ ├── BEDConvert.h │ ├── BoostSerializeDrover.cc │ ├── BoostSerializeDrover.h │ ├── BuildLexiconInteractively.cc │ ├── BuildLexiconInteractively.h │ ├── CMakeLists.txt │ ├── CT_Liver_Perfusion.cc │ ├── CT_Liver_Perfusion.h │ ├── CT_Liver_Perfusion_First_Run.cc │ ├── CT_Liver_Perfusion_First_Run.h │ ├── CT_Liver_Perfusion_Ortho_Views.cc │ ├── CT_Liver_Perfusion_Ortho_Views.h │ ├── CT_Liver_Perfusion_Pharmaco_1Compartment2Input_5Param.cc │ ├── CT_Liver_Perfusion_Pharmaco_1Compartment2Input_5Param.h │ ├── CT_Liver_Perfusion_Pharmaco_1Compartment2Input_Reduced3Param.cc │ ├── CT_Liver_Perfusion_Pharmaco_1Compartment2Input_Reduced3Param.h │ ├── CellularAutomata.cc │ ├── CellularAutomata.h │ ├── ClusterDBSCAN.cc │ ├── ClusterDBSCAN.h │ ├── CombineImages.cc │ ├── CombineImages.h │ ├── CombineMeshes.cc │ ├── CombineMeshes.h │ ├── ComparePixels.cc │ ├── ComparePixels.h │ ├── CompileScript.cc │ ├── CompileScript.h │ ├── ContourBasedRayCastDoseAccumulate.cc │ ├── ContourBasedRayCastDoseAccumulate.h │ ├── ContourBooleanOperations.cc │ ├── ContourBooleanOperations.h │ ├── ContourSimilarity.cc │ ├── ContourSimilarity.h │ ├── ContourViaGeometry.cc │ ├── ContourViaGeometry.h │ ├── ContourViaThreshold.cc │ ├── ContourViaThreshold.h │ ├── ContourVote.cc │ ├── ContourVote.h │ ├── ContourWholeImages.cc │ ├── ContourWholeImages.h │ ├── ContouringAides.cc │ ├── ContouringAides.h │ ├── ConvertContoursToMeshes.cc │ ├── ConvertContoursToMeshes.h │ ├── ConvertContoursToPoints.cc │ ├── ConvertContoursToPoints.h │ ├── ConvertDoseToImage.cc │ ├── ConvertDoseToImage.h │ ├── ConvertImageToDose.cc │ ├── ConvertImageToDose.h │ ├── ConvertImageToMeshes.cc │ ├── ConvertImageToMeshes.h │ ├── ConvertImageToWarp.cc │ ├── ConvertImageToWarp.h │ ├── ConvertMeshesToContours.cc │ ├── ConvertMeshesToContours.h │ ├── ConvertMeshesToPoints.cc │ ├── ConvertMeshesToPoints.h │ ├── ConvertNaNsToAir.cc │ ├── ConvertNaNsToAir.h │ ├── ConvertNaNsToZeros.cc │ ├── ConvertNaNsToZeros.h │ ├── ConvertParametersToTable.cc │ ├── ConvertParametersToTable.h │ ├── ConvertPixelsToPoints.cc │ ├── ConvertPixelsToPoints.h │ ├── ConvertWarpToImage.cc │ ├── ConvertWarpToImage.h │ ├── ConvertWarpToMeshes.cc │ ├── ConvertWarpToMeshes.h │ ├── ConvolveImages.cc │ ├── ConvolveImages.h │ ├── CopyContours.cc │ ├── CopyContours.h │ ├── CopyImages.cc │ ├── CopyImages.h │ ├── CopyLineSamples.cc │ ├── CopyLineSamples.h │ ├── CopyMeshes.cc │ ├── CopyMeshes.h │ ├── CopyPoints.cc │ ├── CopyPoints.h │ ├── CopyTables.cc │ ├── CopyTables.h │ ├── CountObjects.cc │ ├── CountObjects.h │ ├── CountVoxels.cc │ ├── CountVoxels.h │ ├── CropImageDoseToROIs.cc │ ├── CropImageDoseToROIs.h │ ├── CropImages.cc │ ├── CropImages.h │ ├── CropROIDose.cc │ ├── CropROIDose.h │ ├── DCEMRI_IAUC.cc │ ├── DCEMRI_IAUC.h │ ├── DCEMRI_Nonparametric_CE.cc │ ├── DCEMRI_Nonparametric_CE.h │ ├── DICOMExportContours.cc │ ├── DICOMExportContours.h │ ├── DICOMExportImagesAsCT.cc │ ├── DICOMExportImagesAsCT.h │ ├── DICOMExportImagesAsDose.cc │ ├── DICOMExportImagesAsDose.h │ ├── DICOMExportImagesAsMR.cc │ ├── DICOMExportImagesAsMR.h │ ├── DeDuplicateImages.cc │ ├── DeDuplicateImages.h │ ├── DecayDoseOverTimeHalve.cc │ ├── DecayDoseOverTimeHalve.h │ ├── DecayDoseOverTimeJones2014.cc │ ├── DecayDoseOverTimeJones2014.h │ ├── DecimatePixels.cc │ ├── DecimatePixels.h │ ├── DecomposeImagesSVD.cc │ ├── DecomposeImagesSVD.h │ ├── DeleteContours.cc │ ├── DeleteContours.h │ ├── DeleteImages.cc │ ├── DeleteImages.h │ ├── DeleteLineSamples.cc │ ├── DeleteLineSamples.h │ ├── DeleteMeshes.cc │ ├── DeleteMeshes.h │ ├── DeletePoints.cc │ ├── DeletePoints.h │ ├── DeleteTables.cc │ ├── DeleteTables.h │ ├── DetectGrid3D.cc │ ├── DetectGrid3D.h │ ├── DetectShapes3D.cc │ ├── DetectShapes3D.h │ ├── DrawGeometry.cc │ ├── DrawGeometry.h │ ├── DroverDebug.cc │ ├── DroverDebug.h │ ├── DumpAllOrderedImageMetadataToFile.cc │ ├── DumpAllOrderedImageMetadataToFile.h │ ├── DumpAnEncompassedPoint.cc │ ├── DumpAnEncompassedPoint.h │ ├── DumpFilesPartitionedByTime.cc │ ├── DumpFilesPartitionedByTime.h │ ├── DumpImageMeshes.cc │ ├── DumpImageMeshes.h │ ├── DumpImageMetadataOccurrencesToFile.cc │ ├── DumpImageMetadataOccurrencesToFile.h │ ├── DumpPerROIParams_KineticModel_1Compartment2Input_5Param.cc │ ├── DumpPerROIParams_KineticModel_1Compartment2Input_5Param.h │ ├── DumpPixelValuesOverTimeForAnEncompassedPoint.cc │ ├── DumpPixelValuesOverTimeForAnEncompassedPoint.h │ ├── DumpPlanSummary.cc │ ├── DumpPlanSummary.h │ ├── DumpROIContours.cc │ ├── DumpROIContours.h │ ├── DumpROIData.cc │ ├── DumpROIData.h │ ├── DumpROISNR.cc │ ├── DumpROISNR.h │ ├── DumpROISurfaceMeshes.cc │ ├── DumpROISurfaceMeshes.h │ ├── DumpRTPlanMetadataOccurrencesToFile.cc │ ├── DumpRTPlanMetadataOccurrencesToFile.h │ ├── DumpVoxelDoseInfo.cc │ ├── DumpVoxelDoseInfo.h │ ├── EQDXTable.cc │ ├── EQDXTable.h │ ├── EvaluateDoseVolumeStats.cc │ ├── EvaluateDoseVolumeStats.h │ ├── EvaluateNTCPModels.cc │ ├── EvaluateNTCPModels.h │ ├── EvaluateParameters.cc │ ├── EvaluateParameters.h │ ├── EvaluateTCPModels.cc │ ├── EvaluateTCPModels.h │ ├── ExecuteShell.cc │ ├── ExecuteShell.h │ ├── ExplodeImages.cc │ ├── ExplodeImages.h │ ├── ExportContours.cc │ ├── ExportContours.h │ ├── ExportDrover.cc │ ├── ExportDrover.h │ ├── ExportFITSImages.cc │ ├── ExportFITSImages.h │ ├── ExportLineSamples.cc │ ├── ExportLineSamples.h │ ├── ExportOriginalFiles.cc │ ├── ExportOriginalFiles.h │ ├── ExportPointClouds.cc │ ├── ExportPointClouds.h │ ├── ExportSNCImages.cc │ ├── ExportSNCImages.h │ ├── ExportSurfaceMeshes.cc │ ├── ExportSurfaceMeshes.h │ ├── ExportSurfaceMeshesOBJ.cc │ ├── ExportSurfaceMeshesOBJ.h │ ├── ExportSurfaceMeshesOFF.cc │ ├── ExportSurfaceMeshesOFF.h │ ├── ExportSurfaceMeshesPLY.cc │ ├── ExportSurfaceMeshesPLY.h │ ├── ExportSurfaceMeshesSTL.cc │ ├── ExportSurfaceMeshesSTL.h │ ├── ExportTables.cc │ ├── ExportTables.h │ ├── ExportWarps.cc │ ├── ExportWarps.h │ ├── ExtractAlphaBeta.cc │ ├── ExtractAlphaBeta.h │ ├── ExtractImageHistograms.cc │ ├── ExtractImageHistograms.h │ ├── ExtractPointsWarp.cc │ ├── ExtractPointsWarp.h │ ├── ExtractRadiomicFeatures.cc │ ├── ExtractRadiomicFeatures.h │ ├── FVPicketFence.cc │ ├── FVPicketFence.h │ ├── False.cc │ ├── False.h │ ├── FindFiles.cc │ ├── FindFiles.h │ ├── For.cc │ ├── For.h │ ├── ForEachDistinct.cc │ ├── ForEachDistinct.h │ ├── ForEachRTPlan.cc │ ├── ForEachRTPlan.h │ ├── Fork.cc │ ├── Fork.h │ ├── GenerateCalibrationCurve.cc │ ├── GenerateCalibrationCurve.h │ ├── GenerateMapTiles.cc │ ├── GenerateMapTiles.h │ ├── GenerateMeshes.cc │ ├── GenerateMeshes.h │ ├── GenerateSurfaceMask.cc │ ├── GenerateSurfaceMask.h │ ├── GenerateSyntheticImages.cc │ ├── GenerateSyntheticImages.h │ ├── GenerateTable.cc │ ├── GenerateTable.h │ ├── GenerateVirtualDataContourViaThresholdTestV1.cc │ ├── GenerateVirtualDataContourViaThresholdTestV1.h │ ├── GenerateVirtualDataDoseStairsV1.cc │ ├── GenerateVirtualDataDoseStairsV1.h │ ├── GenerateVirtualDataImageSphereV1.cc │ ├── GenerateVirtualDataImageSphereV1.h │ ├── GenerateVirtualDataPerfusionV1.cc │ ├── GenerateVirtualDataPerfusionV1.h │ ├── GenerateWarp.cc │ ├── GenerateWarp.h │ ├── GiveWholeImageArrayABoneWindowLevel.cc │ ├── GiveWholeImageArrayABoneWindowLevel.h │ ├── GiveWholeImageArrayAHeadAndNeckWindowLevel.cc │ ├── GiveWholeImageArrayAHeadAndNeckWindowLevel.h │ ├── GiveWholeImageArrayAThoraxWindowLevel.cc │ ├── GiveWholeImageArrayAThoraxWindowLevel.h │ ├── GiveWholeImageArrayAnAbdominalWindowLevel.cc │ ├── GiveWholeImageArrayAnAbdominalWindowLevel.h │ ├── GiveWholeImageArrayAnAlphaBetaWindowLevel.cc │ ├── GiveWholeImageArrayAnAlphaBetaWindowLevel.h │ ├── GridBasedRayCastDoseAccumulate.cc │ ├── GridBasedRayCastDoseAccumulate.h │ ├── GroupImages.cc │ ├── GroupImages.h │ ├── GrowContours.cc │ ├── GrowContours.h │ ├── HighlightROIs.cc │ ├── HighlightROIs.h │ ├── IfElse.cc │ ├── IfElse.h │ ├── Ignore.cc │ ├── Ignore.h │ ├── ImageRoutineTests.cc │ ├── ImageRoutineTests.h │ ├── ImportDrover.cc │ ├── ImportDrover.h │ ├── ImprintImages.cc │ ├── ImprintImages.h │ ├── InterpolateSlices.cc │ ├── InterpolateSlices.h │ ├── InvokeStandardScript.cc │ ├── InvokeStandardScript.h │ ├── Isolate.cc │ ├── Isolate.h │ ├── IsolatedVoxelFilter.cc │ ├── IsolatedVoxelFilter.h │ ├── LoadFiles.cc │ ├── LoadFiles.h │ ├── LoadFilesInteractively.cc │ ├── LoadFilesInteractively.h │ ├── LogScale.cc │ ├── LogScale.h │ ├── MakeMeshesManifold.cc │ ├── MakeMeshesManifold.h │ ├── MapTableToParameters.cc │ ├── MapTableToParameters.h │ ├── MaskParameters.cc │ ├── MaskParameters.h │ ├── MaskVerbosity.cc │ ├── MaskVerbosity.h │ ├── MaxMinPixels.cc │ ├── MaxMinPixels.h │ ├── MeldDose.cc │ ├── MeldDose.h │ ├── MinkowskiSum3D.cc │ ├── MinkowskiSum3D.h │ ├── ModelIVIM.cc │ ├── ModelIVIM.h │ ├── ModifyContourMetadata.cc │ ├── ModifyContourMetadata.h │ ├── ModifyImageMetadata.cc │ ├── ModifyImageMetadata.h │ ├── ModifyLineSamples.cc │ ├── ModifyLineSamples.h │ ├── ModifyParameters.cc │ ├── ModifyParameters.h │ ├── NegatePixels.cc │ ├── NegatePixels.h │ ├── NoOp.cc │ ├── NoOp.h │ ├── NoneOf.cc │ ├── NoneOf.h │ ├── NormalizeLineSamples.cc │ ├── NormalizeLineSamples.h │ ├── NormalizePixels.cc │ ├── NormalizePixels.h │ ├── NotifyUser.cc │ ├── NotifyUser.h │ ├── OptimizeStaticBeams.cc │ ├── OptimizeStaticBeams.h │ ├── OrderImages.cc │ ├── OrderImages.h │ ├── PartitionContours.cc │ ├── PartitionContours.h │ ├── PerturbPixels.cc │ ├── PerturbPixels.h │ ├── PlotLineSamples.cc │ ├── PlotLineSamples.h │ ├── PlotPerROITimeCourses.cc │ ├── PlotPerROITimeCourses.h │ ├── PointSeparation.cc │ ├── PointSeparation.h │ ├── PollDirectories.cc │ ├── PollDirectories.h │ ├── Polyominoes.cc │ ├── Polyominoes.h │ ├── PreFilterEnormousCTValues.cc │ ├── PreFilterEnormousCTValues.h │ ├── PresentationImage.cc │ ├── PresentationImage.h │ ├── PrintMetadata.cc │ ├── PrintMetadata.h │ ├── PromoteMetadata.cc │ ├── PromoteMetadata.h │ ├── PruneEmptyImageDoseArrays.cc │ ├── PruneEmptyImageDoseArrays.h │ ├── PurgeContours.cc │ ├── PurgeContours.h │ ├── QuantizePixels.cc │ ├── QuantizePixels.h │ ├── QueryUserInteractively.cc │ ├── QueryUserInteractively.h │ ├── RPCReceive.cc │ ├── RPCReceive.h │ ├── RPCSend.cc │ ├── RPCSend.h │ ├── RankPixels.cc │ ├── RankPixels.h │ ├── ReduceNeighbourhood.cc │ ├── ReduceNeighbourhood.h │ ├── RemeshSurfaceMeshes.cc │ ├── RemeshSurfaceMeshes.h │ ├── Repeat.cc │ ├── Repeat.h │ ├── ReportROIData.cc │ ├── ReportROIData.h │ ├── ResampleImages.cc │ ├── ResampleImages.h │ ├── RigidWarpImages.cc │ ├── RigidWarpImages.h │ ├── SDL_Viewer.cc │ ├── SDL_Viewer.h │ ├── SFML_Viewer.cc │ ├── SFML_Viewer.h │ ├── ScalePixels.cc │ ├── ScalePixels.h │ ├── SeamContours.cc │ ├── SeamContours.h │ ├── SelectDirectory.cc │ ├── SelectDirectory.h │ ├── SelectFilename.cc │ ├── SelectFilename.h │ ├── SelectSlicesIntersectingROI.cc │ ├── SelectSlicesIntersectingROI.h │ ├── SelectionIsPresent.cc │ ├── SelectionIsPresent.h │ ├── SimplifyContours.cc │ ├── SimplifyContours.h │ ├── SimplifySurfaceMeshes.cc │ ├── SimplifySurfaceMeshes.h │ ├── SimulateRadiograph.cc │ ├── SimulateRadiograph.h │ ├── Sleep.cc │ ├── Sleep.h │ ├── SpatialBlur.cc │ ├── SpatialBlur.h │ ├── SpatialDerivative.cc │ ├── SpatialDerivative.h │ ├── SpatialSharpen.cc │ ├── SpatialSharpen.h │ ├── SubdivideSurfaceMeshes.cc │ ├── SubdivideSurfaceMeshes.h │ ├── SubsegmentContours.cc │ ├── SubsegmentContours.h │ ├── Subsegment_ComputeDose_VanLuijk.cc │ ├── Subsegment_ComputeDose_VanLuijk.h │ ├── SubtractImages.cc │ ├── SubtractImages.h │ ├── SupersampleImageGrid.cc │ ├── SupersampleImageGrid.h │ ├── TabulateImageMetadata.cc │ ├── TabulateImageMetadata.h │ ├── Terminal_Viewer.cc │ ├── Terminal_Viewer.h │ ├── ThresholdImages.cc │ ├── ThresholdImages.h │ ├── ThresholdOtsu.cc │ ├── ThresholdOtsu.h │ ├── Time_op.cc │ ├── Time_op.h │ ├── Transaction.cc │ ├── Transaction.h │ ├── TrimROIDose.cc │ ├── TrimROIDose.h │ ├── True.cc │ ├── True.h │ ├── UBC3TMRI_DCE.cc │ ├── UBC3TMRI_DCE.h │ ├── UBC3TMRI_DCE_Differences.cc │ ├── UBC3TMRI_DCE_Differences.h │ ├── UBC3TMRI_DCE_Experimental.cc │ ├── UBC3TMRI_DCE_Experimental.h │ ├── UBC3TMRI_IVIM_ADC.cc │ ├── UBC3TMRI_IVIM_ADC.h │ ├── ValidateRTPlan.cc │ ├── ValidateRTPlan.h │ ├── VolumetricCorrelationDetector.cc │ ├── VolumetricCorrelationDetector.h │ ├── VolumetricSpatialBlur.cc │ ├── VolumetricSpatialBlur.h │ ├── VolumetricSpatialDerivative.cc │ ├── VolumetricSpatialDerivative.h │ ├── VoxelRANSAC.cc │ ├── VoxelRANSAC.h │ ├── WarpContours.cc │ ├── WarpContours.h │ ├── WarpImages.cc │ ├── WarpImages.h │ ├── WarpMeshes.cc │ ├── WarpMeshes.h │ ├── WarpPoints.cc │ ├── WarpPoints.h │ ├── While.cc │ ├── While.h │ ├── WidenTable.cc │ └── WidenTable.h ├── PACS_Duplicate_Cleaner.cc ├── PACS_Ingress.cc ├── PACS_Loader.cc ├── PACS_Loader.h ├── PACS_Refresh.cc ├── PLY_File_Loader.cc ├── PLY_File_Loader.h ├── Partition_Drover.cc ├── Partition_Drover.h ├── Regex_Selectors.cc ├── Regex_Selectors.h ├── Rotating_Cube.cc ├── Rotating_Cube.h ├── SNC_File_Loader.cc ├── SNC_File_Loader.h ├── STB_Shim.cc ├── STB_Shim.h ├── STL_File_Loader.cc ├── STL_File_Loader.h ├── Script_Loader.cc ├── Script_Loader.h ├── Simple_Meshing.cc ├── Simple_Meshing.h ├── Standard_Guides.cc.in ├── Standard_Guides.h ├── Standard_Scripts.cc.in ├── Standard_Scripts.h ├── String_Parsing.cc ├── String_Parsing.h ├── Structs.cc ├── Structs.h ├── StructsIOBoostSerialization.h ├── Surface_Meshes.cc ├── Surface_Meshes.h ├── TAR_File_Loader.cc ├── TAR_File_Loader.h ├── Tables.cc ├── Tables.h ├── Thread_Pool.h ├── Transformation_File_Loader.cc ├── Transformation_File_Loader.h ├── Triple_Three.cc ├── Triple_Three.h ├── WindowsIcon.rc ├── Write_File.cc ├── Write_File.h ├── XIM_File_Loader.cc ├── XIM_File_Loader.h ├── XML_File_Loader.cc ├── XML_File_Loader.h ├── XML_Tools.cc ├── XML_Tools.h ├── XYZ_File_Loader.cc ├── XYZ_File_Loader.h ├── YgorImages_Functors │ ├── Compute │ │ ├── AccumulatePixelDistributions.cc │ │ ├── AccumulatePixelDistributions.h │ │ ├── Compare_Images.cc │ │ ├── Compare_Images.h │ │ ├── Contour_Similarity.cc │ │ ├── Contour_Similarity.h │ │ ├── CropToROIs.cc │ │ ├── CropToROIs.h │ │ ├── Detect_Geometry_Clustered_RANSAC.cc │ │ ├── Detect_Geometry_Clustered_RANSAC.h │ │ ├── Extract_Histograms.cc │ │ ├── Extract_Histograms.h │ │ ├── GenerateSurfaceMask.cc │ │ ├── GenerateSurfaceMask.h │ │ ├── Interpolate_Image_Slices.cc │ │ ├── Interpolate_Image_Slices.h │ │ ├── Joint_Pixel_Sampler.cc │ │ ├── Joint_Pixel_Sampler.h │ │ ├── Per_ROI_Time_Courses.cc │ │ ├── Per_ROI_Time_Courses.h │ │ ├── Rank_Pixels.cc │ │ ├── Rank_Pixels.h │ │ ├── Volumetric_Correlation_Detector.cc │ │ ├── Volumetric_Correlation_Detector.h │ │ ├── Volumetric_Neighbourhood_Sampler.cc │ │ ├── Volumetric_Neighbourhood_Sampler.h │ │ ├── Volumetric_Spatial_Blur.cc │ │ ├── Volumetric_Spatial_Blur.h │ │ ├── Volumetric_Spatial_Derivative.cc │ │ └── Volumetric_Spatial_Derivative.h │ ├── ConvenienceRoutines.cc │ ├── ConvenienceRoutines.h │ ├── Grouping │ │ ├── Misc_Functors.cc │ │ └── Misc_Functors.h │ ├── Processing │ │ ├── Average_Pixel_Value.cc │ │ ├── Average_Pixel_Value.h │ │ ├── BEDConversion.cc │ │ ├── BEDConversion.h │ │ ├── CT_Convert_NaNs_to_Air.cc │ │ ├── CT_Convert_NaNs_to_Air.h │ │ ├── CT_Perf_Pixel_Filter.cc │ │ ├── CT_Perf_Pixel_Filter.h │ │ ├── CT_Perfusion_Clip_Search.cc │ │ ├── CT_Perfusion_Clip_Search.h │ │ ├── CT_Reasonable_HU_Window.cc │ │ ├── CT_Reasonable_HU_Window.h │ │ ├── Centralized_Moments.cc │ │ ├── Centralized_Moments.h │ │ ├── Convert_NaNs_to_Zero.cc │ │ ├── Convert_NaNs_to_Zero.h │ │ ├── DBSCAN_Time_Courses.cc │ │ ├── DBSCAN_Time_Courses.h │ │ ├── DCEMRI_AUC_Map.cc │ │ ├── DCEMRI_AUC_Map.h │ │ ├── DCEMRI_S0_Map.cc │ │ ├── DCEMRI_S0_Map.h │ │ ├── DCEMRI_T1_Map.cc │ │ ├── DCEMRI_T1_Map.h │ │ ├── DecayDoseOverTime.cc │ │ ├── DecayDoseOverTime.h │ │ ├── IVIMMRI_ADC_Map.cc │ │ ├── IVIMMRI_ADC_Map.h │ │ ├── ImagePartialDerivative.cc │ │ ├── ImagePartialDerivative.h │ │ ├── In_Image_Plane_Bicubic_Supersample.cc │ │ ├── In_Image_Plane_Bicubic_Supersample.h │ │ ├── In_Image_Plane_Bilinear_Supersample.cc │ │ ├── In_Image_Plane_Bilinear_Supersample.h │ │ ├── In_Image_Plane_Blur.cc │ │ ├── In_Image_Plane_Blur.h │ │ ├── In_Image_Plane_Pixel_Decimate.cc │ │ ├── In_Image_Plane_Pixel_Decimate.h │ │ ├── In_Image_Plane_Sharpen.cc │ │ ├── In_Image_Plane_Sharpen.h │ │ ├── Liver_Kinetic_1Compartment2Input_5Param_Chebyshev_Common.h │ │ ├── Liver_Kinetic_1Compartment2Input_5Param_Chebyshev_FreeformOptimization.cc │ │ ├── Liver_Kinetic_1Compartment2Input_5Param_Chebyshev_FreeformOptimization.h │ │ ├── Liver_Kinetic_1Compartment2Input_5Param_Chebyshev_LevenbergMarquardt.cc │ │ ├── Liver_Kinetic_1Compartment2Input_5Param_Chebyshev_LevenbergMarquardt.h │ │ ├── Liver_Kinetic_1Compartment2Input_5Param_LinearInterp_Common.h │ │ ├── Liver_Kinetic_1Compartment2Input_5Param_LinearInterp_LevenbergMarquardt.cc │ │ ├── Liver_Kinetic_1Compartment2Input_5Param_LinearInterp_LevenbergMarquardt.h │ │ ├── Liver_Kinetic_1Compartment2Input_Reduced3Param_Chebyshev_Common.h │ │ ├── Liver_Kinetic_1Compartment2Input_Reduced3Param_Chebyshev_FreeformOptimization.cc │ │ ├── Liver_Kinetic_1Compartment2Input_Reduced3Param_Chebyshev_FreeformOptimization.h │ │ ├── Liver_Kinetic_Common.h │ │ ├── Logarithmic_Pixel_Scale.cc │ │ ├── Logarithmic_Pixel_Scale.h │ │ ├── Max-Min_Pixel_Value.cc │ │ ├── Max-Min_Pixel_Value.h │ │ ├── Max_Pixel_Value.cc │ │ ├── Max_Pixel_Value.h │ │ ├── Min_Pixel_Value.cc │ │ ├── Min_Pixel_Value.h │ │ ├── Negate_Image.cc │ │ ├── Negate_Image.h │ │ ├── Orthogonal_Slices.cc │ │ ├── Orthogonal_Slices.h │ │ ├── Partitioned_Image_Voxel_Visitor_Mutator.cc │ │ ├── Partitioned_Image_Voxel_Visitor_Mutator.h │ │ ├── Per_ROI_Time_Courses.cc │ │ ├── Per_ROI_Time_Courses.h │ │ ├── Slope_Difference.cc │ │ ├── Slope_Difference.h │ │ ├── Time_Course_Slope_Map.cc │ │ └── Time_Course_Slope_Map.h │ └── Transform │ │ ├── CT_Perfusion_Signal_Diff.cc │ │ ├── CT_Perfusion_Signal_Diff.h │ │ ├── DCEMRI_C_Map.cc │ │ ├── DCEMRI_C_Map.h │ │ ├── DCEMRI_S0_Map_v2.cc │ │ ├── DCEMRI_S0_Map_v2.h │ │ ├── DCEMRI_Signal_Difference_C.cc │ │ ├── DCEMRI_Signal_Difference_C.h │ │ ├── DCEMRI_T1_Map_v2.cc │ │ ├── DCEMRI_T1_Map_v2.h │ │ ├── Pixel_Value_Histogram.cc │ │ ├── Pixel_Value_Histogram.h │ │ ├── Subtract_Spatially_Overlapping_Images.cc │ │ └── Subtract_Spatially_Overlapping_Images.h ├── imebra20121219 │ ├── library │ │ ├── base │ │ │ ├── include │ │ │ │ ├── baseObject.h │ │ │ │ ├── baseStream.h │ │ │ │ ├── charsetConversion.h │ │ │ │ ├── configuration.h │ │ │ │ ├── criticalSection.h │ │ │ │ ├── exception.h │ │ │ │ ├── huffmanTable.h │ │ │ │ ├── memory.h │ │ │ │ ├── memoryStream.h │ │ │ │ ├── nullStream.h │ │ │ │ ├── stream.h │ │ │ │ ├── streamController.h │ │ │ │ ├── streamReader.h │ │ │ │ ├── streamWriter.h │ │ │ │ └── thread.h │ │ │ └── src │ │ │ │ ├── baseObject.cpp │ │ │ │ ├── baseStream.cpp │ │ │ │ ├── charsetConversion.cpp │ │ │ │ ├── criticalSection.cpp │ │ │ │ ├── exception.cpp │ │ │ │ ├── huffmanTable.cpp │ │ │ │ ├── memory.cpp │ │ │ │ ├── memoryStream.cpp │ │ │ │ ├── stream.cpp │ │ │ │ ├── streamController.cpp │ │ │ │ ├── streamReader.cpp │ │ │ │ ├── streamWriter.cpp │ │ │ │ └── thread.cpp │ │ └── imebra │ │ │ ├── include │ │ │ ├── LUT.h │ │ │ ├── MONOCHROME1ToMONOCHROME2.h │ │ │ ├── MONOCHROME1ToRGB.h │ │ │ ├── MONOCHROME2ToRGB.h │ │ │ ├── MONOCHROME2ToYBRFULL.h │ │ │ ├── PALETTECOLORToRGB.h │ │ │ ├── RGBToMONOCHROME2.h │ │ │ ├── RGBToYBRFULL.h │ │ │ ├── RGBToYBRPARTIAL.h │ │ │ ├── VOILUT.h │ │ │ ├── YBRFULLToMONOCHROME2.h │ │ │ ├── YBRFULLToRGB.h │ │ │ ├── YBRPARTIALToRGB.h │ │ │ ├── buffer.h │ │ │ ├── bufferStream.h │ │ │ ├── charsetsList.h │ │ │ ├── codec.h │ │ │ ├── codecFactory.h │ │ │ ├── colorTransform.h │ │ │ ├── colorTransformsFactory.h │ │ │ ├── data.h │ │ │ ├── dataCollection.h │ │ │ ├── dataGroup.h │ │ │ ├── dataHandler.h │ │ │ ├── dataHandlerDate.h │ │ │ ├── dataHandlerDateTime.h │ │ │ ├── dataHandlerDateTimeBase.h │ │ │ ├── dataHandlerNumeric.h │ │ │ ├── dataHandlerString.h │ │ │ ├── dataHandlerStringAE.h │ │ │ ├── dataHandlerStringAS.h │ │ │ ├── dataHandlerStringCS.h │ │ │ ├── dataHandlerStringDS.h │ │ │ ├── dataHandlerStringIS.h │ │ │ ├── dataHandlerStringLO.h │ │ │ ├── dataHandlerStringLT.h │ │ │ ├── dataHandlerStringPN.h │ │ │ ├── dataHandlerStringSH.h │ │ │ ├── dataHandlerStringST.h │ │ │ ├── dataHandlerStringUI.h │ │ │ ├── dataHandlerStringUT.h │ │ │ ├── dataHandlerStringUnicode.h │ │ │ ├── dataHandlerTime.h │ │ │ ├── dataSet.h │ │ │ ├── dicomCodec.h │ │ │ ├── dicomDict.h │ │ │ ├── dicomDir.h │ │ │ ├── drawBitmap.h │ │ │ ├── image.h │ │ │ ├── imebra.h │ │ │ ├── imebraDoc.h │ │ │ ├── jpegCodec.h │ │ │ ├── modalityVOILUT.h │ │ │ ├── transaction.h │ │ │ ├── transform.h │ │ │ ├── transformHighBit.h │ │ │ ├── transformsChain.h │ │ │ ├── viewHelper.h │ │ │ └── waveform.h │ │ │ └── src │ │ │ ├── LUT.cpp │ │ │ ├── MONOCHROME1ToMONOCHROME2.cpp │ │ │ ├── MONOCHROME1ToRGB.cpp │ │ │ ├── MONOCHROME2ToRGB.cpp │ │ │ ├── MONOCHROME2ToYBRFULL.cpp │ │ │ ├── PALETTECOLORToRGB.cpp │ │ │ ├── RGBToMONOCHROME2.cpp │ │ │ ├── RGBToYBRFULL.cpp │ │ │ ├── RGBToYBRPARTIAL.cpp │ │ │ ├── VOILUT.cpp │ │ │ ├── YBRFULLToMONOCHROME2.cpp │ │ │ ├── YBRFULLToRGB.cpp │ │ │ ├── YBRPARTIALToRGB.cpp │ │ │ ├── buffer.cpp │ │ │ ├── charsetsList.cpp │ │ │ ├── codec.cpp │ │ │ ├── codecFactory.cpp │ │ │ ├── colorTransform.cpp │ │ │ ├── colorTransformsFactory.cpp │ │ │ ├── data.cpp │ │ │ ├── dataGroup.cpp │ │ │ ├── dataHandler.cpp │ │ │ ├── dataHandlerDate.cpp │ │ │ ├── dataHandlerDateTime.cpp │ │ │ ├── dataHandlerDateTimeBase.cpp │ │ │ ├── dataHandlerString.cpp │ │ │ ├── dataHandlerStringAE.cpp │ │ │ ├── dataHandlerStringAS.cpp │ │ │ ├── dataHandlerStringCS.cpp │ │ │ ├── dataHandlerStringDS.cpp │ │ │ ├── dataHandlerStringIS.cpp │ │ │ ├── dataHandlerStringLO.cpp │ │ │ ├── dataHandlerStringLT.cpp │ │ │ ├── dataHandlerStringPN.cpp │ │ │ ├── dataHandlerStringSH.cpp │ │ │ ├── dataHandlerStringST.cpp │ │ │ ├── dataHandlerStringUI.cpp │ │ │ ├── dataHandlerStringUT.cpp │ │ │ ├── dataHandlerStringUnicode.cpp │ │ │ ├── dataHandlerTime.cpp │ │ │ ├── dataSet.cpp │ │ │ ├── dicomCodec.cpp │ │ │ ├── dicomDict.cpp │ │ │ ├── dicomDir.cpp │ │ │ ├── drawBitmap.cpp │ │ │ ├── image.cpp │ │ │ ├── jpegCodec.cpp │ │ │ ├── modalityVOILUT.cpp │ │ │ ├── transaction.cpp │ │ │ ├── transform.cpp │ │ │ ├── transformHighBit.cpp │ │ │ ├── transformsChain.cpp │ │ │ ├── viewHelper.cpp │ │ │ └── waveform.cpp │ ├── license.txt │ └── note.txt ├── imgui20210904 │ ├── imconfig.h │ ├── imgui.cpp │ ├── imgui.h │ ├── imgui_demo.cpp │ ├── imgui_draw.cpp │ ├── imgui_impl_opengl3.cpp │ ├── imgui_impl_opengl3.h │ ├── imgui_impl_opengl3_loader.h │ ├── imgui_impl_sdl.cpp │ ├── imgui_impl_sdl.h │ ├── imgui_internal.h │ ├── imgui_tables.cpp │ ├── imgui_widgets.cpp │ ├── imstb_rectpack.h │ ├── imstb_textedit.h │ ├── imstb_truetype.h │ └── license.txt ├── implot20210904 │ ├── LICENSE │ ├── implot.cpp │ ├── implot.h │ ├── implot_demo.cpp │ ├── implot_internal.h │ └── implot_items.cpp ├── pfd20211102 │ └── portable-file-dialogs.h ├── rpc │ ├── CMakeLists.txt │ ├── DCMA.thrift │ ├── Receiver_client.impl.cc │ ├── Receiver_server.impl.cc │ ├── Serialization.cc │ ├── Serialization.h │ ├── compile_example.sh │ ├── compile_thrift.sh │ ├── gen-cpp │ │ ├── DCMA_constants.cc │ │ ├── DCMA_constants.h │ │ ├── DCMA_types.cc │ │ ├── DCMA_types.h │ │ ├── Receiver.cc │ │ ├── Receiver.h │ │ └── Receiver_server.skeleton.cc │ ├── gen-gv │ │ └── DCMA.gv │ ├── gen-html │ │ ├── DCMA.html │ │ ├── index.html │ │ └── style.css │ ├── gen-json │ │ └── DCMA.json │ ├── gen-lua │ │ ├── DCMA_Receiver.lua │ │ ├── DCMA_constants.lua │ │ └── DCMA_ttypes.lua │ ├── gen-markdown │ │ ├── DCMA │ │ └── index │ ├── gen-py │ │ ├── __init__.py │ │ └── dcma │ │ │ ├── __init__.py │ │ │ └── rpc │ │ │ ├── Receiver-remote │ │ │ ├── Receiver.py │ │ │ ├── __init__.py │ │ │ ├── constants.py │ │ │ └── ttypes.py │ └── gen-xml │ │ └── DCMA.xml └── stbnothings20230607 │ ├── LICENSE.txt │ ├── README.md │ ├── stb_image.h │ └── stb_image_write.h ├── sycl ├── CMakeLists.txt ├── GUIDE.md ├── README.md ├── compile_and_install.sh ├── sanitizeInputData.py └── src │ ├── CMakeLists.txt │ ├── Common.cc │ ├── Common.h │ ├── Generate_Expected_Output.cc │ ├── Generate_Test_Inputs.cc │ ├── Perfusion_SCDI.cc │ ├── Perfusion_SCDI.h │ ├── Perfusion_SCSI.cc │ ├── Perfusion_SCSI.h │ └── Run_Model.cc └── unit_tests ├── Alignment_TPSRPM.cc ├── Future_Test.cc ├── Main.cc ├── Thread_Pool.cc ├── compile_and_run.sh └── compile_threads.sh /.clang-format: -------------------------------------------------------------------------------- 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