├── .appveyor.yml ├── .clang-format ├── .git-blame-ignore-revs ├── .gitattributes ├── .github ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── GHA_increase_disk_space.sh │ ├── build-test.yml │ ├── cffconvert.yml │ └── pre-commit-check.yml ├── .gitignore ├── .gitmodules ├── .mailmap ├── .pre-commit-config.yaml ├── .travis.yml ├── CITATION.cff ├── CMakeLists.txt ├── CONTRIBUTING.md ├── INSTALL.txt ├── LICENSE.txt ├── LICENSES ├── Apache-2.0.txt ├── LGPL-2.1.txt └── PARAPET-license.txt ├── README.md ├── VERSION.txt ├── documentation ├── .gitignore ├── EDITOR-CONFIG.md ├── Makefile ├── STIR-UsersGuide.tex ├── STIR-developers-overview.tex ├── STIR-general-overview.tex ├── STIR-glossary.tex ├── STIR-version2-vs-version1.tex ├── STIR_FBP3DRP.pdf ├── STIR_FBP3DRP.rtf ├── a4wide.sty ├── bugs.htm ├── contrib │ ├── Motion_files_KCL │ │ └── Documentation │ │ │ ├── MotionCoordinates.pptx │ │ │ └── Software_Description.docx │ ├── OSMAPOSL_MPI │ │ └── Description.txt │ ├── README.txt │ ├── SAFIR_CListmode_VirtualCylindrical │ │ └── Description.txt │ ├── Shape3D_enhancements_RS_AK │ │ ├── generate_image_upgrade.tex │ │ ├── iopams.sty │ │ ├── iopart.cls │ │ └── setstack.sty │ └── SimSET_STIR │ │ └── Description.txt ├── credits.htm ├── devel │ ├── README.md │ ├── editor-settings.md │ └── git-hooks.md ├── future.htm ├── graphics │ ├── STIR-UsersGuide_PinholeSPECTUB.eps │ ├── STIR-UsersGuide_PinholeSPECTUB.png │ ├── STIR-developers-overviewFig1.eps │ ├── STIR-developers-overviewFig1.png │ ├── STIR-developers-overviewFig10.eps │ ├── STIR-developers-overviewFig10.png │ ├── STIR-developers-overviewFig11.eps │ ├── STIR-developers-overviewFig11.png │ ├── STIR-developers-overviewFig12.eps │ ├── STIR-developers-overviewFig12.png │ ├── STIR-developers-overviewFig2.eps │ ├── STIR-developers-overviewFig2.png │ ├── STIR-developers-overviewFig3.eps │ ├── STIR-developers-overviewFig3.png │ ├── STIR-developers-overviewFig4.eps │ ├── STIR-developers-overviewFig4.png │ ├── STIR-developers-overviewFig7.eps │ ├── STIR-developers-overviewFig7.png │ ├── STIR-developers-overviewFig8.eps │ ├── STIR-developers-overviewFig8.png │ ├── STIR-developers-overviewFig9.eps │ ├── STIR-developers-overviewFig9.png │ ├── STIR-general-overviewFig1.eps │ ├── STIR-general-overviewFig1.png │ ├── STIR-general-overviewFig2.eps │ ├── STIR-general-overviewFig2.png │ ├── STIR-glossary-Fig-span4.eps │ ├── STIR-glossary-Fig-span4.png │ ├── STIR-glossaryFig1.eps │ └── STIR-glossaryFig1.png ├── history.htm ├── release_1.2.htm ├── release_1.3.htm ├── release_1.4.htm ├── release_2.0.htm ├── release_2.1.htm ├── release_2.2.htm ├── release_2.3.htm ├── release_2.4.htm ├── release_2000_07_19.htm ├── release_2001_01_12.htm ├── release_2001_12_20.htm ├── release_2003_06_26.htm ├── release_3.0.htm ├── release_4.0.htm ├── release_4.1.htm ├── release_5.0.htm ├── release_5.1.htm ├── release_5.2.htm ├── release_6.0.htm ├── release_6.1.htm ├── release_6.2.htm ├── release_6.3.htm ├── release_6.4.htm ├── release_notes_skeleton.htm └── support.htm ├── doximages ├── FTMetz.eps ├── FTMetz.jpg ├── Metz.eps ├── Metz.jpg ├── MetzFWHM.eps └── MetzFWHM.jpg ├── examples ├── C++ │ ├── General_Reconstruction │ │ ├── General_Reconstruction.cxx │ │ └── General_Reconstruction.h │ ├── README.md │ ├── using_STIR_LOCAL │ │ ├── CMakeLists.txt │ │ ├── README.md │ │ ├── demo.par │ │ ├── demo1.cxx │ │ ├── demo2.cxx │ │ ├── demo3.cxx │ │ ├── demo4_obj_fun.cxx │ │ ├── demo4_obj_fun.par │ │ ├── demo5_line_search.cxx │ │ ├── demo5_line_search.par │ │ ├── demoPM.par │ │ ├── extra_stir_dirs.cmake │ │ ├── generate_image.par │ │ ├── small.hs │ │ └── small.s │ └── using_installed_STIR │ │ ├── .gitignore │ │ ├── CMakeLists.txt │ │ ├── README.md │ │ └── demo_create_image.cxx ├── GE-Signa-PETMR │ ├── GEAC_to_mu.sh │ ├── GE_HUToMu.par │ ├── NAC_recon.sh │ ├── OSMAPOSLbackground.par │ ├── README.md │ ├── TOF_template.hs │ ├── correct_projdata_for_norm.par │ ├── create_norm_projdata.sh │ ├── download_VQC_data.sh │ ├── generate_zero_atn.par │ ├── howto.md │ ├── lm_to_projdata.par │ ├── process_VQC_data.sh │ ├── register_GEAC.sh │ ├── scatter_and_recon.sh │ ├── sino_and_randoms.sh │ ├── template.hs │ ├── template.s │ └── unlist_and_randoms.sh ├── PET_simulation │ ├── .gitignore │ ├── FBP2D.par │ ├── OSMAPOSL_QP.par │ ├── OSSPS_QP.par │ ├── README.txt │ ├── Shell-scripting-primer.txt │ ├── forward_projector_proj_matrix_ray_tracing.par │ ├── generate_attenuation_image.par │ ├── generate_input_data.sh │ ├── generate_uniform_cylinder.par │ ├── recon_FBP2D.sh │ ├── recon_iterative.sh │ ├── run_reconstruction_without_output.par │ ├── run_simulation.sh │ ├── scatter_simulation.par │ ├── scatter_template.hs │ ├── simulate_data.sh │ └── simulate_scatter.sh ├── README.md ├── ROOT_files │ ├── GATE_test_macro │ │ ├── README.txt │ │ ├── benchPET.mac │ │ ├── digitizer.mac │ │ └── geometry.mac │ └── ROOT_STIR_consistency │ │ ├── .gitignore │ │ ├── DebugScripts │ │ └── debug_consistency_with_root.py │ │ ├── Gate_macros │ │ ├── GateMaterials.db │ │ ├── csorter.mac │ │ ├── digitiser.mac │ │ ├── geometry.mac │ │ ├── main_GATE_macro_template.mac │ │ └── physics.mac │ │ ├── README.md │ │ ├── SourceFiles │ │ ├── generate_image1.par │ │ ├── generate_image2.par │ │ ├── generate_image3.par │ │ ├── generate_image4.par │ │ ├── generate_image5.par │ │ ├── generate_image6.par │ │ ├── generate_image7.par │ │ ├── generate_image8.par │ │ ├── source_test1.mac │ │ ├── source_test2.mac │ │ ├── source_test3.mac │ │ ├── source_test4.mac │ │ ├── source_test5.mac │ │ ├── source_test6.mac │ │ ├── source_test7.mac │ │ └── source_test8.mac │ │ ├── root_header_test_template.hroot │ │ └── run_pretest_script.sh ├── SAFIR-listmode-virtual-scanner │ ├── .gitattributes │ ├── .gitignore │ ├── crystal_map_front.txt │ ├── listmode_input_SAFIR.par │ ├── lm_to_projdata.par │ ├── point_5.clm.safir │ ├── safir_20.hs │ └── safir_20.s ├── SAFIR_genericScanner │ ├── .gitignore │ ├── DualRingPrototype_crystal_map.txt │ ├── OSMAPOSL_QuadraticPrior.par │ ├── README.txt │ ├── coincidencesLM.clm.safir │ ├── listmode_input_SAFIR.par │ ├── lm_to_projdata.par │ ├── muppet.hs │ ├── muppet.s │ ├── template_image.hv │ ├── template_image.v │ └── test.sh ├── Siemens-mMR │ ├── OSMAPOSLbackground.par │ ├── README.md │ ├── correct_projdata.par │ ├── correct_projdata_no_axial_effects.par │ ├── correct_projdata_nogaps.par │ ├── correct_projdata_only_counts.par │ ├── forward_projector_ray_tracing.par │ ├── howto_create_randoms_from_delayed_sino.sh │ ├── howto_recon_sinos.sh │ ├── lm_fansums.par │ ├── lm_fansums_delayed.par │ ├── lm_to_projdata.par │ ├── old_scatter_estimation │ │ └── howto_scatter_and_recon.sh │ ├── postfilter_Gaussian.par │ ├── process_NEMA_data.sh │ ├── scatter_README.md │ ├── scatter_and_recon.sh │ ├── scatter_estimation_par_files │ │ ├── README.md │ │ ├── postfilter_Gaussian_for_mask.par │ │ ├── run_reconstruction.par │ │ ├── scatter_estimation.par │ │ └── tail_fitting.par │ ├── scatter_template.hs │ ├── template_span1.hs │ ├── template_span1.s │ ├── template_span11.hs │ ├── template_span11.s │ └── unlist_and_randoms.sh ├── matlab │ ├── plot_demo.m │ ├── projector_demo.m │ ├── recon_demo.m │ └── recon_demo_gradient.m ├── nifti │ └── disp_4D.nii.gz ├── python │ ├── .gitignore │ ├── README.txt │ ├── ROI_demo.py │ ├── Vision_files_preprocess.py │ ├── construct_projdata_demo.py │ ├── data_analysis │ │ ├── README.md │ │ ├── convert_all_python_to_ipynb.sh │ │ └── plot_GE_singles_info.py │ ├── listmode_demo.py │ ├── listmode_loop_demo.py │ ├── matplotlib_demo.py │ ├── mayavi_demo.py │ ├── plot_projdata_profiles.py │ ├── plot_scanner_LORs.py │ ├── print_scanner_info.py │ ├── projdata_visualisation │ │ ├── BackendTools │ │ │ ├── ImageTools.py │ │ │ ├── STIRInterface.py │ │ │ └── UIGroupboxProjdataDimensions.py │ │ ├── ProjDataVisualisation.py │ │ ├── README.md │ │ └── demo_ProjDataVisualisation.py │ ├── projector_demo.py │ ├── recon_demo.py │ └── recon_demo_gradient.py ├── recon_demo │ ├── .gitignore │ ├── README.txt │ ├── init.hv │ ├── init.v │ ├── recon_demo_OSEM.par │ ├── smalllong.hs │ └── smalllong.s └── samples │ ├── DDSR2D.par │ ├── Estimate_TEW_Scatter.par │ ├── FBP2D.par │ ├── FBP2D_SPECTUB.par │ ├── FBP2D_using_ITK_to_write_image.par │ ├── FBP3DRP.par │ ├── GRD2D.par │ ├── KOSMAPOSL_hkem.par │ ├── KOSMAPOSL_mhkem.par │ ├── MCIR.par │ ├── OSEM_SPECTUB.par │ ├── OSMAPOSL_MRP.par │ ├── OSMAPOSL_NiftyPET.par │ ├── OSMAPOSL_PLS.par │ ├── OSMAPOSL_QuadraticPrior.par │ ├── OSMAPOSL_RDP.par │ ├── OSMAPOSL_emml_with_projector_pair.par │ ├── OSMAPOSL_emml_with_projmatrix.par │ ├── OSMAPOSL_listmode_emml_with_projmatrix.par │ ├── OSMAPOSL_osem_SPECTUB.par │ ├── OSMAPOSL_osem_with_interfiltering.par │ ├── OSSPS_QuadraticPrior.par │ ├── PET_Interfile_header.hs │ ├── PET_TOF_Interfile_header_Signa_PETMR.hs │ ├── PET_TOF_Interfile_header_Signa_PETMR.s │ ├── POSMAPOSL.par │ ├── POSSPS.par │ ├── PatlakPlot.par │ ├── PinholeSPECTUB │ ├── FBP2D_PinholeSPECTUB.par │ ├── OSEM_PinholeSPECTUB.par │ ├── OSOSLMRP_PinholeSPECTUB.par │ ├── OSSPSQP_PinholeSPECTUB.par │ ├── collimator27_cyl.txt │ ├── collimator27_pol.txt │ ├── collimator27_pol_MPH.txt │ ├── detector27.txt │ └── forward_project_PinholeSPECTUB.par │ ├── SPECT_Interfile_header.hs │ ├── SRT2D.par │ ├── SRT2DSPECT.par │ ├── back_projector_parallelproj.par │ ├── back_projector_proj_matrix_ray_tracing.par │ ├── back_projector_proj_matrix_ray_tracing_post_smoothing.par │ ├── compute_sqrt_Hessian_row_sum.par │ ├── correct_projdata.par │ ├── fore.par │ ├── forward_project_SPECTUB.par │ ├── forward_projector_parallelproj.par │ ├── forward_projector_proj_matrix_ray_tracing.par │ ├── forward_projector_proj_matrix_ray_tracing_pre_smoothing.par │ ├── forward_projector_ray_tracing.par │ ├── generate_image.par │ ├── list_ROI_values.par │ ├── list_ROI_values_with_label_image.par │ ├── listmode_input_SAFIR.par │ ├── lm_to_projdata.par │ ├── lm_to_projdata_time_frames.fdef │ ├── lm_to_projdata_time_frames.txt │ ├── mMR_listmode.l │ ├── mMR_listmode.l.hdr │ ├── mMR_sinogram.s │ ├── mMR_sinogram.s.hdr │ ├── multi_file.txt │ ├── postfilter_Gaussian.par │ ├── postfilter_HUToMu.par │ ├── postfilter_Metz.par │ ├── postfilter_median3x3x3.par │ ├── projector_pair_parallelproj.par │ ├── projector_pair_ray_tracing_matrix.par │ ├── root_header.hroot │ ├── root_headerECAT.hroot │ ├── run_reconstruction.par │ ├── scatter_estimation_par_files │ ├── README.md │ ├── postfilter_Gaussian_for_mask.par │ ├── run_reconstruction.par │ ├── scatter_estimation.par │ └── tail_fitting.par │ ├── scatter_simulation.par │ ├── stir_math_ITK_output_file_format.par │ ├── stir_math_multi_output_file_format.par │ ├── stir_math_output_file_format.par │ ├── write_proj_matrix_by_bin.par │ └── write_proj_matrix_by_bin_SPECTUB.par ├── external_helpers ├── CMakeLists.txt └── doxy2swig │ ├── LICENSE │ ├── README.md │ └── doxy2swig.py ├── pre-commit-environment.yml ├── recon_test_pack ├── .gitignore ├── CUDA │ └── OSMAPOSL_test_sim_Parallelproj_CUDARDP.par ├── DDSR2D_test_sim.par ├── FBP2D_test_sim.par ├── FBP3DRP_test_sim.par ├── GRD2D_test_sim.par ├── KOSMAPOSL_test_consistency.par ├── NiftyPET_test.sh ├── OSMAPOSL_test.par ├── OSMAPOSL_test_PMFromFile_QPweights.par ├── OSMAPOSL_test_PM_MRP.par ├── OSMAPOSL_test_PM_QP.par ├── OSMAPOSL_test_PM_QPweights.par ├── OSMAPOSL_test_PM_for_sensitivity.par ├── OSMAPOSL_test_for_sensitivity.par ├── OSMAPOSL_test_lm.par ├── OSMAPOSL_test_lmf.par ├── OSMAPOSL_test_proj.par ├── OSMAPOSL_test_sim_PM.par ├── OSMAPOSL_test_sim_PM_QP.par ├── OSMAPOSL_with_motion_test.par ├── OSSPS_test_PM_QP.par ├── OSSPS_test_PM_QP_subsens1.par ├── OSSPS_test_sim_PM_QPweights.par ├── PET_ACQ_small.l.hdr.STIR ├── README.txt ├── ROI_small_uniform_cylinder.par ├── ROI_uniform_cylinder.par ├── RPTsens_seg3_PM.hv ├── RPTsens_seg3_PM.v ├── RPTsens_seg4.hv ├── RPTsens_seg4.v ├── SPECT │ ├── .gitignore │ ├── PinholeSPECTUB │ │ ├── FBP2D.par │ │ ├── OSEM.par │ │ ├── README.txt │ │ ├── attmap.hv │ │ ├── attmap.v │ │ ├── collimator.txt │ │ ├── detector.txt │ │ ├── init.hv │ │ ├── init.v │ │ ├── input.hs │ │ ├── input.s │ │ ├── mask.hv │ │ ├── mask.v │ │ ├── org │ │ │ ├── FBP.hv │ │ │ ├── FBP.v │ │ │ ├── OSEM_7.hv │ │ │ └── OSEM_7.v │ │ └── run_PinholeSPECTUB_tests.sh │ ├── SPECTUB │ │ ├── FBP2D.par │ │ ├── OSEM_2DPSF.par │ │ ├── OSEM_3DPSF.par │ │ ├── README.txt │ │ ├── attMapRec.hv │ │ ├── attMapRec.v │ │ ├── init.hv │ │ ├── init.v │ │ ├── input.hs │ │ ├── input.s │ │ ├── mask.hv │ │ ├── mask.v │ │ ├── org │ │ │ ├── FBP.hv │ │ │ ├── FBP.v │ │ │ ├── OSEM_2DPSF_16.hv │ │ │ ├── OSEM_2DPSF_16.v │ │ │ ├── OSEM_3DPSF_4.hv │ │ │ └── OSEM_3DPSF_4.v │ │ └── run_SPECTUB_tests.sh │ └── run_SPECT_tests.sh ├── SPECT_test_Interfile_header.hs ├── SPECT_test_Interfile_header.s ├── SRT2DSPECT_test_sim.par ├── SRT2D_test_sim.par ├── Siemens_mMR_seg2.hs ├── Siemens_mMR_seg2.s ├── Utahscat600k_ca_seg4.hs ├── Utahscat600k_ca_seg4.s ├── convecat6_if.inp ├── correct_projdata.par ├── correct_projdata_norm_only.par ├── correct_projdata_simulation.par ├── forward_project_SPECTUB.par ├── forward_projector_proj_matrix_ray_tracing.par ├── frame_single.fdef ├── generate_atten_cylinder.par ├── generate_atten_cylinder_SPECT.par ├── generate_test_object.par ├── generate_uniform_cylinder.par ├── generate_uniform_image.par ├── lm_fansums_delayed.par ├── lm_generate_atten_cylinder.par ├── lm_generate_uniform_cylinder.par ├── lm_to_projdata.par ├── lm_to_projdata_from_ROOT.par ├── postfilter_truncate_circular_FOV.par ├── root_header.hroot ├── run_ML_norm_tests.sh ├── run_ecat_tests.bat ├── run_ecat_tests.sh ├── run_root_GATE.sh ├── run_scatter_tests.sh ├── run_test_SSRB.sh ├── run_test_listmode_recon.sh ├── run_test_simulate_and_recon.sh ├── run_test_simulate_and_recon_with_motion.sh ├── run_test_zoom_image.sh ├── run_tests.bat ├── run_tests.sh ├── run_tests_modelling.sh ├── scatter_cylinder.hs ├── scatter_cylinder.s ├── scatter_simulation.par ├── simulate_data.sh ├── simulate_data_for_tests.sh ├── simulate_scatter.sh ├── small_listmode_file.l ├── template_for_ROOT_scanner.hs ├── template_for_ROOT_scanner.s ├── test_PET_GATE.root ├── test_image_3.hv ├── test_image_3.v ├── test_image_5.hv ├── test_image_5.v ├── test_image_OSSPS_PM_QP_8.hv ├── test_image_OSSPS_PM_QP_8.v ├── test_image_PM_MRP_6.hv ├── test_image_PM_MRP_6.v ├── test_image_PM_QP_6.hv ├── test_image_PM_QP_6.v ├── test_image_PM_QPweights_6.hv ├── test_image_PM_QPweights_6.v ├── test_modelling_input │ ├── ECAT_931_projdata_template.hs │ ├── ECAT_931_projdata_template.s │ ├── POSMAPOSL.par │ ├── POSSPS.par │ ├── PatlakPlot.par │ ├── generate_all1.par │ ├── generate_p0005.par │ ├── generate_p5.par │ ├── plasma.if │ └── time.fdef ├── uncorrect_projdata.par └── write_proj_matrix_by_bin.par ├── scripts ├── CMakeLists.txt ├── IO │ ├── CMakeLists.txt │ ├── convertSiemensInterfileToSTIR.sh │ └── dumpSiemensDicomInfo.sh ├── count ├── create_fdef_from_listmode.sh ├── estimate_scatter.sh ├── force_view_offset_to_zero.sh ├── get_num_voxels.sh ├── maintenance │ ├── CMakeLists.txt │ ├── CVS2hg │ │ ├── README.txt │ │ ├── check_tag.sh │ │ ├── convert-CVS-to-hg.sh │ │ ├── cvs2hg.options │ │ ├── find_dateline_of_rev.sh │ │ ├── find_log_of_rev.sh │ │ ├── not_used │ │ │ ├── STIR-authors.txt │ │ │ ├── STIR-filemap.txt │ │ │ └── cvs2git.options │ │ ├── remove_cvs_keywords.sh │ │ ├── replace_dateline_of_rev.sh │ │ ├── rm_revs.sh │ │ └── rm_revs_dir.sh │ ├── README.txt │ ├── add-PARAPET-license.sed │ ├── change-license.sed │ ├── change-license.sh │ ├── clang-tidy-modernize.md │ ├── git-fame.sh │ └── make_distribution.sh ├── plot_TOF_bins.m ├── stir_divide ├── stir_print_voxel_sizes.sh ├── stir_subtract └── zoom_att_image.sh └── src ├── CMakeLists.txt ├── Doxyfile.in ├── IO ├── CMakeLists.txt ├── ECAT6OutputFileFormat.cxx ├── ECAT7DynamicDiscretisedDensityInputFileFormat.cxx ├── ECAT7DynamicDiscretisedDensityOutputFileFormat.cxx ├── ECAT7OutputFileFormat.cxx ├── ECAT7ParametricDensityOutputFileFormat.cxx ├── GEHDF5ListmodeInputFileFormat.cxx ├── GEHDF5Wrapper.cxx ├── GIPL_ImageFormat.cxx ├── IO_registries.cxx ├── ITKImageInputFileFormat.cxx ├── ITKOutputFileFormat.cxx ├── InputFileFormatRegistry.cxx ├── InputStreamFromROOTFile.cxx ├── InputStreamFromROOTFileForCylindricalPET.cxx ├── InputStreamFromROOTFileForECATPET.cxx ├── InputStreamWithRecordsFromUPENN.cxx ├── InputStreamWithRecordsFromUPENNbin.cxx ├── InputStreamWithRecordsFromUPENNtxt.cxx ├── InterfileDynamicDiscretisedDensityOutputFileFormat.cxx ├── InterfileHeader.cxx ├── InterfileHeaderSiemens.cxx ├── InterfileOutputFileFormat.cxx ├── InterfilePDFSHeaderSPECT.cxx ├── InterfileParametricDiscretisedDensityOutputFileFormat.cxx ├── MultiDynamicDiscretisedDensityInputFileFormat.cxx ├── MultiDynamicDiscretisedDensityOutputFileFormat.cxx ├── MultiParametricDiscretisedDensityOutputFileFormat.cxx ├── OutputFileFormat.cxx ├── OutputFileFormat_default.cxx ├── ecat6_utils.cxx ├── interfile.cxx ├── stir_ecat6.cxx ├── stir_ecat7.cxx └── stir_ecat_common.cxx ├── Shape_buildblock ├── Box3D.cxx ├── CMakeLists.txt ├── DiscretisedShape3D.cxx ├── Ellipsoid.cxx ├── EllipsoidalCylinder.cxx ├── GenerateImage.cxx ├── Shape3D.cxx ├── Shape3DWithOrientation.cxx └── Shape_buildblock_registries.cxx ├── SimSET ├── CMakeLists.txt ├── README.txt ├── TODO.txt ├── conv_SimSET_projdata_to_STIR.cxx ├── conv_to_SimSET_att_image.cxx ├── examples │ ├── generate_uniform_cylinder.par │ ├── howto_run_SimSET.sh │ ├── template_bin.rec │ ├── template_det.rec │ └── template_phg.rec ├── scripts │ ├── CMakeLists.txt │ ├── SimSET_STIR_names.sh │ ├── add_SimSET_results.sh │ ├── conv_SimSET_projdata_to_STIR.sh │ ├── make_hv_from_Simset_params.sh │ ├── mult_num_photons.sh │ ├── run_SimSET.sh │ └── stir_image_to_simset_object.sh └── write_phg_image_info.c ├── analytic ├── DDSR2D │ ├── CMakeLists.txt │ ├── DDSR2D.cxx │ └── DDSR2DReconstruction.cxx ├── FBP2D │ ├── CMakeLists.txt │ ├── FBP2D.cxx │ ├── FBP2DReconstruction.cxx │ └── RampFilter.cxx ├── FBP3DRP │ ├── CMakeLists.txt │ ├── ColsherFilter.cxx │ ├── FBP3DRP.cxx │ └── FBP3DRPReconstruction.cxx ├── GRD2D │ ├── CMakeLists.txt │ ├── GRD2D.cxx │ └── GRD2DReconstruction.cxx ├── SRT2D │ ├── CMakeLists.txt │ ├── SRT2D.cxx │ └── SRT2DReconstruction.cxx └── SRT2DSPECT │ ├── CMakeLists.txt │ ├── SRT2DSPECT.cxx │ └── SRT2DSPECTReconstruction.cxx ├── buildblock ├── ArcCorrection.cxx ├── Array.cxx ├── ArrayFilter1DUsingConvolution.cxx ├── ArrayFilter1DUsingConvolutionSymmetricKernel.cxx ├── ArrayFilter2DUsingConvolution.cxx ├── ArrayFilter3DUsingConvolution.cxx ├── ArrayFilterUsingRealDFTWithPadding.cxx ├── ByteOrder.cxx ├── CMakeLists.txt ├── ChainedDataProcessor.cxx ├── DataSymmetriesForViewSegmentNumbers.cxx ├── DetectorCoordinateMap.cxx ├── DiscretisedDensity.cxx ├── DynamicDiscretisedDensity.cxx ├── DynamicProjData.cxx ├── ExamData.cxx ├── ExamInfo.cxx ├── FilePath.cxx ├── GammaArrayFilter2D.cxx ├── GammaImageFilter2D.cxx ├── GatedDiscretisedDensity.cxx ├── GatedProjData.cxx ├── GeneralisedPoissonNoiseGenerator.cxx ├── GeometryBlocksOnCylindrical.cxx ├── HUToMuImageProcessor.cxx ├── IndexRange.cxx ├── Jamfile ├── KeyParser.cxx ├── ML_norm.cxx ├── MaximalArrayFilter3D.cxx ├── MaximalImageFilter3D.cxx ├── MedianArrayFilter3D.cxx ├── MedianImageFilter3D.cxx ├── MinimalArrayFilter3D.cxx ├── MinimalImageFilter3D.cxx ├── MultipleDataSetHeader.cxx ├── MultipleProjData.cxx ├── NonseparableConvolutionUsingRealDFTImageFilter.cxx ├── NumericType.cxx ├── ParseDiscretisedDensityParameters.cxx ├── ParsingObject.cxx ├── PatientPosition.cxx ├── ProjData.cxx ├── ProjDataFromStream.cxx ├── ProjDataGEHDF5.cxx ├── ProjDataInMemory.cxx ├── ProjDataInfo.cxx ├── ProjDataInfoBlocksOnCylindricalNoArcCorr.cxx ├── ProjDataInfoCylindrical.cxx ├── ProjDataInfoCylindricalArcCorr.cxx ├── ProjDataInfoCylindricalNoArcCorr.cxx ├── ProjDataInfoGeneric.cxx ├── ProjDataInfoGenericNoArcCorr.cxx ├── ProjDataInfoSubsetByView.cxx ├── ProjDataInterfile.cxx ├── Radionuclide.cxx ├── RadionuclideDB.cxx ├── RelatedViewgrams.cxx ├── SSRB.cxx ├── Scanner.cxx ├── Segment.cxx ├── SegmentBySinogram.cxx ├── SegmentByView.cxx ├── SeparableArrayFunctionObject.cxx ├── SeparableCartesianMetzImageFilter.cxx ├── SeparableConvolutionImageFilter.cxx ├── SeparableGaussianArrayFilter.cxx ├── SeparableGaussianImageFilter.cxx ├── SeparableMetzArrayFilter.cxx ├── Sinogram.cxx ├── TextWriter.cxx ├── ThresholdMinToSmallPositiveValueDataProcessor.cxx ├── TimeFrameDefinitions.cxx ├── TimeGateDefinitions.cxx ├── TruncateToCylindricalFOVImageProcessor.cxx ├── Verbosity.cxx ├── Viewgram.cxx ├── VoxelsOnCartesianGrid.cxx ├── WienerArrayFilter2D.cxx ├── WienerImageFilter2D.cxx ├── buildblock_registries.cxx ├── centre_of_gravity.cxx ├── date_time_functions.cxx ├── error.cxx ├── extend_projdata.cxx ├── find_STIR_config.cxx ├── find_fwhm_in_image.cxx ├── getopt.c ├── interfile_keyword_functions.cxx ├── interpolate_projdata.cxx ├── inverse_SSRB.cxx ├── line.cxx ├── linear_regression.cxx ├── multiply_crystal_factors.cxx ├── num_threads.cxx ├── overlap_interpolate.cxx ├── recon_array_functions.cxx ├── scale_sinograms.cxx ├── utilities.cxx ├── warning.cxx └── zoom.cxx ├── cmake ├── BuildMex.cmake ├── FindAllHeaderFiles.cmake ├── FindCERN_ROOT.cmake ├── FindJANSSON.cmake ├── FindLLN.cmake ├── FindNiftyPET.cmake ├── FindNumpy.cmake ├── FindRDF.cmake ├── FindUPENN.cmake ├── STIRConfig.cmake.in ├── STIRConfig.h.in ├── SetC++Version.cmake ├── stir_dirs.cmake ├── stir_exe_targets.cmake ├── stir_lib_target.cmake └── stir_test_exe_targets.cmake ├── config ├── ct_slopes.json ├── radionuclide_info.json └── radionuclide_names.json ├── data_buildblock ├── CMakeLists.txt ├── SinglesRates.cxx ├── SinglesRatesForTimeFrames.cxx ├── SinglesRatesForTimeSlices.cxx ├── SinglesRatesFromECAT7.cxx ├── SinglesRatesFromGEHDF5.cxx ├── SinglesRatesFromSglFile.cxx ├── data_buildblock_registries.cxx └── randoms_from_singles.cxx ├── display ├── CMakeLists.txt ├── display_array.cxx ├── gen.c ├── gen.h ├── mathlinkhelp.c ├── screen.c ├── screen.h └── screengen.c ├── eval_buildblock ├── CMakeLists.txt ├── ROIValues.cxx └── compute_ROI_values.cxx ├── experimental ├── CMakeLists.txt ├── IO │ ├── ECAT7DynamicDiscretisedDensityOutputFileFormat.cxx │ ├── OutputFileFormat_default.cxx │ ├── local_InputFileFormatRegistry.cxx │ └── local_OutputFileFormat_default.cxx ├── README.txt ├── buildblock │ ├── AbsTimeIntervalFromDynamicData.cxx │ ├── AbsTimeIntervalFromECAT7ACF.cxx │ ├── AbsTimeIntervalWithParsing.cxx │ ├── CMakeLists.txt │ ├── DAVArrayFilter3D.cxx │ ├── DAVImageFilter3D.cxx │ ├── ModifiedInverseAveragingImageFilterAll.cxx │ ├── ModifiedInverseAverigingArrayFilter.cxx │ ├── ModifiedInverseAverigingImageFilter.cxx │ ├── NonseparableSpatiallyVaryingFilters.cxx │ ├── NonseparableSpatiallyVaryingFilters3D.cxx │ ├── Quaternion.cxx │ ├── SeparableLowPassArrayFilter.cxx │ ├── SeparableLowPassImageFilter.cxx │ ├── fwd_and_bck_manipulation_for_SAF.cxx │ ├── local_buildblock_registries.cxx │ ├── local_helping_functions.cxx │ └── multiply_plane_scale_factorsImageProcessor.cxx ├── iterative │ └── OSSPS │ │ └── line_search.cxx ├── listmode │ ├── CListModeDataLMF.cxx │ ├── CMakeLists.txt │ └── LmToProjDataWithMC.cxx ├── listmode_utilities │ ├── CMakeLists.txt │ ├── change_lm_time_tags.cxx │ ├── get_singles_info.cxx │ └── lm_to_projdata_with_MC.cxx ├── motion │ ├── CMakeLists.txt │ ├── MatchTrackerAndScanner.cxx │ ├── NonRigidObjectTransformationUsingBSplines.cxx │ ├── PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion.cxx │ ├── Polaris_MT_File.cxx │ ├── RigidObject3DMotion.cxx │ ├── RigidObject3DMotionFromPolaris.cxx │ ├── RigidObject3DTransformation.cxx │ ├── TimeFrameMotion.cxx │ ├── Transform3DObjectImageProcessor.cxx │ ├── local_motion_registries.cxx │ └── transform_3d_object.cxx ├── motion_test │ ├── CMakeLists.txt │ ├── input │ │ ├── ground_truth.nii.gz │ │ └── to_transform.nii.gz │ └── test_BSpline_transformations.cxx ├── motion_utilities │ ├── CMakeLists.txt │ ├── add_planes_to_image.cxx │ ├── find_motion_corrected_norm_factors.cxx │ ├── list_deformation_vectors.cxx │ ├── list_polaris_info.cxx │ ├── match_tracker_and_scanner.cxx │ ├── move_image.cxx │ ├── move_projdata.cxx │ ├── non_rigid_transform.cxx │ ├── remove_corrupted_sinograms.cxx │ ├── report_movement.cxx │ ├── rigid_object_transform_image.cxx │ ├── rigid_object_transform_projdata.cxx │ └── sync_polaris.cxx ├── recon_buildblock │ ├── BinNormalisationFromML2D.cxx │ ├── BinNormalisationSinogramRescaling.cxx │ ├── BinNormalisationUsingProfile.cxx │ ├── CMakeLists.txt │ ├── DataSymmetriesForDensels_PET_CartesianGrid.cxx │ ├── ParametricQuadraticPrior.cxx │ ├── PoissonLogLikelihoodWithLinearModelForMeanAndDynamicProjData.cxx │ ├── PostsmoothingForwardProjectorByBin.cxx │ ├── ProjMatrixByBinSinglePhoton.cxx │ ├── ProjMatrixByBinUsingSolidAngle.cxx │ ├── ProjMatrixByBinWithPositronRange.cxx │ ├── ProjMatrixByDensel.cxx │ ├── ProjMatrixByDenselOnCartesianGridUsingElement.cxx │ ├── ProjMatrixByDenselUsingRayTracing.cxx │ └── local_recon_buildblock_registries.cxx ├── recon_test │ ├── fwdtestDensel.cxx │ └── test_ProjMatrixByBinUsingInterpolation.cxx ├── test │ ├── input │ │ ├── postfilter_nonseparable_with_delta.par │ │ ├── postfilter_nonseparable_with_image_kernel.par │ │ ├── postfilter_separable_with_image_kernel.par │ │ ├── short_triple_frame.fdef │ │ ├── short_triple_plasma.if │ │ ├── triple_blood_data.tac │ │ └── triple_frame.fdef │ ├── test_Fourier.cxx │ ├── test_LmToProjdataWithMC.cxx │ ├── test_Quaternion.cxx │ ├── test_RigidObject3DTransformation.cxx │ ├── test_ecat7_normalisation.sh │ ├── test_nonseparable_convolution_with_image_kernel.sh │ └── test_proj_data_info_LOR.cxx └── utilities │ ├── Bland_Altman_plot.cxx │ ├── CMakeLists.txt │ ├── CoG.cxx │ ├── add_ecat7_header_to_sgl.cxx │ ├── add_side_shields.cxx │ ├── add_time_frame_info.cxx │ ├── apply_plane_rescale_factors.cxx │ ├── change_mhead_file_type.cxx │ ├── compute_gradient.cxx │ ├── compute_plane_rescale_factors.cxx │ ├── create_normfactors.cxx │ ├── create_normfactors3D.cxx │ ├── fillwith1.cxx │ ├── fillwithotherprojdata.cxx │ ├── find_sinogram_rescaling_factors.cxx │ ├── fit_cylinder.cxx │ ├── image_flip_x.cxx │ ├── interpolate_blocks.cxx │ ├── interpolate_projdata.cxx │ ├── inverse_SSRB.cxx │ ├── inverse_proj_data.cxx │ ├── line_profiles_through_projdata.cxx │ ├── list_TAC_ROI_values.cxx │ ├── make_cylinder.cxx │ ├── make_grid_image.cxx │ ├── mode.cxx │ ├── normalizedbckproj.cxx │ ├── precompute_denominator_SPS.cxx │ ├── prepare_projdata.cxx │ ├── remove_sinograms.cxx │ ├── set_blocks_to_value.cxx │ ├── shift_projdata_along_axis.cxx │ ├── show_ecat7_header.cxx │ ├── threshold_norm_data.cxx │ └── zero_projdata_from_norm.cxx ├── include ├── stir │ ├── ArcCorrection.h │ ├── Array.h │ ├── Array.inl │ ├── ArrayFilter1DUsingConvolution.h │ ├── ArrayFilter1DUsingConvolutionSymmetricKernel.h │ ├── ArrayFilter2DUsingConvolution.h │ ├── ArrayFilter3DUsingConvolution.h │ ├── ArrayFilterUsingRealDFTWithPadding.h │ ├── ArrayFunction.h │ ├── ArrayFunction.inl │ ├── ArrayFunctionObject.h │ ├── ArrayFunctionObject_1ArgumentImplementation.h │ ├── ArrayFunctionObject_2ArgumentImplementation.h │ ├── ArrayFwd.h │ ├── Array_complex_numbers.h │ ├── BasicCoordinate.h │ ├── BasicCoordinate.inl │ ├── Bin.h │ ├── Bin.inl │ ├── BoundaryConditions.h │ ├── ByteOrder.h │ ├── ByteOrder.inl │ ├── ByteOrderDefine.h │ ├── CPUTimer.h │ ├── CPUTimer.inl │ ├── CartesianCoordinate2D.h │ ├── CartesianCoordinate2D.inl │ ├── CartesianCoordinate3D.h │ ├── CartesianCoordinate3D.inl │ ├── ChainedDataProcessor.h │ ├── Coordinate2D.h │ ├── Coordinate2D.inl │ ├── Coordinate3D.h │ ├── Coordinate3D.inl │ ├── Coordinate4D.h │ ├── Coordinate4D.inl │ ├── DataProcessor.h │ ├── DataProcessor.inl │ ├── DataSymmetriesForViewSegmentNumbers.h │ ├── Densel.h │ ├── DetectionPosition.h │ ├── DetectionPosition.inl │ ├── DetectionPositionPair.h │ ├── DetectionPositionPair.inl │ ├── DetectorCoordinateMap.h │ ├── DiscretisedDensity.h │ ├── DiscretisedDensity.inl │ ├── DiscretisedDensityOnCartesianGrid.h │ ├── DiscretisedDensityOnCartesianGrid.inl │ ├── DynamicDiscretisedDensity.h │ ├── DynamicDiscretisedDensity.inl │ ├── DynamicProjData.h │ ├── ExamData.h │ ├── ExamInfo.h │ ├── ExamInfo.inl │ ├── FactoryRegistry.h │ ├── FactoryRegistry.inl │ ├── FilePath.h │ ├── FilePath.inl │ ├── FullArrayIterator.h │ ├── FullArrayIterator.inl │ ├── GammaArrayFilter2D.h │ ├── GammaImageFilter2D.h │ ├── GatedDiscretisedDensity.h │ ├── GatedProjData.h │ ├── GeneralisedPoissonNoiseGenerator.h │ ├── GeometryBlocksOnCylindrical.h │ ├── HUToMuImageProcessor.h │ ├── HighResWallClockTimer.h │ ├── HigherPrecision.h │ ├── IO │ │ ├── ECAT6ImageInputFileFormat.h │ │ ├── ECAT6OutputFileFormat.h │ │ ├── ECAT7DynamicDiscretisedDensityInputFileFormat.h │ │ ├── ECAT7DynamicDiscretisedDensityOutputFileFormat.h │ │ ├── ECAT7ImageInputFileFormat.h │ │ ├── ECAT7OutputFileFormat.h │ │ ├── ECAT7ParametricDensityOutputFileFormat.h │ │ ├── ECAT8_32bitListmodeInputFileFormat.h │ │ ├── ECAT962ListmodeInputFileFormat.h │ │ ├── ECAT966ListmodeInputFileFormat.h │ │ ├── FileSignature.h │ │ ├── GEHDF5ListmodeInputFileFormat.h │ │ ├── GEHDF5Wrapper.h │ │ ├── GEHDF5Wrapper.inl │ │ ├── GIPL_ImageFormat.h │ │ ├── ITKImageInputFileFormat.h │ │ ├── ITKOutputFileFormat.h │ │ ├── InputFileFormat.h │ │ ├── InputFileFormatRegistry.h │ │ ├── InputFileFormatRegistry.txx │ │ ├── InputStreamFromROOTFile.h │ │ ├── InputStreamFromROOTFile.inl │ │ ├── InputStreamFromROOTFileForCylindricalPET.h │ │ ├── InputStreamFromROOTFileForCylindricalPET.inl │ │ ├── InputStreamFromROOTFileForECATPET.h │ │ ├── InputStreamFromROOTFileForECATPET.inl │ │ ├── InputStreamWithRecords.h │ │ ├── InputStreamWithRecords.inl │ │ ├── InputStreamWithRecordsFromHDF5.h │ │ ├── InputStreamWithRecordsFromHDF5.inl │ │ ├── InputStreamWithRecordsFromUPENN.h │ │ ├── InputStreamWithRecordsFromUPENN.inl │ │ ├── InputStreamWithRecordsFromUPENNbin.h │ │ ├── InputStreamWithRecordsFromUPENNbin.inl │ │ ├── InputStreamWithRecordsFromUPENNtxt.h │ │ ├── InputStreamWithRecordsFromUPENNtxt.inl │ │ ├── InterfileDynamicDiscretisedDensityInputFileFormat.h │ │ ├── InterfileDynamicDiscretisedDensityOutputFileFormat.h │ │ ├── InterfileHeader.h │ │ ├── InterfileHeaderSiemens.h │ │ ├── InterfileImageInputFileFormat.h │ │ ├── InterfileOutputFileFormat.h │ │ ├── InterfilePDFSHeaderSPECT.h │ │ ├── InterfileParametricDiscretisedDensityInputFileFormat.h │ │ ├── InterfileParametricDiscretisedDensityOutputFileFormat.h │ │ ├── MultiDynamicDiscretisedDensityInputFileFormat.h │ │ ├── MultiDynamicDiscretisedDensityOutputFileFormat.h │ │ ├── MultiParametricDiscretisedDensityInputFileFormat.h │ │ ├── MultiParametricDiscretisedDensityOutputFileFormat.h │ │ ├── OutputFileFormat.h │ │ ├── OutputFileFormat.txx │ │ ├── PENNListmodeInputFileFormat.h │ │ ├── ROOTListmodeInputFileFormat.h │ │ ├── SAFIRCListmodeInputFileFormat.h │ │ ├── ecat6_types.h │ │ ├── ecat6_utils.h │ │ ├── interfile.h │ │ ├── read_data.h │ │ ├── read_data.inl │ │ ├── read_data_1d.h │ │ ├── read_data_1d.inl │ │ ├── read_from_file.h │ │ ├── stir_ecat6.h │ │ ├── stir_ecat7.h │ │ ├── stir_ecat_common.h │ │ ├── test │ │ │ └── test_IO.h │ │ ├── write_data.h │ │ ├── write_data.inl │ │ ├── write_data_1d.h │ │ ├── write_data_1d.inl │ │ └── write_to_file.h │ ├── ImagingModality.h │ ├── IndexRange.h │ ├── IndexRange.inl │ ├── IndexRange2D.h │ ├── IndexRange2D.inl │ ├── IndexRange3D.h │ ├── IndexRange3D.inl │ ├── IndexRange4D.h │ ├── IndexRange4D.inl │ ├── KOSMAPOSL │ │ └── KOSMAPOSLReconstruction.h │ ├── KeyParser.h │ ├── LORCoordinates.h │ ├── LORCoordinates.inl │ ├── ML_norm.h │ ├── MaximalArrayFilter3D.h │ ├── MaximalImageFilter3D.h │ ├── MedianArrayFilter3D.h │ ├── MedianImageFilter3D.h │ ├── MinimalArrayFilter3D.h │ ├── MinimalImageFilter3D.h │ ├── MultipleDataSetHeader.h │ ├── MultipleDataSetHeader.inl │ ├── MultipleProjData.h │ ├── NestedIterator.h │ ├── NestedIterator.inl │ ├── NestedIteratorHelpers.h │ ├── NonseparableConvolutionUsingRealDFTImageFilter.h │ ├── NumericInfo.h │ ├── NumericType.h │ ├── NumericType.inl │ ├── NumericVectorWithOffset.h │ ├── NumericVectorWithOffset.inl │ ├── OSMAPOSL │ │ └── OSMAPOSLReconstruction.h │ ├── OSSPS │ │ └── OSSPSReconstruction.h │ ├── ParseAndCreateFrom.h │ ├── ParseAndCreateFrom.inl │ ├── ParseDiscretisedDensityParameters.h │ ├── ParsingObject.h │ ├── PatientPosition.h │ ├── PixelsOnCartesianGrid.h │ ├── PixelsOnCartesianGrid.inl │ ├── PostFiltering.h │ ├── PostFiltering.inl │ ├── ProjData.h │ ├── ProjData.inl │ ├── ProjDataFromStream.h │ ├── ProjDataFromStream.inl │ ├── ProjDataGEHDF5.h │ ├── ProjDataInMemory.h │ ├── ProjDataInfo.h │ ├── ProjDataInfo.inl │ ├── ProjDataInfoBlocksOnCylindrical.h │ ├── ProjDataInfoBlocksOnCylindricalNoArcCorr.h │ ├── ProjDataInfoCylindrical.h │ ├── ProjDataInfoCylindrical.inl │ ├── ProjDataInfoCylindricalArcCorr.h │ ├── ProjDataInfoCylindricalArcCorr.inl │ ├── ProjDataInfoCylindricalNoArcCorr.h │ ├── ProjDataInfoCylindricalNoArcCorr.inl │ ├── ProjDataInfoGeneric.h │ ├── ProjDataInfoGeneric.inl │ ├── ProjDataInfoGenericNoArcCorr.h │ ├── ProjDataInfoGenericNoArcCorr.inl │ ├── ProjDataInfoSubsetByView.h │ ├── ProjDataInterfile.h │ ├── Radionuclide.h │ ├── RadionuclideDB.h │ ├── RegisteredObject.h │ ├── RegisteredObject.inl │ ├── RegisteredObjectBase.h │ ├── RegisteredParsingObject.h │ ├── RegisteredParsingObject.inl │ ├── RelatedViewgrams.h │ ├── RelatedViewgrams.inl │ ├── RunTests.h │ ├── SSRB.h │ ├── Scanner.h │ ├── Scanner.inl │ ├── Segment.h │ ├── Segment.inl │ ├── SegmentBySinogram.h │ ├── SegmentBySinogram.inl │ ├── SegmentByView.h │ ├── SegmentByView.inl │ ├── SegmentIndices.h │ ├── SegmentIndices.inl │ ├── SeparableArrayFunctionObject.h │ ├── SeparableCartesianMetzImageFilter.h │ ├── SeparableConvolutionImageFilter.h │ ├── SeparableGaussianArrayFilter.h │ ├── SeparableGaussianImageFilter.h │ ├── SeparableMetzArrayFilter.h │ ├── Shape │ │ ├── Box3D.h │ │ ├── CombinedShape3D.h │ │ ├── CombinedShape3D.inl │ │ ├── DiscretisedShape3D.h │ │ ├── DiscretisedShape3D.inl │ │ ├── Ellipsoid.h │ │ ├── EllipsoidalCylinder.h │ │ ├── EllipsoidalCylinder.inl │ │ ├── GenerateImage.h │ │ ├── Shape3D.h │ │ ├── Shape3D.inl │ │ └── Shape3DWithOrientation.h │ ├── Sinogram.h │ ├── Sinogram.inl │ ├── SinogramIndices.h │ ├── SinogramIndices.inl │ ├── StirException.h │ ├── Succeeded.h │ ├── TOF_conversions.h │ ├── TextWriter.h │ ├── ThresholdMinToSmallPositiveValueDataProcessor.h │ ├── TimeFrameDefinitions.h │ ├── TimeGateDefinitions.h │ ├── TimedBlock.h │ ├── TimedObject.h │ ├── TimedObject.inl │ ├── Timer.h │ ├── Timer.inl │ ├── TrivialDataSymmetriesForViewSegmentNumbers.h │ ├── TrivialDataSymmetriesForViewSegmentNumbers.inl │ ├── TruncateToCylindricalFOVImageProcessor.h │ ├── VectorWithOffset.h │ ├── VectorWithOffset.inl │ ├── Verbosity.h │ ├── ViewSegmentNumbers.h │ ├── ViewSegmentNumbers.inl │ ├── Viewgram.h │ ├── Viewgram.inl │ ├── ViewgramIndices.h │ ├── ViewgramIndices.inl │ ├── VoxelsOnCartesianGrid.h │ ├── VoxelsOnCartesianGrid.inl │ ├── WienerArrayFilter2D.h │ ├── WienerImageFilter2D.h │ ├── ZoomOptions.h │ ├── analytic │ │ ├── DDSR2D │ │ │ └── DDSR2DReconstruction.h │ │ ├── FBP2D │ │ │ ├── FBP2DReconstruction.h │ │ │ └── RampFilter.h │ │ ├── FBP3DRP │ │ │ ├── ColsherFilter.h │ │ │ └── FBP3DRPReconstruction.h │ │ ├── GRD2D │ │ │ └── GRD2DReconstruction.h │ │ ├── SRT2D │ │ │ └── SRT2DReconstruction.h │ │ └── SRT2DSPECT │ │ │ └── SRT2DSPECTReconstruction.h │ ├── array_index_functions.h │ ├── array_index_functions.inl │ ├── assign.h │ ├── assign_to_subregion.h │ ├── assign_to_subregion.inl │ ├── centre_of_gravity.h │ ├── common.h │ ├── config │ │ ├── gcc.h │ │ └── visualc.h │ ├── convert_array.h │ ├── convert_array.inl │ ├── convert_range.h │ ├── convert_range.inl │ ├── copy_fill.h │ ├── cross_product.h │ ├── cuda_utilities.h │ ├── data │ │ ├── SinglesRates.h │ │ ├── SinglesRates.inl │ │ ├── SinglesRatesForTimeFrames.h │ │ ├── SinglesRatesForTimeSlices.h │ │ ├── SinglesRatesFromECAT7.h │ │ ├── SinglesRatesFromGEHDF5.h │ │ ├── SinglesRatesFromSglFile.h │ │ └── randoms_from_singles.h │ ├── date_time_functions.h │ ├── decay_correction_factor.h │ ├── deprecated.h │ ├── detail │ │ └── test_if_1d.h │ ├── display.h │ ├── display.inl │ ├── doxygen_doc_for_boost.h │ ├── doxygengroups.h │ ├── doxygenmain.h │ ├── error.h │ ├── evaluation │ │ ├── ROIValues.h │ │ └── compute_ROI_values.h │ ├── extend_projdata.h │ ├── extract_line.h │ ├── extract_line.inl │ ├── find_STIR_config.h │ ├── find_fwhm_in_image.h │ ├── find_fwhm_in_image.inl │ ├── format.h │ ├── geometry │ │ └── line_distances.h │ ├── getopt.h │ ├── index_at_maximum.h │ ├── info.h │ ├── interfile_keyword_functions.h │ ├── interpolate.h │ ├── interpolate_projdata.h │ ├── inverse_SSRB.h │ ├── is_null_ptr.h │ ├── line.h │ ├── linear_regression.h │ ├── linear_regression.inl │ ├── listmode │ │ ├── CListEventCylindricalScannerWithDiscreteDetectors.h │ │ ├── CListEventCylindricalScannerWithViewTangRingRingEncoding.h │ │ ├── CListEventCylindricalScannerWithViewTangRingRingEncoding.inl │ │ ├── CListEventScannerWithDiscreteDetectors.h │ │ ├── CListEventScannerWithDiscreteDetectors.inl │ │ ├── CListModeData.h │ │ ├── CListModeDataECAT.h │ │ ├── CListModeDataECAT8_32bit.h │ │ ├── CListModeDataGEHDF5.h │ │ ├── CListModeDataPENN.h │ │ ├── CListModeDataROOT.h │ │ ├── CListModeDataSAFIR.h │ │ ├── CListRecord.h │ │ ├── CListRecordECAT8_32bit.h │ │ ├── CListRecordECAT962.h │ │ ├── CListRecordECAT966.h │ │ ├── CListRecordGEHDF5.h │ │ ├── CListRecordPENN.h │ │ ├── CListRecordROOT.h │ │ ├── CListRecordROOT.inl │ │ ├── CListRecordSAFIR.h │ │ ├── CListRecordSAFIR.inl │ │ ├── ListEvent.h │ │ ├── ListGatingInput.h │ │ ├── ListModeData.h │ │ ├── ListModeData_dummy.h │ │ ├── ListRecord.h │ │ ├── ListRecordWithGatingInput.h │ │ ├── ListTime.h │ │ ├── LmToProjData.h │ │ ├── LmToProjDataAbstract.h │ │ ├── LmToProjDataBootstrap.h │ │ ├── LmToProjDataWithRandomRejection.h │ │ ├── NiftyPET_listmode │ │ │ └── LmToProjDataNiftyPET.h │ │ ├── SPECTListEvent.h │ │ ├── SPECTListModeData.h │ │ ├── SPECTListRecord.h │ │ └── SPECTListRecordWithGatingInput.h │ ├── make_array.h │ ├── make_array.inl │ ├── min_positive_element.h │ ├── modelling │ │ ├── KineticModel.h │ │ ├── KineticParameters.h │ │ ├── KineticParameters.inl │ │ ├── ModelMatrix.h │ │ ├── ModelMatrix.inl │ │ ├── ParametricDiscretisedDensity.h │ │ ├── ParseAndCreateParametricDiscretisedDensityFrom.h │ │ ├── ParseAndCreateParametricDiscretisedDensityFrom.inl │ │ ├── PatlakPlot.h │ │ ├── PlasmaData.h │ │ ├── PlasmaData.inl │ │ ├── PlasmaSample.h │ │ └── PlasmaSample.inl │ ├── modulo.h │ ├── more_algorithms.h │ ├── more_algorithms.inl │ ├── multiply_crystal_factors.h │ ├── num_threads.h │ ├── numerics │ │ ├── BSplines.h │ │ ├── BSplines1DRegularGrid.h │ │ ├── BSplines1DRegularGrid.inl │ │ ├── BSplinesDetail.inl │ │ ├── BSplinesRegularGrid.h │ │ ├── BSplinesRegularGrid.inl │ │ ├── BSplines_coef.inl │ │ ├── BSplines_weights.inl │ │ ├── FastErf.h │ │ ├── FastErf.inl │ │ ├── IR_filters.h │ │ ├── IR_filters.inl │ │ ├── MatrixFunction.h │ │ ├── MatrixFunction.inl │ │ ├── determinant.h │ │ ├── divide.h │ │ ├── divide.inl │ │ ├── erf.h │ │ ├── erf.inl │ │ ├── fftshift.h │ │ ├── fourier.h │ │ ├── ieeefp.h │ │ ├── integrate_discrete_function.h │ │ ├── integrate_discrete_function.inl │ │ ├── max_eigenvector.h │ │ ├── norm.h │ │ ├── norm.inl │ │ ├── overlap_interpolate.h │ │ ├── overlap_interpolate.inl │ │ ├── sampling_functions.h │ │ ├── sampling_functions.inl │ │ └── stir_NumericalRecipes.h │ ├── recon_array_functions.h │ ├── recon_buildblock │ │ ├── AnalyticReconstruction.h │ │ ├── BackProjectorByBin.h │ │ ├── BackProjectorByBinUsingInterpolation.h │ │ ├── BackProjectorByBinUsingProjMatrixByBin.h │ │ ├── BackProjectorByBinUsingSquareProjMatrixByBin.h │ │ ├── BinNormalisation.h │ │ ├── BinNormalisationFromAttenuationImage.h │ │ ├── BinNormalisationFromECAT7.h │ │ ├── BinNormalisationFromECAT8.h │ │ ├── BinNormalisationFromGEHDF5.h │ │ ├── BinNormalisationFromProjData.h │ │ ├── BinNormalisationPETFromComponents.h │ │ ├── BinNormalisationSPECT.h │ │ ├── BinNormalisationWithCalibration.h │ │ ├── CUDA │ │ │ ├── CudaGibbsPenalty.cuh │ │ │ ├── CudaGibbsPenalty.h │ │ │ └── CudaRelativeDifferencePrior.h │ │ ├── ChainedBinNormalisation.h │ │ ├── DataSymmetriesForBins.h │ │ ├── DataSymmetriesForBins.inl │ │ ├── DataSymmetriesForBins_PET_CartesianGrid.h │ │ ├── DataSymmetriesForBins_PET_CartesianGrid.inl │ │ ├── DataSymmetriesForDensels.h │ │ ├── DataSymmetriesForDensels.inl │ │ ├── DistributedCachingInformation.h │ │ ├── DistributedWorker.h │ │ ├── FilterRootPrior.h │ │ ├── ForwardProjectorByBin.h │ │ ├── ForwardProjectorByBinUsingProjMatrixByBin.h │ │ ├── ForwardProjectorByBinUsingRayTracing.h │ │ ├── FourierRebinning.h │ │ ├── GeneralisedObjectiveFunction.h │ │ ├── GeneralisedPrior.h │ │ ├── GeneralisedPrior.inl │ │ ├── GibbsPenalty.h │ │ ├── GibbsPenalty.inl │ │ ├── GibbsQuadraticPenalty.h │ │ ├── GibbsRelativeDifferencePenalty.h │ │ ├── IterativeReconstruction.h │ │ ├── LogcoshPrior.h │ │ ├── ML_estimate_component_based_normalisation.h │ │ ├── NiftyPET_projector │ │ │ ├── BackProjectorByBinNiftyPET.h │ │ │ ├── ForwardProjectorByBinNiftyPET.h │ │ │ ├── NiftyPETHelper.h │ │ │ └── ProjectorByBinPairUsingNiftyPET.h │ │ ├── PLSPrior.h │ │ ├── Parallelproj_projector │ │ │ ├── BackProjectorByBinParallelproj.h │ │ │ ├── ForwardProjectorByBinParallelproj.h │ │ │ ├── ParallelprojHelper.h │ │ │ └── ProjectorByBinPairUsingParallelproj.h │ │ ├── PinholeSPECTUB_Tools.h │ │ ├── PinholeSPECTUB_Weight3d.h │ │ ├── PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData.h │ │ ├── PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData.txx │ │ ├── PoissonLogLikelihoodWithLinearModelForMean.h │ │ ├── PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion.h │ │ ├── PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion.txx │ │ ├── PoissonLogLikelihoodWithLinearModelForMeanAndListModeData.h │ │ ├── PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin.h │ │ ├── PoissonLogLikelihoodWithLinearModelForMeanAndProjData.h │ │ ├── PostsmoothingBackProjectorByBin.h │ │ ├── PresmoothingForwardProjectorByBin.h │ │ ├── PriorWithParabolicSurrogate.h │ │ ├── ProjDataRebinning.h │ │ ├── ProjMatrixByBin.h │ │ ├── ProjMatrixByBin.inl │ │ ├── ProjMatrixByBinFromFile.h │ │ ├── ProjMatrixByBinPinholeSPECTUB.h │ │ ├── ProjMatrixByBinSPECTUB.h │ │ ├── ProjMatrixByBinUsingInterpolation.h │ │ ├── ProjMatrixByBinUsingRayTracing.h │ │ ├── ProjMatrixElemsForOneBin.h │ │ ├── ProjMatrixElemsForOneBin.inl │ │ ├── ProjMatrixElemsForOneBinValue.h │ │ ├── ProjMatrixElemsForOneBinValue.inl │ │ ├── ProjMatrixElemsForOneDensel.h │ │ ├── ProjMatrixElemsForOneDensel.inl │ │ ├── ProjMatrixElemsForOneDenselValue.h │ │ ├── ProjMatrixElemsForOneDenselValue.inl │ │ ├── ProjectorByBinPair.h │ │ ├── ProjectorByBinPairUsingProjMatrixByBin.h │ │ ├── ProjectorByBinPairUsingSeparateProjectors.h │ │ ├── QuadraticPrior.h │ │ ├── RayTraceVoxelsOnCartesianGrid.h │ │ ├── Reconstruction.h │ │ ├── RelatedBins.h │ │ ├── RelatedBins.inl │ │ ├── RelatedDensels.h │ │ ├── RelatedDensels.inl │ │ ├── RelativeDifferencePrior.h │ │ ├── SPECTUB_Tools.h │ │ ├── SPECTUB_Weight3d.h │ │ ├── SqrtHessianRowSum.h │ │ ├── SumOfGeneralisedObjectiveFunctions.h │ │ ├── SumOfGeneralisedObjectiveFunctions.inl │ │ ├── SymmetryOperation.h │ │ ├── SymmetryOperations_PET_CartesianGrid.h │ │ ├── SymmetryOperations_PET_CartesianGrid.inl │ │ ├── TrivialBinNormalisation.h │ │ ├── TrivialDataSymmetriesForBins.h │ │ ├── distributable.h │ │ ├── distributable.txx │ │ ├── distributableMPICacheEnabled.h │ │ ├── distributable_main.h │ │ ├── distributed_functions.h │ │ ├── distributed_test_functions.h │ │ ├── find_basic_vs_nums_in_subsets.h │ │ └── test │ │ │ ├── ObjectiveFunctionTests.h │ │ │ ├── PoissonLLReconstructionTests.h │ │ │ └── ReconstructionTests.h │ ├── round.h │ ├── round.inl │ ├── scale_sinograms.h │ ├── scatter │ │ ├── CreateTailMaskFromACFs.h │ │ ├── ScatterEstimation.h │ │ ├── ScatterEstimation.inl │ │ ├── ScatterSimulation.h │ │ ├── ScatterSimulation.inl │ │ └── SingleScatterSimulation.h │ ├── shared_ptr.h │ ├── spatial_transformation │ │ ├── GatedSpatialTransformation.h │ │ ├── InvertAxis.h │ │ ├── SpatialTransformation.h │ │ └── warp_image.h │ ├── stir_math.h │ ├── stream.h │ ├── stream.inl │ ├── thresholding.h │ ├── type_traits.h │ ├── unique_ptr.h │ ├── utilities.h │ ├── utilities.inl │ ├── warning.h │ └── zoom.h └── stir_experimental │ ├── AbsTimeInterval.h │ ├── AbsTimeIntervalFromDynamicData.h │ ├── AbsTimeIntervalFromECAT7ACF.h │ ├── AbsTimeIntervalWithParsing.h │ ├── DAVArrayFilter3D.h │ ├── DAVImageFilter3D.h │ ├── Filter.h │ ├── ModifiedInverseAveragingImageFilterAll.h │ ├── ModifiedInverseAverigingArrayFilter.h │ ├── ModifiedInverseAverigingImageFilter.h │ ├── NonseparableSpatiallyVaryingFilters.h │ ├── NonseparableSpatiallyVaryingFilters3D.h │ ├── Quaternion.h │ ├── Quaternion.inl │ ├── SeparableGaussianArrayFilter.h │ ├── SeparableGaussianImageFilter.h │ ├── SeparableLowPassArrayFilter.h │ ├── SeparableLowPassArrayFilter2.h │ ├── SeparableLowPassImageFilter.h │ ├── doxygengroups.h │ ├── fft.h │ ├── fwd_and_bck_manipulation_for_SAF.h │ ├── listmode │ ├── CListModeDataLMF.h │ ├── CListRecordLMF.h │ └── LmToProjDataWithMC.h │ ├── local_helping_functions.h │ ├── modelling │ ├── BloodFrame.h │ ├── BloodFrame.inl │ ├── BloodFrameData.h │ ├── BloodFrameData.inl │ ├── OneParamModel.h │ └── OneParamModel.inl │ ├── motion │ ├── MatchTrackerAndScanner.h │ ├── NonRigidObjectTransformationUsingBSplines.h │ ├── ObjectTransformation.h │ ├── PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion.h │ ├── Polaris_MT_File.h │ ├── RigidObject3DMotion.h │ ├── RigidObject3DMotionFromPolaris.h │ ├── RigidObject3DTransformation.h │ ├── TimeFrameMotion.h │ ├── Transform3DObjectImageProcessor.h │ ├── bin_interpolate.h │ ├── transform_3d_object.h │ └── transform_3d_object.inl │ ├── multiply_plane_scale_factorsImageProcessor.h │ ├── numerics │ ├── linear_extrapolation.h │ ├── more_interpolators.h │ └── more_interpolators.inl │ ├── phantoms │ ├── CylindersWithLineSource.h │ └── Utah.h │ └── recon_buildblock │ ├── BinNormalisationFromML2D.h │ ├── BinNormalisationSinogramRescaling.h │ ├── BinNormalisationUsingProfile.h │ ├── DataSymmetriesForDensels_PET_CartesianGrid.h │ ├── DataSymmetriesForDensels_PET_CartesianGrid.inl │ ├── ParametricQuadraticPrior.h │ ├── PoissonLogLikelihoodWithLinearModelForMeanAndDynamicProjData.h │ ├── PostsmoothingForwardProjectorByBin.h │ ├── ProjMatrixByBinSinglePhoton.h │ ├── ProjMatrixByBinUsingSolidAngle.h │ ├── ProjMatrixByBinWithPositronRange.h │ ├── ProjMatrixByDensel.h │ ├── ProjMatrixByDensel.inl │ ├── ProjMatrixByDenselOnCartesianGridUsingElement.h │ └── ProjMatrixByDenselUsingRayTracing.h ├── iterative ├── KOSMAPOSL │ ├── CMakeLists.txt │ ├── KOSMAPOSL.cxx │ └── KOSMAPOSLReconstruction.cxx ├── OSMAPOSL │ ├── CMakeLists.txt │ ├── OSMAPOSL.cxx │ └── OSMAPOSLReconstruction.cxx ├── OSSPS │ ├── CMakeLists.txt │ ├── OSSPS.cxx │ └── OSSPSReconstruction.cxx ├── POSMAPOSL │ ├── CMakeLists.txt │ └── POSMAPOSL.cxx └── POSSPS │ ├── CMakeLists.txt │ └── POSSPS.cxx ├── listmode_buildblock ├── CListEvent.cxx ├── CListModeDataECAT.cxx ├── CListModeDataECAT8_32bit.cxx ├── CListModeDataGEHDF5.cxx ├── CListModeDataPENN.cxx ├── CListModeDataROOT.cxx ├── CListModeDataSAFIR.cxx ├── CListRecordECAT8_32bit.cxx ├── CListRecordECAT962.cxx ├── CListRecordECAT966.cxx ├── CListRecordPENN.cxx ├── CListRecordROOT.cxx ├── CMakeLists.txt ├── ListEvent.cxx ├── ListModeData.cxx ├── LmToProjData.cxx ├── LmToProjDataAbstract.cxx ├── LmToProjDataBootstrap.cxx ├── LmToProjDataWithRandomRejection.cxx └── NiftyPET_listmode │ └── LmToProjDataNiftyPET.cxx ├── listmode_utilities ├── CMakeLists.txt ├── add_ecat7_header_to_sgl.cxx ├── conv_NiftyPET_stir.cxx ├── list_lm_countrates.cxx ├── list_lm_events.cxx ├── list_lm_info.cxx ├── lm_fansums.cxx ├── lm_to_projdata.cxx ├── lm_to_projdata_NiftyPET.cxx ├── lm_to_projdata_bootstrap.cxx ├── lm_to_projdata_with_random_rejection.cxx ├── print_sgl_values.cxx ├── rebin_sgl_file.cxx └── scan_sgl_file.cxx ├── modelling_buildblock ├── CMakeLists.txt ├── KineticModel.cxx ├── ParametricDiscretisedDensity.cxx ├── PatlakPlot.cxx └── modelling_registries.cxx ├── modelling_utilities ├── CMakeLists.txt ├── apply_patlak_to_images.cxx ├── extract_single_images_from_parametric_image.cxx ├── get_dynamic_images_from_parametric_images.cxx ├── make_parametric_image_from_components.cxx ├── mult_image_parameters.cxx ├── mult_model_with_dyn_images.cxx └── write_patlak_matrix.cxx ├── numerics_buildblock ├── CMakeLists.txt ├── determinant.cxx └── fourier.cxx ├── recon_buildblock ├── AnalyticReconstruction.cxx ├── BackProjectorByBin.cxx ├── BackProjectorByBinUsingInterpolation.cxx ├── BackProjectorByBinUsingInterpolation_3DCho.cxx ├── BackProjectorByBinUsingInterpolation_linear.cxx ├── BackProjectorByBinUsingInterpolation_piecewise_linear.cxx ├── BackProjectorByBinUsingProjMatrixByBin.cxx ├── BackProjectorByBinUsingSquareProjMatrixByBin.cxx ├── BinNormalisation.cxx ├── BinNormalisationFromAttenuationImage.cxx ├── BinNormalisationFromECAT7.cxx ├── BinNormalisationFromECAT8.cxx ├── BinNormalisationFromGEHDF5.cxx ├── BinNormalisationFromProjData.cxx ├── BinNormalisationPETFromComponents.cxx ├── BinNormalisationSPECT.cxx ├── BinNormalisationWithCalibration.cxx ├── CMakeLists.txt ├── CUDA │ ├── CudaGibbsPenaltiesInstantiations.cu │ └── CudaRelativeDifferencePrior.cu ├── ChainedBinNormalisation.cxx ├── DataSymmetriesForBins.cxx ├── DataSymmetriesForBins_PET_CartesianGrid.cxx ├── DataSymmetriesForDensels.cxx ├── DistributedCachingInformation.cxx ├── DistributedWorker.cxx ├── FilterRootPrior.cxx ├── ForwardProjectorByBin.cxx ├── ForwardProjectorByBinUsingProjMatrixByBin.cxx ├── ForwardProjectorByBinUsingRayTracing.cxx ├── ForwardProjectorByBinUsingRayTracing_Siddon.cxx ├── FourierRebinning.cxx ├── GeneralisedObjectiveFunction.cxx ├── GeneralisedPrior.cxx ├── IterativeReconstruction.cxx ├── LogcoshPrior.cxx ├── ML_estimate_component_based_normalisation.cxx ├── NiftyPET_projector │ ├── BackProjectorByBinNiftyPET.cxx │ ├── ForwardProjectorByBinNiftyPET.cxx │ ├── NiftyPETHelper.cxx │ └── ProjectorByBinPairUsingNiftyPET.cxx ├── PLSPrior.cxx ├── Parallelproj_projector │ ├── BackProjectorByBinParallelproj.cxx │ ├── ForwardProjectorByBinParallelproj.cxx │ ├── ParallelprojHelper.cxx │ └── ProjectorByBinPairUsingParallelproj.cxx ├── PinholeSPECTUB_Tools.cxx ├── PinholeSPECTUB_Weight3d.cxx ├── PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData.cxx ├── PoissonLogLikelihoodWithLinearModelForMean.cxx ├── PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion.cxx ├── PoissonLogLikelihoodWithLinearModelForMeanAndListModeData.cxx ├── PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin.cxx ├── PoissonLogLikelihoodWithLinearModelForMeanAndProjData.cxx ├── PostsmoothingBackProjectorByBin.cxx ├── PresmoothingForwardProjectorByBin.cxx ├── ProjDataRebinning.cxx ├── ProjMatrixByBin.cxx ├── ProjMatrixByBinFromFile.cxx ├── ProjMatrixByBinPinholeSPECTUB.cxx ├── ProjMatrixByBinSPECTUB.cxx ├── ProjMatrixByBinUsingInterpolation.cxx ├── ProjMatrixByBinUsingRayTracing.cxx ├── ProjMatrixElemsForOneBin.cxx ├── ProjMatrixElemsForOneDensel.cxx ├── ProjectorByBinPair.cxx ├── ProjectorByBinPairUsingProjMatrixByBin.cxx ├── ProjectorByBinPairUsingSeparateProjectors.cxx ├── QuadraticPrior.cxx ├── RayTraceVoxelsOnCartesianGrid.cxx ├── Reconstruction.cxx ├── RelativeDifferencePrior.cxx ├── SPECTUB_Tools.cxx ├── SPECTUB_Weight3d.cxx ├── SqrtHessianRowSum.cxx ├── SymmetryOperation.cxx ├── SymmetryOperations_PET_CartesianGrid.cxx ├── TrivialBinNormalisation.cxx ├── TrivialDataSymmetriesForBins.cxx ├── distributable.cxx ├── distributableMPICacheEnabled.cxx ├── distributed_functions.cxx ├── distributed_test_functions.cxx ├── find_basic_vs_nums_in_subset.cxx └── recon_buildblock_registries.cxx ├── recon_test ├── CMakeLists.txt ├── bcktest.cxx ├── fwdtest.cxx ├── recontest.cxx ├── test_DataSymmetriesForBins_PET_CartesianGrid.cxx ├── test_FBP2D.cxx ├── test_FBP3DRP.cxx ├── test_OSMAPOSL.cxx ├── test_PoissonLogLikelihoodWithLinearModelForMeanAndListModeWithProjMatrixByBin.cxx ├── test_PoissonLogLikelihoodWithLinearModelForMeanAndProjData.cxx ├── test_blocks_on_cylindrical_projectors.cxx ├── test_consistency_with_GATE.cxx ├── test_data_processor_projectors.cxx ├── test_geometry_blocks_on_cylindrical.cxx └── test_priors.cxx ├── scatter_buildblock ├── CMakeLists.txt ├── CreateTailMaskFromACFs.cxx ├── ScatterEstimation.cxx ├── ScatterSimulation.cxx ├── SingleScatterSimulation.cxx ├── cached_single_scatter_integrals.cxx ├── extradebug.cxx ├── sample_scatter_points.cxx ├── scatter_detection_modelling.cxx ├── scatter_estimate_for_one_scatter_point.cxx ├── scatter_registries.cxx ├── single_scatter_estimate.cxx ├── single_scatter_integrals.cxx └── upsample_and_fit_scatter_estimate.cxx ├── scatter_utilities ├── CMakeLists.txt ├── create_tail_mask_from_ACFs.cxx ├── estimate_scatter.cxx ├── simulate_scatter.cxx └── upsample_and_fit_single_scatter.cxx ├── spatial_transformation_buildblock ├── CMakeLists.txt ├── GatedSpatialTransformation.cxx ├── InvertAxis.cxx ├── SpatialTransformation.cxx ├── spatial_transformation_registries.cxx └── warp_image.cxx ├── swig ├── CMakeLists.txt ├── Makefile ├── README.txt ├── factory_shared.i ├── numpy.i ├── pyfragments.swg ├── stir.i ├── stir_LOR.i ├── stir_array.i ├── stir_coordinates.i ├── stir_dataprocessors.i ├── stir_exam.i ├── stir_listmode.i ├── stir_normalisation.i ├── stir_objectivefunctions.i ├── stir_priors.i ├── stir_projdata.i ├── stir_projdata_coords.i ├── stir_projectors.i ├── stir_reconstruction.i ├── stir_shapes.i ├── stir_voxels.i ├── stir_voxels_IO.i ├── stirextra.py └── test │ ├── matlab │ ├── .gitignore │ ├── test_IO.m │ └── test_buildblock.m │ └── python │ ├── README.md │ ├── test_IO.py │ ├── test_PoissonProjDataObjectiveFunction.py │ ├── test_buildblock.py │ ├── test_listmode.py │ ├── test_numpy.py │ └── test_projdata_profiles.py ├── test ├── CMakeLists.txt ├── IO │ ├── test_IO_DiscretisedDensity.cxx │ ├── test_IO_DynamicDiscretisedDensity.cxx │ ├── test_IO_ITKMulticomponent.cxx │ └── test_IO_ParametricDiscretisedDensity.cxx ├── NiftyPET_projector │ ├── CMakeLists.txt │ └── test_ProjectorNiftyPET_adjoint.cxx ├── input │ ├── test_ECAT6OutputFileFormat.in │ ├── test_ECAT7OutputFileFormat.in │ ├── test_ITKDefaultOutputFileFormat.in │ ├── test_ITKNiftiOutputFileFormat.in │ ├── test_InterfileOutputFileFormat.in │ ├── test_InterfileOutputFileFormat_short.in │ ├── test_MultiOutputFileFormat.in │ ├── test_VAXfloat.in │ └── test_linear_regression.in ├── modelling │ ├── CMakeLists.txt │ ├── input │ │ ├── math_model_matrix.in │ │ ├── model_array.in │ │ ├── plasma.if │ │ ├── time.fdef │ │ └── triple_plasma.if │ ├── test_ParametricDiscretisedDensity.cxx │ └── test_modelling.cxx ├── numerics │ ├── BSplines_timing.cxx │ ├── CMakeLists.txt │ ├── Makefile_BSpline_timings │ ├── test_BSplines.cxx │ ├── test_BSplinesRegularGrid.cxx │ ├── test_BSplinesRegularGrid1D.cxx │ ├── test_Fourier.cxx │ ├── test_IR_filters.cxx │ ├── test_erf.cxx │ ├── test_integrate_discrete_function.cxx │ ├── test_matrices.cxx │ └── test_overlap_interpolate.cxx ├── test_ArcCorrection.cxx ├── test_Array.cxx ├── test_ArrayFilter.cxx ├── test_ByteOrder.cxx ├── test_DateTime.cxx ├── test_DetectionPosition.cxx ├── test_DetectorCoordinateMap.cxx ├── test_DynamicDiscretisedDensity.cxx ├── test_GeneralisedPoissonNoiseGenerator.cxx ├── test_ImagingModality.cxx ├── test_IndexRange.cxx ├── test_KeyParser.cxx ├── test_ML_norm.cxx ├── test_NestedIterator.cxx ├── test_OutputFileFormat.cxx ├── test_ROIs.cxx ├── test_Scanner.cxx ├── test_ScatterSimulation.cxx ├── test_SeparableGaussianArrayFilter.cxx ├── test_SeparableMetzArrayFilter.cxx ├── test_VectorWithOffset.cxx ├── test_VoxelsOnCartesianGrid.cxx ├── test_convert_array.cxx ├── test_coordinates.cxx ├── test_display.cxx ├── test_export_array.cxx ├── test_filename_functions.cxx ├── test_find_fwhm_in_image.cxx ├── test_interpolate.cxx ├── test_interpolate_projdata.cxx ├── test_linear_regression.cxx ├── test_multiple_proj_data.cxx ├── test_proj_data.cxx ├── test_proj_data_in_memory.cxx ├── test_proj_data_info.cxx ├── test_proj_data_info_subsets_pet.cxx ├── test_proj_data_info_subsets_spect.cxx ├── test_proj_data_maths.cxx ├── test_radionuclide.cxx ├── test_stir_math.cxx ├── test_time_of_flight.cxx ├── test_warp_image.cxx └── test_zoom_image.cxx └── utilities ├── CMakeLists.txt ├── GE └── print_GE_singles_values.cxx ├── SPECT_dicom_to_interfile.cxx ├── SSRB.cxx ├── UPENN ├── CMakeLists.txt └── conv_UPENN_projdata_to_STIR.cxx ├── abs_image.cxx ├── apply_normfactors.cxx ├── apply_normfactors3D.cxx ├── attenuation_coefficients_to_projections.cxx ├── back_project.cxx ├── calculate_attenuation_coefficients.cxx ├── compare_image.cxx ├── compare_projdata.cxx ├── compute_sqrt_Hessian_row_sum.cxx ├── construct_randoms_from_GEsingles.cxx ├── construct_randoms_from_singles.cxx ├── conv_GATE_raw_ECAT_projdata_to_interfile.cxx ├── conv_gipl_to_interfile.cxx ├── conv_interfile_to_gipl.cxx ├── convert_to_binary_image.cxx ├── correct_projdata.cxx ├── create_multi_header.cxx ├── create_projdata_template.cxx ├── ctac_to_mu_values.cxx ├── display_projdata.cxx ├── do_linear_regression.cxx ├── ecat ├── CMakeLists.txt ├── conv_to_ecat6.cxx ├── conv_to_ecat7.cxx ├── convecat6_if.cxx ├── copy_ecat7_header.cxx ├── ecat_swap_corners.cxx ├── ifheaders_for_ecat7.cxx ├── is_ecat7_file.cxx └── print_ecat_singles_values.cxx ├── estimate_triple_energy_window_scatter_sinogram.cxx ├── extract_segments.cxx ├── extract_single_images_from_dynamic_image.cxx ├── find_ML_normfactors.cxx ├── find_ML_normfactors3D.cxx ├── find_ML_singles_from_delayed.cxx ├── find_fwhm_in_image.cxx ├── find_maxima_in_image.cxx ├── find_normfactors_from_cylinder_data.cxx ├── find_recovery_coefficients_in_image_quality_phantom_nema_nu4.cxx ├── find_sum_projection_of_viewgram_and_sinogram.cxx ├── forward_project.cxx ├── generate_image.cxx ├── get_time_frame_info.cxx ├── invert_axis.cxx ├── list_ROI_values.cxx ├── list_detector_and_bin_info.cxx ├── list_image_info.cxx ├── list_image_values.cxx ├── list_projdata_info.cxx ├── manip_image.cxx ├── manip_projdata.cxx ├── poisson_noise.cxx ├── postfilter.cxx ├── rebin_projdata.cxx ├── 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