Getting Started
CLI & Scripts Guide
API Reference
PhysioMotion4DBase
PhysioMotion4DBase.__init__()
PhysioMotion4DBase.set_log_level()
PhysioMotion4DBase.set_log_classes()
PhysioMotion4DBase.set_log_all_classes()
PhysioMotion4DBase.get_log_classes()
PhysioMotion4DBase.log_debug()
PhysioMotion4DBase.log_info()
PhysioMotion4DBase.log_warning()
PhysioMotion4DBase.log_error()
PhysioMotion4DBase.log_critical()
PhysioMotion4DBase.log_section()
PhysioMotion4DBase.log_progress()
WorkflowConvertHeartGatedCTToUSD
WorkflowConvertHeartGatedCTToUSD.__init__()
WorkflowConvertHeartGatedCTToUSD.process()
WorkflowConvertCTToVTK
WorkflowConvertCTToVTK.ANATOMY_GROUPS
WorkflowConvertCTToVTK.SEGMENTATION_METHODS
WorkflowConvertCTToVTK.__init__()
WorkflowConvertCTToVTK.run_workflow()
WorkflowConvertCTToVTK.save_surfaces()
WorkflowConvertCTToVTK.save_meshes()
WorkflowConvertCTToVTK.save_combined_surface()
WorkflowConvertCTToVTK.save_combined_mesh()
WorkflowConvertVTKToUSD
WorkflowConvertVTKToUSD.__init__()
WorkflowConvertVTKToUSD.discover_time_series()
WorkflowConvertVTKToUSD.run()
WorkflowCreateStatisticalModel
WorkflowCreateStatisticalModel.sample_meshes
WorkflowCreateStatisticalModel.reference_mesh
WorkflowCreateStatisticalModel.pca_number_of_components
WorkflowCreateStatisticalModel.reference_spatial_resolution
WorkflowCreateStatisticalModel.reference_buffer_factor
WorkflowCreateStatisticalModel.__init__()
WorkflowCreateStatisticalModel.set_pca_number_of_components()
WorkflowCreateStatisticalModel.run_workflow()
WorkflowFitStatisticalModelToPatient
WorkflowFitStatisticalModelToPatient.template_model
WorkflowFitStatisticalModelToPatient.template_model_surface
WorkflowFitStatisticalModelToPatient.template_model_mask
WorkflowFitStatisticalModelToPatient.template_model_roi
WorkflowFitStatisticalModelToPatient.patient_models
WorkflowFitStatisticalModelToPatient.patient_model_surface
WorkflowFitStatisticalModelToPatient.combined_patient_model
WorkflowFitStatisticalModelToPatient.patient_image
WorkflowFitStatisticalModelToPatient.patient_mask
WorkflowFitStatisticalModelToPatient.patient_roi
WorkflowFitStatisticalModelToPatient.mask_dilation_mm
WorkflowFitStatisticalModelToPatient.roi_dilation_mm
WorkflowFitStatisticalModelToPatient.transform_tools
WorkflowFitStatisticalModelToPatient.registrar_icon
WorkflowFitStatisticalModelToPatient.registrar_ants
WorkflowFitStatisticalModelToPatient.use_pca_registration
WorkflowFitStatisticalModelToPatient.pca_model
WorkflowFitStatisticalModelToPatient.pca_number_of_modes
WorkflowFitStatisticalModelToPatient.icp_forward_point_transform
WorkflowFitStatisticalModelToPatient.icp_inverse_point_transform
WorkflowFitStatisticalModelToPatient.icp_template_model_surface
WorkflowFitStatisticalModelToPatient.icp_template_model
WorkflowFitStatisticalModelToPatient.pca_coefficients
WorkflowFitStatisticalModelToPatient.pca_template_model
WorkflowFitStatisticalModelToPatient.pca_template_model_surface
WorkflowFitStatisticalModelToPatient.m2m_forward_transform
WorkflowFitStatisticalModelToPatient.m2m_inverse_transform
WorkflowFitStatisticalModelToPatient.m2m_template_model_surface
WorkflowFitStatisticalModelToPatient.m2i_forward_transform
WorkflowFitStatisticalModelToPatient.m2i_inverse_transform
WorkflowFitStatisticalModelToPatient.m2i_template_model_surface
WorkflowFitStatisticalModelToPatient.m2i_template_labelmap
WorkflowFitStatisticalModelToPatient.registered_template_model
WorkflowFitStatisticalModelToPatient.registered_template_model_surface
WorkflowFitStatisticalModelToPatient.__init__()
WorkflowFitStatisticalModelToPatient.set_mask_dilation_mm()
WorkflowFitStatisticalModelToPatient.set_roi_dilation_mm()
WorkflowFitStatisticalModelToPatient.set_use_pca_registration()
WorkflowFitStatisticalModelToPatient.set_use_mask_to_mask_registration()
WorkflowFitStatisticalModelToPatient.set_use_mask_to_image_registration()
WorkflowFitStatisticalModelToPatient.register_model_to_model_icp()
WorkflowFitStatisticalModelToPatient.register_model_to_model_pca()
WorkflowFitStatisticalModelToPatient.register_mask_to_mask()
WorkflowFitStatisticalModelToPatient.register_labelmap_to_image()
WorkflowFitStatisticalModelToPatient.transform_model()
WorkflowFitStatisticalModelToPatient.run_workflow()
WorkflowReconstructHighres4DCT
WorkflowReconstructHighres4DCT.time_series_images
WorkflowReconstructHighres4DCT.fixed_image
WorkflowReconstructHighres4DCT.reference_frame
WorkflowReconstructHighres4DCT.register_reference
WorkflowReconstructHighres4DCT.prior_weight
WorkflowReconstructHighres4DCT.upsample_to_fixed_resolution
WorkflowReconstructHighres4DCT.registration_method
WorkflowReconstructHighres4DCT.number_of_iterations
WorkflowReconstructHighres4DCT.registrar
WorkflowReconstructHighres4DCT.forward_transforms
WorkflowReconstructHighres4DCT.inverse_transforms
WorkflowReconstructHighres4DCT.losses
WorkflowReconstructHighres4DCT.reconstructed_images
WorkflowReconstructHighres4DCT.__init__()
WorkflowReconstructHighres4DCT.set_number_of_iterations_ants()
WorkflowReconstructHighres4DCT.set_number_of_iterations_icon()
WorkflowReconstructHighres4DCT.set_prior_weight()
WorkflowReconstructHighres4DCT.set_modality()
WorkflowReconstructHighres4DCT.set_mask_dilation()
WorkflowReconstructHighres4DCT.set_fixed_mask()
WorkflowReconstructHighres4DCT.set_moving_masks()
WorkflowReconstructHighres4DCT.register_time_series()
WorkflowReconstructHighres4DCT.reconstruct_time_series()
WorkflowReconstructHighres4DCT.run_workflow()
RegisterImagesBase
RegisterImagesANTs
RegisterImagesGreedy
RegisterImagesICON
RegisterTimeSeriesImages
RegisterModelsICP
RegisterModelsICPITK
RegisterModelsDistanceMaps
RegisterModelsPCA
main()
Developer Guides
Contributing
Additional Resources
physiomotion4d
physiomotion4d.cli
physiomotion4d.cli.convert_ct_to_vtk
physiomotion4d.cli.convert_heart_gated_ct_to_usd
physiomotion4d.cli.convert_vtk_to_usd
physiomotion4d.cli.create_statistical_model
physiomotion4d.cli.fit_statistical_model_to_patient
physiomotion4d.cli.reconstruct_highres_4d_ct
physiomotion4d.cli.visualize_pca_modes
physiomotion4d.contour_tools
physiomotion4d.convert_nrrd_4d_to_3d
physiomotion4d.convert_vtk_to_usd
physiomotion4d.data_download_tools
physiomotion4d.image_tools
physiomotion4d.physiomotion4d_base
physiomotion4d.register_images_ants
physiomotion4d.register_images_base
physiomotion4d.register_images_greedy
physiomotion4d.register_images_icon
physiomotion4d.register_models_distance_maps
physiomotion4d.register_models_icp
physiomotion4d.register_models_icp_itk
physiomotion4d.register_models_pca
physiomotion4d.register_time_series_images
physiomotion4d.segment_anatomy_base
physiomotion4d.segment_chest_total_segmentator
physiomotion4d.segment_heart_simpleware
physiomotion4d.test_tools
physiomotion4d.transform_tools
physiomotion4d.usd_anatomy_tools
physiomotion4d.usd_tools
physiomotion4d.vtk_to_usd
physiomotion4d.vtk_to_usd.converter
physiomotion4d.vtk_to_usd.data_structures
physiomotion4d.vtk_to_usd.material_manager
physiomotion4d.vtk_to_usd.mesh_utils
physiomotion4d.vtk_to_usd.primvar_derivations
physiomotion4d.vtk_to_usd.usd_mesh_converter
physiomotion4d.vtk_to_usd.usd_utils
physiomotion4d.vtk_to_usd.vtk_reader
physiomotion4d.workflow_convert_ct_to_vtk
physiomotion4d.workflow_convert_heart_gated_ct_to_usd
physiomotion4d.workflow_convert_vtk_to_usd
physiomotion4d.workflow_create_statistical_model
physiomotion4d.workflow_fit_statistical_model_to_patient
physiomotion4d.workflow_reconstruct_highres_4d_ct