Getting Started
CLI & Scripts Guide
API Reference
PhysioTwin4DBase
PhysioTwin4DBase.__init__()
PhysioTwin4DBase.set_log_level()
PhysioTwin4DBase.set_log_classes()
PhysioTwin4DBase.set_log_all_classes()
PhysioTwin4DBase.get_log_classes()
PhysioTwin4DBase.log_debug()
PhysioTwin4DBase.log_info()
PhysioTwin4DBase.log_warning()
PhysioTwin4DBase.log_error()
PhysioTwin4DBase.log_critical()
PhysioTwin4DBase.log_section()
PhysioTwin4DBase.log_progress()
WorkflowConvertImageToUSD
WorkflowConvertImageToUSD.__init__()
WorkflowConvertImageToUSD.process()
WorkflowConvertImageToVTK
WorkflowConvertImageToVTK.__init__()
WorkflowConvertImageToVTK.anatomy_groups
WorkflowConvertImageToVTK.process()
WorkflowConvertVTKToUSD
WorkflowConvertVTKToUSD.__init__()
WorkflowConvertVTKToUSD.process()
WorkflowCreateMeanSurface
WorkflowCreateMeanSurface.__init__()
WorkflowCreateMeanSurface.set_number_of_iterations()
WorkflowCreateMeanSurface.set_convergence_tolerance()
WorkflowCreateMeanSurface.set_alignment_transform_type()
WorkflowCreateMeanSurface.set_registration_transform_type()
WorkflowCreateMeanSurface.process()
WorkflowCreateStatisticalModel
WorkflowCreateStatisticalModel.sample_meshes
WorkflowCreateStatisticalModel.reference_mesh
WorkflowCreateStatisticalModel.number_of_pca_components
WorkflowCreateStatisticalModel.reference_spatial_resolution
WorkflowCreateStatisticalModel.reference_buffer_factor
WorkflowCreateStatisticalModel.__init__()
WorkflowCreateStatisticalModel.set_number_of_pca_components()
WorkflowCreateStatisticalModel.process()
WorkflowFitStatisticalModelToPatient
WorkflowFitStatisticalModelToPatient.template_model
WorkflowFitStatisticalModelToPatient.template_model_surface
WorkflowFitStatisticalModelToPatient.template_labelmap
WorkflowFitStatisticalModelToPatient.template_mask
WorkflowFitStatisticalModelToPatient.patient_models
WorkflowFitStatisticalModelToPatient.patient_model_surface
WorkflowFitStatisticalModelToPatient.combined_patient_model
WorkflowFitStatisticalModelToPatient.patient_image
WorkflowFitStatisticalModelToPatient.patient_labelmap
WorkflowFitStatisticalModelToPatient.patient_mask
WorkflowFitStatisticalModelToPatient.mask_dilation_mm
WorkflowFitStatisticalModelToPatient.distancemap_squared_max
WorkflowFitStatisticalModelToPatient.transform_tools
WorkflowFitStatisticalModelToPatient.registrar_ICON
WorkflowFitStatisticalModelToPatient.registrar_Greedy
WorkflowFitStatisticalModelToPatient.use_pca_registration
WorkflowFitStatisticalModelToPatient.pca_model
WorkflowFitStatisticalModelToPatient.number_of_pca_components
WorkflowFitStatisticalModelToPatient.labelmap_interior_object_ids
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.l2l_forward_transform
WorkflowFitStatisticalModelToPatient.l2l_inverse_transform
WorkflowFitStatisticalModelToPatient.l2l_template_model_surface
WorkflowFitStatisticalModelToPatient.l2i_forward_transform
WorkflowFitStatisticalModelToPatient.l2i_inverse_transform
WorkflowFitStatisticalModelToPatient.l2i_template_model_surface
WorkflowFitStatisticalModelToPatient.l2i_template_labelmap
WorkflowFitStatisticalModelToPatient.registered_template_model
WorkflowFitStatisticalModelToPatient.registered_template_model_surface
WorkflowFitStatisticalModelToPatient.__init__()
WorkflowFitStatisticalModelToPatient.set_mask_dilation_mm()
WorkflowFitStatisticalModelToPatient.set_distancemap_squared_max()
WorkflowFitStatisticalModelToPatient.set_labelmap_to_labelmap_icon_weights_path()
WorkflowFitStatisticalModelToPatient.set_use_pca_registration()
WorkflowFitStatisticalModelToPatient.set_use_labelmap_to_labelmap_registration()
WorkflowFitStatisticalModelToPatient.set_use_labelmap_to_image_registration()
WorkflowFitStatisticalModelToPatient.register_model_to_model_icp()
WorkflowFitStatisticalModelToPatient.register_model_to_model_pca()
WorkflowFitStatisticalModelToPatient.register_labelmap_to_labelmap()
WorkflowFitStatisticalModelToPatient.register_labelmap_to_image()
WorkflowFitStatisticalModelToPatient.transform_model()
WorkflowFitStatisticalModelToPatient.process()
WorkflowReconstructHighres4DCT
WorkflowReconstructHighres4DCT.time_series_images
WorkflowReconstructHighres4DCT.reference_image
WorkflowReconstructHighres4DCT.reference_time_frame
WorkflowReconstructHighres4DCT.register_reference_time_frame_to_reference_image
WorkflowReconstructHighres4DCT.upsample_to_fixed_resolution
WorkflowReconstructHighres4DCT.registrar
WorkflowReconstructHighres4DCT.forward_transforms
WorkflowReconstructHighres4DCT.inverse_transforms
WorkflowReconstructHighres4DCT.losses
WorkflowReconstructHighres4DCT.reconstructed_images
WorkflowReconstructHighres4DCT.__init__()
WorkflowReconstructHighres4DCT.set_modality()
WorkflowReconstructHighres4DCT.set_mask_dilation()
WorkflowReconstructHighres4DCT.set_fixed_mask()
WorkflowReconstructHighres4DCT.set_moving_masks()
WorkflowReconstructHighres4DCT.register_time_series()
WorkflowReconstructHighres4DCT.set_upsample_to_fixed_resolution()
WorkflowReconstructHighres4DCT.reconstruct_time_series()
WorkflowReconstructHighres4DCT.process()
WorkflowFinetuneICONRegistration
WorkflowFinetuneICONRegistration.subject_image_files
WorkflowFinetuneICONRegistration.output_dir
WorkflowFinetuneICONRegistration.finetune_name
WorkflowFinetuneICONRegistration.subject_ids
WorkflowFinetuneICONRegistration.subject_labelmap_files
WorkflowFinetuneICONRegistration.subject_mask_files
WorkflowFinetuneICONRegistration.subject_landmark_files
WorkflowFinetuneICONRegistration.__init__()
WorkflowFinetuneICONRegistration.prepare_dataset()
WorkflowFinetuneICONRegistration.prepare_config()
WorkflowFinetuneICONRegistration.expected_weights_path()
WorkflowFinetuneICONRegistration.process()
RegisterImagesBase
RegisterImagesANTS
RegisterImagesGreedy
RegisterImagesICON
RegisterImagesChain
RegisterImagesGreedyICON
RegisterTimeSeriesImages
RegisterModelsICP
RegisterModelsICPITK
RegisterModelsDistanceMaps
RegisterModelsPCA
SubjectManifest
PhaseEntry
parse_manifest()
load_target_array()
load_pca_coefficients()
build_node_features()
mesh_to_edge_index()
compute_edge_features()
reconstruct_reference_points()
PhaseSampleDataset
WorkflowTrainPhysicsNeMo
TrainPhysicsNeMoBase
TrainPhysicsNeMoMGN
TrainPhysicsNeMoMLP
WorkflowInferPhysicsNeMo
WorkflowInferMovement
InferPhysicsNeMoBase
InferPhysicsNeMoMGN
InferPhysicsNeMoMLP
WorkflowEvaluateMovement
main()
Developer Guides
Contributing
Additional Resources
physiotwin4d
physiotwin4d.cli
physiotwin4d.cli.convert_image_4d_to_3d
physiotwin4d.cli.convert_image_to_usd
physiotwin4d.cli.convert_image_to_vtk
physiotwin4d.cli.convert_vtk_to_usd
physiotwin4d.cli.create_statistical_model
physiotwin4d.cli.download_data
physiotwin4d.cli.fit_statistical_model_to_patient
physiotwin4d.cli.infer_physicsnemo
physiotwin4d.cli.reconstruct_highres_4d_ct
physiotwin4d.cli.train_physicsnemo
physiotwin4d.cli.visualize_pca_modes
physiotwin4d.contour_tools
physiotwin4d.convert_image_4d_to_3d
physiotwin4d.convert_vtk_to_usd
physiotwin4d.data_download_tools
physiotwin4d.image_tools
physiotwin4d.infer_physicsnemo_base
physiotwin4d.infer_physicsnemo_mgn
physiotwin4d.infer_physicsnemo_mlp
physiotwin4d.labelmap_tools
physiotwin4d.landmark_tools
physiotwin4d.physicsnemo_tools
physiotwin4d.physiotwin4d_base
physiotwin4d.register_images_ants
physiotwin4d.register_images_base
physiotwin4d.register_images_chain
physiotwin4d.register_images_greedy
physiotwin4d.register_images_greedy_icon
physiotwin4d.register_images_icon
physiotwin4d.register_models_distance_maps
physiotwin4d.register_models_icp
physiotwin4d.register_models_icp_itk
physiotwin4d.register_models_pca
physiotwin4d.register_time_series_images
physiotwin4d.segment_anatomy_base
physiotwin4d.segment_chest_total_segmentator
physiotwin4d.segment_heart_simpleware
physiotwin4d.segment_nv_segment_ct_mri
physiotwin4d.test_tools
physiotwin4d.train_physicsnemo_base
physiotwin4d.train_physicsnemo_mgn
physiotwin4d.train_physicsnemo_mlp
physiotwin4d.transform_tools
physiotwin4d.usd_anatomy_tools
physiotwin4d.usd_tools
physiotwin4d.vtk_to_usd
physiotwin4d.vtk_to_usd.converter
physiotwin4d.vtk_to_usd.data_structures
physiotwin4d.vtk_to_usd.material_manager
physiotwin4d.vtk_to_usd.mesh_utils
physiotwin4d.vtk_to_usd.primvar_derivations
physiotwin4d.vtk_to_usd.usd_mesh_converter
physiotwin4d.vtk_to_usd.usd_utils
physiotwin4d.vtk_to_usd.vtk_reader
physiotwin4d.workflow_convert_image_to_usd
physiotwin4d.workflow_convert_image_to_vtk
physiotwin4d.workflow_convert_vtk_to_usd
physiotwin4d.workflow_create_mean_surface
physiotwin4d.workflow_create_statistical_model
physiotwin4d.workflow_evaluate_movement
physiotwin4d.workflow_finetune_icon_registration
physiotwin4d.workflow_fit_statistical_model_to_patient
physiotwin4d.workflow_infer_movement
physiotwin4d.workflow_infer_physicsnemo
physiotwin4d.workflow_reconstruct_highres_4d_ct
physiotwin4d.workflow_train_physicsnemo