ENH: Made tool naming more consistent with rest of code base by aylward · Pull Request #137 · Project-MONAI/monai-physio

aylward · 2026-09-07T19:45:06Z

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coderabbitai · 2026-09-07T19:45:21Z

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Reviewing files that changed from the base of the PR and between 955d2f8 and 999f8a0.

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.agents/agents/architecture.md
.agents/agents/implementation.md
.agents/agents/testing.md
.agents/skills/test-feature/SKILL.md
AGENTS.md
CLAUDE.md
data/CHOP-Valve4D/README.md
data/Chest-CT/README.md
data/DirLab-4DCT/README.md
data/DirLab-4DCT/fix_downloaded_data.py
data/README.md
data/Slicer-Heart-CT/README.md
docs/api/index.rst
docs/api/physicsnemo/infer.rst
docs/api/physicsnemo/manifest.rst
docs/api/segmentation/base.rst
docs/api/segmentation/nv_segment_ct_mri.rst
docs/api/segmentation/totalsegmentator.rst
docs/api/usd/index.rst
docs/api/usd/tools_for_usd.rst
docs/api/usd/tools_for_usd_anatomy.rst
docs/api/usd/vtk_conversion.rst
docs/api/utilities/image_conversion.rst
docs/api/utilities/index.rst
docs/api/utilities/tools_for_contours.rst
docs/api/utilities/tools_for_data_downloads.rst
docs/api/utilities/tools_for_images.rst
docs/api/utilities/tools_for_labelmaps.rst
docs/api/utilities/tools_for_landmarks.rst
docs/api/utilities/tools_for_tests.rst
docs/api/utilities/tools_for_transforms.rst
docs/api/workflows.rst
docs/architecture.rst
docs/cli_scripts/byod_tutorials.rst
docs/cli_scripts/download_data.rst
docs/cli_scripts/infer_physicsnemo.rst
docs/cookbook/add_a_registration_method.rst
docs/cookbook/add_a_segmentation_method.rst
docs/developer/architecture.rst
docs/developer/core.rst
docs/developer/migration_next.md
docs/developer/registration_images.rst
docs/developer/segmentation.rst
docs/developer/transform_conventions.rst
docs/developer/usd_generation.rst
docs/developer/utilities.rst
docs/developer/workflows.rst
docs/quickstart.rst
docs/tutorials.rst
experiments/Convert_VTK_To_USD/convert_chop_alterra_valve_to_usd.py
experiments/Convert_VTK_To_USD/convert_chop_tpv25_valve_to_usd.py
experiments/Convert_VTK_To_USD/convert_vtk_to_usd_using_class.py
experiments/Heart-Create_Statistical_Model/2-input_surfaces_to_surfaces_aligned.py
experiments/Heart-Create_Statistical_Model/3-registration_based_correspondence.py
experiments/Heart-Create_Statistical_Model/4-surfaces_aligned_correspond_to_pca_inputs.py
experiments/Heart-GatedCT-OptimizedLongitudinalRegistration/0-cardiacGatedCT_segment_and_landmark.py
experiments/Heart-GatedCT-OptimizedLongitudinalRegistration/1-initial_registration.py
experiments/Heart-GatedCT-OptimizedLongitudinalRegistration/3-eval_icon.py
experiments/Heart-GatedCT-OptimizedLongitudinalRegistration/registration_test.py
experiments/Heart-GatedCT_To_USD/0-download_and_convert_4d_to_3d.py
experiments/Heart-GatedCT_To_USD/1-register_images.py
experiments/Heart-GatedCT_To_USD/2-generate_segmentation.py
experiments/Heart-GatedCT_To_USD/3-transform_dynamic_and_static_contours.py
experiments/Heart-GatedCT_To_USD/4-merge_dynamic_and_static_usd.py
experiments/Heart-Simpleware_Segmentation/README.md
experiments/Heart-Simpleware_Segmentation/simpleware_heart_segmentation.py
experiments/Heart-Statistical_Model_To_Patient/heart_model_to_model_icp_itk.py
experiments/Heart-Statistical_Model_To_Patient/heart_model_to_model_registration_pca.py
experiments/Heart-Statistical_Model_To_Patient/heart_model_to_patient.py
experiments/Heart-VTKSeries_To_USD/0-download_and_convert_4d_to_3d.py
experiments/Heart-VTKSeries_To_USD/1-heart_vtkseries_to_usd.py
experiments/Heart_and_Lungs_Motion/0-heart_and_lungs_beating_heart.py
experiments/Heart_and_Lungs_Motion/1-heart_and_lungs_combined.py
experiments/Lung-GatedCT_To_USD/0-register_dirlab_4dct.py
experiments/Lung-GatedCT_To_USD/1-make_dirlab_models.py
experiments/Lung-GatedCT_To_USD/2-paint_dirlab_models.py
experiments/Lung-GatedCT_To_USD/Experiment_ArrangeOnStage.py
experiments/Lung-GatedCT_To_USD/Experiment_CombineModels.py
experiments/Lung-GatedCT_To_USD/data_dirlab_4d_ct.py
experiments/Lung-GatedCT_To_USD_NV/0-register_dirlab_4dct.py
experiments/Lung-GatedCT_To_USD_NV/1-make_dirlab_models.py
experiments/Lung-GatedCT_To_USD_NV/2-paint_dirlab_models.py
experiments/Reconstruct4DCT/reconstruct_4d_ct.py
experiments/Reconstruct4DCT/reconstruct_4d_ct_class.py
src/monai_physio/__init__.py
src/monai_physio/cli/convert_image_to_vtk.py
src/monai_physio/cli/convert_vtk_to_usd.py
src/monai_physio/cli/download_data.py
src/monai_physio/convert_vtk_to_usd.py
src/monai_physio/infer_physicsnemo_mgn.py
src/monai_physio/physicsnemo_tools.py
src/monai_physio/register_images_ants.py
src/monai_physio/register_images_base.py
src/monai_physio/register_images_greedy.py
src/monai_physio/register_models_distance_maps.py
src/monai_physio/register_models_icp.py
src/monai_physio/register_models_icp_itk.py
src/monai_physio/register_models_pca.py
src/monai_physio/register_time_series_images.py
src/monai_physio/segment_anatomy_base.py
src/monai_physio/segment_chest_total_segmentator.py
src/monai_physio/segment_chest_total_segmentator_with_contrast.py
src/monai_physio/segment_heart_simpleware.py
src/monai_physio/segment_heart_simpleware_trimmed_branches.py
src/monai_physio/segment_nv_segment_ct_mri.py
src/monai_physio/tools_for_anatomy_taxonomies.py
src/monai_physio/tools_for_contours.py
src/monai_physio/tools_for_data_downloads.py
src/monai_physio/tools_for_images.py
src/monai_physio/tools_for_labelmaps.py
src/monai_physio/tools_for_landmarks.py
src/monai_physio/tools_for_physicsnemo.py
src/monai_physio/tools_for_tests.py
src/monai_physio/tools_for_transforms.py
src/monai_physio/tools_for_usd.py
src/monai_physio/tools_for_usd_anatomy.py
src/monai_physio/train_physicsnemo_base.py
src/monai_physio/train_physicsnemo_mgn.py
src/monai_physio/train_physicsnemo_physics_informed_motion.py
src/monai_physio/vtk_to_usd/primvar_derivations.py
src/monai_physio/vtk_to_usd/usd_utils.py
src/monai_physio/workflow_convert_image_to_usd.py
src/monai_physio/workflow_convert_image_to_vtk.py
src/monai_physio/workflow_convert_vtk_to_usd.py
src/monai_physio/workflow_create_mean_surface.py
src/monai_physio/workflow_create_statistical_model.py
src/monai_physio/workflow_evaluate_movement.py
src/monai_physio/workflow_fit_statistical_model_to_patient.py
src/monai_physio/workflow_infer_movement.py
src/monai_physio/workflow_infer_physicsnemo.py
src/monai_physio/workflow_reconstruct_highres_4d_ct.py
src/monai_physio/workflow_train_physicsnemo.py
statistics.md
tests/conftest.py
tests/test_contour_mesh_extraction.py
tests/test_convert_vtk_to_usd.py
tests/test_download_data_cli.py
tests/test_download_heart_data.py
tests/test_physics_informed_motion.py
tests/test_register_images_ants.py
tests/test_register_images_greedy.py
tests/test_register_images_icon.py
tests/test_register_time_series_images.py
tests/test_tools_for_anatomy_taxonomies.py
tests/test_tools_for_contours.py
tests/test_tools_for_images.py
tests/test_tools_for_labelmaps.py
tests/test_tools_for_physicsnemo.py
tests/test_tools_for_transforms.py
tests/test_tutorials.py
tests/test_usd_merge.py
tests/test_usd_time_preservation.py
tests/test_vtk_to_usd_library.py
tests/test_workflow_train_physicsnemo.py
tutorials/README.md
tutorials/parameters_base.py
tutorials/parameters_duke_heart_labelmaps.py
tutorials/parameters_duke_heart_physics_informed.py
tutorials/parameters_heart_ct_kcl.py
tutorials/parameters_lung_ct_dirlab.py
tutorials/tutorial_01_heart_gated_ct_to_usd.py
tutorials/tutorial_01_lung_gated_ct_to_usd.py
tutorials/tutorial_02_duke_heart_distancemap_finetune_icon.py
tutorials/tutorial_02_lung_distancemap_finetune_icon.py
tutorials/tutorial_02_lung_finetune_icon.py
tutorials/tutorial_03_heart_reconstruct_highres_4d_ct.py
tutorials/tutorial_03_lung_reconstruct_highres_4d_ct.py
tutorials/tutorial_04_duke_heart_labelmap_to_vtk.py
tutorials/tutorial_04_heart_ct_to_vtk.py
tutorials/tutorial_04_lung_ct_to_vtk.py
tutorials/tutorial_05_duke_heart_vtk_to_usd.py
tutorials/tutorial_05_heart_vtk_to_usd.py
tutorials/tutorial_06_duke_heart_create_statistical_model.py
tutorials/tutorial_06_heart_create_statistical_model.py
tutorials/tutorial_06_lung_create_statistical_model.py
tutorials/tutorial_07_duke_heart_fit_statistical_model_to_patient.py
tutorials/tutorial_07_heart_fit_statistical_model_to_patient.py
tutorials/tutorial_07_lung_fit_statistical_model_to_patient.py
tutorials/tutorial_08_duke_heart_fit_model_to_4d_patients.py
tutorials/tutorial_08_lung_fit_model_to_4d_patients.py
tutorials/tutorial_09_duke_heart_train_physicsnemo_mgn.py
tutorials/tutorial_09_lung_train_physicsnemo_mgn.py
tutorials/tutorial_10_duke_heart_infer_physicsnemo_mgn.py
tutorials/tutorial_10_lung_infer_physicsnemo_mgn.py
tutorials/tutorial_11_duke_heart_evaluate_physicsnemo.py
tutorials/tutorial_11_lung_evaluate_physicsnemo.py
tutorials/tutorial_12_duke_heart_end_to_end_inference.py
tutorials/tutorial_12_lung_end_to_end_inference.py
tutorials/tutorial_13_heart_and_lung_motion.py
tutorials/tutorial_14_duke_heart_shape_parameter_sweep.py
tutorials/tutorial_14_lung_shape_parameter_sweep.py
tutorials/tutorial_15_duke_heart_leave_one_out.py
tutorials/tutorial_15_lung_leave_one_out.py
tutorials/tutorial_16_duke_heart_physics_informed_motion_prep.py
tutorials/tutorial_17_duke_heart_physics_informed_motion_train.py
tutorials/tutorial_18_duke_heart_physics_informed_motion_infer.py
utils/migrate_tools_for_names.py

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