Rename/physiotwin4d#79
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Move src/physiomotion4d -> src/physiotwin4d and physiomotion4d_base.py -> physiotwin4d_base.py, rename PhysioMotion4DBase -> PhysioTwin4DBase, and update all imports, the shared logger name, pyproject.toml packaging metadata (name, console scripts, project URLs, mypy/coverage/ruff config), and tutorials/tests import statements accordingly. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…ents, and infra Bulk text substitution across docs/, experiments/, utils/, .agents/, .github/, .cursor/, data/, and root files (README, AGENTS.md, CLAUDE.md, MANIFEST.in, statistics.md, .readthedocs.yaml). Also renames the internal pm4d abbreviation to pt4d (Sphinx template placeholder and custom.css classes/variables), regenerates docs/API_MAP.md, and bumps the stale 2026.05.07 version references in README.md, docs/changelog.rst, and docs/PYPI_RELEASE_GUIDE.md to 2026.07.0. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Pull request overview
This PR completes the project/package rename from physiomotion4d to physiotwin4d across the library, tests, tutorials/experiments, documentation, and CI/configuration, and introduces the renamed/relocated entry points that go with that new package identity.
Changes:
- Rename imports, docstrings, CLI command names, and references from
physiomotion4d→physiotwin4dthroughout the repo (includingPhysioMotion4DBase→PhysioTwin4DBase). - Update CI/coverage paths and documentation site metadata to the new repo/package name.
- Add
RegisterImagesGreedyICON(Greedy→ICON chain) and add a new CLI entry point for 4D→3D time-series splitting.
Reviewed changes
Copilot reviewed 231 out of 256 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| utils/generate_api_map.py | Update docstring to the new project root name. |
| utils/ai_agent_github_reviews.py | Update agent guidance paths and prompt text for renamed base class and package layout. |
| tutorials/tutorial_10b_cardiac_eval_physicsnemo_mlp.py | Rename tutorial package references and local path examples. |
| tutorials/tutorial_10a_cardiac_eval_physicsnemo_mgn.py | Rename tutorial package references and local path examples. |
| tutorials/tutorial_09b_cardiac_train_physicsnemo_mlp.py | Rename imports/extras text to physiotwin4d. |
| tutorials/tutorial_09a_cardiac_train_physicsnemo_mgn.py | Rename imports/extras text to physiotwin4d. |
| tutorials/tutorial_08_cardiac_fit_model.py | Rename imports/path examples for bring-your-own-data tutorial. |
| tutorials/tutorial_06_reconstruct_highres_4d_ct.py | Rename tutorial imports to physiotwin4d. |
| tutorials/tutorial_05_vtk_to_usd.py | Rename tutorial imports to physiotwin4d. |
| tutorials/tutorial_04_fit_statistical_model_to_patient.py | Rename tutorial imports to physiotwin4d. |
| tutorials/tutorial_03_create_statistical_model.py | Rename tutorial imports to physiotwin4d. |
| tutorials/tutorial_02_ct_to_vtk.py | Rename tutorial imports to physiotwin4d. |
| tutorials/tutorial_01_heart_gated_ct_to_usd.py | Rename tutorial imports to physiotwin4d. |
| tutorials/README.md | Rename tutorial guide branding/CLI references. |
| tests/test_workflow_reconstruct_highres_4d_ct.py | Rename test imports to physiotwin4d. |
| tests/test_workflow_fit_statistical_model_to_patient.py | Rename imports and monkeypatch target module path. |
| tests/test_workflow_fine_tune_icon_registration.py | Rename test imports to physiotwin4d. |
| tests/test_workflow_convert_image_to_vtk.py | Rename test imports to physiotwin4d. |
| tests/test_workflow_convert_image_to_usd.py | Rename test imports to physiotwin4d. |
| tests/test_vtk_to_usd_library.py | Rename tests and narrative to the new package name. |
| tests/test_usd_time_preservation.py | Rename test imports to physiotwin4d. |
| tests/test_usd_merge.py | Rename test imports to physiotwin4d. |
| tests/test_tutorials.py | Rename test env var and path constants for tutorial test mode. |
| tests/test_transform_tools.py | Rename test imports to physiotwin4d. |
| tests/test_segment_heart_simpleware.py | Rename test imports to physiotwin4d. |
| tests/test_segment_heart_simpleware_trimmed_branches.py | Rename test imports to physiotwin4d. |
| tests/test_segment_chest_total_segmentator.py | Rename test imports to physiotwin4d. |
| tests/test_register_time_series_images.py | Rename test imports to physiotwin4d. |
| tests/test_register_models_pca.py | Rename test imports to physiotwin4d. |
| tests/test_register_images_icon.py | Rename test imports to physiotwin4d. |
| tests/test_register_images_greedy.py | Rename test imports to physiotwin4d. |
| tests/test_register_images_greedy_icon.py | Rename test imports to physiotwin4d. |
| tests/test_register_images_chain.py | Rename test imports to physiotwin4d. |
| tests/test_register_images_ants.py | Rename test imports to physiotwin4d. |
| tests/test_labelmap_tools.py | Rename test imports to physiotwin4d. |
| tests/test_import_public_api.py | Validate physiotwin4d.__all__ instead of physiomotion4d.__all__. |
| tests/test_image_tools.py | Rename test imports to physiotwin4d. |
| tests/test_experiments.py | Rename test-mode env var to PHYSIOTWIN_RUNNING_AS_TEST. |
| tests/test_download_heart_data.py | Rename test imports to physiotwin4d. |
| tests/test_download_data_cli.py | Rename CLI import targets to physiotwin4d. |
| tests/test_convert_vtk_to_usd.py | Rename test imports to physiotwin4d. |
| tests/test_convert_image_4d_to_3d.py | Rename test imports to physiotwin4d. |
| tests/test_contour_tools.py | Rename test imports to physiotwin4d. |
| tests/test_cli_smoke.py | Rename CLI module smoke-test targets to physiotwin4d. |
| tests/test_anatomy_taxonomy.py | Rename API references to physiotwin4d. |
| tests/README.md | Rename test documentation and coverage path to src/physiotwin4d. |
| tests/conftest.py | Rename fixture imports and test-tools module initialization import. |
| tests/init.py | Rename test-suite package docstring branding. |
| statistics.md | Rename project branding and example file paths. |
| src/physiotwin4d/workflow_reconstruct_highres_4d_ct.py | Switch workflow base class import to PhysioTwin4DBase. |
| src/physiotwin4d/workflow_fit_statistical_model_to_patient.py | Switch workflow base class import to PhysioTwin4DBase. |
| src/physiotwin4d/workflow_fine_tune_icon_registration.py | Switch workflow base class import to PhysioTwin4DBase and update example paths. |
| src/physiotwin4d/workflow_create_statistical_model.py | Switch workflow base class import to PhysioTwin4DBase. |
| src/physiotwin4d/workflow_convert_vtk_to_usd.py | Switch workflow base class import to PhysioTwin4DBase. |
| src/physiotwin4d/workflow_convert_image_to_vtk.py | Rename top-level examples and base class; update referenced CLI name. |
| src/physiotwin4d/workflow_convert_image_to_usd.py | Rename module docstring branding and base class. |
| src/physiotwin4d/vtk_to_usd/usd_utils.py | Rename coordinate-convention narrative to PhysioTwin4D. |
| src/physiotwin4d/vtk_to_usd/README.md | Rename advanced-library README imports/references. |
| src/physiotwin4d/vtk_to_usd/converter.py | Rename cross-reference to physiotwin4d.ConvertVTKToUSD. |
| src/physiotwin4d/vtk_to_usd/CLAUDE.md | Rename guidance text and code samples to physiotwin4d. |
| src/physiotwin4d/vtk_to_usd/init.py | Rename subpackage docstring and guidance to PhysioTwin4D. |
| src/physiotwin4d/usd_tools.py | Switch USDTools base class to PhysioTwin4DBase. |
| src/physiotwin4d/usd_anatomy_tools.py | Switch USDAnatomyTools base class to PhysioTwin4DBase and update doc refs. |
| src/physiotwin4d/transform_tools.py | Switch TransformTools base class to PhysioTwin4DBase. |
| src/physiotwin4d/test_tools.py | Switch TestTools base class and rename test-mode env var. |
| src/physiotwin4d/simpleware_medical/SimplewareScript_heart_segmentation.py | Rename narrative reference to PhysioTwin4D segmenter class. |
| src/physiotwin4d/simpleware_medical/README.md | Rename integration documentation and code samples. |
| src/physiotwin4d/simpleware_medical/init.py | Rename package docstring branding. |
| src/physiotwin4d/segment_anatomy_base.py | Switch segmenter base class to PhysioTwin4DBase and rename doc refs. |
| src/physiotwin4d/register_models_pca.py | Switch registrar base class and logger name to PhysioTwin4D. |
| src/physiotwin4d/register_models_icp.py | Switch registrar base class and example import. |
| src/physiotwin4d/register_models_icp_itk.py | Switch registrar base class to PhysioTwin4D. |
| src/physiotwin4d/register_models_distance_maps.py | Switch registrar base class and example import. |
| src/physiotwin4d/register_images_greedy_icon.py | Add composite Greedy→ICON registration chain class. |
| src/physiotwin4d/register_images_base.py | Switch registrar base class to PhysioTwin4DBase. |
| src/physiotwin4d/landmark_tools.py | Switch LandmarkTools base class to PhysioTwin4DBase. |
| src/physiotwin4d/labelmap_tools.py | Rename module branding and switch base class. |
| src/physiotwin4d/image_tools.py | Rename module branding and switch base class. |
| src/physiotwin4d/data_download_tools.py | Rename DataDownloadTools docstring branding. |
| src/physiotwin4d/convert_vtk_to_usd.py | Switch converter base class to PhysioTwin4DBase. |
| src/physiotwin4d/convert_image_4d_to_3d.py | Switch converter base class to PhysioTwin4DBase. |
| src/physiotwin4d/contour_tools.py | Switch ContourTools base class to PhysioTwin4DBase. |
| src/physiotwin4d/cli/download_data.py | Rename CLI branding/description strings. |
| src/physiotwin4d/cli/convert_image_4d_to_3d.py | Add CLI for splitting 3D/4D images into 3D frame series. |
| src/physiotwin4d/cli/_method_factories.py | Rename CLI method factory imports to physiotwin4d. |
| src/physiotwin4d/cli/init.py | Rename CLI package docstring branding. |
| src/physiotwin4d/anatomy_taxonomy.py | Rename cross-references to physiotwin4d API consumers. |
| src/physiotwin4d/.gitignore | Add package-local ignores for caches/weights. |
| src/physiotwin4d/init.py | Rename package branding, base class export name, and install guidance strings. |
| MANIFEST.in | Update package data include paths to src/physiotwin4d. |
| experiments/Reconstruct4DCT/reconstruct_4d_ct.py | Rename experiment imports to physiotwin4d. |
| experiments/Reconstruct4DCT/reconstruct_4d_ct_class.py | Rename experiment imports to physiotwin4d. |
| experiments/Lung-VesselsAirways/0-GenData.py | Rename notebook utility import to physiotwin4d. |
| experiments/Lung-GatedCT_To_USD/Experiment_SegReg.py | Rename experiment imports to physiotwin4d. |
| experiments/Lung-GatedCT_To_USD/Experiment_CombineModels.py | Rename experiment imports to physiotwin4d. |
| experiments/Lung-GatedCT_To_USD/Experiment_ArrangeOnStage.py | Rename experiment imports to physiotwin4d. |
| experiments/Lung-GatedCT_To_USD/2-paint_dirlab_models.py | Rename experiment imports to physiotwin4d. |
| experiments/Lung-GatedCT_To_USD/1-make_dirlab_models.py | Rename experiment imports to physiotwin4d. |
| experiments/Lung-GatedCT_To_USD/0-register_dirlab_4dct.py | Rename experiment imports to physiotwin4d. |
| experiments/Heart-VTKSeries_To_USD/1-heart_vtkseries_to_usd.py | Rename experiment imports to physiotwin4d. |
| experiments/Heart-VTKSeries_To_USD/0-download_and_convert_4d_to_3d.py | Rename experiment imports to physiotwin4d. |
| experiments/Heart-Statistical_Model_To_Patient/heart_model_to_patient.py | Rename experiment imports/comments to PhysioTwin4D. |
| experiments/Heart-Statistical_Model_To_Patient/heart_model_to_patient-CHOPValve.py | Rename experiment imports/comments to PhysioTwin4D. |
| experiments/Heart-Statistical_Model_To_Patient/heart_model_to_model_registration_pca.py | Rename experiment imports/comments to PhysioTwin4D. |
| experiments/Heart-Statistical_Model_To_Patient/heart_model_to_model_icp_itk.py | Rename experiment imports/comments to PhysioTwin4D. |
| experiments/Heart-Simpleware_Segmentation/simpleware_heart_segmentation.py | Rename experiment imports/comments to PhysioTwin4D. |
| experiments/Heart-GatedCT-OptimizedLongitudinalRegistration/setup.sh | Rename editable install comment to physiotwin4d. |
| experiments/Heart-GatedCT-OptimizedLongitudinalRegistration/registration_test.py | Rename imports and path examples to PhysioTwin4D. |
| experiments/Heart-GatedCT-OptimizedLongitudinalRegistration/3-eval_icon.py | Rename imports and path examples to PhysioTwin4D. |
| experiments/Heart-GatedCT-OptimizedLongitudinalRegistration/2-finetune_icon.py | Rename imports and path examples to PhysioTwin4D. |
| experiments/Heart-GatedCT-OptimizedLongitudinalRegistration/1-initial_registration.py | Rename imports and path examples to PhysioTwin4D. |
| experiments/Heart-GatedCT-OptimizedLongitudinalRegistration/0-cardiacGatedCT_segment_and_landmark.py | Rename imports and path examples to PhysioTwin4D. |
| experiments/Heart-GatedCT_To_USD/4-merge_dynamic_and_static_usd.py | Rename imports to physiotwin4d. |
| experiments/Heart-GatedCT_To_USD/3-transform_dynamic_and_static_contours.py | Rename imports to physiotwin4d. |
| experiments/Heart-GatedCT_To_USD/2-generate_segmentation.py | Rename imports to physiotwin4d. |
| experiments/Heart-GatedCT_To_USD/1-register_images.py | Rename imports to physiotwin4d. |
| experiments/Heart-GatedCT_To_USD/0-download_and_convert_4d_to_3d.py | Rename imports to physiotwin4d. |
| experiments/Heart-Create_Statistical_Model/README.md | Rename documentation references to PhysioTwin4D. |
| experiments/Heart-Create_Statistical_Model/5-compute_pca_model.py | Rename experiment imports to physiotwin4d. |
| experiments/Heart-Create_Statistical_Model/4-surfaces_aligned_correspond_to_pca_inputs.py | Rename experiment imports to physiotwin4d. |
| experiments/Heart-Create_Statistical_Model/3-registration_based_correspondence.py | Rename experiment imports to physiotwin4d. |
| experiments/Heart-Create_Statistical_Model/2-input_surfaces_to_surfaces_aligned.py | Rename experiment imports to physiotwin4d. |
| experiments/Heart-Create_Statistical_Model/1-input_meshes_to_input_surfaces.py | Rename experiment imports to physiotwin4d. |
| experiments/Convert_VTK_To_USD/convert_vtk_to_usd_using_class.py | Rename experiment imports to physiotwin4d. |
| experiments/Convert_VTK_To_USD/convert_chop_tpv25_valve_to_usd.py | Rename experiment imports to physiotwin4d. |
| experiments/Convert_VTK_To_USD/convert_chop_heart_vtk_to_usd.py | Rename workflow import to physiotwin4d. |
| experiments/Convert_VTK_To_USD/convert_chop_alterra_valve_to_usd.py | Rename experiment imports to physiotwin4d. |
| experiments/Colormap-VTK_To_USD/colormap_vtk_to_usd.py | Rename converter import and output branding string. |
| docs/troubleshooting.rst | Rename install/help text and GitHub issue links. |
| docs/references.rst | Rename citation snippet and GitHub URL. |
| docs/README.md | Rename documentation branding. |
| docs/isaac_for_healthcare.rst | Rename HTML classes/text branding for PhysioTwin4D. |
| docs/faq.rst | Rename FAQ branding and install snippets. |
| docs/developer/workflows.rst | Rename CLI mapping and base-class guidance. |
| docs/developer/utilities.rst | Rename code samples to physiotwin4d. |
| docs/developer/usd_generation.rst | Rename USD entry-point references to physiotwin4d. |
| docs/developer/transform_conventions.rst | Rename API references to physiotwin4d. |
| docs/developer/segmentation.rst | Rename API references to physiotwin4d. |
| docs/developer/registration_models.rst | Rename API references to physiotwin4d. |
| docs/developer/registration_images.rst | Rename API references to physiotwin4d. |
| docs/developer/extending.rst | Rename extension guidance to PhysioTwin4DBase. |
| docs/developer/core.rst | Rename base-class guidance to PhysioTwin4DBase. |
| docs/developer/architecture.rst | Rename architecture branding and base-class reference. |
| docs/contributing.rst | Rename contributing guide branding, clone URLs, and template tokens. |
| docs/conf.py | Rename Sphinx project metadata, GitHub repo name, and template token replacement. |
| docs/cli_scripts/vtk_to_usd.rst | Rename CLI command examples and API references. |
| docs/cli_scripts/overview.rst | Rename CLI prefix and general CLI docs branding. |
| docs/cli_scripts/lung_gated_ct.rst | Rename narrative and API reference. |
| docs/cli_scripts/heart_gated_ct.rst | Rename CLI command examples and API reference. |
| docs/cli_scripts/fit_statistical_model_to_patient.rst | Rename CLI command, install docs, and API reference. |
| docs/cli_scripts/download_data.rst | Rename download CLI and API references. |
| docs/cli_scripts/create_statistical_model.rst | Rename create-model CLI and API references. |
| docs/cli_scripts/brain_vessel_modeling.rst | Rename narrative branding. |
| docs/cli_scripts/best_practices.rst | Rename CLI examples and template token. |
| docs/cli_scripts/4dct_reconstruction.rst | Rename reconstruction CLI and API reference. |
| docs/changelog.rst | Add 2026.07.0 rename note and rename prior release branding. |
| docs/architecture.rst | Rename architecture branding, tokens, and CLI list. |
| docs/api/workflows.rst | Rename module/currentmodule directives and code samples. |
| docs/api/utilities/transform_tools.rst | Rename currentmodule/automodule directives. |
| docs/api/utilities/test_tools.rst | Rename currentmodule/automodule and narrative branding. |
| docs/api/utilities/labelmap_tools.rst | Rename currentmodule/automodule directives. |
| docs/api/utilities/index.rst | Rename currentmodule directive. |
| docs/api/utilities/image_tools.rst | Rename currentmodule/automodule directives. |
| docs/api/utilities/image_conversion.rst | Rename currentmodule/automodule directives. |
| docs/api/utilities/data_download.rst | Rename currentmodule/automodule directives. |
| docs/api/utilities/contour_tools.rst | Rename currentmodule/automodule directives. |
| docs/api/usd/vtk_to_usd_lib.rst | Rename module/currentmodule directives and narrative. |
| docs/api/usd/vtk_conversion.rst | Rename module/currentmodule directives. |
| docs/api/usd/tools.rst | Rename automodule directive target. |
| docs/api/usd/index.rst | Rename currentmodule and code samples. |
| docs/api/usd/anatomy_tools.rst | Rename automodule directive target. |
| docs/api/segmentation/totalsegmentator.rst | Rename module/currentmodule directives and CLI references. |
| docs/api/segmentation/simpleware.rst | Rename module/currentmodule directives and code samples. |
| docs/api/segmentation/index.rst | Rename currentmodule and narrative branding. |
| docs/api/segmentation/base.rst | Rename module/currentmodule directives and guidance. |
| docs/api/registration/time_series.rst | Rename module/currentmodule directives and examples. |
| docs/api/registration/index.rst | Rename currentmodule and narrative branding. |
| docs/api/registration/icon.rst | Rename module/currentmodule directives and examples. |
| docs/api/registration/greedy.rst | Rename module/currentmodule directives and examples. |
| docs/api/registration/base.rst | Rename module/currentmodule directives. |
| docs/api/registration/ants.rst | Rename module/currentmodule directives and examples. |
| docs/api/model_registration/pca.rst | Rename module/currentmodule directives. |
| docs/api/model_registration/index.rst | Rename currentmodule and examples. |
| docs/api/model_registration/icp.rst | Rename module/currentmodule directives. |
| docs/api/model_registration/icp_itk.rst | Rename module/currentmodule directives. |
| docs/api/model_registration/distance_maps.rst | Rename module/currentmodule directives. |
| docs/api/index.rst | Rename API index narrative and class cross-references. |
| docs/api/cli/visualize_pca_modes.rst | Rename automodule directive target. |
| docs/api/cli/reconstruct_highres_4d_ct.rst | Rename automodule directive target. |
| docs/api/cli/index.rst | Rename module/currentmodule directives and narrative. |
| docs/api/cli/fit_statistical_model_to_patient.rst | Rename automodule directive target. |
| docs/api/cli/download_data.rst | Rename automodule directive target. |
| docs/api/cli/create_statistical_model.rst | Rename automodule directive target. |
| docs/api/cli/convert_vtk_to_usd.rst | Rename automodule directive target. |
| docs/api/cli/convert_image_to_vtk.rst | Rename automodule directive target. |
| docs/api/cli/convert_image_to_usd.rst | Rename automodule directive target. |
| docs/api/base.rst | Rename base-class module/currentmodule directives and example code. |
| data/Slicer-Heart-CT/download_and_convert.py | Rename dataset helper script imports to physiotwin4d. |
| data/README.md | Rename data documentation and code samples. |
| data/KCL-Heart-Model/README.md | Rename dataset narrative branding. |
| CLAUDE.md | Update contributor guide coverage path and base-class name. |
| AGENTS.md | Update agent guidance branding, coverage path, and base-class name. |
| .readthedocs.yaml | Rename ReadTheDocs config comment branding. |
| .pre-commit-config.yaml | Update hook file-scoping regex to src/physiotwin4d/. |
| .github/workflows/test-slow.yml | Rename temp venv path and coverage target package name. |
| .github/workflows/README.md | Rename coverage package name in workflow docs. |
| .github/workflows/nightly-health.yml | Rename badge links, venv paths, and coverage target package. |
| .github/workflows/ci.yml | Rename coverage target package and temp venv paths. |
| .github/scripts/build_dashboard.py | Rename dashboard branding, links, and README snippet URLs. |
| .cursor/rules/project-standards.mdc | Rename Cursor rules branding. |
| .agents/skills/test-feature/SKILL.md | Rename skill branding to PhysioTwin4D. |
| .agents/skills/regen-api-map/SKILL.md | Rename skill branding and path references to src/physiotwin4d. |
| .agents/skills/plan/SKILL.md | Rename skill branding to PhysioTwin4D. |
| .agents/skills/impl/SKILL.md | Rename skill branding and key-module references to PhysioTwin4D. |
| .agents/skills/doc-feature/SKILL.md | Rename skill branding to PhysioTwin4D. |
| .agents/skills/commit/SKILL.md | Rename skill branding to PhysioTwin4D. |
| .agents/skills/check-conventions/SKILL.md | Rename convention-audit text and path references to src/physiotwin4d. |
| .agents/agents/testing.md | Rename agent branding and referenced test-tools path. |
| .agents/agents/implementation.md | Rename agent branding and key-module references to PhysioTwin4D. |
| .agents/agents/docs.md | Rename agent branding to PhysioTwin4D. |
| .agents/agents/architecture.md | Rename agent branding and codebase-map paths to src/physiotwin4d. |
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| SSM_MEAN_MESH_FILE = Path("D:/PhysioTwin4D/kcl-heart-pca/pca-vol-kcl/pca_mean.vtu") | ||
| SSM_MODEL_FILE = Path("D:/PhysioTwin4D/kcl-heart-pca/pca-vol-kcl/pca_model.json") |
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