ENH: Produce 4D labelmap and CT images with lung and heart motion

[aylward]

Summary by CodeRabbit

• New Features
  • Added optional surface smoothing and mesh reduction while preserving boundary labels.
  • Added smoothing support for deformation fields.
  • Tutorial 10 now packages predicted surfaces into a 4D USD project.
  • Tutorial 11 now generates warped CT and anatomy labelmap volumes for each combined-motion frame.
• Changes
  • Removed the previous transform-to-USD visualization API.
  • Updated tutorial outputs, checkpoint selection, and cleanup behavior.

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Walkthrough

Changes

Motion workflow updates

Layer / File(s)	Summary
Shared smoothing utilities and transform cleanup src/physiotwin4d/contour_tools.py, src/physiotwin4d/transform_tools.py	Adds surface and deformation-field smoothing helpers and removes the TransformTools USD visualization implementation.
Tutorial 10 prediction and USD assembly tutorials/tutorial_10_byod_eval_physicsnemo_mgn.py	Uses checkpoint epoch 1500, converts predicted surfaces into a 4D USD project, and returns its path.
Tutorial 11 combined-motion volume generation tutorials/tutorial_11_heart_and_lung_motion.py	Blends displacement fields, writes warped CT and labelmap volumes per frame, manages field caching, and includes volume paths in results.

Estimated code review effort: 4 (Complex) | ~45 minutes

Sequence Diagram(s)

Tutorial 11 combined-motion volume flow

sequenceDiagram
  participant Tutorial11
  participant DisplacementFields
  participant CTVolume
  participant LabelmapVolume
  participant CombinedOutputs
  Tutorial11->>DisplacementFields: bilinearly blend phase and stage fields
  DisplacementFields-->>Tutorial11: cached combined field
  Tutorial11->>CTVolume: warp CT with linear interpolation
  Tutorial11->>LabelmapVolume: warp labelmap with nearest-neighbor sampling
  CTVolume-->>CombinedOutputs: combined_ct_###.mha
  LabelmapVolume-->>CombinedOutputs: combined_labelmap_###.mha

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Possibly related PRs

• Project-MONAI/physiotwin4d#85: Refactors WorkflowConvertVTKToUSD, which Tutorial 10 now uses for in-memory predicted surfaces.

Suggested reviewers: copilot

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title accurately captures the main change: generating 4D CT and labelmap outputs for lung and heart motion.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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