ENH: Heart models are now surfaces, save as vtp

[aylward]

Summary by CodeRabbit

• Documentation
  • Updated the heart-fitting tutorial to use .vtp mesh output files.
  • Removed outdated commented examples for custom PCA model paths.

[coderabbitai]

Walkthrough

The heart fitting tutorial now saves template and registered template meshes with .vtp extensions. Commented BYOD PCA model path examples were removed.

Changes

Heart tutorial mesh outputs

Layer / File(s)	Summary
Update mesh output extensions tutorials/tutorial_07_heart_fit_statistical_model_to_patient.py	Template and registered template mesh outputs now use .vtp instead of .vtu.

Estimated code review effort: 1 (Trivial) | ~2 minutes

Possibly related PRs

• Project-MONAI/physiotwin4d#95: Tracks related heart model mesh assets managed through Git LFS.

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.
Title check	✅ Passed	The title clearly summarizes the primary change from volumetric meshes to surface meshes saved in VTP format.
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.

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@tutorials/tutorial_07_heart_fit_statistical_model_to_patient.py`:
- Line 177: Update the registered mesh output path in the tutorial’s
mesh-writing flow to use the filename basename expected by the integration test,
changing only the extension as required by the existing contract. Keep the
producer and consumer names aligned, including any related references to this
output.

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Fix all unresolved CodeRabbit comments on this PR:

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• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: ce0afc8b-3205-47cb-979e-78c52a91e424

📥 Commits

Reviewing files that changed from the base of the PR and between 01a9298 and da0b362.

📒 Files selected for processing (1)

• tutorials/tutorial_07_heart_fit_statistical_model_to_patient.py

[coderabbitai]

🗄️ Data Integrity & Integration | 🟠 Major | ⚡ Quick win

Align the registered mesh filename with the integration test.

Line 177 writes *_template_mesh_registered.vtp, but tests/test_tutorials.py checks for *_template_surface_registered.vtp. The tutorial test will fail because the producer and consumer use different basenames. Preserve the existing filename contract while changing only the extension, or update the test and all consumers together.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@tutorials/tutorial_07_heart_fit_statistical_model_to_patient.py` at line 177,
Update the registered mesh output path in the tutorial’s mesh-writing flow to
use the filename basename expected by the integration test, changing only the
extension as required by the existing contract. Keep the producer and consumer
names aligned, including any related references to this output.

[Copilot]

Pull request overview

This PR updates Tutorial 7’s output artifacts to align with the new convention that heart “models” are treated as surfaces and are saved as VTK PolyData (.vtp) rather than unstructured grids (.vtu).

Changes:

• Remove outdated “BYOD” example paths for .vtu/PCA JSON inputs.
• Update saved template/registered “mesh” outputs from .vtu to .vtp in the tutorial script.

Suppressed comments (1)

tutorials/tutorial_07_heart_fit_statistical_model_to_patient.py:178

• Saving registered_template_model as .vtp assumes the returned dataset is pv.PolyData. Since the workflow returns pv.DataSet here, this can break if the registered model is an UnstructuredGrid. Either keep .vtu for volumetric meshes, or extract a surface before writing .vtp.

    registered_mesh.save(
        str(output_dir / f"{project_name}_template_mesh_registered.vtp")
    )

---

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 36.55%. Comparing base (01a9298) to head (da0b362).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #109   +/-   ##
=======================================
  Coverage   36.55%   36.55%           
=======================================
  Files          72       72           
  Lines        8503     8503           
=======================================
  Hits         3108     3108           
  Misses       5395     5395           

Flag	Coverage Δ
integration-tests	36.35% <ø> (?)
unittests	36.55% <ø> (ø)

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