ENH: Fix directory structure for CHOP-Valve data

[aylward]

Summary by CodeRabbit

• Bug Fixes
  • Updated CHOP-Valve4D dataset downloads and verification to support the revised archive layout.
  • Ensured required CT artifacts and valve-mesh files are correctly detected in the base dataset directory.

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Review details

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 180eedf6-fcf6-4d67-b8a9-cd5a6e9e880c

📥 Commits

Reviewing files that changed from the base of the PR and between 6a78bf0 and aebe894.

📒 Files selected for processing (1)

• src/physiotwin4d/data_download_tools.py

Walkthrough

CHOP-Valve4D release archives are now extracted directly into the base dataset directory. Verification checks for CT artifacts and Alterra or TPV25 valve meshes now inspect that same directory.

Changes

CHOP-Valve4D dataset layout

Layer / File(s)	Summary
Flat archive extraction and verification src/physiotwin4d/data_download_tools.py	Download extraction targets the base dataset directory, and CT, Alterra, and TPV25 verification checks use the updated flat layout.

Estimated code review effort: 2 (Simple) | ~10 minutes

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 matches the main change: fixing the CHOP-Valve data directory structure.
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.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

src/physiotwin4d/data_download_tools.py (1)

247-251: 🎯 Functional Correctness | 🔴 Critical | ⚡ Quick win

Flattened directory paths break data verification and mesh extraction.

Passing data_dir directly to _CHOPValve4DSubdirIsPopulated causes it to look for marker files (like RVOT28-Dias.nii.gz or *.vtk) in the root dataset directory rather than the appropriate subdirectories.

• If the zip archives extract flat into data_dir, Alterra and TPV25 meshes will overwrite each other, and downloading one will cause the other to be skipped (since any(target_dir.glob("*.vtk")) matches both).
• If the zip archives natively contain subdirectories (e.g., CT/), extracting to data_dir avoids double-folders, but the population check will fail because it looks for data_dir / "RVOT28-Dias.nii.gz" instead of data_dir / "CT" / "RVOT28-Dias.nii.gz". This causes VerifyCHOPValve4DData to always fail and triggers re-downloads on every run.

Restore the subdirectory paths for the checks to correctly isolate the assets:

• src/physiotwin4d/data_download_tools.py#L247-L251: Pass data_dir / subdir_name to _CHOPValve4DSubdirIsPopulated instead of target_dir. If you are extracting to data_dir to avoid double-folders, you can keep target_dir = data_dir for the _DownloadAndExtractZip call.
• src/physiotwin4d/data_download_tools.py#L307-L311: Append the respective subdirectory names by passing data_dir / "CT", data_dir / "Alterra", and data_dir / "TPV25" to _CHOPValve4DSubdirIsPopulated.

🤖 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 `@src/physiotwin4d/data_download_tools.py` around lines 247 - 251, The
population check in the download loop must use each asset’s subdirectory rather
than the root data directory. In src/physiotwin4d/data_download_tools.py lines
247-251, pass data_dir / subdir_name to _CHOPValve4DSubdirIsPopulated while
preserving target_dir for extraction; in lines 307-311, pass data_dir / "CT",
data_dir / "Alterra", and data_dir / "TPV25" to the corresponding
_CHOPValve4DSubdirIsPopulated calls.

🤖 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.

Outside diff comments:
In `@src/physiotwin4d/data_download_tools.py`:
- Around line 247-251: The population check in the download loop must use each
asset’s subdirectory rather than the root data directory. In
src/physiotwin4d/data_download_tools.py lines 247-251, pass data_dir /
subdir_name to _CHOPValve4DSubdirIsPopulated while preserving target_dir for
extraction; in lines 307-311, pass data_dir / "CT", data_dir / "Alterra", and
data_dir / "TPV25" to the corresponding _CHOPValve4DSubdirIsPopulated calls.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: d02e7b02-a6d8-4bcb-acd7-9dd0caecd711

📥 Commits

Reviewing files that changed from the base of the PR and between e31c8af and 6a78bf0.

📒 Files selected for processing (1)

• src/physiotwin4d/data_download_tools.py

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