ENH: Specify Python 3.11 for nightly health / remote runner

.github/workflows/nightly-health.yml

@@ -58,7 +58,7 @@ jobs:
         # Python 3.11 is required because the [physicsnemo] extra pulls in
         # nvidia-physicsnemo, which requires Python >= 3.11.
         run: |
-          & py -m venv "$env:RUNNER_TEMP\physiotwin4d-venv"
+          & py -3.11 -m venv "$env:RUNNER_TEMP\physiotwin4d-venv"
           echo "$env:RUNNER_TEMP\physiotwin4d-venv\Scripts" >> $env:GITHUB_PATH
 
       - name: Cache uv packages

.gitignore

@@ -13,6 +13,9 @@ build
 __pycache__
 _version.py
 htmlcov
+.cursor
+.vscode/*
+!.vscode/settings.json
 
 # AI files
 .claude

data/DirLab-4DCT/README.md

@@ -68,7 +68,7 @@ points for registration validation.
 
 ### Dataset Details
 
-- **Format**: `.mhd`/`.raw` (MetaImage format)
+- **Format**: `.mhd` headers + `.img` raw volumes (MetaImage format)
 - **Cases**: 10 patient cases (Case 1-10)
 - **Phases**: 10 respiratory phases per case (T00-T90)
 - **Content**: Non-contrast lung CT

data/README.md

@@ -1,61 +1,33 @@
 # PhysioTwin4D Data Directory
 
-This directory holds the example datasets used by PhysioTwin4D's tutorials,
-experiments, and tests. Each subdirectory is one dataset and has its own
-`README.md` with the download URL(s), directory layout, data sizes, and the
-exact `physiotwin4d-download-data` command for that dataset. This file is
-just the map — see the subdirectory README before downloading anything.
+This directory holds the sample datasets used for experiments, testing, and
+development of the PhysioTwin4D library. Each subdirectory contains one
+dataset and its own `README.md` with download instructions, specifications,
+and citation — this file is just an index; treat the per-dataset READMEs as
+the source of truth.
 
 ## Datasets
 
-| Directory                          | Data Type                                              | Provided By                            | Auto-Download |
-| ----------------------------------- | ------------------------------------------------------- | --------------------------------------- | ------------- |
-| [`Slicer-Heart-CT/`](Slicer-Heart-CT/README.md) | 4D gated cardiac CT (`.seq.nrrd`)         | Jolley Lab (CHOP) / SlicerHeart on GitHub | Yes           |
-| [`DirLab-4DCT/`](DirLab-4DCT/README.md)   | 4D lung CT respiratory benchmark + landmarks (`.mhd/.raw`) | DIR-Lab (Emory / MD Anderson)          | No — manual, may require registration |
-| [`KCL-Heart-Model/`](KCL-Heart-Model/README.md) | Statistical heart shape model meshes (`.vtk`)   | King's College London, via Zenodo       | Yes           |
-| [`CHOP-Valve4D/`](CHOP-Valve4D/README.md) | FEBio valve FE model, converted to VTK/ITK + Simpleware segmentation | Jolley Lab (CHOP), converted by PhysioTwin4D | Yes           |
-
-[`data/test/`](test/README.md) is not a dataset — it is a cache
-automatically managed by the pytest infrastructure (mainly from
-`Slicer-Heart-CT`) and is not used by the workflows, tutorials, or CLIs.
-
-## Downloading Data
-
-Datasets marked **Yes** above can be fetched with the
-`physiotwin4d-download-data` CLI (or the corresponding
-`DataDownloadTools.Download*` method), for example:
-
-```bash
-physiotwin4d-download-data Slicer-Heart-CT --directory data/Slicer-Heart-CT
-physiotwin4d-download-data KCL-Heart-Model --directory data/KCL-Heart-Model
-physiotwin4d-download-data CHOP-Valve4D --directory data/CHOP-Valve4D
-```
-
-Datasets marked **No** must be downloaded by hand following the
-instructions in that dataset's own README (`DirLab-4DCT/README.md`).
-
-### Verification Helpers
-
-Each dataset also has a `DataDownloadTools.Verify*Data()` helper that checks
-whether the expected files are already present, so scripts can skip
-downloading when the data is cached:
-
-```python
-from physiotwin4d import DataDownloadTools
-
-DataDownloadTools.VerifySlicerHeartCTData("data/Slicer-Heart-CT")
-DataDownloadTools.VerifyDirLab4DCTData("data/DirLab-4DCT")
-DataDownloadTools.VerifyKCLHeartModelData("data/KCL-Heart-Model")
-DataDownloadTools.VerifyCHOPValve4DData("data/CHOP-Valve4D")
-```
-
-## Guidelines
-
-- Keep original downloaded data unmodified; write experiment/tutorial
-  results under `experiments/*/results/` or `tutorials/*/results/`, not
-  back into `data/`.
-- Always respect the license and citation requirements of each dataset —
-  see the "Citation" / "Acknowledgement" section in the relevant
-  subdirectory README.
-- If you add a new dataset, add both a row above and a subdirectory
-  `README.md` following the existing datasets as a template.
+| Directory | Description | Provided By | Download | README |
+| --- | --- | --- | --- | --- |
+| `Slicer-Heart-CT/` | 4D cardiac CT with gated cardiac phases | Jolley Lab, Children's Hospital of Philadelphia (CHOP) | Automatic | [Slicer-Heart-CT/README.md](Slicer-Heart-CT/README.md) |
+| `DirLab-4DCT/` | 4D lung CT respiratory motion benchmark | DIR-Lab, MD Anderson Cancer Center / Emory University | Manual | [DirLab-4DCT/README.md](DirLab-4DCT/README.md) |
+| `KCL-Heart-Model/` | Statistical shape model of the heart | King's College London (KCL) | Automatic | [KCL-Heart-Model/README.md](KCL-Heart-Model/README.md) |
+| `CHOP-Valve4D/` | 4D valve reconstruction models | Jolley Lab, CHOP (original FEBio model) | Automatic | [CHOP-Valve4D/README.md](CHOP-Valve4D/README.md) |
+| `test/` | pytest-managed cache; not a downloadable dataset | — | N/A | [test/README.md](test/README.md) |
+
+## Automatic Download
+
+`Slicer-Heart-CT`, `KCL-Heart-Model`, and `CHOP-Valve4D` can be fetched with
+the `physiotwin4d-download-data` CLI or `DataDownloadTools`; see each
+dataset's README for the exact command. `DirLab-4DCT` has no automatic
+downloader — DIR-Lab distributes each case individually and may require
+registration, so it must be obtained manually; see
+[DirLab-4DCT/README.md](DirLab-4DCT/README.md).
+
+## Notes
+
+- Always cite the original data source in publications — see each dataset's
+  README for the required citation.
+- The full set of datasets is ~10-20 GB; ensure adequate disk space before
+  downloading everything.

src/physiotwin4d/vtk_to_usd/usd_utils.py

@@ -163,16 +163,11 @@ def numpy_to_vt_array(array: NDArray, data_type: DataType) -> Any:
         array_uc = array.astype(np.uint8)
         return Vt.UCharArray.FromNumpy(array_uc.flatten())
 
-    elif data_type in [DataType.SHORT, DataType.USHORT]:
+    else:  # DataType.SHORT, DataType.USHORT
         # Convert to int
         array_i = array.astype(np.int32)
         return Vt.IntArray.FromNumpy(array_i.flatten())
 
-    else:
-        # Fallback to float
-        array_f = array.astype(np.float32)
-        return Vt.FloatArray.FromNumpy(array_f.flatten())
-
 
 def get_sdf_value_type(data_type: DataType, num_components: int) -> Sdf.ValueTypeName:
     """Get appropriate SDF value type for primvar creation.
@@ -214,12 +209,9 @@ def get_sdf_value_type(data_type: DataType, num_components: int) -> Sdf.ValueTyp
     elif data_type in [DataType.UCHAR, DataType.CHAR]:
         return Sdf.ValueTypeNames.UCharArray
 
-    elif data_type in [DataType.SHORT, DataType.USHORT]:
+    else:  # DataType.SHORT, DataType.USHORT
         return Sdf.ValueTypeNames.IntArray
 
-    else:
-        return Sdf.ValueTypeNames.FloatArray
-
 
 def sanitize_primvar_name(name: str) -> str:
     """Sanitize a name to be USD-compliant.

tests/README.md

@@ -254,7 +254,7 @@ When creating new tests:
 ## Test Data
 
 ### Slicer-Heart-CT Dataset
-- **Source**: [Slicer-Heart-CT GitHub](https://github.com/Slicer-Heart-CT/Slicer-Heart-CT)
+- **Source**: [SlicerHeart GitHub](https://github.com/SlicerHeart/SlicerHeart)
 - **File**: `TruncalValve_4DCT.seq.nrrd` (~1.2 GB)
 - **Content**: 21-phase pediatric cardiac CT
 - **Usage**: Tests use first 2 time points for speed

tutorials/tutorial_01_heart_gated_ct_to_usd.py

@@ -60,7 +60,7 @@
 Data Required
 -------------
 See data/README.md for download instructions and dataset licensing.
-Dataset: Slicer-Heart-CT - https://github.com/Slicer-Heart-CT/Slicer-Heart-CT
+Dataset: Slicer-Heart-CT - https://github.com/SlicerHeart/SlicerHeart
 This script expects the data to already exist at
 ``data/Slicer-Heart-CT/TruncalValve_4DCT.seq.nrrd``. Run the repository data
 download notebook or download the file manually before running this tutorial.