Tests (#43)

* ENH: Updated reporting of nightly results.
* ENH: Fix link to download slicerheart data
* ENH: Fix coverage reporting
* ENH: Detect more download failures
* ENH: Remove Vista3D due to challenges on blackwell

* TST: Add full type annotations to all test files; include tests/ in mypy
Add return type and parameter annotations to every function in tests/,
satisfying mypy disallow_untyped_defs=true. Extend mypy coverage from
src/ only to src/ tests/ and add a pyproject.toml override so test
modules ignore missing stubs from itk/pyvista.

* FIX: PyVista extract_surface algorithm, ITK snake-case API, TestTools export
Pass algorithm="dataset_surface" to every extract_surface() call to match
the updated PyVista API. Switch segment_anatomy_base.py to the ITK
snake_case functional API (resample_image_filter, etc.). Replace
MultiplyImageFilter with explicit array multiply in transform_tools to
avoid type-dispatch issues. Export TestTools from __init__ and add
__test__=False to suppress spurious pytest collection.

* ENH: Add data/test dir .gitignore

* FIX: Guard against empty ids in segment_connected_component
np.argmax on an empty array raises ValueError; this can occur when the input contains no labeled voxels in the threshold range (e.g. a non-contrast study).

* BUG: Address comments raised by copilot and coderabbit
* BUG: Update baselines for tests

* FIX: Add urllib.error import and fix stale ensemble/simpleware references
urllib.error was used in conftest.py but not imported, causing AttributeError on download failures. Also corrects the segmentation method identifier in troubleshooting docs ('simpleware' -> 'simpleware_heart') and removes stale ensemble references from README and developer docs.

Author: aylward

.claude/.gitignore

@@ -0,0 +1 @@
+settings.local.json

.github/workflows/ci.yml

@@ -107,6 +107,7 @@ jobs:
       uses: codecov/codecov-action@v4
       if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10'
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
         flags: unittests
         name: codecov-unit-${{ matrix.os }}-py${{ matrix.python-version }}
@@ -233,6 +234,7 @@ jobs:
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
         flags: integration-tests
         name: codecov-integration
@@ -317,6 +319,7 @@ jobs:
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
         flags: gpu-tests
         name: codecov-gpu
@@ -380,7 +383,6 @@ jobs:
 # - tests/test_register_images_icon.py (requires CUDA for ICON)
 # - tests/test_transform_tools.py (depends on slow registration tests)
 # - tests/test_segment_chest_total_segmentator.py (requires CUDA for TotalSegmentator)
-# - tests/test_segment_chest_vista_3d.py (requires CUDA for VISTA-3D, 20GB+ RAM)
 #
 # Experiment tests (EXTREMELY SLOW - hours to complete):
 # - tests/test_experiments.py (runs all notebooks in experiments/ subdirectories)

.github/workflows/test-slow.yml

@@ -80,6 +80,7 @@ jobs:
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
         flags: slow-tests-gpu
         name: codecov-slow-gpu

CLAUDE.md

@@ -14,7 +14,7 @@ uv pip install -e .
 ruff check . --fix && ruff format .
 
 # Type checking
-mypy src/
+mypy src/ tests/
 
 # All pre-commit hooks
 pre-commit run --all-files
@@ -28,7 +28,6 @@ py -m pytest tests/test_contour_tools.py::test_extract_surface -v
 
 # Skip GPU-dependent tests
 py -m pytest tests/ --ignore=tests/test_segment_chest_total_segmentator.py \
-              --ignore=tests/test_segment_chest_vista_3d.py \
               --ignore=tests/test_register_images_icon.py
 
 # With coverage

README.md

@@ -7,7 +7,7 @@ PhysioMotion4D is a comprehensive medical imaging package that converts 4D CT sc
 ## 🚀 Key Features
 
 - **Complete 4D Medical Imaging Pipeline**: End-to-end processing from 4D CT data to animated USD models
-- **Multiple AI Segmentation Methods**: TotalSegmentator, VISTA-3D, and ensemble approaches
+- **Multiple AI Segmentation Methods**: TotalSegmentator and Simpleware cardiac segmentation
 - **Deep Learning Registration**: GPU-accelerated image registration using Icon algorithm
 - **NVIDIA Omniverse Integration**: Direct USD file export for medical visualization
 - **Physiological Motion Analysis**: Capture and visualize cardiac and respiratory motion
@@ -106,9 +106,6 @@ print(f"PhysioMotion4D version: {physiomotion4d.__version__}")
   - `WorkflowFitStatisticalModelToPatient`: Model-to-patient registration workflow
 - **Segmentation Classes**: Multiple AI-based chest segmentation implementations
   - `SegmentChestTotalSegmentator`: TotalSegmentator-based segmentation
-  - `SegmentChestVista3D`: VISTA-3D model-based segmentation
-  - `SegmentChestVista3DNIM`: NVIDIA NIM version of VISTA-3D
-  - `SegmentChestEnsemble`: Ensemble segmentation combining multiple methods
   - `SegmentAnatomyBase`: Base class for custom segmentation methods
 - **Registration Classes**: Multiple registration methods for different use cases
   - Image-to-Image Registration:
@@ -142,7 +139,7 @@ print(f"PhysioMotion4D version: {physiomotion4d.__version__}")
 - **AI/ML**: PyTorch, CuPy (CUDA 13 default; CUDA 12 via `[cuda12]` extra), transformers, MONAI
 - **Registration**: icon-registration, unigradicon
 - **Visualization**: USD-core, PyVista
-- **Segmentation**: TotalSegmentator, VISTA-3D models
+- **Segmentation**: TotalSegmentator
 
 ## 🎯 Quick Start
 
@@ -262,11 +259,11 @@ registered_mesh = workflow.run_workflow()
 ### Custom Segmentation
 
 ```python
-from physiomotion4d import SegmentChestVista3D
+from physiomotion4d import SegmentChestTotalSegmentator
 import itk
 
-# Initialize VISTA-3D segmentation
-segmenter = SegmentChestVista3D()
+# Initialize TotalSegmentator segmentation
+segmenter = SegmentChestTotalSegmentator()
 
 # Load and segment image
 image = itk.imread("chest_ct.nrrd")
@@ -578,14 +575,12 @@ pytest tests/test_register_images_greedy.py -v             # Greedy registration
 pytest tests/test_register_images_icon.py -v                # Icon registration
 pytest tests/test_register_time_series_images.py -v         # Time series registration
 pytest tests/test_segment_chest_total_segmentator.py -v     # TotalSegmentator
-pytest tests/test_segment_chest_vista_3d.py -v              # VISTA-3D segmentation
 pytest tests/test_contour_tools.py -v                       # Mesh and contour tools
 pytest tests/test_image_tools.py -v                         # Image processing utilities
 pytest tests/test_transform_tools.py -v                     # Transform operations
 
 # Skip GPU-dependent tests (segmentation and registration)
 pytest tests/ --ignore=tests/test_segment_chest_total_segmentator.py \
-              --ignore=tests/test_segment_chest_vista_3d.py \
               --ignore=tests/test_register_images_icon.py
 
 # Run with coverage report
@@ -594,7 +589,7 @@ pytest tests/ --cov=src/physiomotion4d --cov-report=html
 
 **Test Categories:**
 - **Data Pipeline**: Download, conversion, and preprocessing
-- **Segmentation**: TotalSegmentator and VISTA-3D (GPU required)
+- **Segmentation**: TotalSegmentator (GPU required)
 - **Registration**: ANTs, Icon, and time series methods (slow, ~5-10 min)
 - **Geometry & Visualization**: Contour tools, transform tools, VTK to USD
 - **USD Utilities**: Merging, time preservation, material handling
@@ -637,7 +632,7 @@ Use `/plan` to get an inspection of the affected classes, a numbered implementat
 plan, and a list of open questions — without touching any files.
 
 ```text
-/plan add a confidence-weighted voting mode to SegmentChestEnsemble
+/plan add a new segmentation method to SegmentChestTotalSegmentator
 ```
 
 Claude will read the relevant source, summarize current behavior, list files that
@@ -767,7 +762,7 @@ This project is licensed under the Apache 2.0 License - see the LICENSE file for
 - **NVIDIA Omniverse** team for USD format and visualization platform
 - **MONAI** community for medical imaging AI tools
 - **DirLab** for providing the 4D-CT benchmark datasets
-- **TotalSegmentator** and **VISTA-3D** teams for segmentation models
+- **TotalSegmentator** team for segmentation models
 - **Icon Registration** team for deep learning registration methods
 
 ## 📞 Support

data/test/.gitignore

@@ -0,0 +1,3 @@
+*.hdf
+*.mha
+*.nrrd