Skip to content

Tests #43

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
aylward wants to merge 5 commits into
base: main
Choose a base branch
from
Open

Tests #43

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
f1e3d6f
ENH: Updated reporting of nightly results.
aylward Apr 8, 2026
f9231c3
ENH: Fix link to download slicerheart data
aylward Apr 8, 2026
51e812b
ENH: Fix coverage reporting
aylward Apr 8, 2026
26314ee
ENH: Detect more download failures
aylward Apr 8, 2026
b10c57b
ENH: Remove Vista3D due to challenges on blackwell
aylward Apr 8, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions .claude/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
settings.local.json
4 changes: 3 additions & 1 deletion .github/workflows/ci.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 }}
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand Down
1 change: 1 addition & 0 deletions .github/workflows/test-slow.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
1 change: 0 additions & 1 deletion CLAUDE.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
18 changes: 7 additions & 11 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 ensemble approaches
- **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
Expand Down Expand Up @@ -106,8 +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
Expand Down Expand Up @@ -142,7 +140,7 @@ 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

Expand Down Expand Up @@ -262,11 +260,11 @@ 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")
Comment on lines +263 to 270
Copy link

Copilot AI Apr 8, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

In this example, SegmentChestTotalSegmentator.segment() returns a dict of masks (e.g., result['labelmap'], result['heart']). The snippet below currently assigns to masks = ... and then unpacks multiple values; after switching to TotalSegmentator the example should be updated to use the dict keys instead of tuple unpacking.

Copilot uses AI. Check for mistakes.
Expand Down Expand Up @@ -578,14 +576,12 @@ 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
Expand All @@ -594,7 +590,7 @@ 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
Expand Down Expand Up @@ -767,7 +763,7 @@ 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
Expand Down
Loading
Loading