| CLI flags, defaults, help text |
autoflow/cli.py |
autoflow/api.py, autoflow/config.py, configs/*.json, pyproject.toml |
tests/test_smoke_phantoms.py, tests/test_pressure_gradient_phantom.py |
| Public Python API |
autoflow/api.py, autoflow/__init__.py |
autoflow/config.py, autoflow/processing.py |
tests/test_smoke_phantoms.py, tests/test_pressure_gradient_phantom.py |
| Input collection and batch organization |
autoflow/processing.py, autoflow/algorithms/dicom.py |
autoflow/api.py |
tests/test_smoke_phantoms.py, tests/test_pressure_gradient_phantom.py |
| H5 loading |
autoflow/algorithms/data.py |
autoflow/core/pipeline.py, autoflow/case_types.py |
tests/test_smoke_phantoms.py, tests/test_pressure_gradient_phantom.py |
| DICOM scan and load |
autoflow/algorithms/dicom.py |
autoflow/ui/dicom_confirm.py, autoflow/core/pipeline.py |
manual verification plus smoke and phantom regression only |
| Background phase correction |
autoflow/algorithms/phase_correction.py |
autoflow/algorithms/data.py, autoflow/algorithms/dicom.py, autoflow/cli.py, autoflow/ui/app.py |
tests/test_smoke_phantoms.py, tests/test_pressure_gradient_phantom.py |
| Optional phase unwrapping |
autoflow/algorithms/phase_unwrapping.py, autoflow/core/pipeline.py |
autoflow/core/models.py, autoflow/ui/app.py, autoflow/ui/ortho_viewer.py, autoflow/cli.py |
tests/test_smoke_phantoms.py |
| Segmentation file IO and threshold segmentation |
autoflow/algorithms/segmentation.py |
autoflow/ui/segmentation.py, autoflow/ui/app.py |
tests/test_smoke_phantoms.py |
| nnUNet auto segmentation |
autoflow/algorithms/segmentation.py |
autoflow/processing.py, autoflow/ui/app.py, autoflow/config.py |
manual verification plus smoke and phantom regression only |
| Segmentation state and provenance |
autoflow/core/models.py, autoflow/ui/app.py |
autoflow/ui/segmentation.py, autoflow/algorithms/segmentation.py |
tests/test_smoke_phantoms.py plus manual GUI verification |
| Skeleton |
autoflow/algorithms/preprocess.py, autoflow/algorithms/skeleton.py |
autoflow/core/pipeline.py |
tests/test_smoke_phantoms.py |
| Graph, branch, and path logic |
autoflow/algorithms/graph.py, autoflow/algorithms/branch.py, autoflow/algorithms/paths.py |
autoflow/core/pipeline.py, autoflow/ui/app.py, autoflow/ui/viewer.py |
tests/test_smoke_phantoms.py |
| Plane generation and save logic |
autoflow/algorithms/planes.py, autoflow/plane_io.py |
autoflow/core/pipeline.py, autoflow/ui/app.py |
tests/test_smoke_phantoms.py, tests/test_pressure_gradient_phantom.py |
| Plane metrics and QC |
autoflow/algorithms/metrics.py |
autoflow/core/pipeline.py, autoflow/core/models.py, autoflow/plane_io.py, autoflow/reporting.py, autoflow/ui/app.py, autoflow/ui/ortho_viewer.py |
tests/test_smoke_phantoms.py, tests/test_pressure_gradient_phantom.py, plus manual GUI verification |
| Staged quality report |
autoflow/quality.py |
autoflow/processing.py, autoflow/ui/app.py, docs/en/features/quality-control.md |
tests/test_smoke_phantoms.py plus manual GUI verification |
| WSS, TKE, pressure gradient |
autoflow/algorithms/metrics.py |
autoflow/core/pipeline.py, autoflow/ui/viewer.py, autoflow/ui/ortho_viewer.py, autoflow/rendering/videos.py |
tests/test_smoke_phantoms.py, tests/test_pressure_gradient_phantom.py |
| Vortex kinematics |
autoflow/algorithms/metrics.py |
autoflow/core/models.py, autoflow/core/pipeline.py, autoflow/processing.py, autoflow/ui/app.py, autoflow/ui/ortho_viewer.py, configs/vortex.json |
tests/test_smoke_phantoms.py, tests/test_pressure_gradient_phantom.py |
| Streamlines and pathlines |
autoflow/algorithms/streamlines.py |
autoflow/core/pipeline.py, autoflow/ui/app.py, autoflow/rendering/videos.py |
manual verification plus smoke and phantom regression only |
| GUI main window, menus, and workflow |
autoflow/ui/app.py |
autoflow/config.py, autoflow/ui/launcher.py, autoflow/ui/remote_plotter.py, autoflow/ui/segmentation.py, autoflow/ui/viewer.py |
tests/test_smoke_phantoms.py plus manual GUI verification |
| Ortho viewer and 2D interaction |
autoflow/ui/ortho_viewer.py, autoflow/ui/slice_view.py |
autoflow/ui/app.py |
smoke and phantom regression plus manual GUI verification |
| Offline video rendering |
autoflow/rendering/videos.py |
autoflow/processing.py, autoflow/api.py |
tests/test_smoke_phantoms.py |
| Reporting output |
autoflow/reporting.py, autoflow/processing.py |
autoflow/core/pipeline.py |
tests/test_pressure_gradient_phantom.py |