Quickstart¶

Goal¶

Use this page when you want the shortest path to a successful AutoFlow run.

Install¶

Full local install for GUI, automatic segmentation, and tests:

pip install -e ".[gui,test]"

CLI-only install:

pip install .

Both normal and editable installs include the bundled nnUNet final checkpoint and its required metadata. The gui extra installs both the GUI and nnUNet inference dependencies; there is no separate automatic-segmentation extra.

To enable the optional SpatioTemporal Labeler v0.4.0 exchange workflow, initialize the pinned source submodule and install its extra:

git submodule update --init --recursive
pip install -e ".[gui,labeler]"

Known working test environment in this repo:

~/miniconda3/envs/ryy/bin/python -m pytest tests/test_smoke_phantoms.py tests/test_pressure_gradient_phantom.py -q

Run One H5 Case From The CLI¶

autoflow-run ./data/demo_data.h5 --output-dir ./results/demo

What this does:

load data
generate skeleton
generate graph
generate planes
calculate plane metrics
only run PWV, WSS, TKE, or pressure gradient when requested
only export videos when requested

Typical outputs under ./results/demo/<case_name>/:

multi-group H5 files create one output folder per H5 data-group path, for example stem__StudyA_Series1
planes.json
planes.h5
plane_positions.json
plane_metrics.json
plane_qc.json
quality_report.json
summary.json
source H5 segmask is updated in place for reuse, plus *_auto_segmentation.nii.gz and *_auto_segmentation_feature_*.nii.gz when auto segmentation runs on an H5 input

Run One DICOM Root From The CLI¶

autoflow-run /path/to/dicom_root --output-dir ./results/dicom_batch

Open The GUI¶

autoflow-gui

Typical GUI flow:

File > Open H5 or File > Import DICOM Directory
inspect the case in the 3D view and ortho viewer
if needed, choose or generate segmentation
click Run All
inspect planes, metrics, and derived volumes

Run From Python¶

from autoflow import AutoFlowConfig, run_batch

config = AutoFlowConfig(
    inputs=["./data/demo_data.h5"],
    output_dir="./results/demo",
)
results, last_case_out = run_batch(config)

Common First Steps¶

Batch planes by distance¶

autoflow-run ./data/demo_data.h5 \
  --output-dir ./results/demo \
  --plane-mode distance \
  --cross-section-dist 15 \
  --start-dist 5 \
  --end-dist 0

Default center fixed-step planes¶

Generated planes default to three symmetric planes at 25% of the usable centerline length on either side of the center (fixed_step, center, both). The segmentation filter is enabled by default; disable it with --no-segmentation-filter when working with a binary mask.

Auto segmentation when no segmentation is present¶

autoflow-run ./data/demo_data.h5 \
  --output-dir ./results/demo \
  --autoseg

Opt in to extra metrics and videos¶

autoflow-run ./data/demo_data.h5 \
  --output-dir ./results/demo \
  --with pwv,wss,tke,pg,vortex \
  --video plane,wss,tke,pg

vortex computes whole-volume vorticity, Q-criterion, and swirling strength. It is not a plane-video family, so it is intentionally omitted from --video.