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Outputs

Common Output Files

Output Created when Meaning Main code
planes.json planes exist serialized plane geometry, label_name, and attached summaries autoflow/core/pipeline.py
planes.h5 planes exist one root group per plane with geometry, label_name, path metadata, metrics, and a payload_json mirror autoflow/plane_io.py, autoflow/core/pipeline.py
plane_positions.json planes exist portable v2 plane coordinates with world/local centers, normal, source geometry, group, path rank, and relative path position autoflow/plane_io.py
plane_metrics.json plane metrics run time-resolved plane metrics with explicit plane_index values autoflow/core/pipeline.py
plane_qc.json plane metrics run fork and path QC autoflow/core/pipeline.py
plane_metrics_pixelwise.h5 plane metrics run per-plane pixelwise derived samples autoflow/core/pipeline.py
pwv.json PWV runs successfully PWV fit results for each configured PWV group autoflow/core/pipeline.py, autoflow/algorithms/pwv.py
pwv_<group>.png PWV plotting succeeds per-group two-panel plot with time-to-foot fit and all plane flowrate waveforms autoflow/algorithms/pwv.py
derived_metrics_pixelwise.npz derived metrics run whole-volume WSS, pressure-gradient intermediates, reconstructed relative pressure, optional TKE, and requested vortex-kinematics arrays (uncompressed NPZ for faster export) autoflow/processing.py
quality_report.json every processed case staged automated QC with pass, warn, fail, or not_run checks and suggested review actions autoflow/quality.py, autoflow/processing.py
summary.json every processed case; also updated by GUI video export when present single-case summary including request flags plus stage and video timings autoflow/processing.py, autoflow/ui/app.py
phase_unwrap.npz optional phase-unwrapping run wrapped/unwrapped phase, flow, signed wrap_count, wrap_mask, and mask_used autoflow/processing.py
batch_report.json batch run batch summary report autoflow/api.py, autoflow/processing.py
time_summary.txt batch run timing summary autoflow/api.py, autoflow/processing.py

Video Outputs

Output Created when Meaning
planes_rotate.mp4 plane video export requested from CLI, Python API, or GUI rotating plane overview with configurable index labels that default to planeidx=<index>; MP4 only
streamlines_video.mp4 or streamlines_rotate.mp4 streamlines video export requested from CLI, Python API, or GUI time-resolved streamline movie
wss_video.mp4 or wss_rotate.mp4 wss video export requested from CLI, Python API, or GUI WSS movie
tke_video.mp4 or tke_rotate.mp4 tke video export requested and TKE available TKE movie
pressure_gradient_video.mp4 or pressure_gradient_rotate.mp4 pg video export requested from CLI, Python API, or GUI pressure-gradient movie
relative_pressure_video.mp4 or relative_pressure_rotate.mp4 pg video export requested from CLI, Python API, or GUI relative-pressure movie

Segmentation Sidecars

Output Created when Meaning
*_threshold_segmentation.h5 threshold segmentation succeeds saved threshold segmentation
source input H5 segmask dataset auto segmentation succeeds on an H5 input embedded reusable auto segmentation cache written back into the source H5
*_auto_segmentation.nii.gz auto segmentation succeeds saved predicted segmentation NIfTI used by the run in the same HF/AP/RL geometry convention used by the nnUNet training/export scripts
*_auto_segmentation_feature_*.nii.gz static 3D auto segmentation succeeds saved nnUNet feature-channel NIfTI inputs; grouped 4D preprocessing keeps temporary source maps out of the output directory
user-selected H5, NPY, or NPZ file Segmentation dock Source -> Save... manual save of the active segmentation

Notes

  • derived_metrics_pixelwise.npz stores whole-volume derived arrays
  • When vortex is requested, derived_metrics_pixelwise.npz includes vorticity, vorticity_magnitude, q_criterion, swirling_strength, their phase-peak arrays, and vortex_support_mask.
  • plane_metrics_pixelwise.h5 stores per-plane slice-cellwise samples
  • TKE outputs remain optional and are absent for inputs that do not carry TKE
  • pwv.json is also mirrored into summary.json as pwv_results, pwv_file, and pwv_plot_files
  • summary.json records requested_metrics, requested_videos, stage_times_sec, video_times_sec, pressure_method, centerline_pressure_profiles, and the generated quality report
  • summary.json also records optional phase_unwrap method/device, skip reason, elapsed time, and wrap statistics
  • multi-group H5 inputs write separate case subdirectories whose names include the H5 data-group path
  • GUI Export Videos... also updates summary.json with refreshed videos, refreshed video_times_sec, and a gui_video_export record for that export run
  • planes.json and planes.h5 store per-plane label_name from label_map plus path_info when path metadata is available; grouped multi-label workflows can therefore expose both readable plane labels and path_info.group_name in those files
  • planes.h5 stores each plane as a root group such as plane_0000, plane_0001, and mirrors the full record again as payload_json inside that group
  • GUI scene objects are not saved files, but grouped workflows keep stable internal keys such as segmask_group_<group>, skeleton_<group>, graph_<group>, smooth_path_<group>_<path_idx>, plane_<group>_<plane_idx>, and pathline_<group>_<plane_idx> while showing shorter browser-visible names like plane 5 and pathline 5
  • PWV scene planes are represented as one grouped browser object named PWV planes
  • plane_positions.json uses schema autoflow.plane_positions.v2; center_world_mm is meaningful across cases only when their AutoFlow canonical world-mm frames are registered
  • offline video export writes MP4 only; no GIF fallback is generated