Repository

Outputs

Scripts write run artifacts to outputs/ unless --out-dir is provided.

PAM Outputs

scripts/run_pam.jl typically writes:

  • summary.json: human-readable configuration, source metadata, medium metadata, reconstruction settings, timing information, and analysis metrics.
  • result.jld2: numerical arrays and structured data needed for later reconstruction or analysis.
  • overview.png: source, RF, and reconstruction overview where available.
  • activity_boundaries.png: threshold-dependent active-region boundaries and detection curves for squiggle/network runs.
  • best_threshold_3d.png: selected 3D threshold visualization where applicable.
  • napari_volume.npz: optional 3D visualization volume when generated by the run path.

--from-run-dir creates a new reconstruction output folder and reuses the previous result.jld2 RF data, medium, grid, and source metadata.

Focusing Outputs

scripts/run_focus.jl writes:

  • summary.json
  • result.jld2
  • pressure.png

scripts/compare_focus_estimators.jl writes:

  • summary.json
  • comparison.png

Reading summary.json

The summary file is the best first artifact to inspect. It records the resolved configuration, not just the typed CLI arguments. For PAM, this is important because fit_pam_config may extend the axial domain and simulation duration to fit the selected sources.

For generated activity sources, summary.json also records source counts, centerline metadata, phase/frequency variability, window configuration, and threshold-search results.