Add reproducibility floor + TrackRAD ingestion & integrity harness (Charter Phase 0/1) - #7
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Deterministic run logging with pinned RNGs, git SHA, package versions, and a stable reproducibility checksum written per run. tests/test_repro.py proves determinism across calls and seed-sensitivity (5/5).
Typed TrackRADCase loader reading real fields only (cine frames, tumour mask, JSON sidecars), deterministic case_checksum, patient-level enumeration. Placeholder quarantine: to_smoke_test_bundles refuses without acknowledge_synthetic=True and stamps PLACEHOLDER_TRACKRAD_*. Canonicalises .mha to (T,H,W) and suffix-matches the b-field-strength sidecar — two card-vs-reality discrepancies found by reading real bytes. Charter §3: TrackRAD is an ingestion smoke-test only, never a dose benchmark. tests/test_trackrad_loader.py 10/10, including on real data.
Per-case ingestion checks (loads, frames finite/3D, in-plane isotropic + ~1mm, sidecars present, mask geometry matches frames) with patient-level uniqueness asserted in code, not comment (Charter §2.4). Reproducible per-center scorecard logged to runs/ with a stable sweep_checksum. Verified 12/12 patients clean across 3 centres / 2 field strengths; the gate earned its keep by catching real header rounding on B_002 (fixed the check, not the data). tests/test_trackrad_integrity.py 5/5 (incl. catches injected NaN + mask/frame mismatch).
Charter (CLAUDE.md) defining integrity rules and phase gates, PROGRESS.md tracking phase status against demonstrated evidence, BACKLOG.md for deferred items (MRI-as-geometry-input, tracking service). Ignore runs/ (regenerated provenance logs).
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Summary
Establishes the Charter-driven reproducibility and data-integrity foundation, plus a real-data ingestion path for the TrackRAD2025 asset. Four self-contained commits:
TrackRADCasereading real fields only (cine frames, tumour mask, JSON sidecars), deterministiccase_checksum, patient-level enumeration, and a placeholder quarantine (to_smoke_test_bundlesrefuses withoutacknowledge_synthetic=True, stampsPLACEHOLDER_TRACKRAD_*).sweep_checksum.CLAUDE.md(charter),PROGRESS.md,BACKLOG.md; ignore regeneratedruns/.Scope & integrity notes
b-field-strength.json(suffix-matched), and.mhastores time as the last numpy axis (canonicalised to(T,H,W)).Verification
tests/test_repro.py5/5tests/test_trackrad_loader.py10/10 (incl. on real data)tests/test_trackrad_integrity.py5/5 (incl. catches injected NaN + mask/frame mismatch)Independent of #6 (rebased onto
master); no overlap with the CI-fix PR.