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CellProfiler full-stack contract passes AlignedImageStack into dense scalar callable #342
Description
Owner: H003g runtime repair worker (Codex), under parent integration; source-only diagnosis and repair. Historical #204 selector/input-scope work belonged to Zeno; PR326 is merged, and no current open PR touches the CellProfiler executor. Parent retains the sole installed/native acceptance slot for #338. Please coordinate through this issue before overlapping executor/aligned-payload edits.
Retained H003g candidate-04.py SHA256 7b69ce1f4256e2a64b32ecb1fefd6d22adef7ba3a1d98f5e2a3fc0125eab96b3; native log 1790835483807054701. Exact failure: CellProfilerFunctionContractExecutor.execute_pure_3d -> rescale_intensity -> RescaleIntensityContext.from_settings -> source_data.astype(np.float32, copy=False): TypeError float(AlignedImageStack). Candidate compiled, failed before outputs/counts/result QA. H003g remains an immutable FAILED development repeat, not an acceptance fixture to resubmit.
Investigate typed source/artifact projection and existing materialization authority across nominal contract families; repair via shared owner ABC algorithm and small leaf hooks, capability MI/cooperative super where justified. No function-name switch, np.asarray wrapper fix, mirrored store, or copied executor. Source-only one CPU / 512 MiB / 60-second test shards, no package changes or MCP/native/viewer startup. Synthetic runtime reproducer and draft PR to follow.
Activity
trissim commentedon Oct 1, 2026
Working source checkpoint published as draft PR344 (509bc5c): exact synthetic stack reproduced before fix; 33 executor/reproducer cases passed after, 305672 KiB RSS / 3.08s wall under one-CPU/512MiB/60s gate. Expanding family/mask/provenance/MI-MRO controls now. No MCP/native/viewer, install, or trial changes. Parent retains integration and sole installed acceptance slot after #338.
trissim commentedon Oct 1, 2026
Source checkpoint 63ad7c6 published in draft #344: exact rescale failure occurs with EMPTY kwargs, isolating the composed aligned PRIMARY image; aligned auxiliary images are a separate affected boundary and separately tested. Shared composition ABC owns pixels/masks/provenance, existing nominal strategy dispatch materializes image stacks and preserves non-image domains. 110 source controls passed (all four processing contracts, masks/calibration/exact contributors, named bundles, rejection controls and independent test-capability MRO orders). Original R0 openhcs root passed using the original pinned package and CI Python 3.14. No installed/native/MCP/viewer gate claimed. Broader source checks exposed an independently reproduced unchanged-main fixture mismatch: IPO now returns seven diagnostic planes but the fixture declared none. Runtime repair worker owns this test-only correction via PrimaryObjectDiagnosticPlanes.artifact_specs; 45 consumer checks now pass without production ABI relaxation. Main 7b0ec3f merged normally; final exact-source checks underway. Original R1 is currently unqualified: local NRA cannot import RedundantTypeCheckDetector, and this WT recorded gitlinks are uninitialized. No detector substitution, install/download or narrowed-context pass. Parent owns integration and scheduled installed acceptance after #338. Frozen H003g remains FAILED and untouched.
trissim commentedon Oct 1, 2026
Public PR344 checkpoint a422c4f corrects the engineering authoring recipe only; production remains a14d471. The omitted acquisition rules caused legitimate ORDER/duplicate-address/sidecar admission failures, not a proven intake regression: existing source metadata, METADATA matching and CHANNEL component_identity contracts provide the route. Failed public recipe retained at 327cec9 and earlier archives. Six bounded source-authoring/path/declaration controls pass. Parent owns installed/native acceptance and reports continuous MCP compile/run plus 8192 dense pixel comparisons, max error 1.23e-7, exact declared calibration/first-source scope; no direct carrier/mask or biology/R1 claim. Source-vs-storage input occurrence limits and parent-observed acceptance are documented in docs/refactor/344-engineering-acceptance.rst. No child native/ingestion edit or H003g replay.
Merge pull request #344 from OpenHCSDev/fix/cp-aligned-materializatio…