Fix paired-field Cells measurement identity (#314)

docs/validation/paired_field_csv_314_20260930/PREFLIGHT.json

@@ -0,0 +1,11 @@
+{
+  "command": "/home/ts/bin/agent-resource-check --assert-headroom",
+  "exit_code": 2,
+  "actual_result": {"free_gib": {"/": 8.2, "/dev/shm": 15.5, "/home": 12.5, "/tmp": 11.3}, "level": "warning", "ram_available_gib": 15.6, "reasons": ["/home free 12.5 GiB", "swap used 8.7 GiB"], "swap_used_gib": 8.7},
+  "admission": "20GiB warning only; bounded source worker/scratch",
+  "worker_memory_limit_bytes": 536870912,
+  "cpu_quota_percent": 100,
+  "numeric_threads": 1,
+  "owned_scratch_limit_bytes": 268435456,
+  "owned_scratch": "/home/ts/.cache/agent-scratch/issue314-russell"
+}

docs/validation/paired_field_csv_314_20260930/SHA256SUMS

@@ -0,0 +1,36 @@
+09bc36d6a804f1601315bb842a3c67852ed5d08f5a71b6fc632dd6f7c7a1e12a  docs/validation/paired_field_csv_314_20260930/PREFLIGHT.json
+e935c5bcb0d0bf4da40c68f855bff5afa484c6b1a6e667405004cb06164f0cd7  docs/validation/paired_field_csv_314_20260930/checkpoint.rst
+f7a149a70dd9f82cadd4b1b43eae69a6c70354d04c870113bae2e80d6c697fcf  docs/validation/paired_field_csv_314_20260930/core-census.json.gz
+abcc421cce2ad109a4be6f9bae9c7ffdb80c48725a416bf4db5f60266fe610d5  docs/validation/paired_field_csv_314_20260930/core-census.log
+22a3cbbcc9ac4d15b10c6ae38d5b930fb2a37a687f832f978d29543d803f399b  docs/validation/paired_field_csv_314_20260930/core-overlay.json.gz
+f842402ed5c9f2eb35f5a9abeb97ee7342e1e0269233d2149aab2a3b03ba4318  docs/validation/paired_field_csv_314_20260930/core-overlay.log
+e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855  docs/validation/paired_field_csv_314_20260930/effective-imports-error.log
+6260f67c73bdbb1e138b9733e3100f9c3b82daa032beaa1ab821891a830b8d68  docs/validation/paired_field_csv_314_20260930/effective-imports.json
+2d22257b758889c28b6cc68e230075176e81e94b8b3eb5b93f0c8c0458040102  docs/validation/paired_field_csv_314_20260930/final-policy-exporter.log
+4e6b60bb28c884fddf203e176e39b6b2a8fec79b0db065e2d3fb87bfc11967a1  docs/validation/paired_field_csv_314_20260930/merged-main-census.json
+2a91055d7bc8f70cd70a234c0970babbf0bedf15cfce723dfecd4e028032cbb1  docs/validation/paired_field_csv_314_20260930/merged-main-census.log
+bf1aee9710d476cd67ea9ef6e6a03805d50498d1dd38eb1f3f7e325e7fd2a1bd  docs/validation/paired_field_csv_314_20260930/merged-main-owner.log
+ef34e28b0d9ebe85c9a364f9d64bcba276f1af3de33c782a5452c74d8dd665b5  docs/validation/paired_field_csv_314_20260930/merged-main-related.log
+45bb910ec84bccf47c98eab8d48668058c32f888bf3337eadf6af54ebdcc69a0  docs/validation/paired_field_csv_314_20260930/nra-original-resources.log
+76efdf6231fe3d520aa5aad4ed07aa619696ed0a1bbc0d9ac58207439fbc1d1c  docs/validation/paired_field_csv_314_20260930/nra-original.json
+ca8e2518377ceb506f4b6616de041d8e5901d3abb7d53499aacacd284927f365  docs/validation/paired_field_csv_314_20260930/nra-owner-loop-resources.log
+85fa34cc7c9365e1433cf13cfde3728b93e826212a862d5a896ee50f24215587  docs/validation/paired_field_csv_314_20260930/nra-owner-loop.json
+0ef110ed10150278f09ba7ea4abf837c87f163d834794a99f26731ec3b722a69  docs/validation/paired_field_csv_314_20260930/owned-disposable.tar.gz
+4068fc6aebd829bde62c38c9fd8a9c980ff2480214f9e68d638684cb643d6bef  docs/validation/paired_field_csv_314_20260930/owner-census-delta.json
+d221f41dafd990a5434428d86703b59b1eec66fb99c6537fb40a0c52bdd1205f  docs/validation/paired_field_csv_314_20260930/owner-census-delta.log
+8db82b08046f81c30100fe92751276352cef7f8a444a3297ec4df82ce2d95c0b  docs/validation/paired_field_csv_314_20260930/owner-fixed-corrected.log
+d50a0ddd323c80c4992f46e4a96c8a3a1515c6787ee2ad5f86191357ac964989  docs/validation/paired_field_csv_314_20260930/owner-fixed.log
+d8375d089d79fb532af311d7d3b8f1509d0f21e9e045b7cd14a9ed04a132f509  docs/validation/paired_field_csv_314_20260930/ownership-receipt.rst
+17988389f4355b8274b59fd1141bb8aa5757b6cb6adf94fe879c0b199ca023e3  docs/validation/paired_field_csv_314_20260930/policy-import.log
+6b76484efe7c0bcd2634c61337c0f73018d457338bfb077c05c836ec42e3b481  docs/validation/paired_field_csv_314_20260930/pr-body.md
+77b93b241966cb96c7e7e8e2adc7964d488abbaa14fb2ab94e74ddb1598c3673  docs/validation/paired_field_csv_314_20260930/related-owner-contracts.log
+63ad8bd8fac5a6a06141b607f4d6bd51145a8952ee63bbc9c27c844c07724dcb  docs/validation/paired_field_csv_314_20260930/reproducer-original-built.log
+9aa5f6c2c1dd4b980dc653be3b1fca951a5eb42ba05e2a99709140190f08ffd0  docs/validation/paired_field_csv_314_20260930/reproducer-original.log
+93abbe5307fdb809eae183b7e3fd79f276fb1044b1e889cf95ae3ec754dd36aa  docs/validation/paired_field_csv_314_20260930/ruff-focused.log
+9a5daa28530cfdb8a9a5dfaf7e4469862c7755067be421ee89f83f824ac2a6d7  docs/validation/paired_field_csv_314_20260930/source-anchors-base-empty-snapshot.log
+05d26c97cc6db8b17026c5dfb984b13f5cc667479d0962613118c6d764edc22e  docs/validation/paired_field_csv_314_20260930/source-anchors-base-verified.log
+89e8f8287e324c431d734ec1f3dbb247459ed329ec939cc9478143cf239ccba3  docs/validation/paired_field_csv_314_20260930/source-anchors-base.log
+5e739265347dec1ea5319579c3575f0ca9d4ba12a0a6c4209cbab692196c0b50  docs/validation/paired_field_csv_314_20260930/source-build.log
+1b5332ef5d7e47ae6518191ef1e2564dd03ba02c716ded316439f5103b2b4e25  openhcs/core/source_matching.py
+8eb0468a59f7545bbdbc86e12e0314899942dae444d57cb10bbf1ece2cd10d5b  tests/unit/test_cellprofiler_spreadsheet_export.py
+f106cb03132c41485c6c3dc065481abe80eac0682d25fb3a27cf0e1be093832c  tests/unit/test_source_image_set_identity_policy.py

docs/validation/paired_field_csv_314_20260930/check-installed-parent.py

@@ -0,0 +1,93 @@
+"""Read-only verification of the installed two-well synthetic export control."""
+
+import csv
+import json
+from pathlib import Path
+
+import numpy as np
+import tifffile
+
+from openhcs.core.source_workspace_projection import (
+    VirtualWorkspacePathLookup,
+    VirtualWorkspaceSourceProjection,
+)
+from openhcs.runtime.zmq_execution_observation import ZMQRuntimeExecutionObservationExport
+
+
+def main(root: Path) -> None:
+    receipts = root / "mcp-image-copy-reconnected"
+    status = json.loads((receipts / "receipt-017.json").read_text())
+    execution = status["payload"]["results"][0]["payloads"][0]
+    assert status["returncode"] == 0
+    assert execution["status"] == "complete"
+    assert execution["response"]["execution"]["error"] is None
+    inventory_receipt = json.loads((receipts / "receipt-020.json").read_text())
+    inventory = inventory_receipt["payload"]["results"][0]["payloads"][0]
+    assert inventory_receipt["returncode"] == 0
+    assert inventory["total_count"] == inventory["returned_count"] == 16
+    assert inventory["truncated_count"] == 0
+    cells_record = next(record for record in inventory["records"] if record["key"] == "Cells.csv")
+    assert cells_record["preview"]["truncated"] is False
+    cells = cells_record["preview"]["csv_rows"]
+    assert len(cells) == 4
+    assert {(row["image_number"], row["object_label"]) for row in cells} == {
+        ("1", "1"), ("1", "2"), ("2", "1"), ("2", "2"),
+    }
+    for row in cells:
+        assert row["Parent_Nuclei"] == row["object_label"]
+        assert float(row["AreaShape_Area"]) == 52.0
+        assert float(row["Location_Center_X"]) == float(row["AreaShape_Center_X"])
+        assert float(row["Location_Center_Y"]) == float(row["AreaShape_Center_Y"])
+        assert all(value != "" for value in row.values())
+
+    output = root / "outputs-input-source-fixed" / "synthetic_openhcs"
+    with (output / "results" / "Cells.csv").open(newline="") as handle:
+        assert list(csv.DictReader(handle)) == cells
+    projection = VirtualWorkspaceSourceProjection.from_openhcs_metadata(
+        output, json.loads((output / "openhcs_metadata.json").read_text()),
+    )
+    assert len({(ref.backend, ref.backend_address)
+                for ref in projection.source_refs_by_virtual_path.values()}) == 4
+    for well in ("A01", "B01"):
+        for channel, name, step in (("1", "Nuclei", 0), ("2", "Cells", 1)):
+            relative = f"results/{well}_w{channel}_{name}_step{step}.labels.tif"
+            lookup = VirtualWorkspacePathLookup(relative, str(output / relative))
+            source_projection = projection.require_source_projection_for(lookup)
+            assert source_projection.ref.backend == "disk"
+            assert source_projection.ref.backend_address == relative
+            assert source_projection.image_metadata.source_spatial_domain.source_shape_yx == (32, 32)
+        nuclei = tifffile.imread(output / "results" / f"{well}_w1_Nuclei_step0.labels.tif")
+        expected_nuclei = np.zeros((32, 32), dtype=np.int32)
+        expected_nuclei[5:9, 5:9] = 1
+        expected_nuclei[22:26, 22:26] = 2
+        np.testing.assert_array_equal(nuclei.squeeze(), expected_nuclei)
+        cell_labels = tifffile.imread(output / "results" / f"{well}_w2_Cells_step1.labels.tif")
+        assert set(np.unique(cell_labels)) == {0, 1, 2}
+        assert np.count_nonzero(cell_labels == 1) == np.count_nonzero(cell_labels == 2) == 52
+        dna = tifffile.imread(root / "synthetic" / "TimePoint_1" / f"{well}_s001_w1_z001_t001.tif")
+        expected_dna = np.zeros((32, 32), dtype=np.uint16)
+        expected_dna[5:9, 5:9] = 12000
+        expected_dna[22:26, 22:26] = 18000
+        np.testing.assert_array_equal(dna, expected_dna)
+        actin = tifffile.imread(root / "synthetic" / "TimePoint_1" / f"{well}_s001_w2_z001_t001.tif")
+        np.testing.assert_array_equal(actin, np.full((32, 32), 24000, dtype=np.uint16))
+
+    observation = ZMQRuntimeExecutionObservationExport.read(
+        root / "runtime-observation-input-source-fixed.json",
+    )
+    assert observation.execution_id == "bb932c48-de7a-4867-bbb2-5a090a5aa928"
+    assert dict(observation.execution_success_by_axis) == {"A01": True, "B01": True}
+    close_receipt = json.loads((receipts / "receipt-021.json").read_text())
+    outcome = close_receipt["payload"]["results"][0]["payloads"][0]["outcome"]
+    assert outcome["request_attempted"] and outcome["acknowledged"] and outcome["process_exited"]
+    print("PASS: installed COMPLETE; four complete paired cell rows; four label projections; "
+          "known source pixels unchanged; native export reopens; exact worker closed. "
+          "Physical calibration and biological accuracy are not assessed by this control.")
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("root", type=Path)
+    main(parser.parse_args().root)

docs/validation/paired_field_csv_314_20260930/checkpoint.rst

@@ -0,0 +1,124 @@
+Tested source checkpoint
+========================
+
+Base702b2c2c9563da2636db251f8b734cff215596b8. Source repair only;
+parent owns final integration and actual installed/MCP acceptance.
+
+Production change is confined to SourceImageSetIdentityPolicy.from_source_bindings.
+Shared singleton coordinates across paired primary declarations stay field
+identity. Explicit stacks/grouping keep precedence. Existing component_values()
+owns biological assignment versus physical selector precedence. No exporter,
+shape/secondary module, provenance schema, scope, registry or global package edit.
+
+Original built-source synthetic exporter failed:8 partial rows instead of4
+complete rows for2 fields x2 cells. Corrected source passes100 tests in15.52s
+(wall17.07s, maximumRSS455620KiB) under512MiB cgroup/oneCPU/threads1.
+Includes the real CSV exporter/counts, source binding/provenance contracts,
+measurement source-group alignment, two-versus-three channels, site/well/z/time
+negative controls, explicit stacked/grouped constant axes, physical-selector
+versus biological-coordinate precedence and path fallback without metadata.
+No scientific image read, segmentation, JVM, MCP/server/viewer startup,
+installed-entrypoint or external CellProfiler oracle was performed.
+
+Original failures retained: fresh checkout missing compiled tabular extension
+(reproducer-original.log); real baseline split (reproducer-original-built.log);
+initial production patch had a misplaced generator comma and failed collection
+(owner-fixed.log). Corrected that syntax, not assertions or behavior, before the
+passing owner-fixed-corrected.log. Existing extension declarations were built
+locally without installation or package/source dependency changes (source-build.log).
+The failed complete-context NRA attempt (exit124, maximumRSS524536KiB) returned
+deadline_incomplete JSON: complete=false, deadline_exceeded=true, stage
+parse_python_module, internal budget20s and elapsed22.054s. This corrects the
+earlier empty-JSON description; the raw original was preserved. It remains in
+nra-original.json/nra-original-resources.log; it is not a complete
+R1/semantic proof. Do not repeat with greater global limits. Core syntax census
+and source-witness review are evidence at their actual scope, not global health.
+
+Ruff's initial all-rule check exposes13 inherited findings (import order and
+quoted annotations). Keep unrelated source debt out of this repair; compare
+changed-owner metrics against exact base rather than claiming a clean repository.
+The new test module itself has no Ruff findings. Source/test git diff --check
+passes. Published raw diagnostic logs retain original trailing whitespace;
+an unrestricted evidence-inclusive diff --check flags that whitespace.
+
+Coordination: all7 then-open PR file lists checked. Shared source_bindings.py
+(#206), runtime_image_values.py/runtime_plane_projection.py (#217) remain
+read-only. Direct message addressed to Avicenna on their PR:
+https://github.com/OpenHCSDev/openhcs/pull/217#issuecomment-5920836946.
+No response or coordinated shared edit is claimed; no waiting or new agent call.
+
+H003e immutable REJECT remains untouched. Issue314 is not closed by source tests.
+Source/wheel/MCP continuity and external semantics acceptance remain separate
+parent gates.
+
+Additional source checkpoint before main integration
+---------------------------------------------------
+
+131 distinct source tests pass across the focused owner/exporter and related
+CellProfiler shape, secondary-distance and module-scope shards. The final
+policy/exporter shard is41 passed,4.91s, maximumRSS378400KiB and includes the
+normal from_pipeline_config path. The related shard is30 passed/8 failed,
+maximumRSS518188KiB (below512MiB). Its eight matched-anchor fixture failures
+all reach MeasurementsArtifactType.require_output_subject before this policy:
+legacy synthetic fixtures lack MeasurementSubjectRelation. All eight also fail
+on unmodified main702b2c2c9 (source-anchors-base-verified.log:8 failed/3 passed).
+Parent integration owns disposition of that inherited fixture mismatch; acceptance
+requires properly typed subjects, not weakening the guard. No fixture/assertion
+was relaxed. Earlier baseline snapshot assembly attempts (empty snapshot and
+missing pytest_integration_options) are retained separately as harness failures.
+
+The lightweight one-file NRA loop completed in2.97s/77176KiB, zero findings;
+its actual scan_status is exact_compact_global,79 analyzed detectors,0 omitted,
+complete=true. This is complete ONLY for the selected source_matching.py input,
+not a complete OpenHCS context scan or formal equivalence proof. Full-context
+failure remains retained. Changed-core census at source commit6f636c2afe6d98cc
+adds16 code lines and zero in every other measured syntax category.
+
+Effective OpenHCS imports resolve this worktree (source version0.8.7), not the
+installed distribution metadata0.8.6. Existing editable PolyStore resolves
+/home/ts/wt/openhcs-custom-function-admission-20260929/external/PolyStore,
+clean at1209068f5fc9e4f7025a24ada8a73ef30dd1ddd7. This dependency is unmodified;
+these checks do not prove a frozen gitlink dependency closure or installed parity.
+Exact other effective imports/versions are retained in effective-imports.json.
+
+Merged current main and final handoff
+------------------------------------
+
+Main2b7969f700c33eb7f73f891d975afd1efc0628bb was integrated normally with merge
+commit e3d991e9cf02c496daa7c9df32c73bfde4a7ad00. It changes viewer owners, not
+the repaired policy. Core tree025c72d3ce07962cfbe57c181819bdc6d081e5f3 is byte
+identical between original702b2c2c9 and new main; the changed branch core tree
+is a10ecc8bcf0b4e68576eaa52b6479bd4f661999a. The original fixture and strict
+artifact owner are also unchanged between those main revisions.
+
+Reran both shards on that exact merged head under the same512MiB/oneCPU bounds:
+merged-main-owner.log:101 passed,14.13s, maximumRSS406828KiB;
+merged-main-related.log:30 passed/8 inherited failures,6.01s,387968KiB.
+No budget escalation or stopped-shard replay. These139 distinct selected tests
+therefore have131 passes and8 failures, not a green broad suite. Shape/module/
+secondary contracts pass; the remaining failures occur at the existing strict
+subject guard before the changed policy and have an original-source control.
+Parent integration is the named disposition owner for those fixture failures;
+no active repair by another agent or final acceptance is invented.
+
+merged-main-census.json/log measures exact merged head against new main:
+16 added core code lines and zero other measured syntax-count changes, no parse
+failures, maximumRSS20304KiB. Earlier compact NRA input remains byte-identical.
+No parent viewer/MCP acceptance is attributed to this source-only repair.
+
+Disposal: owned scratch860KiB and build objects400KiB were archived together as
+owned-disposable.tar.gz (309648 bytes,124 archive entries, gzip integrity checked),
+then only /home/ts/.cache/agent-scratch/issue314-russell and this worktree's build/
+were removed. SHA2560ef110ed10150278f09ba7ea4abf837c87f163d834794a99f26731ec3b722a69.
+Removal is recoverable from that archive. Local compiled extensions remain in
+the owned checkout for reproduction; no task-owned persistent worker is active.
+Durable .issue314/ retains instruction extraction and original-source controls.
+SHA256SUMS seals published source/tests/evidence (excluding the manifest itself).
+
+Reproduce from this checkout using the existing Python entrypoint and the exact
+bounded commands retained in merged-main-owner.log/merged-main-related.log.
+The baseline control command and original failing assertions remain in their
+logs; no held-out TIFF, frozen CSV or scientific trial artifact is involved.
+Draft PR317 contains the coherent source repair and original failures. Parent
+owns merge, source-closure/installed/MCP/external-parity acceptance; no installation,
+runtime launch, issue closure or frozen-file mutation is requested or claimed.