Skip to content

Fix paired-field Cells measurement identity (#314) - #317

Merged
trissim merged 9 commits into
mainfrom
fix/paired-field-csv-314-20260930
Oct 1, 2026
Merged

trissim merged 9 commits into
mainfrom
fix/paired-field-csv-314-20260930

Conversation

@trissim

@trissim trissim commented Sep 30, 2026 •

Copy link
Copy Markdown
Collaborator

Summary

Closes #314 and #322. Parent owns integration. Normally merged current main8e478cb21; the existing source-image-set identity owner now distinguishes fixed paired-field coordinates from selected plane membership. Existing NamedSourceBinding.component_values remains assignment/selector authority. Consumers/exporters do not gain CSV joins, copied metadata, module switches or another registry.

The actual installed journey exposed #322: ConvertImageToObjects called image.copy on a metadata-bearing runtime carrier. Its existing NumPy conversion owner now supplies the owned numeric working copy through np.asarray(image).copy(); original main flow, label-builder source, pixels, provenance and declared spacing remain intact. No forwarding shim or guard weakening.

Current evidence

  • Rich/plain and connected/preserved-label regression: original two rich cases fail, two plain controls pass; all repaired cases preserve exact labels, counts, area, source pixels, main identity, provenance/domain and declared XY spacing.
  • 51 focused object-output, source-identity and real exporter checks plus four rendering controls pass at the integrated source.
  • Original unmodified packaged ratchet compares 5,133 metrics against current main with zero positive deltas. Original full-context NRA/R1 deadlines remain incomplete, not formal passes; the owner explicitly said not to block locally/live-verified shipment on NRA.
  • Actual built OpenHCS wheel plus recorded ArrayBridge companion are installed in the isolated candidate. Fresh MCP health reports site-packages, 56 packaged resources and no stale source.
  • Continuous installed MCP inspection/compile/execute/export completes across two tiny synthetic wells. Final executionbb932c48-de7a-4867-bbb2-5a090a5aa928 completes in1.11s, including strict final metadata reconciliation.
  • Native result-directory inventory returns all16 results without truncation. Cells.csv has exactly four complete rows: two objects per independent field, matching parent labels, coexisting location and shape, no blank feature fields, expected52-pixel cell areas. Native CSV previews match disk exactly.
  • Four physical label projections reopen with correct32x32 domains, exact nucleus masks and52-pixel cell identities. All synthetic source images retain their known fixture pixels. The existing gzip-pickle observation owner reopens the exported run and confirms both wells succeeded.
  • Exact owned child is acknowledged closed/process_exited; MCP exits and independent PID/socket checks confirm shutdown. Runtime logs are archived before owned scratch/build cleanup; no duplicate Fiji download or shared installation edit.

Preserved failures and limits

The first installed predecessor failed at image.copy and is retained. The repaired copy then exposed a parent-authored control mistake: KnownCells inherited previous DNA-only main flow instead of selecting original Actin main flow. Reflected schema and existing importer confirm the fix is the existing lazy input_source=PIPELINE_START declaration, not a production fallback. That failure and output remain; final run uses a separate output directory with unchanged algorithms/settings.

A receipt helper initially hit its PTY canonical input-size limit before dispatch. A fresh MCP client reconnects with corrected terminal capture to the same original native child; startup/execution are not replayed and10s observation deadlines are unchanged.

This generic source-binding control does not declare physical calibration; it proves field/row identity in pixels, not installed physical-unit, visual biological QA or a promoted recipe. H003e remains immutable REJECT with no scientific-data access, rerun, retune or held-out/reference answers opened. Full ZIP/R0/R1 completion remains outside this checkpoint.

Canonical receipt: docs/validation/paired_field_csv_314_20260930/installed-parent-checkpoint.rst.

@trissim
trissim marked this pull request as ready for review October 1, 2026 00:41
Copilot AI balanced review requested due to automatic review settings October 1, 2026 00:42

Copilot AI left a comment

Copy link
Copy Markdown

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Copilot was unable to review this pull request because the user who requested the review has reached their quota limit.

@trissim
trissim merged commit 74eac05 into main Oct 1, 2026
1 of 3 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Paired-field cell measurements split across two image numbers and duplicate object rows

2 participants