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Support all in batch coordinate ranges - #156

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codex/support-all-batch-ranges
Open

Support all in batch coordinate ranges#156
arjunrajlab wants to merge 3 commits into
masterfrom
codex/support-all-batch-ranges

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Summary

  • allow users to enter all in Batch XY, Batch Z, and Batch Time fields
  • expand all from dataset IndexXY, IndexZ, and IndexT metadata, with single-position fallbacks for missing dimensions
  • route WorkerClient and direct SAM batching paths through the shared dataset-aware parser
  • support the equivalent all value in Crop range fields and the legacy Cellori loop
  • update interface placeholders and worker documentation

Why

Batch fields previously accepted only numeric ranges such as 1-3, 5-8. The range parser had no dataset-dimension context, so the literal all could not be expanded safely and instead failed numeric parsing. This change centralizes dataset-aware expansion while preserving existing numeric and current-tile behavior.

User impact

Users can now type all (case-insensitive, with surrounding whitespace allowed) to process every available XY position, Z slice, or time point. Datasets without a corresponding IndexRange dimension correctly resolve to coordinate 0.

Validation

  • annotation_utilities: 22 tests passed
  • worker_client: 14 tests passed
  • Crop Docker worker: 15 tests passed
  • Random Squares Docker worker: 3 tests passed
  • Python syntax checks and git diff --check passed

@arjunrajlab
arjunrajlab marked this pull request as ready for review July 19, 2026 11:52

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💡 Codex Review

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Reviewed commit: 5f55e54fe1

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Comment thread workers/annotations/crop/entrypoint.py
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