R2r multiscale#208

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seanmcculloch wants to merge 43 commits intomainfrom

Commits on Apr 22, 2026

split r2r
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detection dev
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fix: split dataset xml generation fix timepoints and calibration transform
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chore: clean diff
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fix: update split xml_to_dataframe with better zarr parser
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feat: split xml ipd

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chore: typo

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docs: inline comment on channel parsing

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chore: .format to f string

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chore: Use os.path.join for path construction in metadata_builder (#168)

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test: Add crop bounds validation for split XML IPD implementation (#169)

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feat(evaluation): add detection_qc module for IP detection sweep analysis

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chore: debug prints
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debug: add diagnostic prints for multiscale loading in IP detection

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debug: move print to ImageReader.fetch_image_data for visibility

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fix: prevent double-appending multiscale level in OME-Zarr paths

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fix: handle zarr arrays without .keys() in diagnostic print

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fix: add root zarr inspection to diagnose missing multiscale levels

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fix: include per-tile zarr path in split tile multiscale resolution

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debug: add detailed diagnostics for image loading and DoG detection

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fix: scale interval bounds for multiscale zarr levels

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refactor: remove verbose diagnostics from production code

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feat(diagnostics): Add comprehensive logging for multiscale IP detection debug

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feat(diagnostics): Add Ray task-level logging with flush

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fix(image_reader): Allow crop_max to equal array dimension - 1

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fix: clamp crop_max bounds to valid array dimensions

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fix: apply split tile crop AFTER downsampling and bounds scaling

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docs: clarify crop_max scaling may produce out-of-bounds values

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fix: explicitly init and shutdown Ray with OS CPU count

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fix: scale crop bounds by total downsampling factor (2^level * dsxy)

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fix: use /scratch/ray/ as Ray temp directory to avoid filling /tmp

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fixes for detection of unsplit xml
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matching and solver working, skip global optimization
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remove _ch_ restriction
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add retry
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Commits on Apr 24, 2026

Commits on Apr 28, 2026

tighten chunk-overlap
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Commits on May 5, 2026

checkpoint
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Commits on May 6, 2026

Commits on May 7, 2026

fix chunks_per_bound double offset
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