fix(impact-reg): masked features, MIND statistics and a worker-safe sentinel - #170
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📝 WalkthroughWalkthroughThe PR updates IMPACT preprocessing, fixed-mask handling, FireANTs mask geometry, and Elastix parameter overrides. It replaces the unresolved read-granularity sentinel with a pickle-stable class. It adds URI-backed OME-Zarr loading, writing, lazy-read handling, and pyramid append restrictions. ChangesIMPACT registration
Patching sentinel serialization
URI-backed OME-Zarr operations
Estimated code review effort: 3 (Moderate) | ~25 minutes Merge Risk: 🟡 Moderate · up to The change can produce incorrect registration scores when a partial moving mask is used because excluded voxels may still affect the metric; this should be addressed or explicitly accepted before merging. A separate localized filesystem error-handling issue also remains for follow-up. Poem
🚥 Pre-merge checks | ✅ 3 | ❌ 2❌ Failed checks (2 warnings)
✅ Passed checks (3 passed)
Full details: Description checkResolution Update the description with the required headings and content: describe the changes and motivation, add related issues or state that none apply, select the applicable change type, document commands run and observed results, complete the checklist, and state whether breaking changes exist. ✨ Finishing Touches 💡 1📝 Generate docstrings 💡
🧪 Generate unit tests (beta)
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Inline comments:
In `@apps/impact_reg/impact_reg_konfai/models/fireants.py`:
- Line 426: Update the mask handling in _ImpactCore.forward before calling
IMPACTReg._compute so the trailing fixed and moving mask channels are
intersected elementwise, then remove the mask channels and pass the combined
mask through the existing uint8 conversion. Ensure partial moving_mask values
are respected.
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apps/impact_reg/impact_reg_konfai/models/elastix_engine.pyapps/impact_reg/impact_reg_konfai/models/fireants.pykonfai/data/patching.py
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Inline comments:
In `@konfai/utils/ome_zarr.py`:
- Line 1134: Update write_ome_zarr to perform the uri.is_uri(store_path) and
non-empty scale_factors validation before creating or writing level 0, raising
the existing rejection error early for remote pyramid writes. Retain the guard
in append_ome_zarr_levels for direct callers.
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Inline comments:
In `@konfai/utils/ome_zarr.py`:
- Line 940: In the metadata upload flow, create the destination directory before
iterating over files: after the existing deletion check and before the loop
containing filesystem.put_file, call filesystem.makedirs(target, exist_ok=True).
Preserve the current upload behavior and ordering.
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Inline comments:
In `@konfai/utils/ome_zarr.py`:
- Line 191: Update the mapper creation in the visible OME-Zarr loading flow to
obtain a filesystem via uri.filesystem(store_path), split the URI target as
required, and call filesystem.get_mapper(target) instead of fsspec.get_mapper;
preserve the existing URL fallback and DatasetManagerError handling.
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…entinel One squashed commit from fix/impact-reg-masked-features (4 commits): - fix(patching): a sentinel keeps its identity across the worker boundary - fix(impact-reg): pass MIND the four statistics it was traced against - fix(impact-reg): a FireANTs mask restricts the feature metric instead of feeding it - fix(impact-reg): a raw elastix override sets a key the map never mentions
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One squashed commit from fix/impact-reg-masked-features (4 commits):
Summary by CodeRabbit
Bug Fixes
New Features