[3/3] Add make_stitched_labels (materialise stitched labels)#1207
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timtreis wants to merge 5 commits into
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[3/3] Add make_stitched_labels (materialise stitched labels)#1207timtreis wants to merge 5 commits into
timtreis wants to merge 5 commits into
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Lock the validation-sweep outcome: at min_confidence=0.5 the deterministic fixture recovers >=50% of cut pieces with no intact false-merges. min_confidence default stays 0.7 (full attainable recall, zero false merges); gap_proximity kept in the 5-feature score. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…bels) PR-C of the scverse#1170 split. Adds sq.experimental.im.make_stitched_labels: reads the stitch_group_id mapping written by assign_stitch_groups and registers a new labels element where each stitched group shares one ID (original labels left untouched), plus an optional collapsed AnnData (one row per group) with configurable merge_strategy. Stacks on PR-B (feature/tiling-stitch-algo) and reuses its full-pipeline tests. Scale rework (must handle 100k x 100k, never materialise the full array): - LUT remap stays lazy; labels present in the image but absent from the QC table (e.g. min_area-filtered cells) pass through instead of indexing OOB. - join_labels is now chunk-aware via dask map_overlap (depth = close_radius+2), never computing the whole image or running a full-frame regionprops. - group aggregation vectorised (argsort+split, pandas groupby) instead of the O(cells x groups) per-group np.where scan. - X aggregation is sparse-safe: sum/mean via sparse matmul, first via sparse gather, other reducers per-group-bounded; the full matrix is never densified. - validate label_id/is_stitched up front; squeeze a leading singleton dim. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…our change - inline equivalent_diameter + largest_contour (single consumer _tiling_stitch) into their call site and delete utils/_geometry.py; keep both guards (1px pad precondition + empty-contour skip). - route _resolve_qc_params through the shared resolve_params helper instead of a duplicated Mapping-validation block; drop the now-dead _QC_FIELDS and unused fields import. utils/_params.py now has two genuine callers. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…le + validation Addresses a max-effort review of the stitched-labels path: - collapsed table no longer sums QC-contract columns: centroid_y/x take the mean of the pieces (a merged cell's position), the per-piece cut-artifact scores take the max (worst piece); merge_strategy now applies only to genuine additive user features. Drops the dtype-restore that re-narrowed/truncated promoted sums and means. - _aggregate_X: sum no longer treated as integer-preserving, so an integer .X promotes to float64 instead of wrapping (uint16 200000 -> 3392); a callable strategy is now applied to singleton groups too (obs/X parity). - multiscale: parse the new element with the resolved scale's transform (not the DataTree base/Identity), so the output overlays correctly; documented as a single-scale element at the QC scale's resolution. - validate label_id (positive, unique, non-NaN) and merge_strategy up front, so bad input fails fast even with write_table=False. - preserve varm (var axis is unchanged); correct the join_labels docstring (it is lazy via map_overlap and bridges seams up to 2*close_radius px, not "forces materialisation"). - add TestReviewFixes regression locks (each fails on the pre-fix code). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #1207 +/- ##
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+ Coverage 75.29% 75.61% +0.31%
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Files 59 59
Lines 8429 8620 +191
Branches 1395 1434 +39
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+ Hits 6347 6518 +171
- Misses 1527 1530 +3
- Partials 555 572 +17
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Completes the tile-cut stitching arc (
[1/3]#1188,[2/3]#1193) with the materialisation step.Usage
Knobs:
merge_strategy(how additive user features aggregate across pieces; default"sum"),join_labels(close the seam so a group is one connected component; stays lazy on dask),write_table,inplace.Also in this PR
utils/_geometry.pyhelpers into their one caller (module deleted) and routed_resolve_qc_paramsthrough the sharedresolve_params. No behaviour change.Closes the #1170 arc.