feat(centroids): add return_area + SpatialData persist to get_centroids#1150
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timtreis wants to merge 7 commits into
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feat(centroids): add return_area + SpatialData persist to get_centroids#1150timtreis wants to merge 7 commits into
timtreis wants to merge 7 commits into
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Surface the per-instance area that the labels bincount already computes (and geometric area for shapes), and add a SpatialData dispatch that writes centroids/area into the element's annotating table, squidpy-style. - `return_area` on all element overloads: labels return the pixel/voxel count (free, already computed); shapes return `pi*r**2` for circles and `geometry.area` for polygons; points raise. Carried as a feature column on the returned Points element. - Harmonise the three element overload signatures (they previously disagreed on `return_background`). - New `get_centroids(sdata, element_name, ..., persist_as="adata")` dispatch: resolves the element's annotating table and writes `obsm["spatial"]` (x, y[, z]) and `obs["area"]` at the element's rows, in place. Raises (pointing to `persist_as="Points"`) when no table annotates the element. No standalone AnnData is ever created. - Element-level `persist_as="adata"` raises, directing to the SpatialData form (which can resolve the table). - Fast path: the table-writing path applies the coordinate transform to the tiny per-instance centroid array in-memory and short-circuits when it is an identity, avoiding the dask `transform()` round-trip. `coordinate_system=None` returns intrinsic coordinates. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## chore/python-3.12-3.14 #1150 +/- ##
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- Coverage 92.43% 92.29% -0.14%
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Files 51 51
Lines 7814 7906 +92
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+ Hits 7223 7297 +74
- Misses 591 609 +18
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…turn type - narrow transformation to BaseTransformation before to_affine_matrix - assert coordinate_system is not None after _validate_persist_args in the element overloads (None is rejected there for persist_as != 'adata') - cast element-dispatch get_centroids results to DaskDataFrame at the two callers (vectorize, datasets); only the SpatialData overload returns SpatialData
…trim docs Correctness: - _write_centroids_into_table: align instance ids via a single get_indexer; raise on a total miss (instance_key dtype != element index) instead of silently writing an all-NaN obsm['spatial']; partial misses (background, filtered instances) still NaN-fill as documented. - refuse to overwrite obsm['spatial'] when an existing array has a different width (would wipe coordinates of other regions sharing the table). - validate coordinate_system on the persist_as='adata' path too. Cleanup (no behavior change): - collapse the three near-identical element overloads into one stacked singledispatch registration delegating to _intrinsic_centroid_frame. - trim verbose docstrings/comments. Tests: instance_key dtype mismatch raises; dimension mismatch refuses to overwrite; invalid-element message updated.
…ds method - persist_as='adata' gains inplace: bool = True (mirrors sanitize_table): inplace=True mutates the resolved table and returns None; inplace=False copies only that AnnData, writes into the copy, returns it (sdata untouched). No whole-SpatialData copy. - add SpatialData.get_centroids(element_name, ...) method delegating to the module function (mirrors sdata.aggregate), so both sd.get_centroids(sdata, ...) and sdata.get_centroids(...) work. Calls the named _get_centroids_sdata overload directly so the full signature type-checks. - widen return type to DaskDataFrame | AnnData | None; update tests.
…edup scatter Correctness hardening (review round 2): - raise a clear error when the element index is non-unique (was a cryptic pandas InvalidIndexError from get_indexer on e.g. duplicate-index shapes). - obsm width-mismatch guard is now 1-D-safe (compare full .shape instead of indexing .shape[1], which raised IndexError on a 1-D obsm['spatial']). - reword the total-miss error (it's 'no shared instances', not only a dtype bug). Cleanup: - reuse the existing _affine_matrix_multiplication helper in _transform_centroid_coords (drops the inline matmul; gives the dead helper a caller). - collapse the duplicated coords/area NaN-fill into a local _scatter(). - _points_from_centroids: df.assign instead of copy-then-mutate. - name the squidpy storage keys (_SPATIAL_KEY/_AREA_KEY) instead of magic strings.
…test assertion - _resolve_annotating_table returns annotators[0] directly (get_element_annotators already yields set[str]; the str() wrap was noise). - extract _assert_obsm_matches_points test helper to remove two near-identical written-obsm vs element-Points comparison blocks.
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Motivation
get_centroidsalready computes per-label pixel counts (np.bincount) when finding label centroids, then discards them, we could store asarea. This PR surfaces that area into an element's annotating table, squidpy-style (obsm["spatial"]/obs["area"]), so downstream tools (e.g. squidpy) and repeated renders can reuse them instead of recomputing.stacked on #1151