hierarchy: dedup _get_ref_coords gather + vectorize voxel→node adjacency#243
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Two safe-and-free cleanups in `hierarchical.py`: - **`_get_ref_coords` redundant gather** — `vals_a` and `vals_b` were computed by the *same* `idxmin[branch_labels_clipped]` expression (same input array, same lookup). Compute once, share the NaN mask. ~6 lines deleted; fewer allocations on the hot motility path (called per-frame inside `_get_motility_stats`). - **`_save_adjacency_maps` voxel→node Python loop** — replaces the nested `for voxel_idx, nodes in enumerate(...): for n in nodes: edges_vn.append((voxel_idx, int(n)))` with `np.repeat` + `np.concatenate`. Only fires when `not skip_nodes` (production default in the napari pipeline). Removes per-edge Python attribute + tuple-allocation overhead — a 1MB-edge frame goes from millions of Python ops to two C-level numpy calls. Bit-identical: verified locally on yeast 2D + 3D fixtures via SHA over all 6 hierarchy outputs (`features_*` + `adjacency_maps`) — all 12 hashes match the post-PR-#242 baseline exactly. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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…ation audit close-out (#244) - now.md: new "Recently shipped" entry covering PRs #241/#242/#243 (vectorized per-label group construction, vectorized _get_branch_stats loops + ADR 0013, _get_ref_coords + vox→node cleanups). Watch list updated to reflect hierarchical's pinning status and the deferred wins (regionprops solidity ~17%, flow_interpolation _get_vector_weights ~28%) that the next perf audit could target. - feature-extraction.md: new Performance section documenting the 4 shipped optimizations + the 3 deferred items, plus a Benchmarks subsection pointing at tests/test_hierarchical_perf.py. Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Two safe-and-free cleanups in `hierarchical.py`:
`_get_ref_coords` redundant gather — `vals_a` and `vals_b` were computed by the same `idxmin[branch_labels_clipped]` expression (same input array, same lookup). Compute once, share the NaN mask. ~6 lines deleted; fewer allocations on the hot motility path (called per-frame inside `_get_motility_stats`).
`_save_adjacency_maps` voxel→node Python loop — replaces the nested `for voxel_idx, nodes in enumerate(...): for n in nodes: edges_vn.append((voxel_idx, int(n)))` with `np.repeat` + `np.concatenate`. Only fires when `not skip_nodes` (production default in the napari pipeline). Removes per-edge Python attribute + tuple-allocation overhead — a 1MB-edge frame goes from millions of Python ops to two C-level numpy calls.
Equivalence bar
Bit-identical. Verified locally on yeast 2D + 3D fixtures via SHA over all 6 hierarchy outputs (`features_voxels` / `features_nodes` / `features_branches` / `features_organelles` / `features_image` / `adjacency_maps`) — all 12 hashes match the post-PR-#242 baseline exactly.
Why
Closing out the 3-PR hierarchical perf audit (PRs #241, #242, this one). cProfile flagged `_save_adjacency_maps` and `_get_ref_coords` as small but allocation-heavy hot paths; this PR captures the trivial wins identified during the audit. No new features, no new tests required (existing 57 tests in `test_hierarchical.py` cover both code paths and pass; SHA verification proves bit-identity).
Test plan
🤖 Generated with Claude Code