merge: expose fast-merge config levers + TPS warp + optimal-site seeding (backward-compatible)#227
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…e config params
Parameterize the formerly-hardcoded fast-merge knobs so they can be tuned per screen:
- evaluate_match: threshold_triangle, threshold_point, threshold_region, ransac_kwargs
- initial_alignment / multistep_alignment: evaluate_kwargs (+ batch_size)
- refine_local_warp: degree, iterations, min_correspondences via warp_kwargs,
threaded through merge_triangle_hash / merge_sbs_phenotype
Wired through scripts/merge/{fast_alignment,fast_merge}.py and rules/merge.smk
(all config.get default None -> lib literal). Defaults unchanged => existing
screens byte-identical.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SAWdQnZAy3WU6bdxy41EgP
Adds two validated two-scope merge levers, both backward-compatible (defaults
off -> byte-identical to the affine path already on this branch):
- TPS warp: `local_refinement` now doubles as the warp-model selector
("polynomial" | "thin_plate_spline"); wire `warp_smoothing` /
`warp_max_correspondences` through scripts/merge/fast_merge.py + merge.smk.
On two-scope OPS merges TPS roughly halves the median residual vs polynomial
while staying stable. String selector is byte-identical to an explicit
warp_kwargs["model"]; a bare truthy keeps the polynomial default.
- find-optimal-site (`seed_optimize`, `seed_topk`): the stage-nearest phenotype
tile is not always the best real overlap when the two scopes have a
metadata-alignment residual. When on, evaluate the top-K nearest tiles per SBS
seed and keep the highest-scoring one per site. Default off = nearest-tile,
unchanged.
Verified: default (local_refinement=None, seed_optimize=False) path untouched;
polynomial selector == explicit model kwarg; TPS routes end-to-end and both
warps recover matches an affine drops on distorted data.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SAWdQnZAy3WU6bdxy41EgP
Cleanup of the merge fast-path (no behavioral change; smoke test identical): - Collapse multiline block comments to single lines across fast_merge.py and fast_alignment.py. - Reorder lib/merge/fast_merge.py high-level -> low-level: merge_triangle_hash, merge_sbs_phenotype, then helpers build_linear_model, refine_local_warp. - Trim refine_local_warp docstring to the file's density; ruff format + check clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SAWdQnZAy3WU6bdxy41EgP
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Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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…nobs Per review of the merge autoresearch results, keep as config-exposed only the levers with measured impact (threshold_triangle, ransac_random_state, local_refinement, warp_degree/iterations/smoothing, seed_optimize/seed_topk). Revert the inert knobs to hardcoded literals in the lib (threshold_point=2, threshold_region=50, batch_size=180, warp min/max_correspondences=30/700). Defaults unchanged => byte-identical. TPS + find-optimal-site kept (validated on Vaishnavi: median 0.08px). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
plot_merge_example / fast_merge_example gain local_refinement + warp_kwargs and apply refine_local_warp to the affine prediction, mirroring merge_sbs_phenotype, so the notebook match preview reflects the levers an operator sets. Notebook-only helper; defaults None => unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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What
Lands the fast-merge improvements onto
mainas 3 focused, backward-compatible commits, cherry-picked frommerge-rotation-fix(which is stacked on the zarr3 line — this PR deliberately excludes all zarr3 changes):feat(merge): expose hardcoded fast-merge levers as backward-compatible config params— parameterizes the formerly-hardcoded knobs (threshold_triangle/point/region,ransac_kwargs,evaluate_kwargs+batch_size, warpdegree/iterations/min_correspondences). Allconfig.get(...)defaultNone→ lib literal. Defaults unchanged ⇒ existing screens byte-identical.feat(merge): thin-plate-spline warp + find-optimal-site seeding (gated)— adds two gated levers:local_refinement="thin_plate_spline"(withwarp_smoothing/warp_max_correspondences) and find-optimal-site seeding (seed_optimize/seed_topk). Both default off ⇒ byte-identical to the affine/nearest-tile path.style(merge): single-line comments, lib high->low order, ruff format— house-style cleanup of the merge fast-path (no behavioral change).Scope
Only 6 files, all in the merge path:
workflow/lib/merge/{fast_merge,hash}.py,workflow/scripts/merge/{fast_alignment,fast_merge}.py,workflow/rules/merge.smk,tests/test_merge_levers.py. No zarr3 / OME-Zarr / HCS files.Testing
tests/test_merge_levers.py(shipped with commit 1) — 3/3 pass: verifies new kwargs at old literals == no kwargs (byte-identical defaults).small_test_analysispipeline gate: running on Slurm; result to follow before merge.Notes
Conflict resolution vs
main: keptmain's required-param semantics (det_range/score/thresholdstay bracket-access) andmain'sconfig["merge"].get(...)style; added the new optional levers in that same style.🤖 Generated with Claude Code