merge(zarr3): expose fast-merge config levers + TPS warp + optimal-site seeding#228
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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
…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, 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
Ports the fast-merge levers onto the zarr3 line (companion to #227 which lands the same change on
main). Same 3 backward-compatible commits, adapted to zarr3's merge code + house style:feat(merge): expose hardcoded fast-merge levers as backward-compatible config paramsfeat(merge): thin-plate-spline warp + find-optimal-site seeding (gated)style(merge): single-line comments, lib high->low order, ruff formatAll levers default to unset ⇒
config.get(...)→None→ lib literal ⇒ existing zarr3 screens byte-identical.Scope
5 merge-path files only:
workflow/lib/merge/{fast_merge,hash}.py,workflow/scripts/merge/{fast_alignment,fast_merge}.py,workflow/rules/merge.smk. No test files.zarr3-specific notes
config.get("merge", {}).get(...)param style used throughout zarr3'smerge.smk(main usesconfig["merge"].get(...)), and preserved zarr3's optionaldet_range/score/thresholdsemantics.threshold_region = 50inevaluate_matchthat was shadowing the (now parameterized)threshold_regionargument.ruff format --check+ruff checkclean; merge modules compile.🤖 Generated with Claude Code