Choose and apply the best reindexing by correlation - #353
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This was referenced Aug 22, 2026
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! This PR was vibe-coded.
Stack
Part 3 of 11 for #31. Depends on #352. Merge bottom-up.
Next branch: codex/phase-alignment-04-reindex-hardening.
What this implements
Adds ReindexingCandidate, ReindexingResult, and reindex_by_correlation(). The public function gates on the ambiguity predicate, evaluates identity plus Gemmi twin-law representatives, applies the highest-scoring operation to a copy, and reports ranked candidates, runner-up correlation, and the score gap.
Amplitudes are squared, normalized by resolution, and scored with signed Pearson correlation. Proper reindexing laws only are considered; hand remains separate.
Tests
End-to-end tests cover nonmutation, correct and identity selections, operation direction, common-HKL matching, amplitude and intensity inputs, and rejection when the unit-cell metric has no alternative indexing.
Reviewer focus
Related: #31 and #174.