leonarski_fandClaude Opus 5
6081b6bc43
Six methods the pages name or describe carried no citation: Padilla & Yeates (the L test), Steller, Bolotovsky & Rossmann (the projection/FFT autoindexing MOSFLM implements), TORO (what ffbidx implements), Krivy & Gruber and the ITA lattice-character table (the reduction and Bravais assignment), Cheetah's peakfinder8 (the per-ring background statistics of the adaptive finder) and Hennequin et al.'s SparseCCL (already credited to traccc, now also to its authors). Each gets its ACKNOWLEDGEMENT.md paragraph, a References entry in CPU_DATA_ANALYSIS.md, and a one-line credit at the algorithm. The Sheriff & Hendrickson / Popov & Bourenkov entry is re-scoped so each claim sits on the paper that supports it - P&B 2003 is titled, and credited for the sigma-aware anisotropy estimation its statistic modelling contains, not for the tensor and its constraints. All DOIs verified against the publishers; the SparseCCL DOI resolves to IEEE document 9049184 (IEEE blocks content scraping, so verified by the resolved document id plus two independent sources). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
58 lines
1.8 KiB
C++
58 lines
1.8 KiB
C++
// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include "FFBIDXIndexer.h"
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#include "PostIndexingRefinement.h"
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// The ffbidx library implements the TORO algorithm:
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// Gasparotto et al. (2024) J. Appl. Cryst. 57, 931-944
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void FFBIDXIndexer::SetupUnitCell(const std::optional<UnitCell> &cell) {
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if (!cell.has_value())
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"FFBIDX requires unit cell");
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reference_unit_cell = cell;
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CrystalLattice l1(cell.value());
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Eigen::Matrix3f m;
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indexer.iCellM() << l1.Vec0().x, l1.Vec0().y, l1.Vec0().z,
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l1.Vec1().x, l1.Vec1().y, l1.Vec1().z,
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l1.Vec2().x, l1.Vec2().y, l1.Vec2().z;
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}
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std::vector<CrystalLattice> FFBIDXIndexer::RunInternal(const std::vector<Coord> &coord, size_t nspots) {
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std::vector<CrystalLattice> ret;
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if (nspots > coord.size())
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nspots = coord.size();
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if (nspots < viable_cell_min_spots)
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return ret;
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assert(nspots <= MAX_SPOT_COUNT);
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assert(coord.size() <= MAX_SPOT_COUNT);
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for (int i = 0; i < coord.size(); i++) {
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indexer.spotX(i) = coord[i].x;
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indexer.spotY(i) = coord[i].y;
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indexer.spotZ(i) = coord[i].z;
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}
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// Index
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indexer.index(1, nspots);
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RefineParameters parameters{
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.viable_cell_min_spots = viable_cell_min_spots,
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.dist_tolerance_vs_reference = dist_tolerance_vs_reference,
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.reference_unit_cell = reference_unit_cell,
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.min_length_A = 1, // doesn't matter
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.max_length_A = 1000, // doesn't matter
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.min_angle_deg = 30,
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.max_angle_deg = 150,
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.indexing_tolerance = indexing_tolerance
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};
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return Refine(coord, nspots, indexer.oCellM(), indexer.oScoreV(), parameters);
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}
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