Jungfraujoch/image_analysis/indexing/FFBIDXIndexer.cpp

// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#include "FFBIDXIndexer.h"
#include "PostIndexingRefinement.h"

// The ffbidx library implements the TORO algorithm:
// Gasparotto et al. (2024) J. Appl. Cryst. 57, 931-944

void FFBIDXIndexer::SetupUnitCell(const std::optional<UnitCell> &cell) {
    if (!cell.has_value())
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "FFBIDX requires unit cell");
    // Given the primitive cell of a centred lattice (IndexingCell); the lattices found are put back
    // into the conventional cell in RunInternal.
    const CrystalLattice l1 = IndexingCell(cell.value());
    reference_unit_cell = l1.GetUnitCell();

    Eigen::Matrix3f m;
    indexer.iCellM() << l1.Vec0().x, l1.Vec0().y, l1.Vec0().z,
            l1.Vec1().x, l1.Vec1().y, l1.Vec1().z,
            l1.Vec2().x, l1.Vec2().y, l1.Vec2().z;
}

std::vector<CrystalLattice> FFBIDXIndexer::RunInternal(const std::vector<Coord> &coord, size_t nspots) {
    std::vector<CrystalLattice> ret;

    if (nspots > coord.size())
        nspots = coord.size();

    if (nspots < viable_cell_min_spots)
        return ret;

    assert(nspots <= MAX_SPOT_COUNT);
    assert(coord.size() <= MAX_SPOT_COUNT);

    for (int i = 0; i < coord.size(); i++) {
        indexer.spotX(i) = coord[i].x;
        indexer.spotY(i) = coord[i].y;
        indexer.spotZ(i) = coord[i].z;
    }

    // Index
    indexer.index(1, nspots);

    RefineParameters parameters{
        .viable_cell_min_spots = viable_cell_min_spots,
        .dist_tolerance_vs_reference = dist_tolerance_vs_reference,
        .reference_unit_cell = reference_unit_cell,
        .min_length_A = 1, // doesn't matter
        .max_length_A = 1000, // doesn't matter
        .min_angle_deg = 30,
        .max_angle_deg = 150,
        .indexing_tolerance = indexing_tolerance
    };

    auto lattices = Refine(coord, nspots, indexer.oCellM(), indexer.oScoreV(), parameters);
    return ToConventional(lattices);
}