Jungfraujoch/image_analysis/IndexAndRefine.cpp

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

#include "IndexAndRefine.h"

#include "bragg_integration/BraggIntegrate2D.h"
#include "bragg_integration/CalcISigma.h"
#include "geom_refinement/XtalOptimizer.h"
#include "indexing/AnalyzeIndexing.h"
#include "indexing/FFTIndexer.h"
#include "lattice_search/LatticeSearch.h"

IndexAndRefine::IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool *indexer)
    : index_ice_rings(x.GetIndexingSettings().GetIndexIceRings()),
      experiment(x),
      geom_(x.GetDiffractionGeometry()),
      indexer_(indexer) {
    if (indexer && x.IsRotationIndexing())
        rotation_indexer = std::make_unique<RotationIndexer>(x, *indexer);
}

IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(DataMessage &msg) {
    IndexingOutcome outcome(experiment);

    if (rotation_indexer) {
        auto result = rotation_indexer->ProcessImage(msg.number, msg.spots);
        if (result) {

            // get rotated lattice
            auto gon = result->axis;
            if (gon) {
                const float angle_deg = gon->GetAngle_deg(msg.number) + gon->GetWedge_deg() / 2.0f;
                outcome.lattice_candidate = result->lattice.Multiply(gon->GetTransformationAngle(-angle_deg));
            }

            outcome.experiment.BeamX_pxl(result->geom.GetBeamX_pxl())
                    .BeamY_pxl(result->geom.GetBeamY_pxl())
                    .DetectorDistance_mm(result->geom.GetDetectorDistance_mm())
                    .PoniRot1_rad(result->geom.GetPoniRot1_rad())
                    .PoniRot2_rad(result->geom.GetPoniRot2_rad())
            .Goniometer(result->axis);
            outcome.symmetry.centering = result->search_result.centering;
            outcome.symmetry.niggli_class = result->search_result.niggli_class;
            outcome.symmetry.crystal_system = result->search_result.system;
        }
        return outcome;
    }

    // Convert input spots to reciprocal space
    std::vector<Coord> recip;
    recip.reserve(msg.spots.size());
    for (const auto &i: msg.spots) {
        if (index_ice_rings || !i.ice_ring)
            recip.push_back(i.ReciprocalCoord(geom_));
    }

    auto indexer_result = indexer_->Run(experiment, recip).get();
    msg.indexing_time_s = indexer_result.indexing_time_s;

    if (indexer_result.lattice.empty())
        return outcome;

    auto latt = indexer_result.lattice[0];
    auto sg = experiment.GetGemmiSpaceGroup();

    // If space group provided => always enforce symmetry in refinement
    // If space group not provided => guess symmetry
    if (sg) {
        // If space group provided but no unit cell fixed, it is better to keep triclinic for now
        if (experiment.GetUnitCell()) {
            outcome.symmetry = LatticeMessage{
                .centering = sg->centring_type(),
                .niggli_class = 0,
                .crystal_system = sg->crystal_system()
            };
        }
        outcome.lattice_candidate = latt;
    } else {
        auto sym_result = LatticeSearch(latt);
        outcome.symmetry = LatticeMessage{
            .centering = sym_result.centering,
            .niggli_class = sym_result.niggli_class,
            .crystal_system = sym_result.system
        };
        outcome.lattice_candidate = sym_result.conventional;
    }

    return outcome;
}

void IndexAndRefine::RefineGeometryIfNeeded(DataMessage &msg, IndexAndRefine::IndexingOutcome &outcome) {
    if (!outcome.lattice_candidate)
        return;

    XtalOptimizerData data{
        .geom = outcome.experiment.GetDiffractionGeometry(),
        .latt = *outcome.lattice_candidate,
        .crystal_system = outcome.symmetry.crystal_system,
        .min_spots = experiment.GetIndexingSettings().GetViableCellMinSpots(),
        .refine_beam_center = true,
        .refine_distance_mm = false,
        .refine_detector_angles = false,
        .max_time = 0.04 // 40 ms is max allowed time for the operation
    };

    if (experiment.IsRotationIndexing()) {
        data.refine_beam_center = false;
        data.refine_rotation_axis = false;
        data.refine_unit_cell = false;
    }

    if (outcome.symmetry.crystal_system == gemmi::CrystalSystem::Trigonal)
        data.crystal_system = gemmi::CrystalSystem::Hexagonal;

    switch (experiment.GetIndexingSettings().GetGeomRefinementAlgorithm()) {
        case GeomRefinementAlgorithmEnum::None:
            break;
        case GeomRefinementAlgorithmEnum::BeamCenter:
            if (XtalOptimizer(data, msg.spots)) {
                outcome.experiment.BeamX_pxl(data.geom.GetBeamX_pxl())
                        .BeamY_pxl(data.geom.GetBeamY_pxl());
                outcome.beam_center_updated = true;
            }
            break;
    }

    outcome.lattice_candidate = data.latt;

    if (outcome.beam_center_updated) {
        msg.beam_corr_x = data.beam_corr_x;
        msg.beam_corr_y = data.beam_corr_y;
    }
}

void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
                                              const SpotFindingSettings &spot_finding_settings,
                                              const CompressedImage &image,
                                              BraggPrediction &prediction,
                                              const IndexAndRefine::IndexingOutcome &outcome) {
    if (!spot_finding_settings.quick_integration)
        return;
    if (!outcome.lattice_candidate)
        return;

    CrystalLattice latt = outcome.lattice_candidate.value();

    if (rotation_indexer) {
        // Use moving average for mosaicity and profile_radius (also add beam center later)
        if (msg.mosaicity_deg)
            msg.mosaicity_deg = rotation_parameters.Mosaicity(msg.mosaicity_deg.value());
        if (msg.profile_radius) {
            msg.profile_radius = rotation_parameters.ProfileRadius(msg.profile_radius.value());
        }
    }

    float ewald_dist_cutoff = 0.001f;
    if (msg.profile_radius)
        ewald_dist_cutoff = msg.profile_radius.value() * 2.0f;

    if (experiment.GetBraggIntegrationSettings().GetFixedProfileRadius_recipA())
        ewald_dist_cutoff = experiment.GetBraggIntegrationSettings().GetFixedProfileRadius_recipA().value() * 3.0f;

    float wedge_deg = 0.0f;
    float mos_deg = 0.1f;

    if (experiment.GetGoniometer().has_value()) {
        wedge_deg = experiment.GetGoniometer()->GetWedge_deg() / 2.0;

        if (msg.mosaicity_deg)
            mos_deg = msg.mosaicity_deg.value();
    }

    const BraggPredictionSettings settings_prediction{
        .high_res_A = experiment.GetBraggIntegrationSettings().GetDMinLimit_A(),
        .ewald_dist_cutoff = ewald_dist_cutoff,
        .max_hkl = 100,
        .centering = outcome.symmetry.centering,
        .wedge_deg = std::fabs(wedge_deg),
        .mosaicity_deg = std::fabs(mos_deg)
    };

    auto nrefl = prediction.Calc(outcome.experiment, latt, settings_prediction);
    auto refl_ret = BraggIntegrate2D(outcome.experiment, image, prediction.GetReflections(), nrefl, msg.number);

    constexpr size_t kMaxReflections = 10000;
    if (refl_ret.size() > kMaxReflections) {
        // Keep only smallest d (highest resolution)
        std::nth_element(refl_ret.begin(),
                         refl_ret.begin() + static_cast<long>(kMaxReflections),
                         refl_ret.end(),
                         [](const Reflection& a, const Reflection& b) {
                             return a.d < b.d;
                         });
        refl_ret.resize(kMaxReflections);

        // Optional: make output ordered by d (nice for downstream / debugging)
        std::sort(refl_ret.begin(), refl_ret.end(),
                  [](const Reflection& a, const Reflection& b) { return a.d < b.d; });
    }

    msg.reflections = std::move(refl_ret);

    CalcISigma(msg);
    CalcWilsonBFactor(msg);

    // Append reflections to the class-wide reflections buffer (thread-safe)
    {
        std::unique_lock ul(reflections_mutex);
        reflections.insert(reflections.end(), msg.reflections.begin(), msg.reflections.end());
    }
}

void IndexAndRefine::ProcessImage(DataMessage &msg,
                                  const SpotFindingSettings &spot_finding_settings,
                                  const CompressedImage &image,
                                  BraggPrediction &prediction) {
    if (!indexer_ || !spot_finding_settings.indexing)
        return;

    msg.indexing_result = false;

    IndexingOutcome outcome = DetermineLatticeAndSymmetry(msg);
    if (!outcome.lattice_candidate)
        return;

    RefineGeometryIfNeeded(msg, outcome);
    if (!outcome.lattice_candidate)
        return;

    if (!AnalyzeIndexing(msg, outcome.experiment, *outcome.lattice_candidate))
        return;

    msg.lattice_type = outcome.symmetry;

    QuickPredictAndIntegrate(msg, spot_finding_settings, image, prediction, outcome);
}

std::optional<RotationIndexerResult> IndexAndRefine::Finalize() {
    if (rotation_indexer)
        return rotation_indexer->GetLattice();
    return {};
}

std::optional<ScaleMergeResult> IndexAndRefine::ScaleRotationData(const ScaleMergeOptions &opts) const {
    std::vector<Reflection> snapshot;
    {
        std::unique_lock ul(reflections_mutex);
        snapshot = reflections;          // cheap copy under lock
    }

    // Need a reasonable number of reflections to make refinement meaningful
    constexpr size_t kMinReflections = 20;
    if (snapshot.size() < kMinReflections)
        return std::nullopt;

    // Build options focused on mosaicity refinement but allow caller override
    ScaleMergeOptions options = opts;

    // If the experiment provides a wedge, propagate it
    if (experiment.GetGoniometer().has_value())
        options.wedge_deg = experiment.GetGoniometer()->GetWedge_deg();

    // If caller left space_group unset, try to pick it from the indexed lattice
    if (!options.space_group.has_value()) {
        auto sg = experiment.GetGemmiSpaceGroup();
        if (sg)
            options.space_group = *sg;
    }

    return ScaleAndMergeReflectionsCeres(snapshot, options);
}