// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#include "SpotAnalyze.h"

#include "geom_refinement/XtalOptimizer.h"
#include "spot_finding/SpotUtils.h"
#include "spot_finding/StrongPixelSet.h"
#include "bragg_integration/BraggIntegrate2D.h"
#include "indexing/AnalyzeIndexing.h"


void SpotAnalyze(const DiffractionExperiment &experiment,
                 const SpotFindingSettings &spot_finding_settings,
                 const std::vector<DiffractionSpot> &spots,
                 const CompressedImage &image,
                 IndexerThreadPool *indexer,
                 DataMessage &output) {
    std::vector<SpotToSave> spots_out;

    auto geom = experiment.GetDiffractionGeometry();
    for (const auto &spot: spots)
        spots_out.push_back(spot.Export(geom));

    if (experiment.GetDatasetSettings().IsDetectIceRings() && spot_finding_settings.ice_ring_width_Q_recipA > 0.0f)
        MarkIceRings(spots_out, spot_finding_settings.ice_ring_width_Q_recipA);

    CountSpots(output, spots_out, spot_finding_settings.cutoff_spot_count_low_res);

    FilterSpotsByCount(spots_out, experiment.GetMaxSpotCount());

    output.spots = spots_out;

    output.resolution_estimate = GetResolution(output.spots);

    if ((indexer != nullptr) && spot_finding_settings.indexing) {
        auto latt_f = indexer->Run(experiment, output);
        auto latt = latt_f.get();

        if (!latt)
            output.indexing_result = false;
        else {
            bool beam_center_updated = false;

            DiffractionExperiment experiment_copy(experiment);
            XtalOptimizerData data{
                .geom = experiment_copy.GetDiffractionGeometry(),
                .latt = latt.value(),
                .crystal_system = experiment.GetCrystalSystem(),
                .centering = experiment.GetCentering(),
                .min_spots = experiment.GetIndexingSettings().GetViableCellMinSpots()
            };

            switch (experiment.GetIndexingSettings().GetGeomRefinementAlgorithm()) {
                case GeomRefinementAlgorithmEnum::None:
                    break;
                case GeomRefinementAlgorithmEnum::BeamCenter:
                    // Settings below ensure that symmetry is not "touched" by the refinement routine
                    data.crystal_system = gemmi::CrystalSystem::Triclinic;
                    data.centering = 'P';
                    // Fall through!
                case GeomRefinementAlgorithmEnum::BeamCenterSymmetry:
                    if (XtalOptimizer(data, output.spots)) {
                        experiment_copy.BeamX_pxl(data.geom.GetBeamX_pxl()).BeamY_pxl(data.geom.GetBeamY_pxl());
                        beam_center_updated = true;
                    }
                    break;
            }

            if (AnalyzeIndexing(output, experiment_copy, data.latt)) {

                float ewald_dist_cutoff = 0.001f;

                if (output.profile_radius)
                    ewald_dist_cutoff = output.profile_radius.value() * 2.0f;
                if (experiment.GetBraggIntegrationSettings().GetFixedProfileRadius_recipA())
                    ewald_dist_cutoff = experiment.GetBraggIntegrationSettings().GetFixedProfileRadius_recipA().value() * 3.0f;

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

                if (spot_finding_settings.quick_integration) {
                    auto res = BraggIntegrate2D(experiment_copy, image, data.latt,
                                                ewald_dist_cutoff, output.number);

                    constexpr size_t kMaxReflections = 10000;
                    if (res.reflections.size() > kMaxReflections) {
                        output.reflections.assign(res.reflections.begin(),
                                                  res.reflections.begin() + kMaxReflections);
                    } else
                        output.reflections = res.reflections;

                    output.b_factor = res.b_factor;
                    output.integration_Isigma = res.Isigma;
                    output.integration_logI = res.logI;
                    output.integration_one_over_d = res.one_over_d;
                }
            }
        }
    }
}