v1.0.0-rc.71

2025-08-28 07:07:01 +02:00
parent 4e3b54f0b0
commit dba807fadd
185 changed files with 267 additions and 1649 deletions
--- a/image_analysis/SpotAnalyze.cpp
+++ b/image_analysis/SpotAnalyze.cpp
@@ -0,0 +1,70 @@
+// 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/SpotAnalysis.h"
+#include "spot_finding/StrongPixelSet.h"
+#include "bragg_integration/BraggIntegrate2D.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));
+
+    CountSpots(output, spots_out, spot_finding_settings.cutoff_spot_count_low_res);
+
+    FilterSpotsByCount(experiment.GetMaxSpotCount(), spots_out, output.spots);
+
+    if ((indexer != nullptr) && spot_finding_settings.indexing) {
+        auto latt_f = indexer->Run(experiment, output);
+        auto latt = latt_f.get();
+
+        if (latt) {
+            DiffractionExperiment experiment_copy(experiment);
+            XtalOptimizerData data{
+                    .geom = experiment_copy.GetDiffractionGeometry(),
+                    .latt = latt.value()
+            };
+            switch (experiment.GetIndexingSettings().GetGeomRefinementAlgorithm()) {
+                case GeomRefinementAlgorithmEnum::None:
+                    break;
+                case GeomRefinementAlgorithmEnum::BeamCenter:
+                    XtalOptimizer(data, output.spots, false);
+                    experiment_copy.BeamX_pxl(data.geom.GetBeamX_pxl()).BeamY_pxl(data.geom.GetBeamY_pxl());
+                    output.beam_center_x = data.geom.GetBeamX_pxl();
+                    output.beam_center_y = data.geom.GetBeamY_pxl();
+                    latt = data.latt;
+                    output.indexing_lattice = data.latt;
+                    break;
+                case GeomRefinementAlgorithmEnum::BeamCenterTetragonal:
+                    XtalOptimizer(data, output.spots, true);
+                    experiment_copy.BeamX_pxl(data.geom.GetBeamX_pxl()).BeamY_pxl(data.geom.GetBeamY_pxl());
+                    output.beam_center_x = data.geom.GetBeamX_pxl();
+                    output.beam_center_y = data.geom.GetBeamY_pxl();
+                    latt = data.latt;
+                    output.indexing_lattice = data.latt;
+                    break;
+            }
+
+            if (spot_finding_settings.quick_integration) {
+                auto res = BraggIntegrate2D(experiment_copy, image, latt.value());
+
+                float res_estimate = sqrtf((res.b_factor.value_or(12.0f) - 12.0f) / 4.0f);
+                if (res_estimate > 1.0 && res_estimate < 4.0)
+                    output.resolution_estimate = res_estimate;
+                output.reflections = res.reflections;
+                output.b_factor = res.b_factor;
+            }
+        }
+    }
+}