From 87a9a0b745fcb4ce3fca20942b1d40ca9d85c1cb Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Sat, 29 Nov 2025 14:07:24 +0100
Subject: [PATCH] SpotAnalyze: Extract spot analysis function into a dedicated

---
 image_analysis/SpotAnalyze.cpp            | 23 ++---------------
 image_analysis/spot_finding/SpotUtils.cpp | 30 ++++++++++++++++++++++-
 image_analysis/spot_finding/SpotUtils.h   |  3 +++
 3 files changed, 34 insertions(+), 22 deletions(-)

diff --git a/image_analysis/SpotAnalyze.cpp b/image_analysis/SpotAnalyze.cpp
index d3fd817e..ea71fb6e 100644
--- a/image_analysis/SpotAnalyze.cpp
+++ b/image_analysis/SpotAnalyze.cpp
@@ -18,27 +18,9 @@ void SpotAnalyze(const DiffractionExperiment &experiment,
                  BraggPrediction &prediction,
                  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 (spot_finding_settings.high_res_gap_Q_recipA.has_value())
-        FilterSpuriousHighResolutionSpots(spots_out, spot_finding_settings.high_res_gap_Q_recipA.value());
-
-    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);
-
-    GenerateSpotPlot(output, spot_finding_settings.high_resolution_limit);
-
-    output.resolution_estimate = GetResolution(spots_out);
-
-    FilterSpotsByCount(spots_out, experiment.GetMaxSpotCount());
-
-    output.spots = spots_out;
+    SpotAnalyze(experiment, spot_finding_settings, spots, output);
 
     if ((indexer != nullptr) && spot_finding_settings.indexing) {
         std::vector<Coord> recip;
@@ -49,8 +31,7 @@ void SpotAnalyze(const DiffractionExperiment &experiment,
                 recip.push_back(i.ReciprocalCoord(geom));
         }
 
-        auto latt_f = indexer->Run(experiment, recip);
-        auto indexer_result = latt_f.get();
+        auto indexer_result = indexer->Run(experiment, recip).get();
         output.indexing_time_s = indexer_result.indexing_time_s;
 
         if (indexer_result.lattice.empty())
diff --git a/image_analysis/spot_finding/SpotUtils.cpp b/image_analysis/spot_finding/SpotUtils.cpp
index 48ee0e86..ad1fb119 100644
--- a/image_analysis/spot_finding/SpotUtils.cpp
+++ b/image_analysis/spot_finding/SpotUtils.cpp
@@ -50,7 +50,7 @@ void FilterSpotsByCount(std::vector<SpotToSave> &input, int64_t count) {
 }
 
 void FilterSpuriousHighResolutionSpots(std::vector<SpotToSave> &spots, float threshold) {
-    std::ranges::sort(spots, [] (SpotToSave &a, SpotToSave &b) {
+    std::ranges::sort(spots, [](SpotToSave &a, SpotToSave &b) {
         return a.d_A > b.d_A;
     });
 
@@ -125,3 +125,31 @@ void GenerateSpotPlot(DataMessage &msg, float d_min_A) {
     msg.spot_plot_intensity = result;
     msg.spot_plot_count = count;
 }
+
+void SpotAnalyze(const DiffractionExperiment &experiment,
+                 const SpotFindingSettings &spot_finding_settings,
+                 const std::vector<DiffractionSpot> &spots,
+                 DataMessage &output) {
+    auto geom = experiment.GetDiffractionGeometry();
+
+    std::vector<SpotToSave> spots_out;
+
+    for (const auto &spot: spots)
+        spots_out.push_back(spot.Export(geom));
+
+    if (spot_finding_settings.high_res_gap_Q_recipA.has_value())
+        FilterSpuriousHighResolutionSpots(spots_out, spot_finding_settings.high_res_gap_Q_recipA.value());
+
+    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);
+
+    GenerateSpotPlot(output, spot_finding_settings.high_resolution_limit);
+
+    output.resolution_estimate = GetResolution(spots_out);
+
+    FilterSpotsByCount(spots_out, experiment.GetMaxSpotCount());
+
+    output.spots = spots_out;
+}
diff --git a/image_analysis/spot_finding/SpotUtils.h b/image_analysis/spot_finding/SpotUtils.h
index bfe880d5..e07c7e5c 100644
--- a/image_analysis/spot_finding/SpotUtils.h
+++ b/image_analysis/spot_finding/SpotUtils.h
@@ -28,4 +28,7 @@ void FilterSpuriousHighResolutionSpots(std::vector<SpotToSave> &spots, float thr
 // For 20 spots or more - take the 95% percentile best high resolution spot
 std::optional<float> GetResolution(const std::vector<SpotToSave> &spots);
 
+void SpotAnalyze(const DiffractionExperiment &experiment, const SpotFindingSettings &settings,
+                 const std::vector<DiffractionSpot> &spots, DataMessage &message);
+
 #endif //JFJOCH_SPOTANALYSIS_H