jfjoch_process: Add photon count threshold for spot finding

docs/CHANGELOG.md

@@ -7,8 +7,8 @@ This is an UNSTABLE release. The release has significant modifications and bug f
 * jfjoch_broker: Allow for asynchronous start to allow overlapping detector configuration with other beamline preparations
 * jfjoch_broker: Goniometer axis name is converted to lowercase
 * jfjoch_broker: Fix bug, where wrong HTTP error codes were returned
-* jfjoch_broker: Improve sigma estimation during merging (K. Takaba)
-
+* jfjoch_process: Improve sigma estimation during merging (K. Takaba)
+* jfjoch_process: Modify spot finding thresholds 
 ### 1.0.0-rc.137
 This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132.
 

image_analysis/spot_finding/SpotFindingSettings.h

@@ -5,6 +5,7 @@
 #define JUNGFRAUJOCH_SPOTFINDINGSETTINGS_H
 
 #include <optional>
+#include <cstdint>
 
 struct SpotFindingSettings {
     bool enable = true;

tools/jfjoch_process.cpp

@@ -51,6 +51,7 @@ void print_usage(Logger &logger) {
     logger.Info("   -c<num>    Max spot count (default: 250)");
     logger.Info("   -W         HDF5 file with analysis results is written");
     logger.Info("   -T<num>    Noise sigma level for spot finding (default: 3.0)");
+    logger.Info("   -t<num>    Photon count threshold for spot finding (default: 10)");
 }
 
 void trim_in_place(std::string& t) {
@@ -135,6 +136,8 @@ int main(int argc, char **argv) {
     bool write_output = false;
     std::optional<int64_t> max_spot_count_override;
     float sigma_spot_finding = 3.0;
+    int64_t photon_count_threshold_spot_finding = 10;
+
     IndexingAlgorithmEnum indexing_algorithm = IndexingAlgorithmEnum::Auto;
 
     ScaleMergeOptions::PartialityModel partiality_model = ScaleMergeOptions::PartialityModel::Fixed;
@@ -148,7 +151,7 @@ int main(int argc, char **argv) {
     }
 
     int opt;
-    while ((opt = getopt(argc, argv, "o:N:s:e:vc:R::FX:xd:S:MP:AD:C:T:W")) != -1) {
+    while ((opt = getopt(argc, argv, "o:N:s:e:vc:R::FX:xd:S:MP:AD:C:T:t:W")) != -1) {
         switch (opt) {
             case 'o':
                 output_prefix = optarg;
@@ -223,6 +226,10 @@ int main(int argc, char **argv) {
                 sigma_spot_finding = atof(optarg);
                 logger.Info("Noise threshold level for spot finding set to {:.2f} sigma", sigma_spot_finding);
                 break;
+            case 't':
+                photon_count_threshold_spot_finding = atoi(optarg);
+                logger.Info("Photon-count threshold level for spot finding set to {:d}", photon_count_threshold_spot_finding);
+                break;
             case 'C': {
                 auto uc = parse_unit_cell_arg(optarg);
                 if (!uc.has_value()) {
@@ -328,6 +335,7 @@ int main(int argc, char **argv) {
     spot_settings.indexing = true;
     spot_settings.high_resolution_limit = d_min_spot_finding;
     spot_settings.signal_to_noise_threshold = sigma_spot_finding;
+    spot_settings.photon_count_threshold = photon_count_threshold_spot_finding;
     if (d_min_scale_merge > 0)
         spot_settings.high_resolution_limit = d_min_spot_finding;