spot-finding option with I/sigma

VERSION

@@ -1 +1 @@
-1.0.0-rc.133
+1.0.0-rc.134

tools/jfjoch_process.cpp

@@ -50,6 +50,7 @@ void print_usage(Logger &logger) {
     logger.Info("   -C<cell>   Fix reference unit cell: -C\"a,b,c,alpha,beta,gamma\" (comma-separated, no spaces; quotes optional)");
     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)");
 }
 
 void trim_in_place(std::string& t) {
@@ -133,6 +134,7 @@ int main(int argc, char **argv) {
     std::optional<UnitCell> fixed_reference_unit_cell;
     bool write_output = false;
     std::optional<int64_t> max_spot_count_override;
+    float sigma_spot_finding = 3.0;
     IndexingAlgorithmEnum indexing_algorithm = IndexingAlgorithmEnum::Auto;
 
     ScaleMergeOptions::PartialityModel partiality_model = ScaleMergeOptions::PartialityModel::Fixed;
@@ -146,7 +148,7 @@ 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:W")) != -1) {
+    while ((opt = getopt(argc, argv, "o:N:s:e:vc:R::FX:xd:S:MP:AD:C:T:W")) != -1) {
         switch (opt) {
             case 'o':
                 output_prefix = optarg;
@@ -217,6 +219,10 @@ int main(int argc, char **argv) {
             case 'A':
                 anomalous_mode = true;
                 break;
+            case 'T':
+                sigma_spot_finding = atof(optarg);
+                logger.Info("Noise threshold level for spot finding set to {:.2f} sigma", sigma_spot_finding);
+                break;
             case 'C': {
                 auto uc = parse_unit_cell_arg(optarg);
                 if (!uc.has_value()) {
@@ -321,6 +327,7 @@ int main(int argc, char **argv) {
     spot_settings.enable = true;
     spot_settings.indexing = true;
     spot_settings.high_resolution_limit = d_min_spot_finding;
+    spot_settings.signal_to_noise_threshold = sigma_spot_finding;
     if (d_min_scale_merge > 0)
         spot_settings.high_resolution_limit = d_min_spot_finding;