jfjoch_process: Handle pixel mask correctly in jfjoch_process

tools/jfjoch_process.cpp

@@ -104,6 +104,7 @@ int main(int argc, char **argv) {
     DiffractionExperiment experiment(dataset->experiment);
     experiment.FilePrefix(output_prefix);
     experiment.Mode(DetectorMode::Standard); // Ensure full image analysis
+    experiment.PixelSigned(false);
 
     // Configure Indexing
     IndexingSettings indexing_settings;
@@ -117,8 +118,8 @@ int main(int argc, char **argv) {
     spot_settings.indexing = true;
 
     // Initialize Analysis Components
-    // Note: dataset->pixel_mask might need conversion depending on type, assuming it fits constructor
-    PixelMask pixel_mask(experiment);
+    PixelMask pixel_mask = dataset->pixel_mask;
+
     // If dataset has a mask you wish to use, you might need to load it into pixel_mask here
     // e.g. pixel_mask.LoadUserMask(dataset->pixel_mask, ...);
 
@@ -135,6 +136,11 @@ int main(int argc, char **argv) {
     start_message.arm_date = dataset->arm_date; // Use original arm date
     start_message.az_int_bin_to_q = mapping.GetBinToQ();
     start_message.az_int_q_bin_count = mapping.GetQBinCount();
+    if (mapping.GetAzimuthalBinCount() > 1)
+        start_message.az_int_bin_to_phi = mapping.GetBinToPhi();
+
+    start_message.pixel_mask["default"] = pixel_mask.GetMask(experiment);
+    start_message.max_spot_count = experiment.GetMaxSpotCount();
 
     std::unique_ptr<FileWriter> writer;
     try {