jfjoch_process: Adapt behavior to write file with processing results and link to original images (to be tested)

tools/jfjoch_process.cpp

@@ -376,15 +376,6 @@ int main(int argc, char **argv) {
     start_message.write_images = write_output;
     start_message.file_format = FileWriterFormat::NXmxIntegrated;
 
-    std::unique_ptr<FileWriter> writer;
-    try {
-        if (!output_prefix.empty())
-            writer = std::make_unique<FileWriter>(start_message);
-    } catch (const std::exception &e) {
-        logger.Error("Failed to initialize file writer: {}", e.what());
-        exit(EXIT_FAILURE);
-    }
-
     // 4. Processing Setup
     int total_images_in_file = reader.GetNumberOfImages();
     if (end_image < 0 || end_image > total_images_in_file)
@@ -405,6 +396,22 @@ int main(int argc, char **argv) {
     std::atomic<uint64_t> total_uncompressed_bytes = 0;
     std::atomic<uint64_t> max_image_number_sent = 0;
 
+    start_message.file_format = FileWriterFormat::NXmxIntegrated;
+    start_message.write_master_file = true;
+    start_message.write_images = false;
+    start_message.number_of_images = images_to_process;
+    start_message.images_per_file = images_to_process;
+    start_message.hdf5_source_data = reader.GetHDF5DataSource(start_image, images_to_process);
+
+    std::unique_ptr<FileWriter> writer;
+    try {
+        if (!output_prefix.empty())
+            writer = std::make_unique<FileWriter>(start_message);
+    } catch (const std::exception &e) {
+        logger.Error("Failed to initialize file writer: {}", e.what());
+        exit(EXIT_FAILURE);
+    }
+
     // Mimic JFJochReceiver lattice handling (IndexAndRefine handles the logic per thread,
     // but we need a central accumulator or use the pool's functionality if IndexAndRefine wraps it)
     // Here we will use per-thread IndexAndRefine which uses the shared thread pool.