v1.0.0-rc.130 (#37)

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.124.

* jfjoch_broker: Rotation indexer has two retries if failes
* jfjoch_broker: Rotation indexer handles small number of rotation images (like test shot)
* jfjoch_broker: Integration calculates background mask based on R2 radius
* jfjoch_process: HDF5 files are not saved by default

Reviewed-on: #37

tools/jfjoch_process.cpp

@@ -45,6 +45,7 @@ void print_usage(Logger &logger) {
     logger.Info("   -P<txt>    Partiality refinement fixed|rot|unity (default: fixed)");
     logger.Info("   -A         Anomalous mode (don't merge Friedel pairs)");
     logger.Info("   -C<cell>   Fix reference unit cell: -C\"a,b,c,alpha,beta,gamma\" (comma-separated, no spaces; quotes optional)");
+    logger.Info("   -W         HDF5 file with analysis results is written");
 }
 
 void trim_in_place(std::string& t) {
@@ -127,6 +128,7 @@ int main(int argc, char **argv) {
     bool anomalous_mode = false;
     std::optional<int> space_group_number;
     std::optional<UnitCell> fixed_reference_unit_cell;
+    bool write_output = false;
 
     ScaleMergeOptions::PartialityModel partiality_model = ScaleMergeOptions::PartialityModel::Fixed;
 
@@ -139,7 +141,7 @@ int main(int argc, char **argv) {
     }
 
     int opt;
-    while ((opt = getopt(argc, argv, "o:N:s:e:vR::Fxd:S:MP:AD:C:")) != -1) {
+    while ((opt = getopt(argc, argv, "o:N:s:e:vR::Fxd:S:MP:AD:C:W")) != -1) {
         switch (opt) {
             case 'o':
                 output_prefix = optarg;
@@ -153,6 +155,9 @@ int main(int argc, char **argv) {
             case 'e':
                 end_image = atoi(optarg);
                 break;
+            case 'W':
+                write_output = true;
+                break;
             case 'v':
                 verbose = true;
                 break;
@@ -316,7 +321,8 @@ int main(int argc, char **argv) {
 
     std::unique_ptr<FileWriter> writer;
     try {
-        writer = std::make_unique<FileWriter>(start_message);
+        if (write_output)
+            writer = std::make_unique<FileWriter>(start_message);
     } catch (const std::exception &e) {
         logger.Error("Failed to initialize file writer: {}", e.what());
         exit(EXIT_FAILURE);
@@ -434,7 +440,8 @@ int main(int argc, char **argv) {
                 std::lock_guard<std::mutex> lock(plots_mutex);
                 plots.Add(msg, profile);
                 // Write Result
-                writer->Write(msg);
+                if (writer)
+                    writer->Write(msg);
             }
 
             // Update max sent tracking
@@ -655,8 +662,10 @@ int main(int argc, char **argv) {
     }
 
     // Write End Message
-    writer->WriteHDF5(end_msg);
-    auto stats = writer->Finalize();
+    if (writer) {
+        writer->WriteHDF5(end_msg);
+        auto stats = writer->Finalize();
+    }
 
     // 6. Report Statistics to Console
     double processing_time = std::chrono::duration<double>(end_time - start_time).count();
@@ -667,7 +676,6 @@ int main(int argc, char **argv) {
     logger.Info("Processing time: {:.2f} s", processing_time);
     logger.Info("Frame rate:      {:.2f} Hz", frame_rate);
     logger.Info("Total throughput:{:.2f} MB/s", throughput_MBs);
-    logger.Info("Images written:  {}", stats.size());
 
     // Print extended stats similar to Receiver
     if (!end_msg.indexing_rate.has_value()) {
@@ -691,12 +699,4 @@ int main(int argc, char **argv) {
         logger.Info("Lattice:         a={:.2f} b={:.2f} c={:.2f} alpha={:.2f} beta={:.2f} gamma={:.2f}",
                     uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
     }
-
-    if (stats.empty()) {
-        logger.Info("Analysis finished with warnings (no files written)");
-        exit(EXIT_FAILURE);
-    } else {
-        logger.Info("Analysis successfully finished");
-        exit(EXIT_SUCCESS);
-    }
 }