v1.0.0-rc.139 (#49)

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.

* jfjoch_broker: Further reduce startup time for DECTRIS detectors by selectively modifying SIMPLON parameters on `/start`
* jfjoch_broker: Further reduce startup time for DECTRIS detectors by not setting beam center and detector distance via SIMPLON API on '/start'
* jfjoch_broker: Add an extra message to ZeroMQ puller ready to monitor Lite worklow preparation time
* jfjoch_broker: Image buffer configuration is postponed for Lite receiver flow till start message is received
* jfjoch_broker: Use nanoseconds internally for frame/image/readout time
* jfjoch_broker: Extra messages added for receiver operation (to be removed after debugging finished)
* jfojch_broker: Improve profiling of different data analysis steps
* jfjoch_broker: Record integration reflection count
* jfjoch_broker: Fix bug where ZeroMQ preview frequency was confusing time units (micro vs. milliseconds)
* jfjoch_broker: Fix bug where '/wait_till_done' got deadlocked
* jfjoch_writer: Fix confusion between NaN and zero in floating-point datasets

**Breaking changes**: detector definition is now using nanoseconds to define minimum frame time, minimum count time and readout time.

Reviewed-on: #49

writer/HDF5DataFilePluginMX.cpp

@@ -93,16 +93,7 @@ void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg,
     spot_count_ice.reserve(images_per_file);
     spot_count_indexed.reserve(images_per_file);
     spot_count_low_res.reserve(images_per_file);
-
-    indexing_time.reserve(images_per_file);
-    spot_finding_time.reserve(images_per_file);
-    integration_time.reserve(images_per_file);
-    refinement_time.reserve(images_per_file);
-    processing_time.reserve(images_per_file);
-    bragg_prediction_time.reserve(images_per_file);
-    preprocessing_time.reserve(images_per_file);
-    compression_time.reserve(images_per_file);
-    azint_time.reserve(images_per_file);
+    integrated_reflections.reserve(images_per_file);
 }
 
 void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number) {
@@ -127,7 +118,7 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
         if (indexing)
             spot_indexed.resize(max_spots * (max_image_number + 1));
         if (indexing)
-            indexed_lattice.resize((max_image_number + 1) * 9);
+            indexed_lattice.resize((max_image_number + 1) * 9, NAN);
     }
 
     uint32_t spot_cnt = std::min(msg.spots.size(), max_spots);
@@ -152,16 +143,6 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
     spot_count_ice[image_number] = msg.spot_count_ice_rings.value_or(0);
     spot_count_low_res[image_number] = msg.spot_count_low_res.value_or(0);
 
-    indexing_time[image_number] = msg.indexing_time_s.value_or(NAN);
-    spot_finding_time[image_number] = msg.spot_finding_time_s.value_or(NAN);
-    integration_time[image_number] = msg.integration_time_s.value_or(NAN);
-    refinement_time[image_number] = msg.refinement_time_s.value_or(NAN);
-    processing_time[image_number] = msg.processing_time_s.value_or(NAN);
-    bragg_prediction_time[image_number] = msg.bragg_prediction_time_s.value_or(NAN);
-    preprocessing_time[image_number] = msg.preprocessing_time_s.value_or(NAN);
-    compression_time[image_number] = msg.compression_time_s.value_or(NAN);
-    azint_time[image_number] = msg.azint_time_s.value_or(NAN);
-
     if (indexing) {
         indexed[image_number] = msg.indexing_result.value_or(0);
         profile_radius[image_number] = msg.profile_radius.value_or(NAN);
@@ -171,6 +152,7 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
         beam_corr_x[image_number] = msg.beam_corr_x.value_or(NAN);
         beam_corr_y[image_number] = msg.beam_corr_y.value_or(NAN);
         spot_count_indexed[image_number] = msg.spot_count_indexed.value_or(0);
+        integrated_reflections[image_number] = msg.integrated_reflections.value_or(0);
 
         if (msg.indexing_lattice) {
             auto tmp = msg.indexing_lattice->GetVector();
@@ -212,25 +194,6 @@ void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
         }
     }
 
-    if (!spot_finding_time.empty())
-        data_file.SaveVector("/entry/MX/spotFindingTime", spot_finding_time.vec())->Units("s");
-    if (!indexing_time.empty())
-        data_file.SaveVector("/entry/MX/indexingTime", indexing_time.vec())->Units("s");
-    if (!integration_time.empty())
-        data_file.SaveVector("/entry/MX/integrationTime", integration_time.vec())->Units("s");
-    if (!refinement_time.empty())
-        data_file.SaveVector("/entry/MX/refinementTime", refinement_time.vec())->Units("s");
-    if (!processing_time.empty())
-        data_file.SaveVector("/entry/MX/processingTime", processing_time.vec())->Units("s");
-    if (!bragg_prediction_time.empty())
-        data_file.SaveVector("/entry/MX/braggPredictionTime", bragg_prediction_time.vec())->Units("s");
-    if (!preprocessing_time.empty())
-        data_file.SaveVector("/entry/MX/preprocessingTime", preprocessing_time.vec())->Units("s");
-    if (!compression_time.empty())
-        data_file.SaveVector("/entry/MX/compressionTime", compression_time.vec())->Units("s");
-    if (!azint_time.empty())
-        data_file.SaveVector("/entry/MX/azIntTime", azint_time.vec())->Units("s");
-
     if (!strong_pixel_count.empty())
         data_file.SaveVector("/entry/MX/strongPixels", strong_pixel_count.vec());
 
@@ -267,4 +230,6 @@ void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
         data_file.SaveVector("/entry/MX/bravais_lattice", bravais_lattice.vec());
     if (!resolution_estimate.empty())
         data_file.SaveVector("/entry/MX/resolutionEstimate", resolution_estimate.vec())->Units("Angstrom");
+    if (!integrated_reflections.empty())
+        data_file.SaveVector("/entry/MX/integratedReflections", integrated_reflections.vec());
 }