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

tests/JFJochReceiverProcessingTest.cpp

@@ -375,6 +375,8 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate", "[JFJoc
     CHECK(receiver_out.status.images_sent == experiment.GetImageNum());
     CHECK(!receiver_out.status.cancelled);
 
+    logger.Info("Processing time {}", receiver_out.processing_time.processing);
+
     // No progress value at the end of measurement
     REQUIRE(!service.GetProgress().has_value());
     auto b_factor = service.GetDataProcessingPlot(
@@ -386,6 +388,82 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate", "[JFJoc
     REQUIRE_NOTHROW(writer_future.get());
 }
 
+TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate_no_spots", "[JFJochReceiver]") {
+    Logger logger(Catch::getResultCapture().getCurrentTestName());
+
+    RegisterHDF5Filter();
+
+    const uint16_t nthreads = 4;
+
+    DiffractionExperiment experiment(DetJF4M());
+    experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
+            .FilePrefix("lyso_test").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
+            .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
+            .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
+    PixelMask pixel_mask(experiment);
+
+    // Load example image
+    HDF5ReadOnlyFile data("../../tests/test_data/compression_benchmark.h5");
+    HDF5DataSet dataset(data, "/entry/data/data");
+    HDF5DataSpace file_space(dataset);
+
+    REQUIRE(file_space.GetDimensions()[2] == experiment.GetXPixelsNum());
+    REQUIRE(file_space.GetDimensions()[1] == experiment.GetYPixelsNum());
+    std::vector<int16_t> image_conv (file_space.GetDimensions()[1] * file_space.GetDimensions()[2]);
+
+    std::vector<hsize_t> start = {4,0,0};
+    std::vector<hsize_t> file_size = {1, file_space.GetDimensions()[1], file_space.GetDimensions()[2]};
+    dataset.ReadVector(image_conv, start, file_size);
+
+    std::vector<int16_t> image_raw_geom(experiment.GetModulesNum() * RAW_MODULE_SIZE);
+    ConvertedToRawGeometry(experiment, image_raw_geom.data(), image_conv.data());
+    logger.Info("Loaded image");
+
+    // Setup acquisition device
+    AcquisitionDeviceGroup aq_devices;
+    std::unique_ptr<HLSSimulatedDevice> test = std::make_unique<HLSSimulatedDevice>(0, 64);
+    for (int m = 0; m < experiment.GetModulesNum(); m++)
+        test->SetInternalGeneratorFrame((uint16_t *) image_raw_geom.data() + m * RAW_MODULE_SIZE, m);
+
+    aq_devices.Add(std::move(test));
+
+    ZMQStream2Pusher pusher({"ipc://*"});
+    pusher.WriterNotificationSocket("ipc://*");
+
+    ZMQImagePuller puller(pusher.GetAddress()[0]);
+    StreamWriter writer(logger, puller);
+    auto writer_future = std::async(std::launch::async, &StreamWriter::Run, &writer);
+
+    JFJochReceiverService service(aq_devices, logger, pusher);
+    service.NumThreads(nthreads);
+    service.Indexing(experiment.GetIndexingSettings());
+
+    // No progress value at the start of measurement
+    REQUIRE(!service.GetProgress().has_value());
+
+    SpotFindingSettings settings = DiffractionExperiment::DefaultDataProcessingSettings();
+    settings.signal_to_noise_threshold = 20; // make sure there are zero spots possible
+    settings.photon_count_threshold = 10000;
+    settings.min_pix_per_spot = 5;
+    settings.max_pix_per_spot = 200;
+    settings.high_resolution_limit = 2.0;
+    settings.low_resolution_limit = 50.0;
+    settings.quick_integration = true;
+    service.SetSpotFindingSettings(settings);
+
+    service.Start(experiment, pixel_mask, nullptr);
+    auto receiver_out = service.Stop();
+
+    CHECK(receiver_out.efficiency == 1.0);
+    REQUIRE(receiver_out.status.indexing_rate);
+    CHECK(receiver_out.status.indexing_rate.value() == 0.0);
+    CHECK(receiver_out.status.images_sent == experiment.GetImageNum());
+    CHECK(!receiver_out.status.cancelled);
+    logger.Info("Processing time {}", receiver_out.processing_time.processing);
+    // No progress value at the end of measurement
+    REQUIRE(!service.GetProgress().has_value());
+    REQUIRE_NOTHROW(writer_future.get());
+}
 
 TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_azint_2d", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());