Add deep learning resolution estimation model from Stanford

2024-02-08 20:15:29 +01:00
parent 1b4ab88f54
commit 8dcecb9685
49 changed files with 650 additions and 194 deletions
--- a/tests/JFJochReceiverProcessingTest.cpp
+++ b/tests/JFJochReceiverProcessingTest.cpp
@@ -173,3 +173,65 @@ TEST_CASE("GenerateResolutionMap") {
    WriteTIFFToFile("ResolutionMap.tiff", spot_finder_resolution_map_int_conv.data(), experiment.GetXPixelsNum(),
                    experiment.GetYPixelsNum(), 4);
 }
+
+TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_resolution", "[JFJochReceiver]") {
+    Logger logger("JFJochIntegrationTest_ZMQ_lysozyme_resolution");
+
+    RegisterHDF5Filter();
+
+    const uint16_t nthreads = 4;
+
+    DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
+    experiment.ImagesPerTrigger(5).NumTriggers(1).DataFileCount(1).UseInternalPacketGenerator(true)
+            .FilePrefix("lyso_test_resolution").ConversionOnFPGA(false)
+            .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).PhotonEnergy_keV(12.4)
+            .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90})
+            .NeuralNetModelPath("../../resonet/traced_resnet_model.pt");
+
+    // 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);
+    test->SetInternalGeneratorFrame(image_raw_geom);
+    aq_devices.Add(std::move(test));
+
+    JFCalibration calib(experiment);
+    HDF5ImagePusher pusher;
+
+    ZMQContext context;
+    context.NumThreads(4);
+
+    JFJochReceiverService service(aq_devices, logger, pusher);
+    service.NumThreads(nthreads);
+
+    SpotFindingSettings settings = DiffractionExperiment::DefaultDataProcessingSettings();
+    settings.signal_to_noise_threshold = 2.5;
+    settings.photon_count_threshold = 5;
+    settings.min_pix_per_spot = 1;
+    settings.max_pix_per_spot = 200;
+    service.SetSpotFindingSettings(settings);
+
+    service.Start(experiment, nullptr);
+    auto receiver_out = service.Stop();
+
+    CHECK(receiver_out.efficiency == 1.0);
+    CHECK(receiver_out.status.indexing_rate == 1.0);
+    CHECK(receiver_out.status.images_sent == experiment.GetImageNum());
+    CHECK(!receiver_out.status.cancelled);
+}