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v1.0.0-rc.40

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leonarski_f
2025-05-28 18:49:27 +02:00
parent aaae74e70b
commit 53c90ee5d8
340 changed files with 9583 additions and 5919 deletions
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tests/JFJochReceiverProcessingTest.cpp
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@@ -16,7 +16,7 @@
#include "../image_pusher/HDF5FilePusher.h"
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index");
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -102,8 +102,200 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT", "[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_fft").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
.OverwriteExistingFiles(true)
.DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
.IndexingAlgorithm(IndexingAlgorithmEnum::FFT)
.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);
// No progress value at the start of measurement
REQUIRE(!service.GetProgress().has_value());
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;
settings.high_resolution_limit = 2.0;
settings.low_resolution_limit = 50.0;
service.SetSpotFindingSettings(settings);
service.Start(experiment, pixel_mask, nullptr);
auto receiver_out = service.Stop();
std::string jpeg;
PreviewJPEGSettings jpeg_settings{
.saturation_value = 10,
.jpeg_quality = 100,
.show_spots = true
};
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
CHECK(receiver_out.efficiency == 1.0);
REQUIRE(receiver_out.status.indexing_rate);
CHECK(receiver_out.status.indexing_rate.value() == 1.0);
CHECK(receiver_out.status.images_sent == experiment.GetImageNum());
CHECK(!receiver_out.status.cancelled);
// No progress value at the end of measurement
REQUIRE(!service.GetProgress().has_value());
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_grid", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
const uint16_t nthreads = 4;
GridScanSettings grid_scan(3, 10.0f, 25.0f, false, true);
DatasetSettings dataset_settings;
dataset_settings.ImagesPerTrigger(7).NumTriggers(1).DetectorDistance_mm(75)
.BeamY_pxl(1136).BeamX_pxl(1090)
.PhotonEnergy_keV(12.4).GridScan(grid_scan)
.SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
DiffractionExperiment experiment(DetJF4M());
experiment.UseInternalPacketGenerator(true).ImagesPerFile(2).ImportDatasetSettings(dataset_settings)
.FilePrefix("lyso_test").JungfrauConvPhotonCnt(false)
.SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true);
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);
// No progress value at the start of measurement
REQUIRE(!service.GetProgress().has_value());
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;
settings.high_resolution_limit = 2.0;
settings.low_resolution_limit = 50.0;
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() == 1.0);
CHECK(receiver_out.status.images_sent == experiment.GetImageNum());
CHECK(!receiver_out.status.cancelled);
auto grid_scan_out = service.GetDataProcessingPlot(
PlotRequest{.type = PlotType::IndexingRate, .experimental_coord = true});
CHECK(grid_scan_out.GetUnits() == MultiLinePlotUnits::Grid_um);
REQUIRE(grid_scan_out.GetPlots().size() == 1);
REQUIRE(grid_scan_out.GetPlots()[0].z.size() == 7);
CHECK(grid_scan_out.GetPlots()[0].z[0] == 1.0f);
CHECK(grid_scan_out.GetPlots()[0].z[1] == 1.0f);
CHECK(grid_scan_out.GetPlots()[0].z[2] == 1.0f);
CHECK(grid_scan_out.GetPlots()[0].z[3] == 1.0f);
CHECK(grid_scan_out.GetPlots()[0].z[4] == 1.0f);
CHECK(grid_scan_out.GetPlots()[0].z[5] == 1.0f);
CHECK(grid_scan_out.GetPlots()[0].z[6] == 1.0f);
CHECK(grid_scan_out.GetPlots()[0].x[5] == 1.5 * 10.0f);
CHECK(grid_scan_out.GetPlots()[0].y[5] == 2.5 * 25.0f);
CHECK(grid_scan_out.GetPlots()[0].x[6] == 2.5 * 10.0f);
CHECK(grid_scan_out.GetPlots()[0].y[6] == 0.5 * 25.0f);
// No progress value at the end of measurement
REQUIRE(!service.GetProgress().has_value());
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_32", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index");
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -189,9 +381,8 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_32", "[JFJochReceiv
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2");
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -289,12 +480,13 @@ TEST_CASE("GenerateResolutionMap") {
RawToConvertedGeometry(experiment, spot_finder_resolution_map_int_conv.data(), spot_finder_resolution_map_int.data());
WriteTIFFToFile("ResolutionMap.tiff", spot_finder_resolution_map_int_conv.data(), experiment.GetXPixelsNum(),
experiment.GetYPixelsNum(), 4);
CompressedImage image(spot_finder_resolution_map_int_conv, experiment.GetXPixelsNum(),
experiment.GetYPixelsNum() );
WriteTIFFToFile("ResolutionMap.tiff", image);
}
TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_ZMQ_ROI");
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -392,13 +584,13 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
auto plot = service.GetDataProcessingPlot(PlotRequest{.type = PlotType::ROISum, .binning = 1});
REQUIRE(plot.size() == 3);
CHECK(plot[0].title == "beam");
REQUIRE(!plot[0].x.empty());
CHECK(plot[0].x[0] == 0);
CHECK(plot[0].y[0] == roi_value);
CHECK(plot[1].title == "roi1");
CHECK(plot[2].title == "roi2");
REQUIRE(plot.GetPlots().size() == 3);
CHECK(plot.GetPlots()[0].title == "beam");
REQUIRE(!plot.GetPlots()[0].x.empty());
CHECK(plot.GetPlots()[0].x[0] == 0);
CHECK(plot.GetPlots()[0].y[0] == roi_value);
CHECK(plot.GetPlots()[1].title == "roi1");
CHECK(plot.GetPlots()[2].title == "roi2");
CHECK(receiver_out.status.roi_beam_sum == roi_value);
CHECK(receiver_out.status.roi_beam_npixel == pixels);
@@ -415,7 +607,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
}
TEST_CASE("JFJochIntegrationTest_ZMQPreview", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_ZMQPreview");
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -478,7 +670,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQPreview", "[JFJochReceiver]") {
}
TEST_CASE("JFJochIntegrationTest_ZMQMetadata", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_ZMQMetadata");
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -536,7 +728,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQMetadata", "[JFJochReceiver]") {
}
TEST_CASE("JFJochIntegrationTest_HDF5FilePusher", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_HDF5FilePusher");
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -569,7 +761,7 @@ TEST_CASE("JFJochIntegrationTest_HDF5FilePusher", "[JFJochReceiver]") {
}
TEST_CASE("JFJochIntegrationTest_HDF5FilePusher_Raw", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_HDF5FilePusher_Raw");
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();