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v1.0.0-rc.36

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leonarski_f
2025-05-05 19:32:22 +02:00
parent 759243d1bf
commit 040cf08386
333 changed files with 22724 additions and 15251 deletions
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tests/JFJochReceiverProcessingTest.cpp
+122 -23
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@@ -9,9 +9,7 @@
#include "../acquisition_device/HLSSimulatedDevice.h"
#include "../writer/HDF5Objects.h"
#include "../receiver/JFJochReceiverService.h"
#include "../common/DiffractionGeometry.h"
#include "../preview/JFJochTIFF.h"
#include "../common/ZMQWrappers.h"
#include "../image_pusher/ZMQStream2Pusher.h"
#include "../writer/StreamWriter.h"
#include "../image_pusher/NonePusher.h"
@@ -24,9 +22,9 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
const uint16_t nthreads = 4;
DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test").JungfrauConvPhotonCnt(false).HDF5MasterFormatVersion(FileWriterFileFormat::NXmxVDS).OverwriteExistingFiles(true)
.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);
@@ -59,7 +57,8 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
ZMQStream2Pusher pusher({"ipc://*"});
pusher.WriterNotificationSocket("ipc://*");
StreamWriter writer(logger, pusher.GetAddress()[0]);
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);
@@ -86,7 +85,8 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
.jpeg_quality = 100,
.show_spots = true
};
REQUIRE_NOTHROW(jpeg = service.GetJPEG(jpeg_settings));
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());
@@ -102,6 +102,94 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_32", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index");
RegisterHDF5Filter();
const uint16_t nthreads = 4;
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_32").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxLegacy).OverwriteExistingFiles(true)
.DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4).BitDepthImage(32).PixelSigned(true)
.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_min_pix_2", "[JFJochReceiver]") {
Logger logger("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2");
@@ -109,9 +197,10 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
const uint16_t nthreads = 4;
DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).OverwriteExistingFiles(true)
.FilePrefix("lyso_test_min_pix_2").JungfrauConvPhotonCnt(false).HDF5MasterFormatVersion(FileWriterFileFormat::NXmxVDS)
.FilePrefix("lyso_test_min_pix_2").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
FileWriterFormat::NXmxVDS)
.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})
.PixelSigned(true);
@@ -142,7 +231,8 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
aq_devices.Add(std::move(test));
ZMQStream2Pusher pusher({"ipc://*"});
StreamWriter writer(logger, pusher.GetAddress()[0]);
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);
@@ -158,16 +248,20 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
service.Start(experiment, pixel_mask, nullptr);
auto receiver_out = service.Stop();
std::string jpeg;
std::string jpeg, jpeg_indexed;
PreviewJPEGSettings jpeg_settings{
.saturation_value = 10,
.jpeg_quality = 100,
.show_spots = true
};
REQUIRE_NOTHROW(jpeg = service.GetJPEG(jpeg_settings));
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_2.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
REQUIRE_NOTHROW(jpeg_indexed = service.GetJPEGFromBuffer(jpeg_settings, ImageBuffer::MaxIndexedImage));
REQUIRE(!jpeg_indexed.empty());
CHECK(receiver_out.efficiency == 1.0);
CHECK(receiver_out.status.indexing_rate == 1.0);
CHECK(receiver_out.status.images_sent == experiment.GetImageNum());
@@ -177,7 +271,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
}
TEST_CASE("GenerateResolutionMap") {
DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
.FilePrefix("lyso_test").JungfrauConvPhotonCnt(false)
.DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
@@ -206,19 +300,21 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
const uint16_t nthreads = 4;
DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
.FilePrefix("lyso_test_roi").JungfrauConvPhotonCnt(false)
.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})
.HDF5MasterFormatVersion(FileWriterFileFormat::NXmxVDS).PixelSigned(true).OverwriteExistingFiles(true);
.SetFileWriterFormat(FileWriterFormat::NXmxVDS).PixelSigned(true).OverwriteExistingFiles(true);
PixelMask pixel_mask(experiment);
experiment.ROI().SetROI(ROIDefinition{
.boxes = {ROIBox("beam", 100, 120, 20, 30)},
.circles = {ROICircle("roi1", 500, 800, 10)}
.circles = {ROICircle("roi1", 500, 800, 10)},
.azimuthal = {ROIAzimuthal("roi2", 4.0, 7.0)}
});
// Load example image
HDF5ReadOnlyFile data("../../tests/test_data/compression_benchmark.h5");
HDF5DataSet dataset(data, "/entry/data/data");
@@ -248,7 +344,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
ConvertedToRawGeometry(experiment, image_raw_geom.data(), image_conv.data());
logger.Info("Loaded image");
auto mask = pixel_mask.GetMaskRaw();
auto mask = pixel_mask.GetMaskRaw(experiment);
uint64_t sat_pixels = 0;
uint64_t err_pixels = 0;
@@ -270,7 +366,8 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
aq_devices.Add(std::move(test));
ZMQStream2Pusher pusher({"ipc://*"});
StreamWriter writer(logger, pusher.GetAddress()[0]);
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);
@@ -286,18 +383,20 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
.show_spots = true,
.show_roi = true
};
REQUIRE_NOTHROW(jpeg = service.GetJPEG(jpeg_settings));
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_roi.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
auto plot = service.GetDataProcessingPlot(PlotRequest{.type = PlotType::ROISum, .binning = 1});
REQUIRE(plot.size() == 2);
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");
CHECK(receiver_out.status.roi_beam_sum == roi_value);
CHECK(receiver_out.status.roi_beam_npixel == pixels);
@@ -320,7 +419,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQPreview", "[JFJochReceiver]") {
const uint16_t nthreads = 4;
DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
.FilePrefix("").JungfrauConvPhotonCnt(false)
.DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4);
@@ -383,7 +482,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQMetadata", "[JFJochReceiver]") {
const uint16_t nthreads = 4;
DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
.FilePrefix("").JungfrauConvPhotonCnt(false)
.DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4);
@@ -441,7 +540,7 @@ TEST_CASE("JFJochIntegrationTest_HDF5FilePusher", "[JFJochReceiver]") {
const uint16_t nthreads = 4;
DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
.FilePrefix("HDF5FilePusherTest").JungfrauConvPhotonCnt(true)
.DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4);
@@ -474,7 +573,7 @@ TEST_CASE("JFJochIntegrationTest_HDF5FilePusher_Raw", "[JFJochReceiver]") {
const uint16_t nthreads = 4;
DiffractionExperiment experiment(DetectorGeometry(1));
DiffractionExperiment experiment(DetJF(1));
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
.FilePrefix("HDF5FilePusherTest_Raw");