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Remove sample identities from the repository; document the rule

Browse Source 
Datasets may be confidential; sample names and measured unit cells committed to
the repo can leak outside the group working on them. Scrub existing occurrences
and add a "No sample identities in the repository" section to CLAUDE.md
(forbidden: sample/dataset names, internal codes, measured cells tied to a
sample; fine: space group / lattice / twinning descriptors).

- Comments: replace internal dataset codes and protein names with the
  crystallographic situation they illustrate (centred vs pseudo-symmetric,
  holohedral, cubic, F-cubic/hexagonal, ...).
- Docs: same, in the analysis/writer/stream references and example configs.
- Tests: rename sample-named identifiers, TEST_CASE names, file prefixes and
  asserted labels to neutral crystallographic names (e.g. tetragonal_uc);
  behaviour unchanged. Reduce the CrystFEL reference PDB to a bare CRYST1 cell
  file (cell.pdb) and rename the reference data file.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-07-15 17:19:43 +02:00
co-authored by Claude Opus 4.8
parent 0f3ccda779
commit abbee2d4dc
27 changed files with 159 additions and 4079 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tests/JFJochReceiverProcessingTest.cpp
+45 -45
View File
@@ -17,7 +17,7 @@
#include "../image_pusher/TCPStreamPusher.h"
#include "../image_puller/TCPImagePuller.h"
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -26,7 +26,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
.FilePrefix("crystal_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});
experiment.SampleTemperature_K(123.0).RingCurrent_mA(115);
@@ -92,7 +92,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
};
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
CHECK(receiver_out.efficiency == 1.0);
@@ -107,7 +107,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_refinement", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -116,7 +116,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement", "[JFJo
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_refinement").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
.FilePrefix("crystal_test_refinement").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})
@@ -184,7 +184,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement", "[JFJo
};
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
CHECK(receiver_out.efficiency == 1.0);
@@ -199,7 +199,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement", "[JFJo
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement_tetragonal", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_refinement_tetragonal", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -208,7 +208,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement_tetragon
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_refinement_tetragonal").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
.FilePrefix("crystal_test_refinement_tetragonal").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
.DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
.SetUnitCell(UnitCell{.a = 78.95, .b = 78.95, .c = 36.9, .alpha = 90, .beta = 90, .gamma = 90})
@@ -277,7 +277,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement_tetragon
};
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
CHECK(receiver_out.efficiency == 1.0);
@@ -292,7 +292,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement_tetragon
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_index_and_integrate", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -301,7 +301,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate", "[JFJoc
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
.FilePrefix("crystal_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);
@@ -366,7 +366,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate", "[JFJoc
};
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
CHECK(receiver_out.efficiency == 1.0);
@@ -388,7 +388,7 @@ 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]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_index_and_integrate_no_spots", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -397,7 +397,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate_no_spots"
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
.FilePrefix("crystal_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);
@@ -465,7 +465,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate_no_spots"
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_azint_2d", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_azint_2d", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -474,7 +474,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_azint_2d", "[JFJochReceiver]") {
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_azim_2d").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
.FilePrefix("crystal_test_azim_2d").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);
@@ -542,7 +542,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_azint_2d", "[JFJochReceiver]") {
REQUIRE(azim_plot.GetPlots()[0].z.size() == 120 * 16);
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_FFT", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -551,7 +551,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT", "[JFJochRecei
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_fft").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
.FilePrefix("crystal_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);
@@ -616,7 +616,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT", "[JFJochRecei
};
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
CHECK(receiver_out.efficiency == 1.0);
@@ -631,7 +631,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT", "[JFJochRecei
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFTW", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_FFTW", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -640,7 +640,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFTW", "[JFJochRece
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_fftw").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
.FilePrefix("crystal_test_fftw").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
.OverwriteExistingFiles(true)
.DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
.IndexingAlgorithm(IndexingAlgorithmEnum::FFTW);
@@ -705,7 +705,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFTW", "[JFJochRece
};
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
CHECK(receiver_out.efficiency == 1.0);
@@ -720,7 +720,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFTW", "[JFJochRece
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_reference", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_FFT_reference", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -729,7 +729,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_reference", "[J
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_fft_ref").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
.FilePrefix("crystal_test_fft_ref").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
.OverwriteExistingFiles(true)
.DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
.IndexingAlgorithm(IndexingAlgorithmEnum::FFT)
@@ -795,7 +795,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_reference", "[J
};
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
CHECK(receiver_out.efficiency == 1.0);
@@ -810,7 +810,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_reference", "[J
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_wrong_reference", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_FFT_wrong_reference", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -819,7 +819,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_wrong_reference
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_fft_wrongref").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
.FilePrefix("crystal_test_fft_wrongref").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
.OverwriteExistingFiles(true)
.DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
.IndexingAlgorithm(IndexingAlgorithmEnum::FFT)
@@ -885,7 +885,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_wrong_reference
};
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
CHECK(receiver_out.efficiency == 1.0);
@@ -900,7 +900,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_wrong_reference
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_grid", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_grid", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -916,7 +916,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_grid", "[JFJochRece
DiffractionExperiment experiment(DetJF4M());
experiment.UseInternalPacketGenerator(true).ImagesPerFile(2).ImportDatasetSettings(dataset_settings)
.FilePrefix("lyso_test_grid").JungfrauConvPhotonCnt(false)
.FilePrefix("crystal_test_grid").JungfrauConvPhotonCnt(false)
.SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true);
PixelMask pixel_mask(experiment);
@@ -1010,7 +1010,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_grid", "[JFJochRece
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_32", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_32", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -1019,7 +1019,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_32", "[JFJochReceiv
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_32").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxLegacy).OverwriteExistingFiles(true)
.FilePrefix("crystal_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);
@@ -1082,7 +1082,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_32", "[JFJochReceiv
};
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
CHECK(receiver_out.efficiency == 1.0);
@@ -1097,7 +1097,7 @@ 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]") {
TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_min_pix_2", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -1106,7 +1106,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).OverwriteExistingFiles(true)
.FilePrefix("lyso_test_min_pix_2").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
.FilePrefix("crystal_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})
@@ -1164,7 +1164,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
};
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_min_pix_2.jpeg", std::ios::binary);
std::ofstream f("crystal_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));
@@ -1181,7 +1181,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
TEST_CASE("GenerateResolutionMap") {
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
.FilePrefix("lyso_test").JungfrauConvPhotonCnt(false)
.FilePrefix("crystal_test").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});
@@ -1211,7 +1211,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
.FilePrefix("lyso_test_roi").JungfrauConvPhotonCnt(false)
.FilePrefix("crystal_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})
.SetFileWriterFormat(FileWriterFormat::NXmxVDS).PixelSigned(true).OverwriteExistingFiles(true);
@@ -1297,7 +1297,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
REQUIRE(!jpeg.empty());
std::ofstream f("lyso_processing_test_roi.jpeg", std::ios::binary);
std::ofstream f("crystal_processing_test_roi.jpeg", std::ios::binary);
f.write(jpeg.data(), jpeg.size());
auto plot = service.GetDataProcessingPlot(PlotRequest{.type = PlotType::ROISum, .binning = 1});
@@ -1577,7 +1577,7 @@ TEST_CASE("JFJochIntegrationTest_HDF5FilePusher_Raw", "[JFJochReceiver]") {
CHECK(!receiver_out.status.cancelled);
}
TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_no_processing", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_TCP_crystal_no_processing", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -1586,7 +1586,7 @@ TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_no_processing", "[JFJochReceiver]"
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_tcp_no_processing").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
.FilePrefix("crystal_test_tcp_no_processing").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});
experiment.SampleTemperature_K(123.0).RingCurrent_mA(115);
@@ -1654,7 +1654,7 @@ TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_no_processing", "[JFJochReceiver]"
CHECK(ack == experiment.GetImageNum());
}
TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_spot_and_index", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_TCP_crystal_spot_and_index", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -1663,7 +1663,7 @@ TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_spot_and_index", "[JFJochReceiver]
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_tcp").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
.FilePrefix("crystal_test_tcp").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});
experiment.SampleTemperature_K(123.0).RingCurrent_mA(115);
@@ -1796,7 +1796,7 @@ TEST_CASE("JFJochIntegrationTest_TCP_calibration", "[JFJochReceiver]") {
REQUIRE_NOTHROW(writer_future.get());
}
TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_spot_and_index_single_file", "[JFJochReceiver]") {
TEST_CASE("JFJochIntegrationTest_TCP_crystal_spot_and_index_single_file", "[JFJochReceiver]") {
Logger logger(Catch::getResultCapture().getCurrentTestName());
RegisterHDF5Filter();
@@ -1805,7 +1805,7 @@ TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_spot_and_index_single_file", "[JFJ
DiffractionExperiment experiment(DetJF4M());
experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
.FilePrefix("lyso_test_tcp_single_file").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxIntegrated).OverwriteExistingFiles(true)
.FilePrefix("crystal_test_tcp_single_file").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxIntegrated).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});
experiment.SampleTemperature_K(123.0).RingCurrent_mA(115);