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Fix tests + trim unnecessary variables in DataProcessingSettings

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leonarski_f committed 2023-11-16 19:58:24 +01:00
1 parent 4307a670eb
commit 0d3cb19a2e
9 files changed
+37 -51
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broker/JFJochBroker.cpp
-6
View File
@@ -11,11 +11,8 @@ inline DataProcessingSettings Convert(const JFJochProtoBuf::DataProcessingSettin
ret.photon_count_threshold = input.photon_count_threshold();
ret.min_pix_per_spot = input.min_pix_per_spot();
ret.max_pix_per_spot = input.max_pix_per_spot();
ret.local_bkg_size = input.local_bkg_size();
ret.high_resolution_limit = input.high_resolution_limit();
ret.low_resolution_limit = input.low_resolution_limit();
ret.bkg_estimate_low_q = input.bkg_estimate_low_q();
ret.bkg_estimate_high_q = input.bkg_estimate_high_q();
ret.preview_indexed_only = input.preview_indexed_only();
return ret;
}
@@ -26,11 +23,8 @@ inline JFJochProtoBuf::DataProcessingSettings Convert(const DataProcessingSettin
ret.set_photon_count_threshold(input.photon_count_threshold);
ret.set_min_pix_per_spot(input.min_pix_per_spot);
ret.set_max_pix_per_spot(input.max_pix_per_spot);
ret.set_local_bkg_size(input.local_bkg_size);
ret.set_high_resolution_limit(input.high_resolution_limit);
ret.set_low_resolution_limit(input.low_resolution_limit);
ret.set_bkg_estimate_low_q(input.bkg_estimate_low_q);
ret.set_bkg_estimate_high_q(input.bkg_estimate_high_q);
ret.set_preview_indexed_only(input.preview_indexed_only);
return ret;
}
common/DiffractionExperiment.cpp
+8 -7
View File
@@ -702,8 +702,6 @@ void DiffractionExperiment::CheckDataProcessingSettings(const DataProcessingSett
check_min("Photon count threshold", settings.photon_count_threshold, 0);
check_min("Minimum pixels per spot", settings.min_pix_per_spot, 1);
check_min("Maximum pixels per spot", settings.max_pix_per_spot, settings.min_pix_per_spot + 1);
check_min("Local background size", settings.local_bkg_size, 2);
check_max("Local background size", settings.local_bkg_size, 7);
if (settings.high_resolution_limit > 0) {
check_min("Spot finding high resolution limit", settings.high_resolution_limit, 0.5);
check_max("Spot finding high resolution limit", settings.high_resolution_limit, 50.0);
@@ -715,19 +713,14 @@ void DiffractionExperiment::CheckDataProcessingSettings(const DataProcessingSett
check_min("Spot finding low resolution limit", settings.low_resolution_limit, 1.0);
check_max("Spot finding low resolution limit", settings.low_resolution_limit, 50.0);
}
check_min("Background estimate lowQ", settings.bkg_estimate_low_q, 0.0);
check_min("Background estimate highQ", settings.bkg_estimate_high_q, settings.bkg_estimate_low_q);
}
DataProcessingSettings DiffractionExperiment::DefaultDataProcessingSettings() {
DataProcessingSettings ret{};
ret.local_bkg_size = 5;
ret.signal_to_noise_threshold = 3;
ret.photon_count_threshold = 16;
ret.min_pix_per_spot = 1;
ret.max_pix_per_spot = 50;
ret.bkg_estimate_low_q = 2 * M_PI / 5.0;
ret.bkg_estimate_high_q= 2 * M_PI / 3.0;
return ret;
}
@@ -974,3 +967,11 @@ DiffractionExperiment::GetDetectorModuleConfig(const std::vector<AcquisitionDevi
}
return ret;
}
float DiffractionExperiment::GetLowQForBkgEstimate_recipA() const {
return 2 * static_cast<float>(M_PI) / 5.0;
}
float DiffractionExperiment::GetHighQForBkgEstimate_recipA() const {
return 2 * static_cast<float>(M_PI) / 3.0;
}
common/DiffractionExperiment.h
+3
View File
@@ -248,6 +248,9 @@ public:
float GetHighQForRadialInt_recipA() const;
float GetQSpacingForRadialInt_recipA() const;
float GetLowQForBkgEstimate_recipA() const;
float GetHighQForBkgEstimate_recipA() const;
int64_t GetSpaceGroupNumber() const;
int64_t GetStorageCellNumber() const;
grpc/jfjoch.proto
-3
View File
@@ -156,11 +156,8 @@ message DataProcessingSettings {
int64 photon_count_threshold = 2; // Threshold in photon counts
int64 min_pix_per_spot = 3; // Minimum pixels per spot
int64 max_pix_per_spot = 4; // Maximum pixels per spot
int64 local_bkg_size = 5; // NBX/NBY parameter
float high_resolution_limit = 6;
float low_resolution_limit = 7;
float bkg_estimate_low_q = 8;
float bkg_estimate_high_q = 9;
bool preview_indexed_only = 10;
}
image_analysis/DataProcessingSettings.h
-3
View File
@@ -10,11 +10,8 @@ struct DataProcessingSettings {
int64_t photon_count_threshold; // Threshold in photon counts
int64_t min_pix_per_spot; // Minimum pixels per spot
int64_t max_pix_per_spot; // Maximum pixels per spot
int64_t local_bkg_size; // NBX/NBY parameter
float high_resolution_limit;
float low_resolution_limit;
float bkg_estimate_low_q;
float bkg_estimate_high_q;
bool preview_indexed_only;
};
python/jfjoch_pb2.py
+24 -24
View File
@@ -13,23 +13,23 @@ _sym_db = _symbol_database.Default()
DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n\x0cjfjoch.proto\x12\x0eJFJochProtoBuf\"\x07\n\x05\x45mpty\"W\n\x08UnitCell\x12\t\n\x01\x61\x18\x01 \x01(\x02\x12\t\n\x01\x62\x18\x02 \x01(\x02\x12\t\n\x01\x63\x18\x03 \x01(\x02\x12\r\n\x05\x61lpha\x18\x04 \x01(\x02\x12\x0c\n\x04\x62\x65ta\x18\x05 \x01(\x02\x12\r\n\x05gamma\x18\x06 \x01(\x02\")\n\x06Vector\x12\t\n\x01x\x18\x01 \x01(\x02\x12\t\n\x01y\x18\x02 \x01(\x02\x12\t\n\x01z\x18\x03 \x01(\x02\"|\n\x10RotationSettings\x12\x17\n\x0fstart_angle_deg\x18\x01 \x01(\x02\x12 \n\x18\x61ngle_incr_per_image_deg\x18\x02 \x01(\x02\x12-\n\rrotation_axis\x18\x03 \x01(\x0b\x32\x16.JFJochProtoBuf.Vector\"\x1c\n\x04Plot\x12\t\n\x01x\x18\x01 \x03(\x02\x12\t\n\x01y\x18\x02 \x03(\x02\"\xb1\x04\n\x0f\x44\x61tasetSettings\x12\x1a\n\x12images_per_trigger\x18\x01 \x01(\x03\x12\x10\n\x08ntrigger\x18\x02 \x01(\x03\x12:\n\x11\x66pga_pixel_output\x18\x03 \x01(\x0e\x32\x1f.JFJochProtoBuf.FPGAPixelOutput\x12\x11\n\tsummation\x18\x04 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DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n\x0cjfjoch.proto\x12\x0eJFJochProtoBuf\"\x07\n\x05\x45mpty\"W\n\x08UnitCell\x12\t\n\x01\x61\x18\x01 \x01(\x02\x12\t\n\x01\x62\x18\x02 \x01(\x02\x12\t\n\x01\x63\x18\x03 \x01(\x02\x12\r\n\x05\x61lpha\x18\x04 \x01(\x02\x12\x0c\n\x04\x62\x65ta\x18\x05 \x01(\x02\x12\r\n\x05gamma\x18\x06 \x01(\x02\")\n\x06Vector\x12\t\n\x01x\x18\x01 \x01(\x02\x12\t\n\x01y\x18\x02 \x01(\x02\x12\t\n\x01z\x18\x03 \x01(\x02\"|\n\x10RotationSettings\x12\x17\n\x0fstart_angle_deg\x18\x01 \x01(\x02\x12 \n\x18\x61ngle_incr_per_image_deg\x18\x02 \x01(\x02\x12-\n\rrotation_axis\x18\x03 \x01(\x0b\x32\x16.JFJochProtoBuf.Vector\"\x1c\n\x04Plot\x12\t\n\x01x\x18\x01 \x03(\x02\x12\t\n\x01y\x18\x02 \x03(\x02\"\xb1\x04\n\x0f\x44\x61tasetSettings\x12\x1a\n\x12images_per_trigger\x18\x01 \x01(\x03\x12\x10\n\x08ntrigger\x18\x02 \x01(\x03\x12:\n\x11\x66pga_pixel_output\x18\x03 \x01(\x0e\x32\x1f.JFJochProtoBuf.FPGAPixelOutput\x12\x11\n\tsummation\x18\x04 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_builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, globals())
_builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, 'jfjoch_pb2', globals())
if _descriptor._USE_C_DESCRIPTORS == False:
DESCRIPTOR._options = None
_COMPRESSION._serialized_start=2753
_COMPRESSION._serialized_end=2837
_DETECTORMODE._serialized_start=2839
_DETECTORMODE._serialized_end=2929
_STATE._serialized_start=2931
_STATE._serialized_end=3025
_FPGAPIXELOUTPUT._serialized_start=3027
_FPGAPIXELOUTPUT._serialized_end=3100
_PLOTTYPE._serialized_start=3102
_PLOTTYPE._serialized_end=3225
_COMPRESSION._serialized_start=2672
_COMPRESSION._serialized_end=2756
_DETECTORMODE._serialized_start=2758
_DETECTORMODE._serialized_end=2848
_STATE._serialized_start=2850
_STATE._serialized_end=2944
_FPGAPIXELOUTPUT._serialized_start=2946
_FPGAPIXELOUTPUT._serialized_end=3019
_PLOTTYPE._serialized_start=3021
_PLOTTYPE._serialized_end=3144
_EMPTY._serialized_start=32
_EMPTY._serialized_end=39
_UNITCELL._serialized_start=41
@@ -55,17 +55,17 @@ if _descriptor._USE_C_DESCRIPTORS == False:
_RADIALINTEGRATIONPROFILES._serialized_start=1647
_RADIALINTEGRATIONPROFILES._serialized_end=1734
_DATAPROCESSINGSETTINGS._serialized_start=1737
_DATAPROCESSINGSETTINGS._serialized_end=2052
_MEASUREMENTSTATISTICS._serialized_start=2055
_MEASUREMENTSTATISTICS._serialized_end=2384
_BROKERSTATUS._serialized_start=2387
_BROKERSTATUS._serialized_end=2524
_DETECTORLISTELEMENT._serialized_start=2526
_DETECTORLISTELEMENT._serialized_end=2598
_DETECTORLIST._serialized_start=2600
_DETECTORLIST._serialized_end=2718
_DETECTORSELECTION._serialized_start=2720
_DETECTORSELECTION._serialized_end=2751
_GRPC_JFJOCHBROKER._serialized_start=3228
_GRPC_JFJOCHBROKER._serialized_end=4594
_DATAPROCESSINGSETTINGS._serialized_end=1971
_MEASUREMENTSTATISTICS._serialized_start=1974
_MEASUREMENTSTATISTICS._serialized_end=2303
_BROKERSTATUS._serialized_start=2306
_BROKERSTATUS._serialized_end=2443
_DETECTORLISTELEMENT._serialized_start=2445
_DETECTORLISTELEMENT._serialized_end=2517
_DETECTORLIST._serialized_start=2519
_DETECTORLIST._serialized_end=2637
_DETECTORSELECTION._serialized_start=2639
_DETECTORSELECTION._serialized_end=2670
_GRPC_JFJOCHBROKER._serialized_start=3147
_GRPC_JFJOCHBROKER._serialized_end=4513
# @@protoc_insertion_point(module_scope)
receiver/JFJochReceiver.cpp
+2 -4
View File
@@ -444,10 +444,8 @@ void JFJochReceiver::FrameTransformationThread() {
}
if (rad_int_profile_image) {
uint16_t rad_int_min_bin = std::floor(
rad_int_mapping->QToBin(local_data_processing_settings.bkg_estimate_low_q));
uint16_t rad_int_max_bin = std::ceil(
rad_int_mapping->QToBin(local_data_processing_settings.bkg_estimate_high_q));
uint16_t rad_int_min_bin = std::floor(rad_int_mapping->QToBin(experiment.GetLowQForBkgEstimate_recipA()));
uint16_t rad_int_max_bin = std::ceil(rad_int_mapping->QToBin(experiment.GetHighQForBkgEstimate_recipA()));
float bkg_estimate_val = rad_int_profile_image->GetMeanValueOfBins(rad_int_min_bin, rad_int_max_bin);
bkg_estimate.AddElement(image_number, bkg_estimate_val);
receiver/JFJochReceiverTest.cpp
-1
View File
@@ -24,7 +24,6 @@ JFJochReceiverOutput RunJFJochReceiverTest(AcquisitionDeviceGroup &aq_devices, I
settings.photon_count_threshold = 5;
settings.min_pix_per_spot = 3;
settings.max_pix_per_spot = 200;
settings.local_bkg_size = 5;
service.SetDataProcessingSettings(settings);
service.Start(x, &calib);
tests/JFJochFullIntegrationTest.cpp
-3
View File
@@ -792,9 +792,6 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot", "[JFJochReceiver]") {
settings.max_pix_per_spot = 200;
settings.low_resolution_limit = 80.0;
settings.high_resolution_limit = 2.5;
settings.bkg_estimate_high_q = 0.0;
settings.bkg_estimate_low_q = 0.0;
settings.local_bkg_size = 5;
REQUIRE_NOTHROW(state_machine.SetDataProcessingSettings(settings));