From 99741ae5c53ba879ad66c26583da52ebf951ef44 Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Sat, 21 Oct 2023 19:51:21 +0200 Subject: [PATCH] ADU histogram: Save --- common/ADUHistogram.cpp | 26 +++++++++++ common/ADUHistogram.h | 20 +++++++++ common/CMakeLists.txt | 4 +- frame_serialize/CBORMessages.h | 2 + frame_serialize/CborUtil.h | 3 ++ frame_serialize/JFJochFrameDeserializer.cpp | 48 ++++++++++++--------- frame_serialize/JFJochFrameSerializer.cpp | 16 ++++--- grpc/jfjoch.proto | 1 + python/jfjoch_pb2.py | 20 ++++----- receiver/JFJochReceiver.cpp | 16 ++++++- receiver/JFJochReceiver.h | 5 ++- writer/HDF5DataFile.cpp | 4 ++ writer/HDF5DataFile.h | 1 + 13 files changed, 125 insertions(+), 41 deletions(-) create mode 100644 common/ADUHistogram.cpp create mode 100644 common/ADUHistogram.h diff --git a/common/ADUHistogram.cpp b/common/ADUHistogram.cpp new file mode 100644 index 00000000..1b998d75 --- /dev/null +++ b/common/ADUHistogram.cpp @@ -0,0 +1,26 @@ +// Copyright (2019-2023) Paul Scherrer Institute + +#include "ADUHistogram.h" + +ADUHistogram::ADUHistogram() : histogram(ADU_HISTO_BIN_COUNT) { + +} + +void ADUHistogram::Add(const DeviceOutput &output) { + std::unique_lock ul(m); + for (int i = 0; i < ADU_HISTO_BIN_COUNT; i++) + histogram[i] += output.adu_histogram[i]; +} + +const std::vector &ADUHistogram::GetHistogram() const { + return histogram; +} + +void ADUHistogram::GetPlot(JFJochProtoBuf::Plot &plot) const { + std::unique_lock ul(m); + + for (int i = 0; i < ADU_HISTO_BIN_COUNT; i++) { + plot.add_x(ADU_HISTO_BIN_WIDTH * i + ADU_HISTO_BIN_WIDTH / 2); + plot.add_y(histogram[i]); + } +} \ No newline at end of file diff --git a/common/ADUHistogram.h b/common/ADUHistogram.h new file mode 100644 index 00000000..837ab698 --- /dev/null +++ b/common/ADUHistogram.h @@ -0,0 +1,20 @@ +// Copyright (2019-2023) Paul Scherrer Institute + +#ifndef JUNGFRAUJOCH_ADUHISTOGRAM_H +#define JUNGFRAUJOCH_ADUHISTOGRAM_H + +#include +#include +#include "../receiver/AcquisitionDevice.h" + +class ADUHistogram { + mutable std::mutex m; + std::vector histogram; +public: + explicit ADUHistogram(); + void Add(const DeviceOutput &output); + const std::vector& GetHistogram() const; + void GetPlot(JFJochProtoBuf::Plot &plot) const; +}; + +#endif //JUNGFRAUJOCH_ADUHISTOGRAM_H diff --git a/common/CMakeLists.txt b/common/CMakeLists.txt index 96eae103..dbdd5a2c 100644 --- a/common/CMakeLists.txt +++ b/common/CMakeLists.txt @@ -48,7 +48,9 @@ ADD_LIBRARY( CommonFunctions STATIC CUDAWrapper.cpp CUDAWrapper.h NUMAHWPolicy.cpp - NUMAHWPolicy.h) + NUMAHWPolicy.h + ADUHistogram.cpp + ADUHistogram.h) TARGET_LINK_LIBRARIES(CommonFunctions Compression FrameSerialize libzmq JFCalibration JFJochProtoBuf -lrt) diff --git a/frame_serialize/CBORMessages.h b/frame_serialize/CBORMessages.h index 897aff29..4d34c4c2 100644 --- a/frame_serialize/CBORMessages.h +++ b/frame_serialize/CBORMessages.h @@ -48,6 +48,8 @@ struct DataMessage { std::string series_unique_id; uint64_t series_id; + + std::vector adu_histogram; }; struct GoniometerAxis { diff --git a/frame_serialize/CborUtil.h b/frame_serialize/CborUtil.h index b19656d2..f032b6aa 100644 --- a/frame_serialize/CborUtil.h +++ b/frame_serialize/CborUtil.h @@ -8,6 +8,7 @@ constexpr const CborTag TagMultiDimArray = 40; constexpr const CborTag TagDECTRISCompression = 56500; +// rfc8746 constexpr const CborTag TagFloatLE = 0b01010101; constexpr const CborTag TagUnsignedInt8Bit = 0b01000000; constexpr const CborTag TagSignedInt8Bit = 0b01001000; @@ -18,4 +19,6 @@ constexpr const CborTag TagSignedInt16BitLE = 0b01001101; constexpr const CborTag TagUnsignedInt32BitLE = 0b01000110; constexpr const CborTag TagSignedInt32BitLE = 0b01001110; +constexpr const CborTag TagUnsignedInt64BitLE = 0b01000111; + #endif //JUNGFRAUJOCH_CBORUTIL_H diff --git a/frame_serialize/JFJochFrameDeserializer.cpp b/frame_serialize/JFJochFrameDeserializer.cpp index 78af72c6..c884fc75 100644 --- a/frame_serialize/JFJochFrameDeserializer.cpp +++ b/frame_serialize/JFJochFrameDeserializer.cpp @@ -108,26 +108,6 @@ inline std::pair GetRational(CborValue &value) { return ret; } -inline void GetCBORFloatArray(CborValue &value, std::vector &v) { - if (GetCBORTag(value) != TagFloatLE) - throw JFJochException(JFJochExceptionCategory::CBORError, "Incorrect array type tag"); - auto len = GetCBORArrayLen(value); - if (len > 0) { - CborValue array_value; - - v.resize(len); - - cborErr(cbor_value_enter_container(&value, &array_value)); - - for (int i = 0; i < len; i++) - v[i] = GetCBORFloat(array_value); - - cborErr(cbor_value_leave_container(&value, &array_value)); - } else - cbor_value_advance(&value); -} - - inline std::pair GetCBORDimension2DArray(CborValue &value) { std::pair ret; @@ -179,6 +159,32 @@ inline std::pair GetCBORByteString(CborValue &value) { return {ptr, len}; } +inline void GetCBORFloatArray(CborValue &value, std::vector &v) { + if (GetCBORTag(value) != TagFloatLE) + throw JFJochException(JFJochExceptionCategory::CBORError, "Incorrect array type tag"); + + auto [ptr, len] = GetCBORByteString(value); + + if (len % sizeof(float)) + throw JFJochException(JFJochExceptionCategory::CBORError, "Size mismatch"); + + v.resize(len / sizeof(float)); + memcpy(v.data(), ptr, len); +} + +inline void GetCBORUInt64Array(CborValue &value, std::vector &v) { + if (GetCBORTag(value) != TagUnsignedInt64BitLE) + throw JFJochException(JFJochExceptionCategory::CBORError, "Incorrect array type tag"); + + auto [ptr, len] = GetCBORByteString(value); + + if (len % sizeof(uint64_t)) + throw JFJochException(JFJochExceptionCategory::CBORError, "Size mismatch"); + + v.resize(len / sizeof(uint64_t)); + memcpy(v.data(), ptr, len); +} + inline void GetCBORTypedArray(CBORImage &v, CborValue &value) { CborTag tag = GetCBORTag(value); @@ -401,6 +407,8 @@ void JFJochFrameDeserializer::ProcessImageMessageUserDataElement(CborValue &valu data_message.storage_cell = GetCBORUInt(map_value) & UINT32_MAX; else if (key == "bunch_id") data_message.bunch_id = GetCBORUInt(map_value); + else if (key == "adu_histogram") + GetCBORUInt64Array(map_value, data_message.adu_histogram); else cbor_value_advance(&map_value); } diff --git a/frame_serialize/JFJochFrameSerializer.cpp b/frame_serialize/JFJochFrameSerializer.cpp index 9ff86ebb..cf51d881 100644 --- a/frame_serialize/JFJochFrameSerializer.cpp +++ b/frame_serialize/JFJochFrameSerializer.cpp @@ -126,16 +126,16 @@ inline void CBOR_ENC_2D_TYPED_ARRAY(CborEncoder &encoder, const CBORImage& image } inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector& v) { - CborEncoder arrayEncoder; - cborErr(cbor_encode_text_stringz(&encoder, key)); cborErr(cbor_encode_tag(&encoder, TagFloatLE)); - cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, v.size())); + cborErr(cbor_encode_byte_string(&encoder, (uint8_t *) v.data(), v.size() * sizeof(float))); +} - for (const auto &i : v) - cborErr(cbor_encode_float(&arrayEncoder, i)); - cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder)); +inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector& v) { + cborErr(cbor_encode_text_stringz(&encoder, key)); + cborErr(cbor_encode_tag(&encoder, TagUnsignedInt64BitLE)); + cborErr(cbor_encode_byte_string(&encoder, (uint8_t *) v.data(), v.size() * sizeof(uint64_t))); } inline void CBOR_ENC_RATIONAL(CborEncoder &encoder, const char* key, uint64_t numerator, uint64_t denominator) { @@ -422,7 +422,7 @@ void JFJochFrameSerializer::SerializeImage(const DataMessage& message) { message.timestamp_base); cborErr(cbor_encode_text_stringz(&mapEncoder, "user_data")); - cborErr(cbor_encoder_create_map(&mapEncoder, &userDataMapEncoder, 10)); + cborErr(cbor_encoder_create_map(&mapEncoder, &userDataMapEncoder, 11)); CBOR_ENC(userDataMapEncoder, "magic_number", user_data_magic_number); CBOR_ENC(userDataMapEncoder, "spots", message.spots); @@ -434,6 +434,8 @@ void JFJochFrameSerializer::SerializeImage(const DataMessage& message) { CBOR_ENC(userDataMapEncoder, "receiver_available_send_buffers", message.receiver_available_send_buffers); CBOR_ENC(userDataMapEncoder, "receiver_aq_dev_delay", message.receiver_aq_dev_delay); CBOR_ENC(userDataMapEncoder, "storage_cell", (uint64_t) message.storage_cell); + CBOR_ENC(userDataMapEncoder, "adu_histogram", message.adu_histogram); + cborErr(cbor_encoder_close_container(&mapEncoder, &userDataMapEncoder)); CBOR_ENC(mapEncoder, "data", message.image); diff --git a/grpc/jfjoch.proto b/grpc/jfjoch.proto index 37ce28b7..256be2e0 100644 --- a/grpc/jfjoch.proto +++ b/grpc/jfjoch.proto @@ -285,6 +285,7 @@ enum PlotType { SPOT_COUNT = 2; INDEXING_RATE = 3; INDEXING_RATE_PER_FILE = 4; + ADU_HISTOGRAM = 5; } message PlotRequest { diff --git a/python/jfjoch_pb2.py b/python/jfjoch_pb2.py index fc233b8b..96dc6ab7 100644 --- a/python/jfjoch_pb2.py +++ b/python/jfjoch_pb2.py @@ -13,7 +13,7 @@ _sym_db = 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_builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, globals()) _builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, 'jfjoch_pb2', globals()) @@ -31,7 +31,7 @@ if _descriptor._USE_C_DESCRIPTORS == False: _STATE._serialized_start=9365 _STATE._serialized_end=9459 _PLOTTYPE._serialized_start=9461 - _PLOTTYPE._serialized_end=9565 + _PLOTTYPE._serialized_end=9584 _EMPTY._serialized_start=32 _EMPTY._serialized_end=39 _UNITCELL._serialized_start=41 @@ -128,12 +128,12 @@ if _descriptor._USE_C_DESCRIPTORS == False: _DETECTORLIST._serialized_end=9055 _DETECTORSELECTION._serialized_start=9057 _DETECTORSELECTION._serialized_end=9088 - _GRPC_JFJOCHRECEIVER._serialized_start=9568 - _GRPC_JFJOCHRECEIVER._serialized_end=10335 - _GRPC_JFJOCHWRITER._serialized_start=10338 - _GRPC_JFJOCHWRITER._serialized_end=10540 - _GRPC_JFJOCHDETECTOR._serialized_start=10543 - _GRPC_JFJOCHDETECTOR._serialized_end=10929 - _GRPC_JFJOCHBROKER._serialized_start=10932 - _GRPC_JFJOCHBROKER._serialized_end=12621 + _GRPC_JFJOCHRECEIVER._serialized_start=9587 + _GRPC_JFJOCHRECEIVER._serialized_end=10354 + _GRPC_JFJOCHWRITER._serialized_start=10357 + _GRPC_JFJOCHWRITER._serialized_end=10559 + _GRPC_JFJOCHDETECTOR._serialized_start=10562 + _GRPC_JFJOCHDETECTOR._serialized_end=10948 + _GRPC_JFJOCHBROKER._serialized_start=10951 + _GRPC_JFJOCHBROKER._serialized_end=12640 # @@protoc_insertion_point(module_scope) diff --git a/receiver/JFJochReceiver.cpp b/receiver/JFJochReceiver.cpp index ce05c621..6838e6cd 100644 --- a/receiver/JFJochReceiver.cpp +++ b/receiver/JFJochReceiver.cpp @@ -8,6 +8,7 @@ #include "../jungfrau/JFPedestalCalc.h" #include "../image_analysis/IndexerWrapper.h" #include "../common/DiffractionGeometry.h" +#include "../common/ADUHistogram.h" inline std::string time_UTC(const std::chrono::time_point &input) { auto time_ms = std::chrono::duration_cast(input.time_since_epoch()).count(); @@ -344,7 +345,7 @@ void JFJochReceiver::MeasurePedestalThread(uint16_t data_stream, uint16_t module void JFJochReceiver::MiniSummationThread(int d, int m, size_t image_number, bool &send_image, FrameTransformation &transformation, DataMessage &message, std::vector &conversion, - RadialIntegrationProfile *profile) { + ADUHistogram& adu_histogram, RadialIntegrationProfile *profile) { for (int j = 0; j < experiment.GetSummation(); j++) { size_t frame_number = image_number * experiment.GetSummation() + j; acquisition_device[d]->Counters().WaitForFrame(frame_number + 2); @@ -370,6 +371,9 @@ void JFJochReceiver::MiniSummationThread(int d, int m, size_t image_number, bool if (profile) profile->Add(*acquisition_device[d]->GetDeviceOutput(frame_number, m)); + adu_histogram.Add(*acquisition_device[d]->GetDeviceOutput(frame_number, m)); + adu_histogram_total.Add(*acquisition_device[d]->GetDeviceOutput(frame_number, m)); + if (experiment.GetConversionOnCPU()) { auto &conv = conversion.at(experiment.GetFirstModuleOfDataStream(d) + m); transformation.ProcessModule(conv, src, m, d); @@ -434,6 +438,7 @@ void JFJochReceiver::FrameTransformationThread() { message.timestamp_base = 10*1000*1000; message.exptime_base = 10*1000*1000; message.indexing_result = 0; + ADUHistogram adu_histogram; bool send_preview = false; bool send_bkg_estimate = false; @@ -463,7 +468,7 @@ void JFJochReceiver::FrameTransformationThread() { this, d, m, image_number, std::ref(send_image), std::ref(transformation), std::ref(message), std::ref(*conversion), - rad_int_profile_image.get())); + std::ref(adu_histogram), rad_int_profile_image.get())); message.receiver_aq_dev_delay = max_delay; } else { for (int j = 0; j < experiment.GetSummation(); j++) { @@ -497,6 +502,8 @@ void JFJochReceiver::FrameTransformationThread() { } else transformation.ProcessModule(src, m, d); + adu_histogram.Add(*acquisition_device[d]->GetDeviceOutput(frame_number, m)); + adu_histogram_total.Add(*acquisition_device[d]->GetDeviceOutput(frame_number, m)); if (rad_int_profile_image) rad_int_profile_image->Add(*acquisition_device[d]->GetDeviceOutput(frame_number, m)); @@ -572,6 +579,8 @@ void JFJochReceiver::FrameTransformationThread() { *rad_int_profile_per_file[image_number % experiment.GetDataFileCount()] += *rad_int_profile_image; } + message.adu_histogram = adu_histogram.GetHistogram(); + if (send_preview) preview_publisher->Publish(experiment, transformation.GetPreview16BitImage(), @@ -784,6 +793,9 @@ JFJochProtoBuf::Plot JFJochReceiver::GetPlots(const JFJochProtoBuf::PlotRequest case JFJochProtoBuf::INDEXING_RATE_PER_FILE: indexing_solution_per_file.GetPlot(ret); break; + case JFJochProtoBuf::ADU_HISTOGRAM: + adu_histogram_total.GetPlot(ret); + break; default: // Do nothing break; diff --git a/receiver/JFJochReceiver.h b/receiver/JFJochReceiver.h index 9fed7c17..71d0f4ce 100644 --- a/receiver/JFJochReceiver.h +++ b/receiver/JFJochReceiver.h @@ -29,6 +29,7 @@ #include "../jungfrau/JFCalibration.h" #include "../jungfrau/JFConversionFixedPoint.h" +#include "../common/ADUHistogram.h" class JFJochReceiver { DiffractionExperiment experiment; @@ -42,6 +43,8 @@ class JFJochReceiver { std::vector> frame_transformation_futures; std::vector> data_acquisition_futures; + ADUHistogram adu_histogram_total; + std::unique_ptr rad_int_mapping; std::unique_ptr rad_int_profile; std::vector> rad_int_profile_per_file; @@ -111,7 +114,7 @@ class JFJochReceiver { void MiniSummationThread(int d, int m, size_t image_number, bool &send_image, FrameTransformation &transformation, DataMessage &message, std::vector &conversion, - RadialIntegrationProfile *profile); + ADUHistogram& adu_histogram, RadialIntegrationProfile *profile); void Cancel(const JFJochException &e); void FinalizeMeasurement(); JFJochProtoBuf::DataProcessingSettings GetDataProcessingSettings(); diff --git a/writer/HDF5DataFile.cpp b/writer/HDF5DataFile.cpp index ce76b2e4..d0a285fb 100644 --- a/writer/HDF5DataFile.cpp +++ b/writer/HDF5DataFile.cpp @@ -61,6 +61,7 @@ void HDF5DataFile::CreateFile() { result_group->NXClass("NXcollection"); rad_int_group = std::make_unique(*data_file, "/entry/result/rad_int"); + adu_histo_group = std::make_unique(*data_file, "/entry/result/adu_histogram"); HDF5DataSpace data_space({1, ypixel, xpixel},{H5S_UNLIMITED, ypixel, xpixel}); data_set = std::make_unique(*data_file, "/entry/data/data", data_type, data_space, dcpl); @@ -154,6 +155,9 @@ void HDF5DataFile::Write(const DataMessage &msg, uint64_t image_number) { if (!msg.rad_int_profile.empty() && (msg.rad_int_profile.size() == rad_int_bin_to_q.size())) rad_int_group->SaveVector("img" + std::to_string(image_number), msg.rad_int_profile); + + if (!msg.adu_histogram.empty()) + adu_histo_group->SaveVector("img" + std::to_string(image_number), msg.adu_histogram); } HDF5DataFileStatistics HDF5DataFile::GetStatistics() const { diff --git a/writer/HDF5DataFile.h b/writer/HDF5DataFile.h index 13548b9a..0478c475 100644 --- a/writer/HDF5DataFile.h +++ b/writer/HDF5DataFile.h @@ -29,6 +29,7 @@ class HDF5DataFile { std::unique_ptr result_group = nullptr; std::unique_ptr rad_int_group = nullptr; + std::unique_ptr adu_histo_group = nullptr; size_t xpixel; size_t ypixel;