Files
Jungfraujoch/receiver/JFJochReceiver.cpp

587 lines
24 KiB
C++

// Copyright (2019-2024) Paul Scherrer Institute
#include "JFJochReceiver.h"
#include <thread>
#include "../image_analysis/MXAnalyzer.h"
#include "../common/DiffractionGeometry.h"
#include "ImageMetadata.h"
#include "../common/time_utc.h"
#include "../common/PixelMask.h"
JFJochReceiver::JFJochReceiver(const DiffractionExperiment& in_experiment,
const JFCalibration *in_calibration,
AcquisitionDeviceGroup &in_aq_device,
ImagePusher &in_image_sender,
Logger &in_logger, int64_t in_forward_and_sum_nthreads,
const NUMAHWPolicy &in_numa_policy,
const SpotFindingSettings &in_spot_finding_settings,
PreviewImage &in_preview_image,
PreviewImage &in_preview_image_indexed,
SendBuffer &buf) :
experiment(in_experiment),
calibration(nullptr),
send_buf_ctrl(experiment, buf),
acquisition_device(in_aq_device),
logger(in_logger),
image_pusher(in_image_sender),
frame_transformation_nthreads(in_forward_and_sum_nthreads),
ndatastreams(experiment.GetDataStreamsNum()),
data_acquisition_ready(ndatastreams),
frame_transformation_ready((experiment.GetImageNum() > 0) ? frame_transformation_nthreads : 0),
numa_policy(in_numa_policy),
adu_histogram_module(experiment.GetModulesNum()),
az_int_mapping(experiment),
plots(experiment, az_int_mapping),
spot_finding_settings(in_spot_finding_settings),
preview_image(in_preview_image),
preview_image_indexed(in_preview_image_indexed),
serialmx_filter(experiment)
{
if (experiment.GetDetectorSetup().GetDetectorType() == DetectorType::JUNGFRAU)
calibration = in_calibration;
push_images_to_writer = (experiment.GetImageNum() > 0) && (!experiment.GetFilePrefix().empty());
if (acquisition_device.size() < ndatastreams)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Number of acquisition devices has to match data streams");
if (frame_transformation_nthreads <= 0)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Number of threads must be more than zero");
logger.Info("NUMA policy: {}", numa_policy.GetName());
for (int d = 0; d < ndatastreams; d++) {
acquisition_device[d].PrepareAction(experiment);
acquisition_device[d].SetSpotFinderParameters(spot_finding_settings);
logger.Debug("Acquisition device {} prepared", d);
}
logger.Info("Data acquisition devices ready");
if (experiment.GetImageNum() > 0) {
SendStartMessage();
SendCalibration();
for (int i = 0; i < experiment.GetImageNum(); i++)
images_to_go.Put(i);
// Setup frames summation and forwarding
for (uint32_t i = 0; i < frame_transformation_nthreads; i++) {
auto handle = std::async(std::launch::async, &JFJochReceiver::FrameTransformationThread,
this, i);
frame_transformation_futures.emplace_back(std::move(handle));
}
logger.Info("Image compression/forwarding threads started");
frame_transformation_ready.wait();
logger.Info("Image compression/forwarding threads ready");
}
for (int d = 0; d < ndatastreams; d++)
data_acquisition_futures.emplace_back(std::async(std::launch::async, &JFJochReceiver::AcquireThread,
this, d));
data_acquisition_ready.wait();
start_time = std::chrono::system_clock::now();
measurement = std::async(std::launch::async, &JFJochReceiver::FinalizeMeasurement, this);
logger.Info("Receiving data started");
}
void JFJochReceiver::SendStartMessage() {
if (!push_images_to_writer)
return;
StartMessage message{};
experiment.FillMessage(message);
message.arm_date = time_UTC(std::chrono::system_clock::now());
message.az_int_bin_number = az_int_mapping.GetBinNumber();
message.az_int_bin_to_q = az_int_mapping.GetBinToQ();
message.write_master_file = true;
PixelMask pixel_mask(experiment);
if (calibration)
pixel_mask.LoadDetectorBadPixelMask(calibration->CalculateMask(), 1);
std::vector<uint32_t> nexus_mask;
nexus_mask = pixel_mask.GetMask(experiment);
size_t xpixel = experiment.GetXPixelsNum();
size_t ypixel = experiment.GetYPixelsNum();
CompressedImage image{
.data = (uint8_t *) nexus_mask.data(),
.size = nexus_mask.size() * sizeof(nexus_mask[0]),
.xpixel = xpixel,
.ypixel = ypixel,
.pixel_depth_bytes = sizeof(nexus_mask[0]),
.pixel_is_signed = false,
.pixel_is_float = false,
.algorithm = CompressionAlgorithm::NO_COMPRESSION,
.channel = "default"
};
message.AddPixelMask(image);
image_pusher.StartDataCollection(message);
}
void JFJochReceiver::SendCalibration() {
if ((calibration == nullptr) || !experiment.GetSaveCalibration() || !push_images_to_writer)
return;
JFJochBitShuffleCompressor compressor(CompressionAlgorithm::BSHUF_LZ4);
size_t xpixel = RAW_MODULE_COLS;
size_t ypixel = experiment.GetModulesNum() * RAW_MODULE_LINES;
for (int sc = 0; sc < experiment.GetStorageCellNumber(); sc++) {
for (int gain = 0; gain < 3; gain++) {
if (experiment.IsFixedGainG1() && (gain != 1))
continue;
auto v = compressor.Compress(calibration->GetPedestal(gain, sc));
std::string channel = "pedestal_G" + std::to_string(gain);
if (experiment.GetStorageCellNumber() > 1)
channel += "_sc" + std::to_string(sc);
CompressedImage image{
.data = v.data(),
.size = v.size(),
.xpixel = (size_t) xpixel,
.ypixel = (size_t) ypixel,
.pixel_depth_bytes = 2,
.pixel_is_signed = false,
.pixel_is_float = false,
.algorithm = CompressionAlgorithm::BSHUF_LZ4,
.channel = channel
};
image_pusher.SendCalibration(image);
}
}
}
void JFJochReceiver::AcquireThread(uint16_t data_stream) {
try {
NUMAHWPolicy::RunOnNode(acquisition_device[data_stream].GetNUMANode());
} catch (const JFJochException &e) {
logger.Warning("NUMA bind error {} for device thread {} - continuing without binding", e.what(), data_stream);
}
try {
if (calibration != nullptr)
acquisition_device[data_stream].InitializeCalibration(experiment, *calibration);
size_t m_offset = experiment.GetFirstModuleOfDataStream(data_stream);
acquisition_device[data_stream].InitializeROIMap(experiment);
std::vector<float> tmp(RAW_MODULE_SIZE);
for (int m = 0; m < experiment.GetModulesNum(data_stream); m++) {
CalcSpotFinderResolutionMap(tmp.data(), experiment, m_offset + m);
acquisition_device[data_stream].InitializeSpotFinderResolutionMap(tmp.data(), m);
CalcAzIntCorrRawCoord(tmp.data(), experiment, m_offset + m);
acquisition_device[data_stream].InitializeIntegrationMap(az_int_mapping.GetPixelToBinMappingRaw().data()
+ (m_offset + m) * RAW_MODULE_SIZE,
tmp.data(), m);
}
frame_transformation_ready.wait();
logger.Debug("Device thread {} start FPGA action", data_stream);
acquisition_device[data_stream].StartAction(experiment);
} catch (const JFJochException &e) {
Cancel(e);
data_acquisition_ready.count_down();
logger.ErrorException(e);
logger.Warning("Device thread {} done due to an error", data_stream);
return;
}
data_acquisition_ready.count_down();
try {
bool send_wr_to_fpga_immediately = (experiment.GetImageNum() == 0);
logger.Debug("Device thread {} wait for FPGA action complete", data_stream);
acquisition_device[data_stream].WaitForActionComplete(send_wr_to_fpga_immediately);
} catch (const JFJochException &e) {
logger.ErrorException(e);
Cancel(e);
logger.ErrorException(e);
logger.Warning("Device thread {} done due to an error", data_stream);
return;
}
logger.Info("Device thread {} done", data_stream);
}
void JFJochReceiver::RetrievePedestal() {
try {
if ((experiment.GetDetectorMode() == DetectorMode::PedestalG0)
|| ((experiment.GetDetectorMode() == DetectorMode::PedestalG1)
&& experiment.IsFixedGainG1())) {
pedestal_result.resize(experiment.GetModulesNum() * experiment.GetStorageCellNumber());
for (int s = 0; s < experiment.GetStorageCellNumber(); s++) {
for (int d = 0; d < ndatastreams; d++) {
for (int m = 0; m < experiment.GetModulesNum(d); m++) {
size_t offset = experiment.GetModulesNum() * s + experiment.GetFirstModuleOfDataStream(d) + m;
JFModulePedestal pedestal(16384);
try {
pedestal.ImportFPGAPedestal(acquisition_device[d].GetDeviceOutputPedestal(s, m));
} catch (const JFJochException& e) {
logger.Warning("Pedestal not collected for module {} storage cell {}", s, m);
}
pedestal_result[offset] = pedestal;
pedestal_result[offset].SetCollectionTime(start_time.time_since_epoch().count() / 1e9);
}
}
}
} else if ((experiment.GetDetectorMode() == DetectorMode::PedestalG1)
|| (experiment.GetDetectorMode() == DetectorMode::PedestalG2)) {
pedestal_result.resize(experiment.GetModulesNum());
for (int d = 0; d < ndatastreams; d++) {
for (int m = 0; m < experiment.GetModulesNum(d); m++) {
size_t offset = experiment.GetFirstModuleOfDataStream(d) + m;
JFModulePedestal pedestal(16384);
try {
pedestal.ImportFPGAPedestal(acquisition_device[d].GetDeviceOutputPedestal(
(experiment.GetStorageCellNumber() == 2) ? 1 : 0, m));
} catch (const JFJochException& e) {
logger.Warning("Pedestal not collected for module {}", m);
}
pedestal_result[offset] = pedestal;
pedestal_result[offset].SetCollectionTime(start_time.time_since_epoch().count() / 1e9);
}
}
}
} catch (const JFJochException& e) {
logger.ErrorException(e);
}
}
void JFJochReceiver::FrameTransformationThread(uint32_t threadid) {
std::unique_ptr<MXAnalyzer> analyzer;
try {
numa_policy.Bind(threadid);
analyzer = std::make_unique<MXAnalyzer>(experiment);
} catch (const JFJochException &e) {
frame_transformation_ready.count_down();
logger.Error("Thread setup error {}", e.what());
Cancel(e);
return;
}
FrameTransformation transformation(experiment);
frame_transformation_ready.count_down();
uint16_t az_int_min_bin = std::floor(az_int_mapping.QToBin(experiment.GetLowQForBkgEstimate_recipA()));
uint16_t az_int_max_bin = std::ceil(az_int_mapping.QToBin(experiment.GetHighQForBkgEstimate_recipA()));
uint64_t image_number;
while (images_to_go.Get(image_number) != 0) {
try {
logger.Debug("Frame transformation thread - trying to get image {}", image_number);
// If data acquisition is finished and fastest frame for the first device is behind
acquisition_device[0].Counters().WaitForFrame(image_number + 1);
logger.Debug("Frame transformation thread - frame arrived {}", image_number + 1);
if (acquisition_device[0].Counters().IsAcquisitionFinished() &&
(acquisition_device[0].Counters().GetFastestFrameNumber() < image_number)) {
logger.Debug("Frame transformation thread - skipping image {}", image_number);
continue;
}
DataMessage message{};
message.number = image_number;
message.original_number = image_number;
message.user_data = experiment.GetImageAppendix();
message.series_id = experiment.GetSeriesID();
message.series_unique_id = experiment.GetSeriesIDString();
ImageMetadata metadata(experiment);
AzimuthalIntegrationProfile az_int_profile_image(az_int_mapping);
auto local_spot_finding_settings = GetSpotFindingSettings();
logger.Debug("Frame transformation thread - processing image from FPGA {}", image_number);
for (int d = 0; d < ndatastreams; d++) {
for (int m = 0; m < experiment.GetModulesNum(d); m++) {
acquisition_device[d].Counters().WaitForFrame(image_number + 1, m);
if (acquisition_device[d].Counters().IsAnyPacketCollected(image_number, m)) {
const DeviceOutput* output = acquisition_device[d].GetDeviceOutput(image_number, m);
metadata.Process(output);
size_t module_abs_number = experiment.GetFirstModuleOfDataStream(d) + m;
adu_histogram_module[module_abs_number].Add(*output);
az_int_profile_image.Add(*output);
analyzer->ReadFromFPGA(output, local_spot_finding_settings, module_abs_number);
transformation.ProcessModule(output, d);
} else
transformation.FillNotCollectedModule(m, d);
acquisition_device[d].FrameBufferRelease(image_number, m);
}
auto delay = acquisition_device[d].Counters().CalculateDelay(image_number);
UpdateMaxDelay(delay);
if (delay > message.receiver_aq_dev_delay)
message.receiver_aq_dev_delay = delay;
}
metadata.Export(message, 256 * experiment.GetModulesNum() * experiment.GetSummation());
if (message.image_collection_efficiency == 0.0f) {
plots.AddEmptyImage(message);
continue;
}
analyzer->Process(message, local_spot_finding_settings);
message.receiver_free_send_buf = send_buf_ctrl.GetAvailBufLocations();
message.az_int_profile = az_int_profile_image.GetResult();
message.bkg_estimate = az_int_profile_image.GetMeanValueOfBins(az_int_min_bin, az_int_max_bin);
plots.Add(message, image_number % experiment.GetTimePointNumber(), az_int_profile_image);
preview_image.UpdateImage(transformation.GetImage(), message.spots);
if (message.indexing_result)
preview_image_indexed.UpdateImage(transformation.GetImage(), message.spots);
images_collected++;
if (!push_images_to_writer)
continue;
if (!serialmx_filter.ApplyFilter(message)) {
images_skipped++;
continue;
}
auto loc = send_buf_ctrl.GetBufLocation();
if (loc == nullptr)
continue;
auto writer_buffer = (uint8_t *)loc->get_ptr();
CBORStream2Serializer serializer(writer_buffer, experiment.GetSendBufferLocationSize());
PrepareCBORImage(message, experiment, nullptr, 0);
serializer.SerializeImage(message);
if (experiment.GetSendBufferLocationSize() - serializer.GetImageAppendOffset()
< experiment.GetMaxCompressedSize())
throw JFJochException(JFJochExceptionCategory::ArrayOutOfBounds, "Not enough memory to save image");
size_t image_size = transformation.CompressImage(writer_buffer + serializer.GetImageAppendOffset());
serializer.AppendImage(image_size);
compressed_size += image_size;
image_pusher.SendImage(writer_buffer, serializer.GetBufferSize(), message.number, loc);
images_sent++; // Handle case when image not sent properly
UpdateMaxImage(message.number);
logger.Debug("Frame transformation thread - done sending image {} / {}", image_number, message.number);
} catch (const JFJochException &e) {
logger.ErrorException(e);
Cancel(e);
}
}
logger.Debug("Sum&compression thread done");
}
float JFJochReceiver::GetEfficiency() const {
uint64_t expected_packets = 0;
uint64_t received_packets = 0;
for (int d = 0; d < ndatastreams; d++) {
expected_packets += acquisition_device[d].Counters().GetExpectedPackets();
received_packets += acquisition_device[d].Counters().GetTotalPackets();
}
if ((expected_packets == received_packets) || (expected_packets == 0))
return 1.0;
else
return received_packets / static_cast<double>(expected_packets);
}
void JFJochReceiver::Cancel(bool silent) {
if (!silent) {
// Remote abort: This tells FPGAs to stop, but doesn't do anything to CPU code
logger.Warning("Cancelling on request");
cancelled = true;
}
for (int d = 0; d < ndatastreams; d++)
acquisition_device[d].Cancel();
}
void JFJochReceiver::Cancel(const JFJochException &e) {
logger.Error("Cancelling data collection due to exception");
logger.ErrorException(e);
// Error abort: This tells FPGAs to stop and also prevents deadlock in CPU code, by setting abort to 1
cancelled = true;
for (int d = 0; d < ndatastreams; d++)
acquisition_device[d].Cancel();
}
float JFJochReceiver::GetProgress() const {
int64_t frames = experiment.GetImageNum();
if (frames == 0)
frames = experiment.GetFrameNum();
if ((frames == 0) || (acquisition_device[0].Counters().IsAcquisitionFinished()))
return 1.0;
else
return static_cast<float>(acquisition_device[0].Counters().GetSlowestFrameNumber()) / static_cast<float>(frames);
}
void JFJochReceiver::FinalizeMeasurement() {
if (!frame_transformation_futures.empty()) {
for (auto &future: frame_transformation_futures)
future.get();
logger.Info("All processing threads done");
}
if (push_images_to_writer) {
EndMessage message{};
message.max_image_number = max_image_number_sent;
message.images_collected_count = images_collected;
message.images_sent_to_write_count = images_sent;
message.max_receiver_delay = max_delay;
message.efficiency = GetEfficiency();
message.end_date = time_UTC(std::chrono::system_clock::now());
message.series_id = experiment.GetSeriesID();
message.series_unique_id = experiment.GetSeriesIDString();
message.az_int_result["dataset"] = plots.GetAzIntProfile();
for (int i = 0; i < experiment.GetTimePointNumber(); i++)
message.az_int_result["file" + std::to_string(i)] = plots.GetAzIntProfilePerFile(i);
for (int i = 0; i < adu_histogram_module.size(); i++)
message.adu_histogram["module" + std::to_string(i)] = adu_histogram_module[i].GetHistogram();
if (!image_pusher.EndDataCollection(message))
logger.Error("End message not sent via ZeroMQ (time-out)");
logger.Info("Disconnected from writers");
}
if (experiment.GetImageNum() > 0) {
for (int d = 0; d < ndatastreams; d++)
acquisition_device[d].Cancel();
}
end_time = std::chrono::system_clock::now();
for (auto &future : data_acquisition_futures)
future.get();
RetrievePedestal();
logger.Info("Devices stopped");
if (!send_buf_ctrl.CheckIfBufferReturned(std::chrono::seconds(10))) {
logger.Error("Send commands not finalized in 10 seconds");
throw JFJochException(JFJochExceptionCategory::ZeroMQ, "Send commands not finalized in 10 seconds");
}
logger.Info("Receiving data done");
}
void JFJochReceiver::SetSpotFindingSettings(const SpotFindingSettings &in_spot_finding_settings) {
std::unique_lock<std::mutex> ul(spot_finding_settings_mutex);
DiffractionExperiment::CheckDataProcessingSettings(in_spot_finding_settings);
spot_finding_settings = in_spot_finding_settings;
for (int i = 0; i < ndatastreams; i++)
acquisition_device[i].SetSpotFinderParameters(spot_finding_settings);
}
void JFJochReceiver::StopReceiver() {
if (measurement.valid()) {
measurement.get();
logger.Info("Receiver stopped");
}
}
JFJochReceiver::~JFJochReceiver() {
if (measurement.valid())
measurement.get();
}
SpotFindingSettings JFJochReceiver::GetSpotFindingSettings() {
std::unique_lock<std::mutex> ul(spot_finding_settings_mutex);
return spot_finding_settings;
}
MultiLinePlot JFJochReceiver::GetPlots(const PlotRequest &request) {
return plots.GetPlots(request);
}
void JFJochReceiver::UpdateMaxImage(uint64_t image_number) {
std::unique_lock<std::mutex> ul(max_image_number_sent_mutex);
if (image_number + 1 > max_image_number_sent)
max_image_number_sent = image_number + 1;
}
void JFJochReceiver::UpdateMaxDelay(uint64_t delay) {
std::unique_lock<std::mutex> ul(max_delay_mutex);
if (delay > max_delay)
max_delay = delay;
}
JFJochReceiverOutput JFJochReceiver::GetStatistics() const {
JFJochReceiverOutput ret;
for (int d = 0; d < ndatastreams; d++) {
for (int m = 0; m < acquisition_device[d].Counters().GetModuleNumber(); m++) {
ret.expected_packets.push_back(acquisition_device[d].Counters().GetExpectedPacketsPerModule());
ret.received_packets.push_back(acquisition_device[d].Counters().GetTotalPackets(m));
}
}
ret.efficiency = GetEfficiency();
ret.start_time_ms = std::chrono::duration_cast<std::chrono::milliseconds>(start_time.time_since_epoch()).count();
ret.end_time_ms = std::chrono::duration_cast<std::chrono::milliseconds>(end_time.time_since_epoch()).count();
ret.pedestal_result = pedestal_result;
ret.status = GetStatus();
return ret;
}
JFJochReceiverStatus JFJochReceiver::GetStatus() const {
JFJochReceiverStatus ret;
ret.indexing_rate = plots.GetIndexingRate();
ret.bkg_estimate = plots.GetBkgEstimate();
if ((experiment.GetImageNum() > 0) && (compressed_size > 0)) {
ret.compressed_ratio = static_cast<double> ((images_sent + images_skipped)
* experiment.GetPixelDepth()
* experiment.GetModulesNum()
* RAW_MODULE_SIZE)
/ static_cast<double> (compressed_size);
}
ret.progress = GetProgress();
ret.compressed_size = compressed_size;
ret.max_receive_delay = max_delay;
ret.max_image_number_sent = max_image_number_sent;
ret.images_collected = images_collected;
ret.images_sent = images_sent;
ret.images_skipped = images_skipped;
ret.cancelled = cancelled;
return ret;
}
void JFJochReceiver::GetXFELEventCode(std::vector<uint64_t> &v) const {
if (experiment.IsPulsedSource())
plots.GetXFELEventCode(v);
}
void JFJochReceiver::GetXFELPulseID(std::vector<uint64_t> &v) const {
if (experiment.IsPulsedSource())
plots.GetXFELPulseID(v);
}