The analysis read the --model file itself, four to five times per run (the model kind, every validation, molecular replacement, the stills reference intensities) and located the PAE sidecar from the file name. The library is to do no file I/O, so the model now arrives in memory: - RugnuxModel (image_analysis/structure_refinement/RugnuxModel.h): the gemmi structure as read, whether it is ModelCIF, the PAE matrix where a prediction came with one, and the name the report gives it. - ParseRugnuxModel / ReadRugnuxModelFile (writer/RugnuxModelFile.h, in JFJochRugnuxFiles): bytes in, gzip by magic, PDB/mmCIF by content, _ma_qa_metric detection as before; the file reader takes the PAE JSON from the same place PaePathFor named. - ProcessConfig::model replaces model_path; PrepareSearchModel, RunMolecularReplacement, ValidateAgainstModel and ModelReferenceIntensities take the model; result fields name it by model_name. - rugnux reads the model before the run starts and stops with an error where the file holds no model (it used to run and report the model as not validated). The viewer reads it when the job is set up. - The broker parses an uploaded model at once and answers 400 where it is not one; it keeps the parsed model in memory, with no temporary directory or file. It takes no PAE. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
403 lines
17 KiB
C++
403 lines
17 KiB
C++
// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include "JFJochReceiverService.h"
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#include "JFJochReceiverRugnux.h"
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#include "../common/ThreadAffinity.h"
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#include "../rugnux/RugnuxDefaults.h"
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#include "JFJochReceiverFPGA.h"
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#include "JFJochReceiverLite.h"
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#include "../preview/JFJochJPEG.h"
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#include "../preview/JFJochTIFF.h"
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JFJochReceiverService::JFJochReceiverService(AcquisitionDeviceGroup &in_aq_devices,
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Logger &in_logger, ImagePusher &pusher,
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size_t send_buffer_size_MiB)
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: aq_devices(in_aq_devices),
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logger(in_logger),
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image_buffer(send_buffer_size_MiB * 1024 * 1024),
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image_pusher(pusher),
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spot_finding_settings(DiffractionExperiment::DefaultDataProcessingSettings()) {
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}
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JFJochReceiverService &JFJochReceiverService::RugnuxLive(bool enable, std::shared_ptr<const RugnuxModel> model,
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int reserved_cpus, double deadline_s) {
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std::unique_lock ul_state(state_mutex);
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if (state != ReceiverState::Idle)
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throw JFJochException(JFJochExceptionCategory::WrongDAQState,
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"Cannot change rugnux settings during data collection");
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rugnux_enable = enable;
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rugnux_model = std::move(model);
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rugnux_reserved_cpus = reserved_cpus;
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rugnux_deadline_s = deadline_s;
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return *this;
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}
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RugnuxLiveSnapshot JFJochReceiverService::GetRugnuxStatus() const {
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return rugnux_status.Get();
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}
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JFJochReceiverService &JFJochReceiverService::NumThreads(int64_t input) {
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if (input <= 0)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Thread number must be above zero");
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nthreads = input;
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return *this;
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}
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void JFJochReceiverService::FinalizeMeasurementChangeState() {
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std::unique_lock ul(state_mutex);
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state = ReceiverState::Idle;
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measurement_done.notify_all();
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}
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void JFJochReceiverService::FinalizeMeasurement() {
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try {
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receiver->StopReceiver();
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} catch (...) {
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FinalizeMeasurementChangeState();
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throw;
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}
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FinalizeMeasurementChangeState();
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}
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std::optional<JFJochReceiverStatus> JFJochReceiverService::GetStatus() {
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return receiver_status.GetStatus();
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}
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void JFJochReceiverService::Preflight(const DiffractionExperiment &experiment) {
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// Same condition JFJochReceiver uses to decide whether it pushes to a writer at all: with no
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// images or no file prefix nothing is written, so there is nothing to check.
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if ((experiment.GetImageNum() <= 0) || experiment.GetFilePrefix().empty())
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return;
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// FillMessage alone, which is what makes this frame small: the per-pixel arrays that dominate a
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// real start message - the pixel mask, the azimuthal-integration map, the ROI map - are added
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// by JFJochReceiver::SendStartMessage and are not here. Measured on a JUNGFRAU 9M: 1.4 kB
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// against 543 kB for the start message that follows. It is deliberately the whole of
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// FillMessage rather than the handful of fields the check reads today, so that the writer sees
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// the same description of the run it will be given at start - a hand-picked subset would
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// answer for a different set of file names the day the check learns to read one more field.
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StartMessage message{};
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experiment.FillMessage(message);
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image_pusher.Preflight(message);
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}
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void JFJochReceiverService::Start(const DiffractionExperiment &experiment,
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const PixelMask &pixel_mask,
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const JFCalibration *calibration,
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std::shared_ptr<ImagePuller> puller) {
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std::unique_lock ul_state(state_mutex); // unique lock, as it will destroy and create receiver object
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if (state != ReceiverState::Idle)
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throw JFJochException(JFJochExceptionCategory::WrongDAQState, "Receiver not idle, cannot start");
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try {
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auto nthreads_local = nthreads;
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if (experiment.IsCPUSummation())
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nthreads_local = 4;
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// First clean-up old measurement
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receiver.reset();
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preview_image.Configure(experiment, pixel_mask);
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switch (experiment.GetDetectorType()) {
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case DetectorType::EIGER:
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case DetectorType::JUNGFRAU:
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receiver = std::make_unique<JFJochReceiverFPGA>(experiment, pixel_mask,
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calibration,
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aq_devices, image_pusher,
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logger,
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nthreads_local,
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spot_finding_settings,
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receiver_status,
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plots,
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image_buffer,
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zmq_preview_socket.get(),
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zmq_metadata_socket.get(),
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indexer_thread_pool.get());
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break;
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case DetectorType::DECTRIS:
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if (puller)
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image_puller = puller;
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else {
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image_puller = std::make_shared<ZMQImagePuller>(
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experiment.GetDetectorSetup().GetDECTRISStream2Addr());
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}
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if (rugnux_enable && RugnuxRotationData(experiment)) {
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receiver = std::make_unique<JFJochReceiverRugnux>(
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experiment, pixel_mask, *image_puller, image_pusher, logger, nthreads_local,
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std::max<int>(1, static_cast<int>(AvailableCpus()) - rugnux_reserved_cpus),
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rugnux_model, rugnux_deadline_s, rugnux_status, spot_finding_settings, receiver_status, plots, image_buffer,
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zmq_preview_socket.get(), zmq_metadata_socket.get());
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break;
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}
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receiver = std::make_unique<JFJochReceiverLite>(experiment,
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pixel_mask,
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*image_puller,
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image_pusher,
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logger,
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nthreads_local,
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spot_finding_settings,
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receiver_status,
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plots,
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image_buffer,
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zmq_preview_socket.get(),
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zmq_metadata_socket.get(),
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indexer_thread_pool.get());
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break;
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}
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measurement = std::async(std::launch::async, &JFJochReceiverService::FinalizeMeasurement, this);
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state = ReceiverState::Running;
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} catch (const std::exception &e) {
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// The receiver never started, so drop the status its base constructor had already reset -
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// otherwise /status and /statistics keep reporting a zero-progress run that never happened,
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// until the next start overwrites it.
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receiver_status.Clear();
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receiver_status.SetProgress({});
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logger.ErrorException(e);
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throw;
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}
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}
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void JFJochReceiverService::Cancel(bool silent) {
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std::unique_lock ul(state_mutex);
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if (state == ReceiverState::Running)
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receiver->Cancel(silent);
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}
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JFJochReceiverOutput JFJochReceiverService::Stop() {
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std::unique_lock ul(state_mutex);
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measurement_done.wait(ul, [this] { return (state != ReceiverState::Running); });
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if (state != ReceiverState::Idle)
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throw JFJochException(JFJochExceptionCategory::WrongReceiverState, "Receiver in weird state");
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try {
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if (measurement.valid())
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measurement.get();
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} catch (JFJochException &e) {
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logger.ErrorException(e);
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throw;
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}
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if (!receiver) {
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logger.Warning("Request to stop while receiver not running");
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throw JFJochException(JFJochExceptionCategory::WrongReceiverState, "Receiver idle, cannot stop");
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}
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return receiver->GetFinalStatistics();
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}
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void JFJochReceiverService::SetSpotFindingSettings(const SpotFindingSettings &settings) {
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try {
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std::unique_lock ul(state_mutex);
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DiffractionExperiment::CheckDataProcessingSettings(settings);
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spot_finding_settings = settings;
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if (state != ReceiverState::Idle)
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receiver->SetSpotFindingSettings(settings);
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} catch (std::exception &e) {
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logger.ErrorException(e);
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throw;
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}
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}
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MultiLinePlot JFJochReceiverService::GetDataProcessingPlot(const PlotRequest &request) {
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return plots.GetPlots(request);
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}
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void JFJochReceiverService::GetPlotRaw(std::vector<float> &v, PlotType type, const std::string &roi) {
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plots.GetPlotRaw(v, type, roi);
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}
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std::vector<AcquisitionDeviceNetConfig> JFJochReceiverService::GetNetworkConfig() {
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return aq_devices.GetNetworkConfig();
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}
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void JFJochReceiverService::LoadInternalGeneratorImage(const DiffractionExperiment &experiment,
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const std::vector<uint16_t> &image,
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uint64_t image_number) {
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std::vector<uint16_t> raw_geom, eiger_geom;
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const uint16_t *frame;
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if (image.size() == RAW_MODULE_SIZE * experiment.GetModulesNum()) {
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frame = image.data();
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} else if (image.size() == experiment.GetPixelsNum()) {
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raw_geom.resize(RAW_MODULE_SIZE * experiment.GetModulesNum());
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ConvertedToRawGeometry(experiment, raw_geom.data(), image.data());
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frame = raw_geom.data();
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} else
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Size of input array with raw expected image is wrong");
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for (int i = 0; i < experiment.GetDataStreamsNum(); i++) {
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uint32_t module0 = experiment.GetFirstModuleOfDataStream(i);
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switch (experiment.GetDetectorSetup().GetDetectorType()) {
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case DetectorType::EIGER:
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eiger_geom.resize(RAW_MODULE_SIZE);
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for (int m = 0; m < experiment.GetModulesNum(i); m++) {
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RawToEigerInput(eiger_geom.data(), frame + (module0 + m) * RAW_MODULE_SIZE);
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aq_devices[i].SetInternalGeneratorFrame(eiger_geom.data(),
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m + experiment.GetModulesNum(i) * image_number);
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}
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break;
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case DetectorType::JUNGFRAU:
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for (int m = 0; m < experiment.GetModulesNum(i); m++)
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aq_devices[i].SetInternalGeneratorFrame(frame + (module0 + m) * RAW_MODULE_SIZE,
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m + experiment.GetModulesNum(i) * image_number);
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break;
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default:
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Detector not supported");
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}
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}
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}
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void JFJochReceiverService::GetXFELEventCode(std::vector<uint64_t> &v) const {
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plots.GetXFELEventCode(v);
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}
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void JFJochReceiverService::GetXFELPulseID(std::vector<uint64_t> &v) const {
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plots.GetXFELPulseID(v);
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}
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std::vector<DeviceStatus> JFJochReceiverService::GetDeviceStatus() const {
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return aq_devices.GetDeviceStatus();
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}
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std::optional<float> JFJochReceiverService::GetProgress() const {
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return receiver_status.GetProgress();
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}
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JFJochReceiverService &JFJochReceiverService::PreviewSocket(const std::string &addr, const std::optional<int32_t> &watermark) {
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if (!addr.empty()) {
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logger.Info("ZeroMQ preview socket available at {}", addr);
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zmq_preview_socket = std::make_unique<ZMQPreviewSocket>(addr, watermark);
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}
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return *this;
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}
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JFJochReceiverService &JFJochReceiverService::MetadataSocket(const std::string &addr) {
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if (!addr.empty()) {
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logger.Info("ZeroMQ metadata socket available at {}", addr);
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zmq_metadata_socket = std::make_unique<ZMQMetadataSocket>(addr);
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}
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return *this;
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}
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std::string JFJochReceiverService::GetPreviewSocketAddress() const {
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if (zmq_preview_socket)
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return zmq_preview_socket->GetAddress();
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return "";
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}
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std::string JFJochReceiverService::GetMetadataSocketAddress() const {
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if (zmq_metadata_socket)
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return zmq_metadata_socket->GetAddress();
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return "";
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}
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JFJochReceiverService &JFJochReceiverService::PreviewSocketSettings(const ZMQPreviewSettings &input) {
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if (zmq_preview_socket)
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zmq_preview_socket->ImportSettings(input);
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return *this;
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}
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JFJochReceiverService &JFJochReceiverService::MetadataSocketSettings(const ZMQMetadataSettings &input) {
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if (zmq_metadata_socket)
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zmq_metadata_socket->ImportSettings(input);
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return *this;
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}
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ZMQPreviewSettings JFJochReceiverService::GetPreviewSocketSettings() const {
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if (zmq_preview_socket)
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return zmq_preview_socket->GetSettings();
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return {};
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}
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ZMQMetadataSettings JFJochReceiverService::GetMetadataSocketSettings() const {
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if (zmq_metadata_socket)
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return zmq_metadata_socket->GetSettings();
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return {};
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}
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void JFJochReceiverService::GetStartMessageFromBuffer(std::vector<uint8_t> &v) {
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image_buffer.GetStartMessage(v);
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}
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bool JFJochReceiverService::GetImageFromBuffer(std::vector<uint8_t> &v, int64_t image_number) {
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return image_buffer.GetImage(v, image_number);
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}
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std::string JFJochReceiverService::GetJPEGFromBuffer(const PreviewImageSettings &settings, int64_t image_number) {
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std::vector<uint8_t> cbor_image;
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if (!image_buffer.GetImage(cbor_image, image_number))
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return {};
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return preview_image.GenerateImage(settings, cbor_image);
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}
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std::string JFJochReceiverService::GetTIFFFromBuffer(int64_t image_number) {
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std::vector<uint8_t> cbor_image;
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if (!image_buffer.GetImage(cbor_image, image_number))
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return {};
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return PreviewImage::GenerateTIFF(cbor_image);
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}
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ImageBufferStatus JFJochReceiverService::GetImageBufferStatus() const {
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return image_buffer.GetStatus();
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}
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void JFJochReceiverService::ClearResults() {
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std::unique_lock ul(state_mutex);
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if (state != ReceiverState::Idle)
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throw JFJochException(JFJochExceptionCategory::WrongDAQState,
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"Cannot clear results during data collection");
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receiver_status.Clear();
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receiver_status.SetProgress({});
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plots.Clear();
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image_buffer.Finalize(std::chrono::milliseconds(2500));
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}
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void JFJochReceiverService::ClearImageBuffer() {
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std::unique_lock ul(state_mutex);
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// Clearing image buffer during data collection could be catastrophic, so better protect here, even if redundant
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// with JFJochStateMachine
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if (state == ReceiverState::Idle)
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image_buffer.Finalize(std::chrono::milliseconds(2500));
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else
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throw JFJochException(JFJochExceptionCategory::WrongDAQState,
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"Cannot clear image buffer during data collection");
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}
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JFJochReceiverService &JFJochReceiverService::Indexing(const IndexingSettings &input) {
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std::unique_lock ul(state_mutex);
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// Clearing image buffer during data collection could be catastrophic, so better protect here, even if redundant
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// with JFJochStateMachine
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if (state == ReceiverState::Idle) {
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// Release the previous run's receiver first. It holds a raw pointer to the indexer pool and
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// its own GPU resources; keeping it alive while we rebuild the pool means a fresh GPU indexer
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// has to coexist with a stale receiver (e.g. after a failed acquisition start, where the
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// receiver is stopped but not destroyed until the next Start), which can make the GPU indexer
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// initialisation fail. Destroying the receiver before the pool also avoids the dangling
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// pointer. Safe here: state is Idle, so no measurement is using it.
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receiver.reset();
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logger.Info("Resetting indexing thread pool");
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indexer_thread_pool.reset();
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if (input.GetAlgorithm() != IndexingAlgorithmEnum::None) {
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logger.Info("Creating indexing thread pool...");
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indexer_thread_pool = std::make_unique<IndexerThreadPool>(input);
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logger.Info(" ... done");
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}
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return *this;
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} else
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throw JFJochException(JFJochExceptionCategory::WrongDAQState,
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"Cannot change indexing settings during data collection");
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}
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ImagePusherStatus JFJochReceiverService::GetImagePusherStatus() const {
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return image_pusher.GetStatus();
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}
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