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>
410 lines
15 KiB
C++
410 lines
15 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 "JFJochServices.h"
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#include "../common/JFJochException.h"
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#include "../detector_control/SLSDetectorWrapper.h"
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#include "../detector_control/DectrisDetectorWrapper.h"
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JFJochServices::JFJochServices(Logger &in_logger) : logger(in_logger) {}
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void JFJochServices::Preflight(const DiffractionExperiment& experiment) {
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if (receiver == nullptr)
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return;
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receiver->Preflight(experiment);
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}
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void JFJochServices::Start(const DiffractionExperiment& experiment,
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const PixelMask &pixel_mask,
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const JFCalibration *calibration) {
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logger.Info("Measurement start for: {}", experiment.GetFilePrefix());
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cannot_stop_detector = false;
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if (receiver == nullptr) {
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logger.Info(" Done!");
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return;
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}
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logger.Info(" ... receiver start");
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if (image_puller)
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image_puller->ResumeAndClear();
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receiver->Start(experiment, pixel_mask, calibration, image_puller);
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// From here the receiver is running asynchronously. If starting the detector fails, stop the
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// receiver again so the service returns to idle and the run can be retried without
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// re-initialising. The detector failure is then propagated (a critical detector error stays
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// critical, so the broker still goes to the Error state).
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try {
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std::shared_lock ul(detector_mutex);
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if (detector && !experiment.IsUsingInternalPacketGen()) {
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logger.Info(" ... detector start");
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detector->Start(experiment);
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}
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} catch (const std::exception &e) {
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logger.Error(" ... detector failed to start ({}) - stopping detector and receiver", e.what());
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// Best-effort cleanup - it must not replace the original detector exception (which may be
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// critical), so swallow anything it throws and let the throw below re-raise e. The detector
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// may have partially armed before failing, so stop it too; otherwise it lingers in a BUSY
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// state and the next start fails with "detector busy" until a manual re-initialisation.
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try {
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{
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std::shared_lock ul(detector_mutex);
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if (detector)
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detector->Stop();
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}
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receiver->Cancel(false);
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receiver->Stop();
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} catch (const std::exception &stop_error) {
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logger.Warning("Stop after failed start reported: {}", stop_error.what());
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}
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throw;
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}
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logger.Info(" Done!");
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}
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void JFJochServices::Off() {
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// Disconnect explicitly rather than relying on the destructor: the receiver service keeps its
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// own shared_ptr to the puller of the last run, so dropping this one does not necessarily close
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// the socket, and a puller left connected keeps taking its share of the detector stream.
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if (image_puller)
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image_puller->Disconnect();
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image_puller.reset();
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std::unique_ptr<DetectorWrapper> old_detector;
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{
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std::unique_lock ul(detector_mutex);
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old_detector = std::move(detector);
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}
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if (old_detector) {
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old_detector->Deactivate();
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// destroyed here, outside lock
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}
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}
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void JFJochServices::On(DiffractionExperiment &x) {
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if (x.IsUsingInternalPacketGen() || (receiver == nullptr)) {
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std::unique_lock ul(detector_mutex);
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detector.reset();
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} else {
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logger.Info("Detector on");
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// The previous puller has to be disconnected before the new one connects. Dropping the
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// shared_ptr is not enough: the receiver service keeps its own reference to the puller of
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// the last run, so the socket would stay open - and two PULL sockets on the same DECTRIS
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// stream share the messages round-robin, so the old one silently swallows half of the
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// stream, the start message included. The run then never starts and the receiver waits for
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// a start message that has already been thrown away.
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if (image_puller)
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image_puller->Disconnect();
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std::unique_ptr<DetectorWrapper> new_detector;
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switch (x.GetDetectorType()) {
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case DetectorType::EIGER:
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case DetectorType::JUNGFRAU:
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new_detector = std::make_unique<SLSDetectorWrapper>();
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image_puller.reset();
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break;
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case DetectorType::DECTRIS:
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new_detector = std::make_unique<DectrisDetectorWrapper>();
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image_puller = std::make_shared<ZMQImagePuller>(x.GetDetectorSetup().GetDECTRISStream2Addr());
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image_puller->Suspend();
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break;
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}
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new_detector->Initialize(x, receiver->GetNetworkConfig());
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{
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std::unique_lock ul(detector_mutex);
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detector = std::move(new_detector);
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}
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logger.Info(" ... done");
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}
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}
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JFJochServicesOutput JFJochServices::Stop() {
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JFJochServicesOutput ret;
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// Captured as an exception_ptr (not a copied JFJochException) so the dynamic type survives: a
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// critical hardware fault (e.g. PCIeDeviceException) must stay critical when re-thrown, otherwise
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// slicing it to a plain JFJochException would send the state machine to Idle instead of Error.
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std::exception_ptr exception;
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bool detector_error = false;
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if (receiver != nullptr) {
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try {
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{
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std::shared_lock ul(detector_mutex);
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if (detector) {
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logger.Info("Wait for detector idle");
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DetectorState state = detector->GetState();
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while ((!cannot_stop_detector)
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&& ((state == DetectorState::WAITING) || (state == DetectorState::BUSY))) {
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// check detector state every 100 ms - every check is an HTTP request for DECTRIS
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std::this_thread::sleep_for(std::chrono::milliseconds(100));
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state = detector->GetState();
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}
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if (state == DetectorState::IDLE) {
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logger.Info(" ... detector idle");
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receiver->Cancel(true); // cancel silently
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} else {
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logger.Error(" ... detector not idle: state {}{}; {}", to_string(state),
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cannot_stop_detector ? " (stop command failed)" : "",
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detector->GetErrorDescription());
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receiver->Cancel(false);
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detector_error = true;
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}
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}
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}
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logger.Info("Wait for receiver done");
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ret.receiver_output = receiver->Stop();
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if (image_puller)
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image_puller->Suspend();
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logger.Info(" ... Receiver efficiency: {} % Max delay: {} Compression ratio {}x",
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static_cast<int>(ret.receiver_output.efficiency * 100.0),
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ret.receiver_output.status.max_receive_delay.value_or(0),
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static_cast<int>(std::round(ret.receiver_output.status.compressed_ratio.value_or(1))));
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if (ret.receiver_output.efficiency < 1.0) {
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for (int i = 0; i < ret.receiver_output.received_packets.size(); i++) {
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if (ret.receiver_output.received_packets[i] != ret.receiver_output.expected_packets[i])
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logger.Info(" ... Module: {} Packets received: {} out of {}", i,
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ret.receiver_output.received_packets[i], ret.receiver_output.expected_packets[i]);
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}
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}
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// A writer that broke mid-run (e.g. a lost connection) leaves a truncated file. This is
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// reported to the caller via receiver_output.writer_err (the state machine surfaces it as
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// an error message) - it is not a detector fault, so it does not need re-initialisation.
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logger.Info(" ... finished with success");
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} catch (const JFJochException &e) {
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logger.Error(" ... finished with error {}", e.what());
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exception = std::current_exception();
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}
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} else {
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logger.Info("No receiver - sleeping for 30 seconds");
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std::this_thread::sleep_for(std::chrono::seconds(30));
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logger.Info("Sleep done");
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}
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// A detector fault must win over an ordinary receiver/writer error: it needs re-initialisation,
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// so raise the critical exception first. If only the receiver failed, the run can be retried from
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// Idle, so that ordinary error is raised second.
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if (detector_error)
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throw JFJochCriticalException("Error in detector operation");
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if (exception)
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std::rethrow_exception(exception);
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return ret;
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}
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void JFJochServices::Cancel() {
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std::shared_lock ul(detector_mutex);
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if (detector) {
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// Best effort - if detector cannot be stopped, this is OK, important to still stop receiver
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try {
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detector->Stop();
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} catch (const std::exception &e) {
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logger.Error("Cannot stop detector: {}", e.what());
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cannot_stop_detector = true;
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} catch (...) {
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cannot_stop_detector = true;
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}
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}
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if (receiver != nullptr)
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receiver->Cancel(false);
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}
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JFJochServices &JFJochServices::Receiver(JFJochReceiverService *input) {
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receiver = input;
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return *this;
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}
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std::optional<JFJochReceiverStatus> JFJochServices::GetReceiverStatus() const {
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if (receiver == nullptr)
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return {};
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return receiver->GetStatus();
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}
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std::optional<float> JFJochServices::GetReceiverProgress() const {
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if (receiver == nullptr)
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return {};
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return receiver->GetProgress();
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}
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MultiLinePlot JFJochServices::GetPlots(const PlotRequest &request) {
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if (receiver == nullptr)
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return {};
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return receiver->GetDataProcessingPlot(request);
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}
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void JFJochServices::GetPlotRaw(std::vector<float> &v, PlotType type, const std::string &roi) {
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if (receiver != nullptr)
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receiver->GetPlotRaw(v, type, roi);
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}
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void JFJochServices::SetSpotFindingSettings(const SpotFindingSettings &settings) {
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if (receiver)
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receiver->SetSpotFindingSettings(settings);
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}
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void JFJochServices::Trigger() {
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std::shared_lock ul(detector_mutex);
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if (detector && (receiver != nullptr))
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detector->Trigger();
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}
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std::optional<DetectorStatus> JFJochServices::GetDetectorStatus() const {
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std::shared_lock ul(detector_mutex, std::defer_lock);
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if (ul.try_lock_for(std::chrono::milliseconds(500)) && detector)
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return detector->GetStatus();
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return {};
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}
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std::string JFJochServices::GetPreviewJPEG(const PreviewImageSettings &settings, int64_t image_number) const {
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if (receiver != nullptr)
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return receiver->GetJPEGFromBuffer(settings, image_number);
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else
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return {};
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}
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std::string JFJochServices::GetPreviewTIFF(int64_t image_number) const {
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if (receiver != nullptr)
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return receiver->GetTIFFFromBuffer(image_number);
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else
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return "";
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}
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void JFJochServices::ConfigureDetector(const DiffractionExperiment &experiment) {
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std::unique_lock ul(detector_mutex); // While configuring detector ensure exclusive access (even though pointer is not modified here)
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if (detector)
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detector->Configure(experiment);
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}
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void JFJochServices::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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if (receiver)
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receiver->LoadInternalGeneratorImage(experiment, image, image_number);
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}
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void JFJochServices::GetXFELPulseID(std::vector<uint64_t> &v) const {
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if (receiver)
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receiver->GetXFELPulseID(v);
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}
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void JFJochServices::GetXFELEventCode(std::vector<uint64_t> &v) const {
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if (receiver)
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receiver->GetXFELEventCode(v);
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}
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std::vector<DeviceStatus> JFJochServices::GetDeviceStatus() const {
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std::vector<DeviceStatus> ret;
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if (receiver)
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ret = receiver->GetDeviceStatus();
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return ret;
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}
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ZMQPreviewSettings JFJochServices::GetPreviewSocketSettings() {
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if (receiver)
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return receiver->GetPreviewSocketSettings();
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return {};
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}
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ZMQMetadataSettings JFJochServices::GetMetadataSocketSettings() {
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if (receiver)
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return receiver->GetMetadataSocketSettings();
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return {};
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}
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void JFJochServices::SetPreviewSocketSettings(const ZMQPreviewSettings &input) {
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if (receiver)
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receiver->PreviewSocketSettings(input);
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}
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void JFJochServices::SetMetadataSocketSettings(const ZMQMetadataSettings &input) {
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if (receiver)
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receiver->MetadataSocketSettings(input);
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}
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void JFJochServices::GetStartMessageFromBuffer(std::vector<uint8_t> &v) {
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if (receiver)
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return receiver->GetStartMessageFromBuffer(v);
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}
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bool JFJochServices::GetImageFromBuffer(std::vector<uint8_t> &v, int64_t image_number) {
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if (receiver)
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return receiver->GetImageFromBuffer(v, image_number);
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return false;
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}
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ImageBufferStatus JFJochServices::GetImageBufferStatus() const {
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if (receiver)
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return receiver->GetImageBufferStatus();
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else return ImageBufferStatus{.total_slots = 0, .available_slots = 0};
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}
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void JFJochServices::ClearImageBuffer() const {
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if (receiver)
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receiver->ClearImageBuffer();
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}
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void JFJochServices::ClearResults() const {
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if (receiver)
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receiver->ClearResults();
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}
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void JFJochServices::LoadDetectorPixelMask(PixelMask &mask) {
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std::shared_lock ul(detector_mutex);
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if (detector)
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detector->LoadPixelMask(mask);
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}
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void JFJochServices::SetupIndexing(const IndexingSettings &input) {
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if (receiver)
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receiver->Indexing(input);
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}
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void JFJochServices::SetRugnuxLive(const RugnuxLiveSettings &input) {
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if (receiver)
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receiver->RugnuxLive(input.enable, input.model, input.reserved_cpus, input.deadline_s);
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rugnux = input;
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}
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RugnuxLiveSettings JFJochServices::GetRugnuxLive() const {
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return rugnux;
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}
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RugnuxLiveSnapshot JFJochServices::GetRugnuxStatus() const {
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if (receiver)
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return receiver->GetRugnuxStatus();
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return {};
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}
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void JFJochServices::SetRugnuxModel(std::shared_ptr<const RugnuxModel> model, int64_t size_bytes) {
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RugnuxLiveSettings s = rugnux;
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s.model = std::move(model);
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s.model_size_bytes = s.model ? size_bytes : 0;
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SetRugnuxLive(s);
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}
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LiveCollection *JFJochServices::GetLiveCollection() {
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return receiver ? receiver->GetLiveCollection() : nullptr;
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}
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ImagePusherStatus JFJochServices::GetImagePusherStatus() const {
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if (receiver)
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return receiver->GetImagePusherStatus();
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return {
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.pusher_type = ImagePusherType::None,
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.address = {},
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.connected_writers = 0
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};
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}
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