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* `rugnux --model` adopts the model's space group as a label where the data were merged in its enantiomorph, instead of reindexing the reflections - which swapped I(+) with I(-). * `rugnux --model` warns, naming the atom, when the anomalous density at the model's atoms comes out inverted, which means the data and the model are in opposite hands. * `rugnux --model` writes an anomalous difference map (`<prefix>_anom.ccp4`) when the merge kept the Bijvoet split, and names the ten model atoms it peaks highest on as `ANOMALOUS_SITE_01`..`_10`. * `MEAN_ATOM_DENSITY_SIGMA` is read from the map by cubic rather than linear interpolation and comes out around a tenth higher; it is no longer comparable with the figure earlier versions printed. * `rugnux --model` reads an mmCIF coordinate file as well as a PDB one, gzipped or not, taking the format from the file's content rather than its name. * A model `rugnux --model` cannot use is reported as a `WARNING:` line in the results report instead of only in the log. * The rugnux results report has a `10. MODEL VALIDATION` section when `--model` was given; `REPORT_VERSION` is 4, `WARNINGS` moves to section 11 and no existing key changed. * The rugnux results report records how the run was invoked, what it cost and what it ran on: `COMMAND_LINE=`, `WALL_TIME=` and `GPU_COUNT=` / `GPU=`. * rugnux says which GPUs it can see before it starts processing. * `rugnux --export-unmerged` also writes `<prefix>_unmerged.mtz` on a `--no-merge` run, and is ignored on a run with no output prefix instead of writing a file called `_unmerged.mtz`. * `/start` asks the writer whether the run can be written before the detector is armed, so a run whose master file already exists, or whose output directory cannot be created, is refused up front with the writer's own message. This needs the TCP image stream or the built-in HDF5 writer; the ZeroMQ stream is unchanged. * A calibration that fails goes to `Error` carrying the reason instead of `Inactive`, so `/wait_till_done` and `/wait_until_running` report it; a cancelled calibration still goes to `Inactive`. * `/wait_till_done` answers 500 with the message when a collection ended in an error. A cancelled collection and a collection that only triggered a warning still answer 200. * A pending start failure is discarded by `/cancel` and `/deactivate`, as it already was by `/start` and `/initialize`. * `/scan_result` no longer reports the previous run's images after a collection that failed to start, or after `/deactivate`. * The TCP image stream protocol version is 4. `jfjoch_writer` and `jfjoch_broker` have to be of the same release, as before. Reviewed-on: #75
357 lines
12 KiB
C++
357 lines
12 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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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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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 5 ms
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std::this_thread::sleep_for(std::chrono::milliseconds(5));
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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 in error state");
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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 (...) {
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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::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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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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