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Jungfraujoch/broker/JFJochServices.cpp
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v1.0.0-rc.157 (#67)
This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.

* rugnux: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`.
* rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling.
* rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics.
* rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1.
* rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group.
* rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix.
* jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation.
* jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning.
* jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint.
* jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed).
* jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types.
* jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails.
* jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak.
* Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation.
* CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67

Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-07-11 07:19:11 +02:00

351 lines
12 KiB
C++

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "JFJochServices.h"
#include "../common/JFJochException.h"
#include "../detector_control/SLSDetectorWrapper.h"
#include "../detector_control/DectrisDetectorWrapper.h"
JFJochServices::JFJochServices(Logger &in_logger) : logger(in_logger) {}
void JFJochServices::Start(const DiffractionExperiment& experiment,
const PixelMask &pixel_mask,
const JFCalibration *calibration) {
logger.Info("Measurement start for: {}", experiment.GetFilePrefix());
cannot_stop_detector = false;
if (receiver == nullptr) {
logger.Info(" Done!");
return;
}
logger.Info(" ... receiver start");
if (image_puller)
image_puller->ResumeAndClear();
receiver->Start(experiment, pixel_mask, calibration, image_puller);
// From here the receiver is running asynchronously. If starting the detector fails, stop the
// receiver again so the service returns to idle and the run can be retried without
// re-initialising. The detector failure is then propagated (a critical detector error stays
// critical, so the broker still goes to the Error state).
try {
std::shared_lock ul(detector_mutex);
if (detector && !experiment.IsUsingInternalPacketGen()) {
logger.Info(" ... detector start");
detector->Start(experiment);
}
} catch (const std::exception &e) {
logger.Error(" ... detector failed to start ({}) - stopping detector and receiver", e.what());
// Best-effort cleanup - it must not replace the original detector exception (which may be
// critical), so swallow anything it throws and let the throw below re-raise e. The detector
// may have partially armed before failing, so stop it too; otherwise it lingers in a BUSY
// state and the next start fails with "detector busy" until a manual re-initialisation.
try {
{
std::shared_lock ul(detector_mutex);
if (detector)
detector->Stop();
}
receiver->Cancel(false);
receiver->Stop();
} catch (const std::exception &stop_error) {
logger.Warning("Stop after failed start reported: {}", stop_error.what());
}
throw;
}
logger.Info(" Done!");
}
void JFJochServices::Off() {
image_puller.reset();
std::unique_ptr<DetectorWrapper> old_detector;
{
std::unique_lock ul(detector_mutex);
old_detector = std::move(detector);
}
if (old_detector) {
old_detector->Deactivate();
// destroyed here, outside lock
}
}
void JFJochServices::On(DiffractionExperiment &x) {
if (x.IsUsingInternalPacketGen() || (receiver == nullptr)) {
std::unique_lock ul(detector_mutex);
detector.reset();
} else {
logger.Info("Detector on");
std::unique_ptr<DetectorWrapper> new_detector;
switch (x.GetDetectorType()) {
case DetectorType::EIGER:
case DetectorType::JUNGFRAU:
new_detector = std::make_unique<SLSDetectorWrapper>();
image_puller.reset();
break;
case DetectorType::DECTRIS:
new_detector = std::make_unique<DectrisDetectorWrapper>();
image_puller = std::make_shared<ZMQImagePuller>(x.GetDetectorSetup().GetDECTRISStream2Addr());
image_puller->Suspend();
break;
}
new_detector->Initialize(x, receiver->GetNetworkConfig());
{
std::unique_lock ul(detector_mutex);
detector = std::move(new_detector);
}
logger.Info(" ... done");
}
}
JFJochServicesOutput JFJochServices::Stop() {
JFJochServicesOutput ret;
// Captured as an exception_ptr (not a copied JFJochException) so the dynamic type survives: a
// critical hardware fault (e.g. PCIeDeviceException) must stay critical when re-thrown, otherwise
// slicing it to a plain JFJochException would send the state machine to Idle instead of Error.
std::exception_ptr exception;
bool detector_error = false;
if (receiver != nullptr) {
try {
{
std::shared_lock ul(detector_mutex);
if (detector) {
logger.Info("Wait for detector idle");
DetectorState state = detector->GetState();
while ((!cannot_stop_detector)
&& ((state == DetectorState::WAITING) || (state == DetectorState::BUSY))) {
// check detector state every 5 ms
std::this_thread::sleep_for(std::chrono::milliseconds(5));
state = detector->GetState();
}
if (state == DetectorState::IDLE) {
logger.Info(" ... detector idle");
receiver->Cancel(true); // cancel silently
} else {
logger.Error(" ... detector in error state");
receiver->Cancel(false);
detector_error = true;
}
}
}
logger.Info("Wait for receiver done");
ret.receiver_output = receiver->Stop();
if (image_puller)
image_puller->Suspend();
logger.Info(" ... Receiver efficiency: {} % Max delay: {} Compression ratio {}x",
static_cast<int>(ret.receiver_output.efficiency * 100.0),
ret.receiver_output.status.max_receive_delay.value_or(0),
static_cast<int>(std::round(ret.receiver_output.status.compressed_ratio.value_or(1))));
if (ret.receiver_output.efficiency < 1.0) {
for (int i = 0; i < ret.receiver_output.received_packets.size(); i++) {
if (ret.receiver_output.received_packets[i] != ret.receiver_output.expected_packets[i])
logger.Info(" ... Module: {} Packets received: {} out of {}", i,
ret.receiver_output.received_packets[i], ret.receiver_output.expected_packets[i]);
}
}
// A writer that broke mid-run (e.g. a lost connection) leaves a truncated file. This is
// reported to the caller via receiver_output.writer_err (the state machine surfaces it as
// an error message) - it is not a detector fault, so it does not need re-initialisation.
logger.Info(" ... finished with success");
} catch (const JFJochException &e) {
logger.Error(" ... finished with error {}", e.what());
exception = std::current_exception();
}
} else {
logger.Info("No receiver - sleeping for 30 seconds");
std::this_thread::sleep_for(std::chrono::seconds(30));
logger.Info("Sleep done");
}
// A detector fault must win over an ordinary receiver/writer error: it needs re-initialisation,
// so raise the critical exception first. If only the receiver failed, the run can be retried from
// Idle, so that ordinary error is raised second.
if (detector_error)
throw JFJochCriticalException("Error in detector operation");
if (exception)
std::rethrow_exception(exception);
return ret;
}
void JFJochServices::Cancel() {
std::shared_lock ul(detector_mutex);
if (detector) {
// Best effort - if detector cannot be stopped, this is OK, important to still stop receiver
try {
detector->Stop();
} catch (...) {
cannot_stop_detector = true;
}
}
if (receiver != nullptr)
receiver->Cancel(false);
}
JFJochServices &JFJochServices::Receiver(JFJochReceiverService *input) {
receiver = input;
return *this;
}
std::optional<JFJochReceiverStatus> JFJochServices::GetReceiverStatus() const {
if (receiver == nullptr)
return {};
return receiver->GetStatus();
}
std::optional<float> JFJochServices::GetReceiverProgress() const {
if (receiver == nullptr)
return {};
return receiver->GetProgress();
}
MultiLinePlot JFJochServices::GetPlots(const PlotRequest &request) {
if (receiver == nullptr)
return {};
return receiver->GetDataProcessingPlot(request);
}
void JFJochServices::GetPlotRaw(std::vector<float> &v, PlotType type, const std::string &roi) {
if (receiver != nullptr)
receiver->GetPlotRaw(v, type, roi);
}
void JFJochServices::SetSpotFindingSettings(const SpotFindingSettings &settings) {
if (receiver)
receiver->SetSpotFindingSettings(settings);
}
void JFJochServices::Trigger() {
std::shared_lock ul(detector_mutex);
if (detector && (receiver != nullptr))
detector->Trigger();
}
std::optional<DetectorStatus> JFJochServices::GetDetectorStatus() const {
std::shared_lock ul(detector_mutex, std::defer_lock);
if (ul.try_lock_for(std::chrono::milliseconds(500)) && detector)
return detector->GetStatus();
return {};
}
std::string JFJochServices::GetPreviewJPEG(const PreviewImageSettings &settings, int64_t image_number) const {
if (receiver != nullptr)
return receiver->GetJPEGFromBuffer(settings, image_number);
else
return {};
}
std::string JFJochServices::GetPreviewTIFF(int64_t image_number) const {
if (receiver != nullptr)
return receiver->GetTIFFFromBuffer(image_number);
else
return "";
}
void JFJochServices::ConfigureDetector(const DiffractionExperiment &experiment) {
std::unique_lock ul(detector_mutex); // While configuring detector ensure exclusive access (even though pointer is not modified here)
if (detector)
detector->Configure(experiment);
}
void JFJochServices::LoadInternalGeneratorImage(const DiffractionExperiment &experiment,
const std::vector<uint16_t> &image,
uint64_t image_number) {
if (receiver)
receiver->LoadInternalGeneratorImage(experiment, image, image_number);
}
void JFJochServices::GetXFELPulseID(std::vector<uint64_t> &v) const {
if (receiver)
receiver->GetXFELPulseID(v);
}
void JFJochServices::GetXFELEventCode(std::vector<uint64_t> &v) const {
if (receiver)
receiver->GetXFELEventCode(v);
}
std::vector<DeviceStatus> JFJochServices::GetDeviceStatus() const {
std::vector<DeviceStatus> ret;
if (receiver)
ret = receiver->GetDeviceStatus();
return ret;
}
ZMQPreviewSettings JFJochServices::GetPreviewSocketSettings() {
if (receiver)
return receiver->GetPreviewSocketSettings();
return {};
}
ZMQMetadataSettings JFJochServices::GetMetadataSocketSettings() {
if (receiver)
return receiver->GetMetadataSocketSettings();
return {};
}
void JFJochServices::SetPreviewSocketSettings(const ZMQPreviewSettings &input) {
if (receiver)
receiver->PreviewSocketSettings(input);
}
void JFJochServices::SetMetadataSocketSettings(const ZMQMetadataSettings &input) {
if (receiver)
receiver->MetadataSocketSettings(input);
}
void JFJochServices::GetStartMessageFromBuffer(std::vector<uint8_t> &v) {
if (receiver)
return receiver->GetStartMessageFromBuffer(v);
}
bool JFJochServices::GetImageFromBuffer(std::vector<uint8_t> &v, int64_t image_number) {
if (receiver)
return receiver->GetImageFromBuffer(v, image_number);
return false;
}
ImageBufferStatus JFJochServices::GetImageBufferStatus() const {
if (receiver)
return receiver->GetImageBufferStatus();
else return ImageBufferStatus{.total_slots = 0, .available_slots = 0};
}
void JFJochServices::ClearImageBuffer() const {
if (receiver)
receiver->ClearImageBuffer();
}
void JFJochServices::LoadDetectorPixelMask(PixelMask &mask) {
std::shared_lock ul(detector_mutex);
if (detector)
detector->LoadPixelMask(mask);
}
void JFJochServices::SetupIndexing(const IndexingSettings &input) {
if (receiver)
receiver->Indexing(input);
}
ImagePusherStatus JFJochServices::GetImagePusherStatus() const {
if (receiver)
return receiver->GetImagePusherStatus();
return {
.pusher_type = ImagePusherType::None,
.address = {},
.connected_writers = 0
};
}