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Jungfraujoch/receiver/JFJochReceiverService.cpp
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leonarski_f 511be0c366
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v1.0.0-rc.165 (#75)
* `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
2026-08-27 22:16:54 +02:00

364 lines
15 KiB
C++

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "JFJochReceiverService.h"
#include "JFJochReceiverFPGA.h"
#include "JFJochReceiverLite.h"
#include "../preview/JFJochJPEG.h"
#include "../preview/JFJochTIFF.h"
JFJochReceiverService::JFJochReceiverService(AcquisitionDeviceGroup &in_aq_devices,
Logger &in_logger, ImagePusher &pusher,
size_t send_buffer_size_MiB)
: aq_devices(in_aq_devices),
logger(in_logger),
image_buffer(send_buffer_size_MiB * 1024 * 1024),
image_pusher(pusher),
spot_finding_settings(DiffractionExperiment::DefaultDataProcessingSettings()) {
}
JFJochReceiverService &JFJochReceiverService::NumThreads(int64_t input) {
if (input <= 0)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Thread number must be above zero");
nthreads = input;
return *this;
}
void JFJochReceiverService::FinalizeMeasurementChangeState() {
std::unique_lock ul(state_mutex);
state = ReceiverState::Idle;
measurement_done.notify_all();
}
void JFJochReceiverService::FinalizeMeasurement() {
try {
receiver->StopReceiver();
} catch (...) {
FinalizeMeasurementChangeState();
throw;
}
FinalizeMeasurementChangeState();
}
std::optional<JFJochReceiverStatus> JFJochReceiverService::GetStatus() {
return receiver_status.GetStatus();
}
void JFJochReceiverService::Preflight(const DiffractionExperiment &experiment) {
// Same condition JFJochReceiver uses to decide whether it pushes to a writer at all: with no
// images or no file prefix nothing is written, so there is nothing to check.
if ((experiment.GetImageNum() <= 0) || experiment.GetFilePrefix().empty())
return;
// FillMessage alone, which is what makes this frame small: the per-pixel arrays that dominate a
// real start message - the pixel mask, the azimuthal-integration map, the ROI map - are added
// by JFJochReceiver::SendStartMessage and are not here. Measured on a JUNGFRAU 9M: 1.4 kB
// against 543 kB for the start message that follows. It is deliberately the whole of
// FillMessage rather than the handful of fields the check reads today, so that the writer sees
// the same description of the run it will be given at start - a hand-picked subset would
// answer for a different set of file names the day the check learns to read one more field.
StartMessage message{};
experiment.FillMessage(message);
image_pusher.Preflight(message);
}
void JFJochReceiverService::Start(const DiffractionExperiment &experiment,
const PixelMask &pixel_mask,
const JFCalibration *calibration,
std::shared_ptr<ImagePuller> puller) {
std::unique_lock ul_state(state_mutex); // unique lock, as it will destroy and create receiver object
if (state != ReceiverState::Idle)
throw JFJochException(JFJochExceptionCategory::WrongDAQState, "Receiver not idle, cannot start");
try {
auto nthreads_local = nthreads;
if (experiment.IsCPUSummation())
nthreads_local = 4;
// First clean-up old measurement
receiver.reset();
preview_image.Configure(experiment, pixel_mask);
switch (experiment.GetDetectorType()) {
case DetectorType::EIGER:
case DetectorType::JUNGFRAU:
receiver = std::make_unique<JFJochReceiverFPGA>(experiment, pixel_mask,
calibration,
aq_devices, image_pusher,
logger,
nthreads_local,
spot_finding_settings,
receiver_status,
plots,
image_buffer,
zmq_preview_socket.get(),
zmq_metadata_socket.get(),
indexer_thread_pool.get());
break;
case DetectorType::DECTRIS:
if (puller)
image_puller = puller;
else {
image_puller = std::make_shared<ZMQImagePuller>(
experiment.GetDetectorSetup().GetDECTRISStream2Addr());
}
receiver = std::make_unique<JFJochReceiverLite>(experiment,
pixel_mask,
*image_puller,
image_pusher,
logger,
nthreads_local,
spot_finding_settings,
receiver_status,
plots,
image_buffer,
zmq_preview_socket.get(),
zmq_metadata_socket.get(),
indexer_thread_pool.get());
break;
}
measurement = std::async(std::launch::async, &JFJochReceiverService::FinalizeMeasurement, this);
state = ReceiverState::Running;
} catch (const std::exception &e) {
// The receiver never started, so drop the status its base constructor had already reset -
// otherwise /status and /statistics keep reporting a zero-progress run that never happened,
// until the next start overwrites it.
receiver_status.Clear();
receiver_status.SetProgress({});
logger.ErrorException(e);
throw;
}
}
void JFJochReceiverService::Cancel(bool silent) {
std::unique_lock ul(state_mutex);
if (state == ReceiverState::Running)
receiver->Cancel(silent);
}
JFJochReceiverOutput JFJochReceiverService::Stop() {
std::unique_lock ul(state_mutex);
measurement_done.wait(ul, [this] { return (state != ReceiverState::Running); });
if (state != ReceiverState::Idle)
throw JFJochException(JFJochExceptionCategory::WrongReceiverState, "Receiver in weird state");
try {
if (measurement.valid())
measurement.get();
} catch (JFJochException &e) {
logger.ErrorException(e);
throw;
}
if (!receiver) {
logger.Warning("Request to stop while receiver not running");
throw JFJochException(JFJochExceptionCategory::WrongReceiverState, "Receiver idle, cannot stop");
}
return receiver->GetFinalStatistics();
}
void JFJochReceiverService::SetSpotFindingSettings(const SpotFindingSettings &settings) {
try {
std::unique_lock ul(state_mutex);
DiffractionExperiment::CheckDataProcessingSettings(settings);
spot_finding_settings = settings;
if (state != ReceiverState::Idle)
receiver->SetSpotFindingSettings(settings);
} catch (std::exception &e) {
logger.ErrorException(e);
throw;
}
}
MultiLinePlot JFJochReceiverService::GetDataProcessingPlot(const PlotRequest &request) {
return plots.GetPlots(request);
}
void JFJochReceiverService::GetPlotRaw(std::vector<float> &v, PlotType type, const std::string &roi) {
plots.GetPlotRaw(v, type, roi);
}
std::vector<AcquisitionDeviceNetConfig> JFJochReceiverService::GetNetworkConfig() {
return aq_devices.GetNetworkConfig();
}
void JFJochReceiverService::LoadInternalGeneratorImage(const DiffractionExperiment &experiment,
const std::vector<uint16_t> &image,
uint64_t image_number) {
std::vector<uint16_t> raw_geom, eiger_geom;
const uint16_t *frame;
if (image.size() == RAW_MODULE_SIZE * experiment.GetModulesNum()) {
frame = image.data();
} else if (image.size() == experiment.GetPixelsNum()) {
raw_geom.resize(RAW_MODULE_SIZE * experiment.GetModulesNum());
ConvertedToRawGeometry(experiment, raw_geom.data(), image.data());
frame = raw_geom.data();
} else
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Size of input array with raw expected image is wrong");
for (int i = 0; i < experiment.GetDataStreamsNum(); i++) {
uint32_t module0 = experiment.GetFirstModuleOfDataStream(i);
switch (experiment.GetDetectorSetup().GetDetectorType()) {
case DetectorType::EIGER:
eiger_geom.resize(RAW_MODULE_SIZE);
for (int m = 0; m < experiment.GetModulesNum(i); m++) {
RawToEigerInput(eiger_geom.data(), frame + (module0 + m) * RAW_MODULE_SIZE);
aq_devices[i].SetInternalGeneratorFrame(eiger_geom.data(),
m + experiment.GetModulesNum(i) * image_number);
}
break;
case DetectorType::JUNGFRAU:
for (int m = 0; m < experiment.GetModulesNum(i); m++)
aq_devices[i].SetInternalGeneratorFrame(frame + (module0 + m) * RAW_MODULE_SIZE,
m + experiment.GetModulesNum(i) * image_number);
break;
default:
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Detector not supported");
}
}
}
void JFJochReceiverService::GetXFELEventCode(std::vector<uint64_t> &v) const {
plots.GetXFELEventCode(v);
}
void JFJochReceiverService::GetXFELPulseID(std::vector<uint64_t> &v) const {
plots.GetXFELPulseID(v);
}
std::vector<DeviceStatus> JFJochReceiverService::GetDeviceStatus() const {
return aq_devices.GetDeviceStatus();
}
std::optional<float> JFJochReceiverService::GetProgress() const {
return receiver_status.GetProgress();
}
JFJochReceiverService &JFJochReceiverService::PreviewSocket(const std::string &addr, const std::optional<int32_t> &watermark) {
if (!addr.empty()) {
logger.Info("ZeroMQ preview socket available at {}", addr);
zmq_preview_socket = std::make_unique<ZMQPreviewSocket>(addr, watermark);
}
return *this;
}
JFJochReceiverService &JFJochReceiverService::MetadataSocket(const std::string &addr) {
if (!addr.empty()) {
logger.Info("ZeroMQ metadata socket available at {}", addr);
zmq_metadata_socket = std::make_unique<ZMQMetadataSocket>(addr);
}
return *this;
}
std::string JFJochReceiverService::GetPreviewSocketAddress() const {
if (zmq_preview_socket)
return zmq_preview_socket->GetAddress();
return "";
}
std::string JFJochReceiverService::GetMetadataSocketAddress() const {
if (zmq_metadata_socket)
return zmq_metadata_socket->GetAddress();
return "";
}
JFJochReceiverService &JFJochReceiverService::PreviewSocketSettings(const ZMQPreviewSettings &input) {
if (zmq_preview_socket)
zmq_preview_socket->ImportSettings(input);
return *this;
}
JFJochReceiverService &JFJochReceiverService::MetadataSocketSettings(const ZMQMetadataSettings &input) {
if (zmq_metadata_socket)
zmq_metadata_socket->ImportSettings(input);
return *this;
}
ZMQPreviewSettings JFJochReceiverService::GetPreviewSocketSettings() const {
if (zmq_preview_socket)
return zmq_preview_socket->GetSettings();
return {};
}
ZMQMetadataSettings JFJochReceiverService::GetMetadataSocketSettings() const {
if (zmq_metadata_socket)
return zmq_metadata_socket->GetSettings();
return {};
}
void JFJochReceiverService::GetStartMessageFromBuffer(std::vector<uint8_t> &v) {
image_buffer.GetStartMessage(v);
}
bool JFJochReceiverService::GetImageFromBuffer(std::vector<uint8_t> &v, int64_t image_number) {
return image_buffer.GetImage(v, image_number);
}
std::string JFJochReceiverService::GetJPEGFromBuffer(const PreviewImageSettings &settings, int64_t image_number) {
std::vector<uint8_t> cbor_image;
if (!image_buffer.GetImage(cbor_image, image_number))
return {};
return preview_image.GenerateImage(settings, cbor_image);
}
std::string JFJochReceiverService::GetTIFFFromBuffer(int64_t image_number) {
std::vector<uint8_t> cbor_image;
if (!image_buffer.GetImage(cbor_image, image_number))
return {};
return PreviewImage::GenerateTIFF(cbor_image);
}
ImageBufferStatus JFJochReceiverService::GetImageBufferStatus() const {
return image_buffer.GetStatus();
}
void JFJochReceiverService::ClearImageBuffer() {
std::unique_lock ul(state_mutex);
// Clearing image buffer during data collection could be catastrophic, so better protect here, even if redundant
// with JFJochStateMachine
if (state == ReceiverState::Idle)
image_buffer.Finalize(std::chrono::milliseconds(2500));
else
throw JFJochException(JFJochExceptionCategory::WrongDAQState,
"Cannot clear image buffer during data collection");
}
JFJochReceiverService &JFJochReceiverService::Indexing(const IndexingSettings &input) {
std::unique_lock ul(state_mutex);
// Clearing image buffer during data collection could be catastrophic, so better protect here, even if redundant
// with JFJochStateMachine
if (state == ReceiverState::Idle) {
// Release the previous run's receiver first. It holds a raw pointer to the indexer pool and
// its own GPU resources; keeping it alive while we rebuild the pool means a fresh GPU indexer
// has to coexist with a stale receiver (e.g. after a failed acquisition start, where the
// receiver is stopped but not destroyed until the next Start), which can make the GPU indexer
// initialisation fail. Destroying the receiver before the pool also avoids the dangling
// pointer. Safe here: state is Idle, so no measurement is using it.
receiver.reset();
logger.Info("Resetting indexing thread pool");
indexer_thread_pool.reset();
if (input.GetAlgorithm() != IndexingAlgorithmEnum::None) {
logger.Info("Creating indexing thread pool...");
indexer_thread_pool = std::make_unique<IndexerThreadPool>(input);
logger.Info(" ... done");
}
return *this;
} else
throw JFJochException(JFJochExceptionCategory::WrongDAQState,
"Cannot change indexing settings during data collection");
}
ImagePusherStatus JFJochReceiverService::GetImagePusherStatus() const {
return image_pusher.GetStatus();
}