485 lines
23 KiB
C++
485 lines
23 KiB
C++
// SPDX-FileCopyrightText: 2026 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 "JFJochReceiverRugnux.h"
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#include <cmath>
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#include <filesystem>
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#include <sys/resource.h>
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#include <sys/syscall.h>
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#include <unistd.h>
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#include "spdlog/fmt/fmt.h"
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#include "JFJochReceiverLite.h"
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#include "../common/ParallelFor.h"
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#include "../frame_serialize/CBORStream2Deserializer.h"
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#include "../rugnux/RugnuxLive.h"
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#include "../rugnux/ResultReport.h"
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#include "../writer/RugnuxResultBlocks.h"
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using namespace std::chrono_literals;
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namespace {
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int64_t SteadyNowNs() {
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return std::chrono::duration_cast<std::chrono::nanoseconds>(
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std::chrono::steady_clock::now().time_since_epoch()).count();
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}
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double SecondsSince(int64_t ns) {
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return static_cast<double>(SteadyNowNs() - ns) / 1e9;
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}
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// A run reachable for Cut while it exists: registered in `slot` (under `m`, cancelled at once where the
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// cut came first) and taken off again before it is destroyed, an exception included.
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class Reachable {
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std::mutex &m;
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Rugnux *&slot;
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public:
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Reachable(std::mutex &m, Rugnux *&slot, Rugnux &run, const bool &cut, const std::atomic<bool> &cancelled)
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: m(m), slot(slot) {
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std::unique_lock ul(m);
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slot = &run;
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if (cut || cancelled)
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run.Cancel();
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}
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~Reachable() {
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std::unique_lock ul(m);
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slot = nullptr;
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}
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};
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// What rugnux reports as it goes: its per-image results into the receiver's plots and scan
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// result, which a later pass over the same image overwrites - so the canonical pass, the last to
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// read every image, is what stays - and its steps into the log.
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class LiveObserver : public RugnuxObserver {
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JFJochReceiverPlots &plots;
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ScanResultGenerator &scan_result;
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const AzimuthalIntegrationMapping &mapping;
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RugnuxLiveStatus &status;
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Logger &logger;
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public:
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LiveObserver(JFJochReceiverPlots &plots, ScanResultGenerator &scan_result,
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const AzimuthalIntegrationMapping &mapping, RugnuxLiveStatus &status, Logger &logger)
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: plots(plots), scan_result(scan_result), mapping(mapping), status(status), logger(logger) {}
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void OnImageProcessed(const DataMessage &msg) override {
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plots.Add(msg, AzimuthalIntegrationProfile(mapping));
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scan_result.Add(msg);
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}
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void OnProgress(uint64_t done, uint64_t total) override { status.Progress(done, total); }
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void OnStep(const std::string &title) override {
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status.Step(title);
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logger.Info("rugnux: {}", title);
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}
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void OnNote(const std::string &text) override {
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status.Note(text);
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logger.Info("rugnux: {}", text);
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}
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};
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}
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JFJochReceiverRugnux::JFJochReceiverRugnux(const DiffractionExperiment &in_experiment,
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const PixelMask &in_pixel_mask,
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ImagePuller &in_image_puller,
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ImagePusher &in_image_pusher,
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Logger &in_logger,
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int64_t in_forward_nthreads,
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int in_rugnux_nthreads,
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const std::string &in_model_path,
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double in_deadline_s,
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RugnuxLiveStatus &in_live_status,
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const SpotFindingSettings &in_spot_finding_settings,
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JFJochReceiverCurrentStatus &in_current_status,
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JFJochReceiverPlots &in_plots,
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ImageBuffer &in_image_buffer,
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ZMQPreviewSocket *in_zmq_preview_socket,
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ZMQMetadataSocket *in_zmq_metadata_socket)
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: JFJochReceiver(in_experiment, in_image_buffer, in_image_pusher, in_current_status, in_plots,
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in_spot_finding_settings, in_logger, in_pixel_mask, in_zmq_preview_socket,
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in_zmq_metadata_socket, nullptr),
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image_puller(in_image_puller),
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reader(in_image_buffer),
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forward_nthreads(JFJochReceiverLite::NumberOfDataAnalysisThreads(in_forward_nthreads, in_experiment)),
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rugnux_nthreads(in_rugnux_nthreads),
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model_path(in_model_path),
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deadline_s(in_deadline_s),
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live_status(in_live_status),
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measurement_started(1),
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forward_started(forward_nthreads) {
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logger.Info("Starting {} forward threads; rugnux runs on {} threads while the images arrive",
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forward_nthreads, rugnux_nthreads);
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for (int i = 0; i < forward_nthreads; i++)
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forward_futures.emplace_back(std::async(std::launch::async, &JFJochReceiverRugnux::ForwardThread, this, i));
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measurement = std::async(std::launch::async, &JFJochReceiverRugnux::MeasurementThread, this);
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forward_started.wait();
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}
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JFJochReceiverRugnux::~JFJochReceiverRugnux() {
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cancelled = true;
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reader.Ended();
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{
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std::unique_lock ul(rugnux_m);
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if (rugnux != nullptr)
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rugnux->Cancel();
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if (probe != nullptr)
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probe->Cancel();
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}
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try {
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if (measurement.valid())
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measurement.get();
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} catch (const std::exception &e) {
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logger.Error("ReceiverRugnux teardown failed: {}", e.what());
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}
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}
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void JFJochReceiverRugnux::MeasurementThread() {
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std::future<void> rugnux_done, probe_done;
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try {
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// Waiting for the start message, as JFJochReceiverLite::MeasurementThread.
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std::optional<std::chrono::steady_clock::time_point> give_up_at;
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auto msg = image_puller.PollImage();
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while (!cancelled && (!msg.has_value() || !msg->cbor || !msg->cbor->start_message)) {
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if (detector_finished && !give_up_at)
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give_up_at = std::chrono::steady_clock::now() + StartMessageGrace;
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if (give_up_at && (std::chrono::steady_clock::now() > *give_up_at)) {
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logger.Error("Detector finished, but no start message arrived - abandoning measurement");
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cancelled = true;
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break;
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}
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msg = image_puller.PollImage();
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}
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if (cancelled) {
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current_status.SetProgress({});
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current_status.SetStatus(GetStatus());
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measurement_started.count_down();
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return;
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}
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Configure(msg->cbor->start_message.value());
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image_buffer.StartMeasurement(experiment);
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start_time = std::chrono::system_clock::now();
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SendStartMessage();
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// Rugnux reads the images back from the buffer, so it needs one slot per image: a slot taken
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// again would hand it a later image. Without that the collection is only forwarded.
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const auto slots = image_buffer.GetStatus().total_slots;
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live_status.Start(experiment.GetImageNum());
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if (slots < experiment.GetImageNum()) {
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logger.Error("Image buffer holds {} images, the collection has {}: no rugnux analysis for it",
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slots, experiment.GetImageNum());
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live_status.Finish(RugnuxLiveState::Skipped, "the image buffer cannot hold the whole collection");
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} else {
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// The start message as the writer gets it, so rugnux sees the dataset an HDF5 master states.
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std::vector<uint8_t> start_cbor;
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image_buffer.GetStartMessage(start_cbor);
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reader.Open(CBORStream2Deserialize(start_cbor)->start_message.value());
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char dir_template[] = "/tmp/jfjoch_rugnux_XXXXXX";
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if (mkdtemp(dir_template) == nullptr)
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throw JFJochException(JFJochExceptionCategory::FileWriteError, "Cannot create rugnux scratch directory");
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scratch_dir = dir_template;
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rugnux_done = std::async(std::launch::async, &JFJochReceiverRugnux::RugnuxThread, this);
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probe_done = std::async(std::launch::async, &JFJochReceiverRugnux::ProbeThread, this);
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}
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measurement_started.count_down();
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} catch (const JFJochException &e) {
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logger.ErrorException(e);
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Cancel(e);
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measurement_started.count_down();
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throw;
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}
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logger.Info("Receiving started");
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for (auto &f: forward_futures)
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f.get();
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reader.Ended();
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images_done = true;
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live_status.LastImage();
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const int64_t last_image = last_image_ns.load();
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logger.Info("Receiving finished, {} images", images_collected.load());
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if (rugnux_done.valid()) {
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// The fixed cutoff: the analysis gets deadline_s after the last image, then gives what it has.
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if (deadline_s > 0 && rugnux_done.wait_for(std::chrono::duration<double>(deadline_s))
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== std::future_status::timeout)
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Cut("deadline");
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rugnux_done.wait();
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logger.Info("rugnux live: done {:.2f} s after the last image", SecondsSince(last_image));
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}
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if (probe_done.valid())
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probe_done.wait();
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current_status.SetProgress(1.0);
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current_status.SetStatus(GetStatus());
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SendEndMessage();
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const double end_sent_s = SecondsSince(last_image);
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if (!image_buffer.CheckIfBufferReturned(SendFinalizeTimeout)) {
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logger.Error("Send commands not finalized in {} seconds", SendFinalizeTimeout.count());
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throw JFJochException(JFJochExceptionCategory::ZeroMQ, "Send commands not finalized in "
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+ std::to_string(SendFinalizeTimeout.count()) + " seconds");
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}
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if (push_images_to_writer)
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writer_error = image_pusher.Finalize();
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if (last_image > 0 && rugnux_done.valid()) {
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const double written_s = SecondsSince(last_image);
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live_status.Latency(written_s);
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logger.Info("rugnux live: last image -> all written {:.2f} s (end message sent at {:.2f} s)",
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written_s, end_sent_s);
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}
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if (!scratch_dir.empty()) {
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std::error_code ec;
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std::filesystem::remove_all(scratch_dir, ec);
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}
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end_time = std::chrono::system_clock::now();
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current_status.SetProgress({});
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current_status.SetStatus(GetStatus());
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}
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void JFJochReceiverRugnux::RugnuxThread() {
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// Below the forward threads: every thread rugnux starts inherits this, so an image arriving finds a
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// core however busy rugnux keeps the machine.
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// The process-wide ParallelFor pool is not started by this thread, so it is lowered separately.
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setpriority(PRIO_PROCESS, static_cast<id_t>(syscall(SYS_gettid)), 10);
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parallel_detail::WorkerPool::Instance().SetNice(10);
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try {
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const auto dataset = reader.GetDataset();
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const RugnuxLiveSetup setup = MakeRugnuxLiveSetup(*dataset, rugnux_nthreads, scratch_dir + "/p", model_path);
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LiveObserver observer(plots, scan_result, *az_int_mapping, live_status, logger);
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ProcessResult result;
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{
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Rugnux process(reader, setup.experiment, *dataset->pixel_mask, setup.config);
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Reachable reachable(rugnux_m, rugnux, process, cut, cancelled);
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result = process.Run(&observer);
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}
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// The verdict and summary of the report a `rugnux` run writes, without writing it.
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const ReportDocument doc = BuildReportDocument(scratch_dir + "/p", experiment.GetFilePrefix(),
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setup.experiment, result);
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std::vector<std::string> warnings;
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for (const auto &w: doc.warnings)
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if (!w.developer_only)
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warnings.push_back(w.text);
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live_status.Result(doc.verdict, doc.verdict_text, doc.summary_rows, warnings);
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live_status.Finish(result.cancelled ? RugnuxLiveState::Cancelled : RugnuxLiveState::Done);
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std::unique_lock ul(rugnux_m);
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rugnux_result = std::move(result);
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} catch (const std::exception &e) {
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logger.Error("rugnux live: {}", e.what());
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live_status.Finish(RugnuxLiveState::Failed, e.what());
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}
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if (!parallel_detail::WorkerPool::Instance().SetNice(0))
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logger.Warning("rugnux live: the ParallelFor pool stays at nice 10 - raising it back needs CAP_SYS_NICE");
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}
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void JFJochReceiverRugnux::ProbeThread() {
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// Rugnux waits for half the sweep before it decides on a lattice. In the meantime the machine is
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// idle, so a small run of its own indexes the first 60 degrees and says at once whether there is
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// a crystal - quick feedback for the person at the beamline, above all where there is none. It
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// decides nothing for the run, which goes on as it would without it.
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constexpr double PROBE_DEG = 60.0;
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setpriority(PRIO_PROCESS, static_cast<id_t>(syscall(SYS_gettid)), 10);
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try {
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const auto dataset = reader.GetDataset();
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const auto gonio = dataset->experiment.GetGoniometer();
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if (!gonio || gonio->GetIncrement_deg() == 0.0f)
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return;
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const int64_t frames = std::lround(PROBE_DEG / std::abs(gonio->GetIncrement_deg()));
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if (2 * frames > static_cast<int64_t>(reader.GetNumberOfImages()))
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return; // a sweep this short is decided on soon enough by the run itself
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RugnuxLiveSetup setup = MakeRugnuxLiveSetup(*dataset, rugnux_nthreads, "", "");
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setup.config.end_image = static_cast<int>(frames);
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setup.config.rotation_postrefine_geometry = false;
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setup.config.run_scaling = false;
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ProcessResult r;
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{
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Rugnux probe_run(reader, setup.experiment, *dataset->pixel_mask, setup.config);
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Reachable reachable(rugnux_m, probe, probe_run, cut, cancelled);
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r = probe_run.Run(nullptr);
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}
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if (r.consensus_cell && r.rotation_lattice_type) {
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const auto &c = *r.consensus_cell;
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live_status.Probe(fmt::format("lattice on the first {:.0f} deg: {}-centred {}, {:.1f} {:.1f} {:.1f} "
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"{:.1f} {:.1f} {:.1f}, {:.0f}% of the images indexed", PROBE_DEG,
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r.rotation_lattice_type->centering,
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gemmi::crystal_system_str(r.rotation_lattice_type->crystal_system),
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c.a, c.b, c.c, c.alpha, c.beta, c.gamma,
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100.0 * r.indexing_rate.value_or(0.0f)));
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} else
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live_status.Probe(fmt::format("no lattice on the first {:.0f} deg", PROBE_DEG));
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} catch (const NoLatticeFound &e) {
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live_status.Probe(fmt::format("no lattice on the first {:.0f} deg: {}", PROBE_DEG, e.reason));
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} catch (const std::exception &e) {
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logger.Warning("rugnux live: the lattice probe failed: {}", e.what());
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}
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logger.Info("rugnux live: lattice probe - {}", live_status.Get().probe);
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}
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void JFJochReceiverRugnux::AddToEndMessage(EndMessage &message) {
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std::unique_lock ul(rugnux_m);
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if (!rugnux_result)
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return;
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const EndMessage &r = rugnux_result->end_message;
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message.indexing_rate = r.indexing_rate;
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message.bkg_estimate = r.bkg_estimate;
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message.spindle_blind_fraction = r.spindle_blind_fraction;
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message.ice_ring_score_mean = r.ice_ring_score_mean;
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message.az_int_result = r.az_int_result;
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message.rotation_lattice = r.rotation_lattice;
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message.rotation_lattice_type = r.rotation_lattice_type;
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message.rotation_extra_lattices = r.rotation_extra_lattices;
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message.unit_cell = r.unit_cell;
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message.space_group_name = r.space_group_name;
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message.space_group_number = r.space_group_number;
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message.reindex_matrix = r.reindex_matrix;
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message.refined_beam_center_x = r.refined_beam_center_x;
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message.refined_beam_center_y = r.refined_beam_center_y;
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message.refined_poni_rot1 = r.refined_poni_rot1;
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message.refined_poni_rot2 = r.refined_poni_rot2;
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message.refined_poni_rot3 = r.refined_poni_rot3;
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message.refined_rotation_axis = r.refined_rotation_axis;
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// Merged data, map coefficients and placed model, for the writer to write beside the master. Only
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// here, with rugnux_result set: every file in scratch_dir is then whole - rugnux writes synchronously
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// and a cut never stops a write half-way - while a run that threw may have left one half-written.
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FillRugnuxResultBlocks(scratch_dir + "/p", message);
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}
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void JFJochReceiverRugnux::Configure(const StartMessage &msg) {
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// As JFJochReceiverLite::Configure.
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if ((experiment.GetXPixelsNum() != msg.image_size_x)
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|| (experiment.GetYPixelsNum() != msg.image_size_y))
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Mismatch in detector size");
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if (fabs(experiment.GetPixelSize_mm() - msg.pixel_size_x * 1e3) > 1e-7)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Mismatch in pixel size");
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experiment.Detector().Description(msg.detector_description);
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experiment.Detector().SerialNumber(msg.detector_serial_number);
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experiment.Detector().SensorMaterial(msg.sensor_material);
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experiment.Detector().SensorThickness_um(msg.sensor_thickness * 1e6);
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experiment.Detector().SaturationLimit(SaturationLimitFromValue(msg.saturation_value));
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experiment.Detector().CountRateCorrectionApplied(msg.countrate_correction_enabled);
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experiment.Detector().CountRateCorrectionLookupTable(msg.countrate_correction_lookup_table);
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experiment.Detector().FlatfieldApplied(msg.flatfield_enabled);
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experiment.Detector().VirtualPixelInterpolationApplied(msg.virtual_pixel_interpolation_enabled);
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experiment.ApplyPixelMask(false);
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experiment.Detector().BitDepthImage(msg.bit_depth_image);
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experiment.PixelSigned(msg.pixel_signed);
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}
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void JFJochReceiverRugnux::ForwardThread(uint32_t id) {
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forward_started.count_down();
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measurement_started.wait();
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while (!cancelled && !end_message_received) {
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try {
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auto msg = image_puller.PollImage(std::chrono::milliseconds(5));
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if (!msg.has_value() || !msg->cbor)
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continue;
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if (msg->cbor->end_message) {
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end_message_received = true;
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} else if (msg->cbor->calibration) {
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if (push_images_to_writer)
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image_pusher.SendCalibration(msg->cbor->calibration.value());
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} else if (msg->cbor->data_message) {
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last_image_ns = SteadyNowNs();
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live_status.ImageReceived();
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DataMessage data_msg = msg->cbor->data_message.value();
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++images_collected;
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const auto compressed_size_img = data_msg.image.GetCompressedSize();
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const auto uncompressed_size_img = data_msg.image.GetUncompressedSize();
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compressed_size += compressed_size_img;
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uncompressed_size += uncompressed_size_img;
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UpdateMaxImageReceived(data_msg.number);
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data_msg.original_number = data_msg.number;
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data_msg.user_data = experiment.GetImageAppendix();
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data_msg.run_number = experiment.GetRunNumber();
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data_msg.run_name = experiment.GetRunName();
|
|
data_msg.receiver_buf_available = image_buffer.GetAvailSlots();
|
|
data_msg.receiver_aq_dev_delay = image_puller.GetCurrentFifoUtilization();
|
|
if (compressed_size_img > 0)
|
|
data_msg.compression_ratio = static_cast<float>(uncompressed_size_img)
|
|
/ static_cast<float>(compressed_size_img);
|
|
|
|
auto loc = image_buffer.GetImageSlot();
|
|
if (loc == nullptr)
|
|
writer_queue_full = true;
|
|
else {
|
|
auto writer_buffer = (uint8_t *) loc->GetImage();
|
|
CBORStream2Serializer serializer(writer_buffer, experiment.GetImageBufferLocationSize());
|
|
serializer.SerializeImage(data_msg);
|
|
loc->SetImageNumber(data_msg.number);
|
|
loc->SetImageSize(serializer.GetBufferSize());
|
|
loc->SetIndexed(false);
|
|
loc->ReadyToSend();
|
|
|
|
if (zmq_preview_socket != nullptr)
|
|
zmq_preview_socket->SendImage(writer_buffer, serializer.GetBufferSize());
|
|
if (zmq_metadata_socket != nullptr)
|
|
zmq_metadata_socket->AddDataMessage(data_msg);
|
|
if (push_images_to_writer) {
|
|
if (image_pusher.SendImage(*loc))
|
|
++images_sent;
|
|
} else
|
|
loc->release();
|
|
UpdateMaxImageSent(data_msg.number);
|
|
}
|
|
}
|
|
UpdateMaxDelay(image_puller.GetCurrentFifoUtilization());
|
|
current_status.SetProgress(GetProgress());
|
|
current_status.SetStatus(GetStatus());
|
|
} catch (const JFJochException &e) {
|
|
logger.ErrorException(e);
|
|
Cancel(e);
|
|
}
|
|
}
|
|
}
|
|
|
|
void JFJochReceiverRugnux::Cancel(bool silent) {
|
|
detector_finished = true;
|
|
// The silent cancel is the detector reading idle at the end of every collection: rugnux goes on.
|
|
if (silent)
|
|
return;
|
|
// /cancel is the one way in for the beamline, which cannot tell the collection from its analysis: it
|
|
// ends the collection while the images still arrive, as JFJochReceiverLite does, and in every case
|
|
// cuts the analysis, so the end message goes out at once with what rugnux has established.
|
|
if (!images_done)
|
|
JFJochReceiver::Cancel(silent);
|
|
Cut("cancel");
|
|
}
|
|
|
|
void JFJochReceiverRugnux::Cut(const std::string &reason) {
|
|
std::unique_lock ul(rugnux_m);
|
|
if (cut || rugnux_result)
|
|
return;
|
|
cut = true;
|
|
reader.Ended(); // no image is waited for any more
|
|
if (rugnux != nullptr)
|
|
rugnux->Cancel();
|
|
if (probe != nullptr)
|
|
probe->Cancel();
|
|
live_status.Cut(reason);
|
|
logger.Info("rugnux live: analysis cut ({}) - the end message carries what is established", reason);
|
|
}
|
|
|
|
void JFJochReceiverRugnux::StopReceiver() {
|
|
if (measurement.valid()) {
|
|
measurement.get();
|
|
logger.Info("Receiver stopped");
|
|
}
|
|
}
|
|
|
|
float JFJochReceiverRugnux::GetEfficiency() const {
|
|
if (experiment.GetFrameNum() == 0)
|
|
return 0;
|
|
return static_cast<float>(images_collected) / static_cast<float>(experiment.GetFrameNum());
|
|
}
|
|
|
|
float JFJochReceiverRugnux::GetProgress() const {
|
|
if (experiment.GetFrameNum() == 0)
|
|
return 0.0;
|
|
return static_cast<float>(max_image_number_received) / static_cast<float>(experiment.GetFrameNum());
|
|
}
|