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Jungfraujoch/reader/JFJochStartMessageReader.h
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leonarski_fandFilip Leonarski 19b135186d
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v1.0.0-rc.175 (#85)
* Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`).
* Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection.
* Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS).
* Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead.
* Rugnux: On macOS, Bragg integration runs on the Apple GPU.
* Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand.
* Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`.
* Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit.
* Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed.
* Rugnux: The beam-stop shadow is found correctly on tilted detectors.
* Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement.
* jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps.
* jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection.
* jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images.
* Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges.

---------

Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home>
Reviewed-on: #85
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-10-16 15:34:43 +02:00

57 lines
2.3 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#pragma once
#include <condition_variable>
#include <mutex>
#include <stdexcept>
#include <string>
#include <vector>
#include "JFJochReader.h"
#include "HDF5ImageSource.h"
// The broker that reported a collection's data files can no longer be heard from, and an image this
// reader was asked for has not been reported: it will never be read.
class LiveCollectionLost : public std::runtime_error {
public:
explicit LiveCollectionLost(const std::string &what) : std::runtime_error(what) {}
};
// Reads a collection while it is being written: the dataset comes from its start message, as the
// broker sends it, and the images straight from the data files - /entry/data/data in each - once the
// broker reports a file closed and renamed into place (FileClosed). A read of an image whose file has
// not been reported waits for it; after Ended it returns false for an image no file holds, and after
// Lost it throws. The master file is never read.
class JFJochStartMessageReader : public JFJochReader {
public:
// master_path: where the collection's master file will be; the data files are next to it.
void Open(const StartMessage &start, const std::string &master_path);
void FileClosed(uint64_t file_number, uint64_t image_count);
void Ended();
void Lost(const std::string &why);
[[nodiscard]] uint64_t GetNumberOfImages() const override;
void Close() override;
bool ReadRawImage(int64_t image_number, JFJochReaderRawImage &image) override;
std::vector<SpotToSave> ReadSpots(int64_t image) const override { return {}; }
private:
bool LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset, DataMessage &message,
std::vector<uint8_t> &buffer, int64_t image_number, bool update_dataset) override;
// Waits until the file of this image is reported; false when the collection ended without it.
bool WaitForImage(int64_t image_number);
HDF5ImageSource image_source_;
uint64_t number_of_images_ = 0;
uint64_t images_per_file_ = 1;
std::mutex m_;
std::condition_variable cv_;
std::vector<int64_t> file_images_; // per data file: images it holds, -1 while not reported
bool ended_ = false;
std::string lost_;
};