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Jungfraujoch/writer/FileWriter.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

68 lines
3.4 KiB
C++

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#pragma once
#include <numeric>
#include "HDF5DataFile.h"
#include "../common/JFJochMessages.h"
#include "../common/ZMQWrappers.h"
#include "HDF5NXmx.h"
#include <functional>
#include <set>
#include <unordered_set>
class FileWriter {
FileWriterFormat format = FileWriterFormat::NXmxLegacy;
StartMessage start_message;
std::unique_ptr<NXmx> master_file;
std::vector<std::unique_ptr<HDF5DataFile> > files;
std::vector<HDF5DataFileStatistics> stats;
std::unique_ptr<ZMQSocket> finalized_file_socket;
std::function<void(const HDF5DataFileStatistics &)> file_closed_callback;
std::unordered_set<uint64_t> closed_files;
// File numbers with a live HDF5DataFile, in order. CloseOldFiles walks this and not `files`, whose
// slots stay (empty) for every file of the run - a thousand of them for a long run, visited on every
// image.
std::set<uint64_t> open_files;
constexpr static uint64_t close_file_lag_images = 1000;
constexpr static uint64_t default_images_per_file = 1000;
void CreateHDF5MasterFile(const StartMessage& msg);
static void CheckOutputFilesAvailable(const StartMessage &msg, FileWriterFormat format);
void AddStats(const std::optional<HDF5DataFileStatistics>& s);
void CloseFile(uint64_t file_number);
void CloseOldFiles(uint64_t current_image_number);
public:
// check_overwrite_at_start: fail the constructor if an output file already
// exists and overwrite is off. Only safe for transports with a back-channel
// (direct HDF5 pusher, TCP) that can report the failure to the broker before
// acquisition arms. The ZeroMQ pusher is fire-and-forget with no back-channel,
// so it must pass false: the writer then falls back to writing .tmp files and
// failing at the final rename (see docs/JFJOCH_WRITER.md).
// trusted_path: the caller supplied the output prefix itself (offline rugnux / the viewer's
// processing), so the multi-user CheckPath guard - which forbids absolute paths and '..' traversal
// for remotely-supplied prefixes - is skipped, allowing an absolute output path. The broker/writer
// never set it, so their behaviour is unchanged.
explicit FileWriter(const StartMessage &request, bool check_overwrite_at_start = true,
bool trusted_path = false);
// Everything the constructor does before it opens anything: the path guard, creating the
// output directory and checking that no output file is in the way. Sent to the writer as a
// PREFLIGHT frame before the detector is armed, so a run that cannot be written is refused
// while refusing it is still free. Shares its code with the constructor, so a pre-flight that
// passes cannot be contradicted by the start that follows it.
static void Preflight(const StartMessage &request, bool trusted_path = false);
void Write(const DataMessage& msg);
void WriteHDF5(const DataMessage& msg);
void WriteHDF5(const CompressedImage& msg);
void WriteHDF5(const EndMessage& msg);
std::vector<HDF5DataFileStatistics> Finalize();
void SetupFinalizedFileSocket(const std::string &addr);
// Called for every data file once it is closed and renamed into place.
void FileClosedCallback(std::function<void(const HDF5DataFileStatistics &)> callback);
std::optional<std::string> GetZMQAddr();
};