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