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Jungfraujoch/reader/JFJochReader.h
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v1.0.0-rc.178 (#88)
* Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`).
* Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels.
* Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL.
* jfjoch_viewer: Opens the same XFEL file formats.
* Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL.
* Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded.
* jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start.

Reviewed-on: #88
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-10-21 11:20:01 +02:00

69 lines
2.6 KiB
C++

// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#ifndef JFJOCHIMAGEREADER_H
#define JFJOCHIMAGEREADER_H
#include <unordered_set>
#include <map>
#include <mutex>
#include "../common/JFJochMessages.h"
#include "../common/Plot.h"
#include "../common/ROIBox.h"
#include "../common/DiffractionExperiment.h"
#include "JFJochReaderDataset.h"
#include "JFJochReaderImage.h"
#include "JFJochReaderSpots.h"
class JFJochReader {
// Reads each of its inputs' frames through them (JFJochMultiReader.h).
friend class JFJochMultiReader;
mutable std::mutex m;
std::shared_ptr<JFJochReaderDataset> dataset;
virtual bool LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset,
DataMessage& message,
std::vector<uint8_t> &buffer,
int64_t image_number,
bool update_dataset) = 0;
mutable std::mutex summation_mutex;
void SummationThread(int64_t image0,
int64_t n_image,
int64_t image_jump,
JFJochReaderImage &image);
protected:
void SetStartMessage(const std::shared_ptr<JFJochReaderDataset> &val);
DiffractionExperiment default_experiment;
public:
virtual ~JFJochReader() = default;
JFJochReader& Experiment(const DiffractionExperiment& experiment);
std::shared_ptr<const JFJochReaderDataset> GetDataset() const;
[[nodiscard]] virtual uint64_t GetNumberOfImages() const = 0;
virtual void Close() = 0;
std::shared_ptr<JFJochReaderImage> LoadImage(int64_t image_number, int64_t summation_factor = 1);
void UpdateGeomMetadata(const DiffractionExperiment& experiment);
void UpdateUserMask(const std::vector<uint32_t>& mask);
// Read one image into a raw image the caller owns, false where there is nothing to read. A
// worker that walks a whole sweep hands the same object back on every frame and so keeps its
// buffer: GetRawImage() allocates a fresh one per call, which on a 4-byte 16 Mpx frame is 72 MB
// of untouched pages the decoder then faults in one by one, measurably more than the decode.
virtual bool ReadRawImage(int64_t image_number, JFJochReaderRawImage &image) = 0;
// The same image in a freshly allocated raw image.
std::shared_ptr<JFJochReaderRawImage> GetRawImage(int64_t image_number);
virtual std::vector<SpotToSave> ReadSpots(int64_t image) const = 0;
std::shared_ptr<JFJochReaderSpots> ReadAllSpots(int64_t start_image, int64_t end_image, int64_t stride = 1) const;
};
#endif //JFJOCHIMAGEREADER_H