leonarski_fandClaude Opus 5.5
6557ba87f4
Every input is a file named on the command line, read in the order given (a shell glob gives them sorted by name); a directory is refused with the glob form to use instead. - Several Jungfraujoch/NXmx masters of stills are read as one run (JFJochMultiReader): their images one after another, the pixel masks combined, the per-image efficiency placed at each input's images. They must share the detector, wavelength (0.1%), distance (0.1 mm) and beam centre (1 px), since stills geometry refinement refines one geometry for all frames; rotation sweeps are refused. The log gives the indexing rate of each input beside the run's (ProcessResult::image_indexed). - SACLA HDF5 / CXI (JFJochCrystFELReader::ReadFiles, ReadCXI, Open) and XTC (JFJochXTCReader::ReadFiles) take the list of files instead of scanning a directory; CanReadCXI and xtc::CanRead accept only a file; ListFiles and xtc::CollectStreams are gone. - Several inputs must be one format, --mode mx, and stored files (no broker, no --simulate-live); one frame of a CBF/marCCD/SMV sweep still names the whole sweep. Validated: two Jungfraujoch lysozyme stills runs together (49,920 frames, known cell) 57.1% indexed (59.3% / 54.9% per run), 1.22 A, CC1/2 0.986, R_split 8.8%, REFMAC R/R-free 0.253/0.269 against 0.257/0.273 for the earlier hand-built combined master. Rotation: 5reo and lyso_x10sa_90deg_1 unchanged. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
69 lines
2.6 KiB
C++
69 lines
2.6 KiB
C++
// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#ifndef JFJOCHIMAGEREADER_H
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#define JFJOCHIMAGEREADER_H
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#include <unordered_set>
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#include <map>
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#include <mutex>
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#include "../common/JFJochMessages.h"
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#include "../common/Plot.h"
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#include "../common/ROIBox.h"
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#include "../common/DiffractionExperiment.h"
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#include "JFJochReaderDataset.h"
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#include "JFJochReaderImage.h"
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#include "JFJochReaderSpots.h"
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class JFJochReader {
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// Reads each of its inputs' frames through them (JFJochMultiReader.h).
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friend class JFJochMultiReader;
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mutable std::mutex m;
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std::shared_ptr<JFJochReaderDataset> dataset;
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virtual bool LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset,
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DataMessage& message,
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std::vector<uint8_t> &buffer,
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int64_t image_number,
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bool update_dataset) = 0;
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mutable std::mutex summation_mutex;
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void SummationThread(int64_t image0,
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int64_t n_image,
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int64_t image_jump,
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JFJochReaderImage &image);
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protected:
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void SetStartMessage(const std::shared_ptr<JFJochReaderDataset> &val);
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DiffractionExperiment default_experiment;
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public:
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virtual ~JFJochReader() = default;
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JFJochReader& Experiment(const DiffractionExperiment& experiment);
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std::shared_ptr<const JFJochReaderDataset> GetDataset() const;
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[[nodiscard]] virtual uint64_t GetNumberOfImages() const = 0;
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virtual void Close() = 0;
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std::shared_ptr<JFJochReaderImage> LoadImage(int64_t image_number, int64_t summation_factor = 1);
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void UpdateGeomMetadata(const DiffractionExperiment& experiment);
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void UpdateUserMask(const std::vector<uint32_t>& mask);
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// Read one image into a raw image the caller owns, false where there is nothing to read. A
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// worker that walks a whole sweep hands the same object back on every frame and so keeps its
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// buffer: GetRawImage() allocates a fresh one per call, which on a 4-byte 16 Mpx frame is 72 MB
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// of untouched pages the decoder then faults in one by one, measurably more than the decode.
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virtual bool ReadRawImage(int64_t image_number, JFJochReaderRawImage &image) = 0;
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// The same image in a freshly allocated raw image.
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std::shared_ptr<JFJochReaderRawImage> GetRawImage(int64_t image_number);
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virtual std::vector<SpotToSave> ReadSpots(int64_t image) const = 0;
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std::shared_ptr<JFJochReaderSpots> ReadAllSpots(int64_t start_image, int64_t end_image, int64_t stride = 1) const;
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};
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#endif //JFJOCHIMAGEREADER_H
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