leonarski_fandClaude Opus 5
5f78fc156f
A series of one file per image was laid out end to end: the rotation start came from the first file and the step from the difference between the first two, so a series with frames missing came out compressed - one 179.8 degree deposited sweep of 1108 files out of 1800 was read as 111 degrees, and every frame past the first gap was analysed at the wrong spindle angle. Indexing then found a lattice that took 4% of the validation spots, and two other gapped series aborted outright with "it is not this crystal's lattice". Every one of these formats writes each image's own start angle in its own header, so the sweep is fully recoverable. The new reader/SweepLayout places each frame at the slot its own angle puts it in and leaves a missing frame as a gap - a slot with no file, which ReadRawImage reports as nothing to read, which every image loop in the pipeline already passes over. The goniometer's start + increment * image_number is then the true angle of every image, and the sweep range, the per-10-degree delta-CC1/2 batches and the sweep-quality ledger all read the rotation the headers describe. The rotation step is the smallest move between two frames that really are adjacent, not the first pair. The three readers shared this code by duplication; it is now written once. The same place refuses what is not a sweep rather than averaging it into one: headers that disagree about the detector distance, the beam centre, the wavelength or the oscillation width, angles that do not sit on a single step (a folder of screening shots), or two frames claiming the same angle - each naming the frames. A series that does not turn at all is left exactly as it was. A directory holding fewer files than its own numbering spans is also reported, with both counts: that is the signal that a sweep was not unpacked or copied whole, which otherwise shows up only as a resolution nobody can explain. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_013nW6FNRP1bBJJ8pfHiByAT
62 lines
2.7 KiB
C++
62 lines
2.7 KiB
C++
// SPDX-FileCopyrightText: 2026 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 <string>
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#include <vector>
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#include "JFJochReader.h"
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#include "MiniCBF.h"
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// Reads a rotation sweep straight from a directory of PILATUS miniCBF files - the form most
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// facilities still archive - with no conversion step and no libcbf.
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//
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// The sweep's geometry comes from the first file's header; the rotation angle of each image comes
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// from its own header, which costs only the bytes up to the binary separator. Images are decoded on
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// demand, one per call, so any number of workers can read at once - there is no global lock as there
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// is on the HDF5 path, HDF5 not being thread-safe.
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//
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// A raw CBF carries no analysis results, so this reader has no spots, no reflections and no snapshots;
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// the dataset it builds is the geometry, the mask and nothing else, exactly as a plain DECTRIS file
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// with no /entry/MX would give.
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class JFJochCBFReader : public JFJochReader {
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std::vector<std::string> files_;
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std::shared_ptr<JFJochReaderDataset> dataset_;
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minicbf::Header header0_;
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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) override;
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// Decodes one image into the caller's byte buffer (RawByteBuffer or std::vector<uint8_t>) and
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// returns the image that points at it. The compressed file is read through scratch, which the
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// caller keeps between frames.
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template <class Buffer>
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CompressedImage DecodeInto(int64_t image_number, Buffer &buffer, std::vector<uint8_t> &scratch) const;
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public:
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~JFJochCBFReader() override = default;
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// True if the path names something this reader can open: a miniCBF file, or a directory holding
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// at least one. Cheap - it reads a few kB at most.
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static bool CanRead(const std::string &path);
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// path is a directory of *.cbf, or one *.cbf inside the sweep to take the whole directory from.
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void ReadFiles(const std::string &path);
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[[nodiscard]] uint64_t GetNumberOfImages() const override;
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void Close() override;
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// Whether the sweep really has an image at this point. A deposited series can be missing frames,
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// and they are kept as gaps so that every image keeps the spindle angle its own header states;
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// ReadRawImage hands such a slot back as "nothing to read".
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[[nodiscard]] bool HasImage(int64_t image_number) const;
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bool ReadRawImage(int64_t image_number, JFJochReaderRawImage &image) override;
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[[nodiscard]] std::vector<SpotToSave> ReadSpots(int64_t image) const override;
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};
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