leonarski_fandClaude Opus 5
dc16a00271
Most facilities still archive rotation data as a directory of miniCBF frames, which until now had to be converted to HDF5 before rugnux could see it. Nothing in that format needs a CIF parser or a library: it is an ASCII header, four separator bytes, then one byte-offset compressed image, and every value the reader wants sits on a "# " comment line or a MIME line. MiniCBF holds the format itself - header parse and the byte-offset decoder, which is a running value with deltas stored smallest-container-first. Verified byte-exact against dxtbx on PILATUS 6M, 6M-F, 300K, silicon and CdTe sensors, and three sensor thicknesses. JFJochCBFReader is a sibling of JFJochHDF5Reader under the JFJochReader base. NAMING ANY FRAME READS ITS WHOLE SWEEP: the sweep is identified by the template (prefix + digit count) the named frame belongs to, not by "every .cbf in the directory", so a directory holding two sweeps does not splice two crystals together. Naming a directory takes the sweep with the most frames in it. Images decode on demand, one per call, so any number of workers can read at once - there is no global lock as there is on the HDF5 path, HDF5 not being thread-safe. A raw CBF carries no analysis results, so the dataset it builds is the geometry, the mask and nothing else, exactly as a plain DECTRIS file with no /entry/MX gives. Two header quirks are handled because real files have them: the sensor material is written "Silicon" where the rest of the code compares against "CdTe", and the thickness unit is sometimes omitted. Headers are not a fixed size either - one set carries 6335 bytes - so the parse runs to the binary separator rather than over a fixed prefix. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
55 lines
2.3 KiB
C++
55 lines
2.3 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.
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template <class Buffer>
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CompressedImage DecodeInto(int64_t image_number, Buffer &buffer) 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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std::shared_ptr<JFJochReaderRawImage> GetRawImage(int64_t image_number) override;
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[[nodiscard]] std::vector<SpotToSave> ReadSpots(int64_t image) const override;
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};
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