leonarski_fandClaude Opus 5
df3696e6e2
Firmware 1.x writes the same three values under different names. Try the NXmx spelling first and
the old one only if it is absent:
detector/distance <- detector/detector_distance
detector/saturation_value <- detectorSpecific/countrate_correction_count_cutoff
sample/transformations <- sample/goniometer
This cannot change what a current file reads: every modern Eiger master carries BOTH spellings.
Measured on thirteen masters from ten facilities, firmware release-2020.2.1 through
release-2024.1.1 - all of them write detector_distance and countrate_correction_count_cutoff beside
the NXmx names, and a goniometer group beside the transformations one.
The goniometer is the one that matters. A goniometer is only ever set from that one group, so a
file whose axes are somewhere else was not an error - it was read as STILLS, silently, and the run
completed with the wrong answer. The old layout also tags no axis with transformation_type and
gives no vector, both of which ReadAxis required, so absence now means two different things by
layout: in a transformations group it still means "not an axis" (that is how AXISNAME_end and the
width scalars are skipped), while in the legacy group every leaf IS an axis and the companions are
recognised by name instead. A missing direction defaults to the one every DECTRIS master since has
written and says so in a warning rather than assuming it silently; a wrong guess there does not
index, so it is visible, and the rotation first pass tries the opposite sign anyway.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
83 lines
4.1 KiB
C++
83 lines
4.1 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 <memory>
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#include <optional>
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#include <string>
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#include <unordered_map>
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#include <vector>
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#include "JFJochReaderDataset.h"
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#include "HDF5ImageSource.h"
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#include "../common/JFJochMessages.h"
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#include "../common/SpotToSave.h"
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#include "../common/GoniometerAxis.h"
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#include "../common/DiffractionExperiment.h"
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#include "../common/DiffractionGeometry.h"
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#include "../image_analysis/IntegrationOutcome.h"
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// Metadata side of the reader: everything read from one master file that is NOT raw pixels -
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// dataset-level metadata (geometry, mask, ROI definitions, azimuthal mapping, the per-image plot
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// arrays) and per-image metadata (spots, reflections, MX scalars, azimuthal profile, lattice).
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//
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// This is the swappable part: a dataset can have several metadata sources over the same images
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// (the original _master.h5 plus reprocessing _process.h5 snapshots). Per-image metadata is
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// located either through the shared image source (original file: metadata sits in the same files
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// as the pixels) or in this master at the global index (integrated _process.h5 snapshot).
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//
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// HDF5 is not thread-safe; all calls must be made with the global hdf5_mutex held by the caller.
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class HDF5MetadataSource {
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public:
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struct OpenResult {
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HDF5ImageLocator::Layout image_layout; // layout implied by this master (for the image source)
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uint64_t number_of_images = 0;
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};
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// Parse a master file's dataset-level metadata into a JFJochReaderDataset. default_experiment
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// seeds the dataset's experiment. Returns the image layout it implies; the caller decides
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// whether to use it to configure the shared image source.
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OpenResult Open(const std::string &filename, const DiffractionExperiment &default_experiment);
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// How per-image metadata is located: with image_source set, metadata is co-located with the
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// pixels (original file); when null it lives in this master at the global index.
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void UseImageSourceForMetadata(const HDF5ImageSource *image_source) { image_source_ = image_source; }
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std::shared_ptr<JFJochReaderDataset> Dataset() const { return dataset_; }
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uint64_t NumberOfImages() const { return number_of_images; }
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// Per-image metadata (spots, azimuthal profile, MX scalars, lattice, reflections) into msg.
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void FillPerImage(DataMessage &message, int64_t image_number,
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const std::shared_ptr<const JFJochReaderDataset> &dataset) const;
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std::vector<SpotToSave> ReadSpots(int64_t image) const;
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// True if the file stores spot-finding results (/entry/MX); a plain DECTRIS file has none.
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[[nodiscard]] bool HasSpots() const;
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std::vector<IntegrationOutcome> ReadReflections(size_t start_image, std::optional<size_t> end_image) const;
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CompressedImage ReadCalibration(std::vector<uint8_t> &tmp, const std::string &name) const;
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private:
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std::shared_ptr<HDF5ReadOnlyFile> master_file;
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std::string master_filename;
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std::shared_ptr<JFJochReaderDataset> dataset_;
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DiffractionGeometry cached_geom;
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uint64_t number_of_images = 0;
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const HDF5ImageSource *image_source_ = nullptr;
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// Inverse of dataset_->source_image_number (original image number -> local index in this
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// master). Empty for a 1:1 source; populated when this metadata covers a subset of images.
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std::unordered_map<int64_t, int64_t> image_to_local_;
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// Translate a global/original image number to the local index in this metadata source, or
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// nullopt if this source does not cover that image. Identity for a 1:1 source.
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std::optional<int64_t> ToLocalIndex(int64_t image_number) const;
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HDF5ImageLocator::Location ResolveMeta(int64_t global) const;
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// group is where the axes live: /entry/sample/transformations (NXmx) or
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// /entry/sample/goniometer (DECTRIS firmware 1.x, which tags no axis and gives no vector).
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std::optional<GoniometerAxis> ReadAxis(HDF5Object *file, const std::string &name,
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const std::string &group);
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void ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDataset &dataset) const;
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};
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