leonarski_f
9434878c92
Build Packages / build:rpm (ubuntu2404_nocuda) (push) Successful in 12m46s
Build Packages / build:rpm (rocky8_nocuda) (push) Successful in 14m27s
Build Packages / build:rpm (ubuntu2204_nocuda) (push) Successful in 15m5s
Build Packages / build:rpm (rocky8_sls9) (push) Successful in 15m1s
Build Packages / build:rpm (rocky9_nocuda) (push) Successful in 15m7s
Build Packages / build:rpm (rocky9_sls9) (push) Successful in 15m6s
Build Packages / build:rpm (rocky8) (push) Successful in 13m25s
Build Packages / XDS test (neggia plugin) (push) Successful in 9m46s
Build Packages / XDS test (durin plugin) (push) Successful in 10m14s
Build Packages / Generate python client (push) Successful in 16s
Build Packages / Create release (push) Skipped
Build Packages / build:rpm (rocky9) (push) Successful in 13m1s
Build Packages / build:rpm (ubuntu2204) (push) Successful in 11m33s
Build Packages / XDS test (JFJoch plugin) (push) Successful in 10m45s
Build Packages / Build documentation (push) Successful in 47s
Build Packages / build:rpm (ubuntu2404) (push) Successful in 12m17s
Build Packages / DIALS test (push) Successful in 13m39s
Build Packages / Unit tests (push) Failing after 58m55s
Complete the image/metadata decoupling. JFJochHDF5Reader is now a thin JFJochReader
facade composing one shared HDF5ImageSource (raw pixels) with a name->HDF5MetadataSource
map and an active selection ("snapshots").
- HDF5MetadataSource owns one master file: dataset-level parse (Open, ex-ReadFile),
per-image metadata (FillPerImage, ex-LoadImage_i), ReadSpots/ReadReflections/
ReadCalibration, and the master-first helpers. It locates per-image metadata either via
the shared image source (original file: metadata co-located with pixels) or in its own
master at the global index (integrated _process.h5 snapshot) - so switching snapshots
never reloads pixels.
- Facade adds RegisterSnapshot/SetActiveSnapshot/SnapshotNames/ActiveSnapshot; ReadFile
registers the original as "Original". All existing JFJochReader callers are unchanged.
- The global hdf5_mutex is taken once in the facade; the sources assume it is held.
Adds JFJochReader_Snapshots test (original _master.h5 + a reprocessing _process.h5 over
the same images: pixels stay from the original, metadata follows the active snapshot).
Verified: tests/jfjoch_test [HDF5] (80 cases / 1810 assertions), plus jfjoch_process/
azint/extract_hkl/scale and jfjoch_viewer all build against the refactored reader.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
69 lines
3.3 KiB
C++
69 lines
3.3 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
|
|
// SPDX-License-Identifier: GPL-3.0-only
|
|
|
|
#pragma once
|
|
|
|
#include <memory>
|
|
#include <optional>
|
|
#include <string>
|
|
#include <vector>
|
|
|
|
#include "JFJochReaderDataset.h"
|
|
#include "HDF5ImageSource.h"
|
|
#include "../common/JFJochMessages.h"
|
|
#include "../common/SpotToSave.h"
|
|
#include "../common/GoniometerAxis.h"
|
|
#include "../common/DiffractionExperiment.h"
|
|
#include "../common/DiffractionGeometry.h"
|
|
#include "../image_analysis/IntegrationOutcome.h"
|
|
|
|
// Metadata side of the reader: everything read from one master file that is NOT raw pixels -
|
|
// dataset-level metadata (geometry, mask, ROI definitions, azimuthal mapping, the per-image plot
|
|
// arrays) and per-image metadata (spots, reflections, MX scalars, azimuthal profile, lattice).
|
|
//
|
|
// This is the swappable part: a dataset can have several metadata sources over the same images
|
|
// (the original _master.h5 plus reprocessing _process.h5 snapshots). Per-image metadata is
|
|
// located either through the shared image source (original file: metadata sits in the same files
|
|
// as the pixels) or in this master at the global index (integrated _process.h5 snapshot).
|
|
//
|
|
// HDF5 is not thread-safe; all calls must be made with the global hdf5_mutex held by the caller.
|
|
class HDF5MetadataSource {
|
|
public:
|
|
struct OpenResult {
|
|
HDF5ImageLocator::Layout image_layout; // layout implied by this master (for the image source)
|
|
uint64_t number_of_images = 0;
|
|
};
|
|
|
|
// Parse a master file's dataset-level metadata into a JFJochReaderDataset. default_experiment
|
|
// seeds the dataset's experiment. Returns the image layout it implies; the caller decides
|
|
// whether to use it to configure the shared image source.
|
|
OpenResult Open(const std::string &filename, const DiffractionExperiment &default_experiment);
|
|
|
|
// How per-image metadata is located: with image_source set, metadata is co-located with the
|
|
// pixels (original file); when null it lives in this master at the global index.
|
|
void UseImageSourceForMetadata(const HDF5ImageSource *image_source) { image_source_ = image_source; }
|
|
|
|
std::shared_ptr<JFJochReaderDataset> Dataset() const { return dataset_; }
|
|
uint64_t NumberOfImages() const { return number_of_images; }
|
|
|
|
// Per-image metadata (spots, azimuthal profile, MX scalars, lattice, reflections) into msg.
|
|
void FillPerImage(DataMessage &message, int64_t image_number,
|
|
const std::shared_ptr<const JFJochReaderDataset> &dataset) const;
|
|
|
|
std::vector<SpotToSave> ReadSpots(int64_t image) const;
|
|
std::vector<IntegrationOutcome> ReadReflections(size_t start_image, std::optional<size_t> end_image) const;
|
|
CompressedImage ReadCalibration(std::vector<uint8_t> &tmp, const std::string &name) const;
|
|
|
|
private:
|
|
std::shared_ptr<HDF5ReadOnlyFile> master_file;
|
|
std::string master_filename;
|
|
std::shared_ptr<JFJochReaderDataset> dataset_;
|
|
DiffractionGeometry cached_geom;
|
|
uint64_t number_of_images = 0;
|
|
const HDF5ImageSource *image_source_ = nullptr;
|
|
|
|
HDF5ImageLocator::Location ResolveMeta(int64_t global) const;
|
|
std::optional<GoniometerAxis> ReadAxis(HDF5Object *file, const std::string &name);
|
|
void ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDataset &dataset) const;
|
|
};
|