leonarski_f
23d27f30c4
Decouple the raw-pixel side of JFJochHDF5Reader from the rest as the first step toward swappable per-dataset metadata snapshots. - HDF5ImageLocator: single owner of the legacy/VDS/contiguous layout resolution plus a persistent open-file cache, replacing the four duplicated resolvers (GetImageLocation, ReadSpots, ReadReflections) and their per-call file caches. Also hosts the source-mapping logic (former GetHDF5DataSource body). - HDF5ImageSource: raw-pixel reading (locator + LoadImageDataset); the part whose links to files stay fixed while the metadata master may change. - JFJochHDF5Reader keeps a thin GetImageLocation/GetRawImage/GetHDF5DataSource that delegate to image_source_; the six layout members are gone, parsed into a local Layout handed to the source at the end of ReadFile. Cache cleared on Close(). Verified: tests/jfjoch_test [HDF5] (79 cases / 1775 assertions), and jfjoch_process/azint/extract_hkl/scale relink unchanged. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
67 lines
2.5 KiB
C++
67 lines
2.5 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
|
|
// SPDX-License-Identifier: GPL-3.0-only
|
|
|
|
#include "HDF5ImageSource.h"
|
|
#include "../common/JFJochException.h"
|
|
|
|
void HDF5ImageSource::Configure(HDF5ImageLocator::Layout layout) {
|
|
locator_.Configure(std::move(layout));
|
|
}
|
|
|
|
void HDF5ImageSource::Clear() {
|
|
locator_.Clear();
|
|
}
|
|
|
|
HDF5ImageLocator::Location HDF5ImageSource::Resolve(int64_t global) const {
|
|
return locator_.Resolve(global);
|
|
}
|
|
|
|
std::vector<HDF5DataSourceMessage> HDF5ImageSource::GetSourceMapping(uint64_t first_image,
|
|
std::optional<uint64_t> image_count,
|
|
uint64_t total_images) const {
|
|
return locator_.GetSourceMapping(first_image, image_count, total_images);
|
|
}
|
|
|
|
CompressedImage HDF5ImageSource::ReadImageAt(std::vector<uint8_t> &buffer,
|
|
const HDF5ImageLocator::Location &loc) const {
|
|
return LoadImageDataset(buffer, *loc.file, loc.local_index);
|
|
}
|
|
|
|
CompressedImage HDF5ImageSource::LoadImageDataset(std::vector<uint8_t> &tmp, HDF5Object &file, hsize_t number) {
|
|
std::vector<hsize_t> start = {static_cast<hsize_t>(number), 0, 0};
|
|
|
|
const std::string dataset_name = "/entry/data/data";
|
|
|
|
HDF5DataSet dataset(file, dataset_name);
|
|
HDF5DataSpace dataspace(dataset);
|
|
HDF5DataType datatype(dataset);
|
|
HDF5Dcpl dcpl(dataset);
|
|
|
|
if (dataspace.GetNumOfDimensions() != 3)
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"/entry/data/data dataset must be 3D");
|
|
|
|
auto dim = dataspace.GetDimensions();
|
|
|
|
CompressionAlgorithm algorithm = CompressionAlgorithm::NO_COMPRESSION;
|
|
auto chunk_size = dcpl.GetChunking();
|
|
|
|
if ((chunk_size.size() == 3) && (chunk_size[0] == 1) && (chunk_size[1] == dim[1]) && (chunk_size[2] == dim[2])) {
|
|
dataset.ReadDirectChunk(tmp, start);
|
|
algorithm = dcpl.GetCompression();
|
|
} else {
|
|
dataset.ReadVectorToU8(tmp, start, {1, dim[1], dim[2]});
|
|
algorithm = CompressionAlgorithm::NO_COMPRESSION;
|
|
}
|
|
|
|
if (datatype.IsFloat())
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"Float datasets not supported at this time");
|
|
|
|
return {
|
|
tmp, dim[2], dim[1],
|
|
CalcImageMode(datatype.GetElemSize(), datatype.IsFloat(), datatype.IsSigned()),
|
|
algorithm
|
|
};
|
|
}
|