115 lines
4.0 KiB
C++
115 lines
4.0 KiB
C++
// Copyright (2019-2022) Paul Scherrer Institute
|
|
// SPDX-License-Identifier: GPL-3.0-or-later
|
|
|
|
#include "HDF5DataFile.h"
|
|
#include "../compression/JFJochCompressor.h"
|
|
|
|
HDF5DataFile::HDF5DataFile(const std::string &in_filename, int64_t width, int64_t height,
|
|
int64_t pixel_depth_byte, bool is_signed, CompressionAlgorithm compression,
|
|
size_t in_max_spots) : data_type(pixel_depth_byte, is_signed),
|
|
max_spots(in_max_spots) {
|
|
max_image_number = 0;
|
|
nimages = 0;
|
|
|
|
if (max_spots > 256)
|
|
throw JFJochException(JFJochExceptionCategory::ArrayOutOfBounds, "Max spot count must be less than 256 for performance reasons");
|
|
|
|
filename = in_filename;
|
|
|
|
xpixel = width;
|
|
ypixel = height;
|
|
|
|
dcpl.SetCompression(compression, pixel_depth_byte, JFJochBitShuffleCompressor::DefaultBlockSize);
|
|
dcpl.SetChunking( {1, ypixel, xpixel});
|
|
}
|
|
|
|
HDF5DataFile::~HDF5DataFile() {
|
|
data_set.reset();
|
|
|
|
if (!spot_count.empty()) {
|
|
HDF5Group group(*data_file, "/entry/result");
|
|
group.NXClass("NXcollection");
|
|
std::vector<hsize_t> dims = {spot_count.size(), max_spots};
|
|
group.SaveVector("nPeaks", spot_count);
|
|
group.SaveVector("peakXPosRaw", spot_x, dims, CompressionAlgorithm::BSHUF_LZ4);
|
|
group.SaveVector("peakYPosRaw", spot_y, dims, CompressionAlgorithm::BSHUF_LZ4);
|
|
group.SaveVector("peakTotalIntensity", spot_intensity, dims, CompressionAlgorithm::BSHUF_LZ4);
|
|
group.SaveVector("indexingResult", indexing_result);
|
|
|
|
HDF5Group group_exp(*data_file, "/entry/jungfrau");
|
|
group_exp.NXClass("NXcollection");
|
|
group_exp.SaveVector("bunch_id", bunch_id);
|
|
group_exp.SaveVector("info", jf_info);
|
|
group_exp.SaveVector("timestamp", timestamp);
|
|
}
|
|
|
|
data_file.reset();
|
|
}
|
|
|
|
void HDF5DataFile::CreateFile() {
|
|
data_file = std::make_unique<HDF5File>(filename, true,false, false);
|
|
HDF5Group(*data_file, "/entry").NXClass("NXentry");
|
|
HDF5Group(*data_file, "/entry/data").NXClass("NXdata");
|
|
|
|
HDF5DataSpace data_space({1, ypixel, xpixel},{H5S_UNLIMITED, ypixel, xpixel});
|
|
data_set = std::make_unique<HDF5DataSet>(*data_file, "/entry/data/data", data_type, data_space, dcpl);
|
|
|
|
spot_count.resize(1);
|
|
spot_x.resize(max_spots);
|
|
spot_y.resize(max_spots);
|
|
spot_intensity.resize(max_spots);
|
|
indexing_result.resize(1);
|
|
bunch_id.resize(1);
|
|
jf_info.resize(1);
|
|
timestamp.resize(1);
|
|
}
|
|
|
|
void HDF5DataFile::Write(const DataMessage &msg, uint64_t image_number) {
|
|
std::lock_guard<std::mutex> lock(hdf5_mutex);
|
|
if (!data_file)
|
|
CreateFile();
|
|
|
|
if (image_number > max_image_number) {
|
|
max_image_number = image_number;
|
|
data_set->SetExtent({max_image_number+1, ypixel, xpixel});
|
|
spot_count.resize(max_image_number + 1);
|
|
spot_x.resize(max_spots * (max_image_number + 1));
|
|
spot_y.resize(max_spots * (max_image_number + 1));
|
|
spot_intensity.resize(max_spots * (max_image_number + 1));
|
|
indexing_result.resize(max_image_number + 1);
|
|
bunch_id.resize(max_image_number + 1);
|
|
jf_info.resize(max_image_number + 1);
|
|
timestamp.resize(max_image_number + 1);
|
|
}
|
|
|
|
nimages++;
|
|
data_set->WriteDirectChunk(msg.image.data, msg.image.size, {image_number, 0, 0});
|
|
|
|
size_t cnt = std::min(msg.spots.size(), max_spots);
|
|
|
|
spot_count[image_number] = cnt;
|
|
|
|
for (int i = 0; i < cnt; i++) {
|
|
spot_x[max_spots * image_number + i] = msg.spots[i].x;
|
|
spot_y[max_spots * image_number + i] = msg.spots[i].y;
|
|
spot_intensity[max_spots * image_number + i] = msg.spots[i].intensity;
|
|
}
|
|
|
|
indexing_result[image_number] = msg.indexing_result;
|
|
bunch_id[image_number] = msg.bunch_id;
|
|
jf_info[image_number] = msg.jf_info;
|
|
timestamp[image_number] = msg.timestamp;
|
|
}
|
|
|
|
size_t HDF5DataFile::GetMaxImageNumber() const {
|
|
return max_image_number;
|
|
}
|
|
|
|
size_t HDF5DataFile::GetNumImages() const {
|
|
return nimages;
|
|
}
|
|
|
|
std::string HDF5DataFile::GetFilename() const {
|
|
return filename;
|
|
}
|