133 lines
4.1 KiB
C++
133 lines
4.1 KiB
C++
// Copyright (2019-2023) Paul Scherrer Institute
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#include <sys/stat.h>
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#include "HDF5DataFile.h"
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#include "../compression/JFJochCompressor.h"
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#include "HDF5DataFilePluginAzInt.h"
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#include "HDF5DataFilePluginMX.h"
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#include "HDF5DataFilePluginXFEL.h"
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#include "HDF5DataFilePluginJUNGFRAU.h"
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#include "../include/spdlog/fmt/fmt.h"
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HDF5DataFile::HDF5DataFile(const std::string &in_filename,
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const std::vector<float>& in_rad_int_bin_to_q,
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int32_t in_image_low,
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size_t in_max_spots) {
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xpixel = 0;
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ypixel = 0;
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max_image_number = 0;
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nimages = 0;
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filename = in_filename;
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image_low = in_image_low;
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tmp_filename = fmt::format("{}.tmp{:8x}", filename, std::chrono::system_clock::now().time_since_epoch().count());
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plugins.emplace_back(std::make_unique<HDF5DataFilePluginJUNGFRAU>());
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plugins.emplace_back(std::make_unique<HDF5DataFilePluginAzInt>(in_rad_int_bin_to_q));
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plugins.emplace_back(std::make_unique<HDF5DataFilePluginXFEL>());
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plugins.emplace_back(std::make_unique<HDF5DataFilePluginMX>(in_max_spots));
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}
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std::optional<HDF5DataFileStatistics> HDF5DataFile::Close() {
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if (!data_file)
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return {};
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HDF5Group group_exp(*data_file, "/entry/detector");
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group_exp.NXClass("NXcollection");
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group_exp.SaveVector("timestamp", timestamp);
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group_exp.SaveVector("exptime", exptime);
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group_exp.SaveVector("number", number);
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for (auto &p: plugins)
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p->WriteFinal(*data_file);
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if (data_set) {
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data_set
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->Attr("image_nr_low", (int32_t) (image_low + 1))
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.Attr("image_nr_high", (int32_t) (image_low + 1 + max_image_number));
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data_set.reset();
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}
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data_file.reset();
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std::rename(tmp_filename.c_str(), filename.c_str());
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closed = true;
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HDF5DataFileStatistics ret;
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ret.max_image_number = max_image_number;
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ret.total_images = nimages;
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ret.filename = filename;
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return ret;
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}
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HDF5DataFile::~HDF5DataFile() {
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if (data_file) {
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try {
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Close();
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} catch (...) {}
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}
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}
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void HDF5DataFile::CreateFile(const DataMessage& msg) {
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HDF5Dcpl dcpl;
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HDF5DataType data_type(msg.image.pixel_depth_bytes, msg.image.pixel_is_signed);
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xpixel = msg.image.xpixel;
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ypixel = msg.image.ypixel;
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dcpl.SetCompression(msg.image.algorithm, msg.image.pixel_depth_bytes, JFJochBitShuffleCompressor::DefaultBlockSize);
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dcpl.SetChunking( {1, ypixel, xpixel});
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if (msg.image.pixel_is_signed) {
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if (msg.image.pixel_depth_bytes == 2)
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dcpl.SetFillValue16(INT16_MIN);
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else
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dcpl.SetFillValue32(INT32_MIN);
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}
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data_file = std::make_unique<HDF5File>(tmp_filename);
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chmod(tmp_filename.c_str(), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP); // default permissions
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HDF5Group(*data_file, "/entry").NXClass("NXentry");
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HDF5Group(*data_file, "/entry/data").NXClass("NXdata");
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HDF5DataSpace data_space({1, ypixel, xpixel}, {H5S_UNLIMITED, ypixel, xpixel});
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data_set = std::make_unique<HDF5DataSet>(*data_file, "/entry/data/data", data_type, data_space, dcpl);
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for (auto &p: plugins)
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p->OpenFile(*data_file, msg);
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}
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void HDF5DataFile::Write(const DataMessage &msg, uint64_t image_number) {
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if (closed)
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return;
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bool new_file = false;
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if (!data_file) {
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CreateFile(msg);
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new_file = true;
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}
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if (new_file || (static_cast<int64_t>(image_number) > max_image_number)) {
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max_image_number = image_number;
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data_set->SetExtent({max_image_number+1, ypixel, xpixel});
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timestamp.resize(max_image_number + 1);
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exptime.resize(max_image_number + 1);
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number.resize(max_image_number + 1);
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}
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nimages++;
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data_set->WriteDirectChunk(msg.image.data, msg.image.size, {image_number, 0, 0});
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for (auto &p: plugins)
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p->Write(msg, image_number);
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timestamp[image_number] = msg.timestamp;
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exptime[image_number] = msg.exptime;
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number[image_number] = (msg.original_number) ? msg.original_number.value() : msg.number;
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}
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size_t HDF5DataFile::GetNumImages() const {
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return nimages;
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}
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