mirror of
https://github.com/slsdetectorgroup/aare.git
synced 2026-02-20 05:38:41 +01:00
works for hdf5, needs refactoring
This commit is contained in:
162
src/Hdf5File.cpp
162
src/Hdf5File.cpp
@@ -10,7 +10,8 @@ Hdf5File::Hdf5File(const std::filesystem::path &fname, const std::string &mode)
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: m_master(fname) {
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m_mode = mode;
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if (mode == "r") {
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open_file();
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open_data_file();
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open_header_files();
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} else {
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throw std::runtime_error(LOCATION +
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"Unsupported mode. Can only read Hdf5Files.");
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@@ -66,12 +67,9 @@ DetectorType Hdf5File::detector_type() const {
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}
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void Hdf5File::seek(size_t frame_index) {
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// check if the frame number is greater than the total frames
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// if frame_number == total_frames, then the next read will throw an error
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if (frame_index > total_frames()) {
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throw std::runtime_error(
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fmt::format("frame number {} is greater than total frames {}",
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frame_index, total_frames()));
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m_data_file->seek(frame_index);
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for (size_t i = 0; i != header_dataset_names.size(); ++i) {
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m_header_files[i]->seek(frame_index);
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}
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m_current_frame = frame_index;
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};
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@@ -86,6 +84,37 @@ xy Hdf5File::geometry() { return m_master.geometry(); }
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DetectorHeader Hdf5File::read_header(const std::filesystem::path &fname) {
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DetectorHeader h{};
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std::vector<std::unique_ptr<H5Handles>> handles;
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try {
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for (size_t i = 0; i != header_dataset_names.size(); ++i) {
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handles.push_back(std::make_unique<H5Handles>(fname.string(), metadata_group_name+ header_dataset_names[i], 1));
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}
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handles[0]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.frameNumber)));
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handles[1]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.expLength)));
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handles[2]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.packetNumber)));
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handles[3]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.bunchId)));
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handles[4]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.timestamp)));
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handles[5]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.modId)));
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handles[6]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.row)));
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handles[7]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.column)));
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handles[8]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.reserved)));
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handles[9]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.debug)));
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handles[10]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.roundRNumber)));
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handles[11]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.detType)));
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handles[12]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.version)));
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handles[13]->get_frame_into(0, reinterpret_cast<std::byte *>(&(h.packetMask)));
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fmt::print("Read 1D header for frame {}\n", 0);
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} catch (const H5::Exception &e) {
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handles.clear();
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fmt::print("Exception type: {}\n", typeid(e).name());
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e.printErrorStack();
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throw std::runtime_error(
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LOCATION + "\nCould not to access header datasets in given file.");
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}
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FILE *fp = fopen(fname.string().c_str(), "r");
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if (!fp)
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throw std::runtime_error(
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@@ -114,27 +143,35 @@ size_t Hdf5File::bytes_per_pixel() const { return m_master.bitdepth() / 8; }
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void Hdf5File::get_frame_into(size_t frame_index, std::byte *frame_buffer,
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DetectorHeader *header) {
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get_data_into(frame_index, frame_buffer);
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get_header_into(frame_index, header);
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}
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// Check if the frame number is valid
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if (frame_index < 0 || frame_index >= m_total_frames) {
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throw std::runtime_error(LOCATION + "Invalid frame number");
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}
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// Define the hyperslab to select the 2D slice for the given frame number
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hsize_t offset[3] = {static_cast<hsize_t>(frame_index), 0, 0};
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hsize_t count[3] = {1, m_rows, m_cols};
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dataspace->selectHyperslab(H5S_SELECT_SET, count, offset);
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// Define the memory space for the 2D slice
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hsize_t dimsm[2] = {m_rows, m_cols};
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H5::DataSpace memspace(2, dimsm);
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// Read the data into the provided 2D array
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dataset->read(frame_buffer, m_datatype, memspace, dataspace);
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void Hdf5File::get_data_into(size_t frame_index, std::byte *frame_buffer) {
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m_data_file->get_frame_into(frame_index, frame_buffer);
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fmt::print("Read 2D data for frame {}\n", frame_index);
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}
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void Hdf5File::get_header_into(size_t frame_index, DetectorHeader *header) {
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if (header) {
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m_header_files[0]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->frameNumber)));
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m_header_files[1]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->expLength)));
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m_header_files[2]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->packetNumber)));
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m_header_files[3]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->bunchId)));
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m_header_files[4]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->timestamp)));
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m_header_files[5]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->modId)));
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m_header_files[6]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->row)));
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m_header_files[7]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->column)));
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m_header_files[8]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->reserved)));
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m_header_files[9]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->debug)));
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m_header_files[10]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->roundRNumber)));
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m_header_files[11]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->detType)));
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m_header_files[12]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->version)));
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m_header_files[13]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&(header->packetMask)));
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fmt::print("Read 1D header for frame {}\n", frame_index);
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}
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}
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std::vector<Frame> Hdf5File::read_n(size_t n_frames) {
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// TODO: implement this in a more efficient way
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std::vector<Frame> frames;
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@@ -146,48 +183,45 @@ std::vector<Frame> Hdf5File::read_n(size_t n_frames) {
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}
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size_t Hdf5File::frame_number(size_t frame_index) {
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if (frame_index >= m_master.frames_in_file()) {
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throw std::runtime_error(LOCATION + " Frame number out of range");
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}
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size_t subfile_id = frame_index / m_master.max_frames_per_file();
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/*if (subfile_id >= subfiles.size()) {
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throw std::runtime_error(
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LOCATION + " Subfile out of range. Possible missing data.");
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}*/
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return 1; // subfiles[subfile_id][0]->frame_number(
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// frame_index % m_master.max_frames_per_file());
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uint64_t fnum{0};
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m_header_files[0]->get_frame_into(frame_index, reinterpret_cast<std::byte *>(&fnum));
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return fnum;
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}
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Hdf5File::~Hdf5File() {}
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const std::string Hdf5File::metadata_group_name = "/entry/data/";
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const std::vector<std::string> Hdf5File::header_dataset_names = {
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"frame number",
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"exp length or sub exposure time",
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"packets caught",
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"detector specific 1",
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"timestamp",
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"mod id",
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"row",
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"column",
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"detector specific 2",
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"detector specific 3",
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"detector specific 4",
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"detector type",
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"detector header version",
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"packets caught bit mask"
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};
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void Hdf5File::open_file() {
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void Hdf5File::open_data_file() {
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if (m_mode != "r")
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throw std::runtime_error(LOCATION +
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"Unsupported mode. Can only read Hdf5 files.");
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try {
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file = std::make_unique<H5::H5File>(m_master.master_fname().string(),
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H5F_ACC_RDONLY);
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dataset = std::make_unique<H5::DataSet>(
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file->openDataSet(metadata_group_name + "/data"));
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dataspace = std::make_unique<H5::DataSpace>(dataset->getSpace());
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int rank = dataspace->getSimpleExtentNdims();
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if (rank != 3) {
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throw std::runtime_error(
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LOCATION + "Expected rank of '/data' dataset to be 3. Got " +
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std::to_string(rank));
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}
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hsize_t dims[3];
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dataspace->getSimpleExtentDims(dims, nullptr);
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m_total_frames = dims[0];
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m_rows = dims[1];
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m_cols = dims[2];
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m_datatype = dataset->getDataType();
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fmt::print("Dataset dimensions: frames = {}, rows = {}, cols = {}\n",
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m_data_file = std::make_unique<H5Handles>(m_master.master_fname().string(), metadata_group_name + "/data", 3);
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m_total_frames = m_data_file->dims[0];
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m_rows = m_data_file->dims[1];
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m_cols = m_data_file->dims[2];
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fmt::print("Data Dataset dimensions: frames = {}, rows = {}, cols = {}\n",
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m_total_frames, m_rows, m_cols);
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} catch (const H5::Exception &e) {
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file->close();
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m_data_file.reset();
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fmt::print("Exception type: {}\n", typeid(e).name());
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e.printErrorStack();
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throw std::runtime_error(
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@@ -195,4 +229,24 @@ void Hdf5File::open_file() {
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}
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}
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void Hdf5File::open_header_files() {
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if (m_mode != "r")
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throw std::runtime_error(LOCATION +
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"Unsupported mode. Can only read Hdf5 files.");
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try {
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for (size_t i = 0; i != header_dataset_names.size(); ++i) {
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m_header_files.push_back(std::make_unique<H5Handles>(m_master.master_fname().string(), metadata_group_name + header_dataset_names[i], 1));
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fmt::print("{} Dataset dimensions: size = {}\n",
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header_dataset_names[i], m_header_files[i]->dims[0]);
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}
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} catch (const H5::Exception &e) {
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m_header_files.clear();
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m_data_file.reset();
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fmt::print("Exception type: {}\n", typeid(e).name());
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e.printErrorStack();
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throw std::runtime_error(
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LOCATION + "\nCould not to access header datasets in master file.");
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}
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}
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} // namespace aare
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