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https://github.com/slsdetectorgroup/aare.git
synced 2025-06-06 12:50:40 +02:00
refactored a bit
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parent
55236ce6cc
commit
76b8872fe6
@ -9,13 +9,13 @@
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namespace aare {
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struct H5Handles {
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std::string file_name{};
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std::string dataset_name{};
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std::string file_name;
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std::string dataset_name;
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H5::H5File file;
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H5::DataSet dataset;
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H5::DataSpace dataspace;
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H5::DataType datatype;
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std::unique_ptr<H5::DataSpace> memspace{nullptr};
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std::unique_ptr<H5::DataSpace> memspace;
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std::vector<hsize_t>dims;
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std::vector<hsize_t> count;
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std::vector<hsize_t> offset;
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@ -26,59 +26,60 @@ struct H5Handles {
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file(fname, H5F_ACC_RDONLY),
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dataset(file.openDataSet(dname)),
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dataspace(dataset.getSpace()),
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datatype(dataset.getDataType())
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{
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// get dimensions
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int rank = dataspace.getSimpleExtentNdims();
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dims.resize(rank);
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dataspace.getSimpleExtentDims(dims.data(), nullptr);
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// to slice 1 frame with hyperslab
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count.push_back(1);
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offset.push_back(0);
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// header datasets
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if (rank == 1) {
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memspace = std::make_unique<H5::DataSpace>(H5S_SCALAR);
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}
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// header virtual datasets
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else if (rank == 2) {
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memspace = std::make_unique<H5::DataSpace>(H5S_SCALAR);
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count.push_back(1);
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offset.push_back(0);
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}
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// data dataset
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else {
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hsize_t dimsm[2] = {dims[1], dims[2]};
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memspace = std::make_unique<H5::DataSpace>(2, dimsm);
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count.push_back(dims[1]);
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count.push_back(dims[2]);
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offset.push_back(0);
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offset.push_back(0);
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datatype(dataset.getDataType()) {
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intialize_dimensions();
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initialize_memspace();
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}
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};
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void seek(size_t frame_index) {
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if (frame_index >= dims[0]) {
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throw std::runtime_error(LOCATION + "Invalid frame number");
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}
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offset[0] = static_cast<hsize_t>(frame_index);
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};
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}
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void get_frame_into(size_t frame_index, std::byte *frame_buffer) {
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void get_data_into(size_t frame_index, std::byte *frame_buffer) {
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seek(frame_index);
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//LOG(logDEBUG) << "data offset:" << offset << " count:" << count;
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//std::cout << "offset:" << offset << " count:" << count << std::endl;
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dataspace.selectHyperslab(H5S_SELECT_SET, count.data(), offset.data());
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dataset.read(frame_buffer, datatype, *memspace, dataspace);
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};
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}
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void get_header_into(size_t frame_index, int part_index, std::byte *header_buffer) {
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seek(frame_index);
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offset[1] = part_index;
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//LOG(logDEBUG) << "header offset:" << offset << " count:" << count;
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offset[1] = static_cast<hsize_t>(part_index);
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//std::cout << "offset:" << offset << " count:" << count << std::endl;
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dataspace.selectHyperslab(H5S_SELECT_SET, count.data(), offset.data());
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dataset.read(header_buffer, datatype, *memspace, dataspace);
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};
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}
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private:
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void intialize_dimensions() {
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int rank = dataspace.getSimpleExtentNdims();
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dims.resize(rank);
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dataspace.getSimpleExtentDims(dims.data(), nullptr);
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}
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void initialize_memspace() {
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int rank = dataspace.getSimpleExtentNdims();
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count.clear();
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offset.clear();
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// header datasets or header virtual datasets
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if (rank == 1 || rank == 2) {
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count = std::vector<hsize_t>(rank, 1); // slice 1 value
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offset = std::vector<hsize_t>(rank, 0);
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memspace = std::make_unique<H5::DataSpace>(H5S_SCALAR);
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} else if (rank >= 3) {
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// data dataset (frame x height x width)
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count = {1, dims[1], dims[2]};
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offset = {0, 0, 0};
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hsize_t dims_image[2] = {dims[1], dims[2]};
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memspace = std::make_unique<H5::DataSpace>(2, dims_image);
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} else {
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throw std::runtime_error(LOCATION + "Invalid rank for dataset: " + std::to_string(rank));
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}
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}
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};
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/**
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@ -79,6 +79,8 @@ size_t Hdf5File::bitdepth() const { return m_master.bitdepth(); }
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xy Hdf5File::geometry() { return m_master.geometry(); }
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size_t Hdf5File::n_modules() const { return m_master.n_modules(); }
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Hdf5MasterFile Hdf5File::master() const { return m_master; }
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size_t Hdf5File::bytes_per_pixel() const { return m_master.bitdepth() / 8; }
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DetectorHeader Hdf5File::read_header(const std::filesystem::path &fname) {
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DetectorHeader h{};
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@ -113,20 +115,6 @@ DetectorHeader Hdf5File::read_header(const std::filesystem::path &fname) {
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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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fmt::format("Could not open: {} for reading", fname.string()));
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size_t const rc = fread(reinterpret_cast<char *>(&h), sizeof(h), 1, fp);
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if (rc != 1)
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throw std::runtime_error(LOCATION + "Could not read header from file");
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if (fclose(fp)) {
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throw std::runtime_error(LOCATION + "Could not close file");
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}
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return h;
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}
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@ -138,18 +126,15 @@ Frame Hdf5File::get_frame(size_t frame_index) {
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return f;
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}
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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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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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LOG(logINFOBLUE) << "Reading frame " << frame_index;
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get_data_into(frame_index, frame_buffer);
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if (header) {
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for (size_t part_idx = 0; part_idx != m_master.n_modules(); ++part_idx) {
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// fmt::print("Reading header for module {}\n", part_idx);
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get_header_into(frame_index, part_idx, header);
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header++;
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}
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@ -157,7 +142,7 @@ void Hdf5File::get_frame_into(size_t frame_index, std::byte *frame_buffer,
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}
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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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m_data_file->get_data_into(frame_index, frame_buffer);
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}
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void Hdf5File::get_header_into(size_t frame_index, int part_index, DetectorHeader *header) {
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@ -176,7 +161,7 @@ void Hdf5File::get_header_into(size_t frame_index, int part_index, DetectorHeade
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m_header_files[11]->get_header_into(frame_index, part_index, reinterpret_cast<std::byte *>(&(header->detType)));
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m_header_files[12]->get_header_into(frame_index, part_index, reinterpret_cast<std::byte *>(&(header->version)));
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m_header_files[13]->get_header_into(frame_index, part_index, reinterpret_cast<std::byte *>(&(header->packetMask)));
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LOG(logDEBUG5) << "Read 1D header for frame " << frame_index;
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LOG(logDEBUG) << "Read 1D header for frame " << frame_index;
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} catch (const H5::Exception &e) {
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fmt::print("Exception type: {}\n", typeid(e).name());
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e.printErrorStack();
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