mirror of
https://github.com/slsdetectorgroup/slsDetectorPackage.git
synced 2025-06-17 23:37:14 +02:00
Generalize HDF5 reader for 3- or 4-dimensional datasets
This commit is contained in:
@ -2,215 +2,217 @@
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#include "ansi.h"
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#include <string.h>
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#include <algorithm>
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#include <fmt/ranges.h>
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HDF5File::HDF5File () {
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//InitializeParameters();
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//InitializeParameters(); //old
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}
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HDF5File::~HDF5File () {
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if(frame_index_list)
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delete [] frame_index_list;
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if(current_image)
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delete [] current_image;
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}
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void HDF5File::InitializeParameters () {
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/*
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memset(file_name, 0, MAX_STR_LENGTH); //awkward, initializes all file_name characters to 0
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file = -1;
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dataspace = -1;
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//memspace = -1;
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dataset = -1;
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number_of_frames = 0;
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frame_index_list = NULL;
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current_image = NULL;
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*/
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for (int i = 0; i < RANK; ++i) {
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file_dims[i] = 0; //also awkward
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chunk_dims[i] = 0;
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frame_offset[i] = 0;
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}
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void HDF5File::SetImageDataPath (std::string const& name) { data_datasetname = name; }
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void HDF5File::SetFrameIndexPath (std::string const& name) { index_datasetname = name; }
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void HDF5File::InitializeDimensions () {
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rank = H5Sget_simple_extent_ndims(dataspace);
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file_dims.resize(rank);
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H5Sget_simple_extent_dims(dataspace, file_dims.data(), nullptr);
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std::cout << "Dataset dimensions: (";
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for (size_t i = 0; i < file_dims.size(); ++i) {
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std::cout << file_dims[i];
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if (i < file_dims.size() - 1) std::cout << ", ";
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}
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std::cout << ")\n";
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}
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std::vector<hsize_t> HDF5File::GetDatasetDimensions() {
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return file_dims;
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}
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std::vector<hsize_t> HDF5File::GetChunkDimensions() {
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return chunk_dims;
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}
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bool HDF5File::ValidateDimensions () {
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// validate rank
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if(rank != RANK) {
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cprintf(RED,"rank found %d. Expected %d\n", rank, RANK);
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std::cerr << "Error: Rank could not be validated\n";
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return false;
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}
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// validate file dimensions of x and y (assuming those are the last two dimensions of the dataset)
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if ( (file_dims[file_dims.size()-2] != DEFAULT_X_DIMS) || (file_dims[file_dims.size()-1] != DEFAULT_Y_DIMS) ) {
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cprintf(RED,"file dimensions of x found %llu. Expected %d\n", file_dims[file_dims.size()-2], DEFAULT_X_DIMS);
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cprintf(RED,"file dimensions of y found %llu. Expected %d\n", file_dims[file_dims.size()-1], DEFAULT_Y_DIMS);
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std::cerr << "Error: Dataset dimensions could not be validated\n";
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return false;
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}
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cprintf(GREEN, "File rank & dimensions validated.");
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return true;
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}
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bool HDF5File::ReadChunkDimensions () {
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// Get layout
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hid_t plist_id = H5Dget_create_plist(dataset);
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if (H5Pget_layout (plist_id) != H5D_CHUNKED) {
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cprintf(RED,"NOTE: Dataset is not chunked!\n");
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std::cerr << "Error: Dataset is not chunked\n";
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return false;
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}
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// Get Chunk Dimensions
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int rank_chunk = H5Pget_chunk (plist_id, 0, nullptr);
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chunk_dims.resize(rank_chunk);
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H5Pget_chunk (plist_id, rank_chunk, chunk_dims.data());
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std::cout << "Chunk dimensions: (";
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for (size_t i = 0; i < chunk_dims.size(); ++i) {
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std::cout << chunk_dims[i];
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if (i < chunk_dims.size() - 1) std::cout << ", ";
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}
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std::cout << ")\n";
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H5Pclose (plist_id);
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return true;
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}
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bool HDF5File::ValidateChunkDimensions () {
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// validate rank
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if(chunk_dims.size() != rank) {
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cprintf(RED,"Chunk rank does not match dataset rank! Found %d. Expected %d\n", chunk_dims.size(), rank);
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std::cerr << "Error: Chunk rank does not match dataset rank\n";
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return false;
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}
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// validate chunk dimensions of x and y (assuming those are the last two dimensions of the dataset)
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if ( (chunk_dims[chunk_dims.size()-2] != DEFAULT_CHUNK_X_DIMS) || (chunk_dims[chunk_dims.size()-1] != DEFAULT_CHUNK_Y_DIMS) ) {
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cprintf(RED,"file dimensions of x found %llu. Expected %d\n", chunk_dims[chunk_dims.size()-2], DEFAULT_CHUNK_X_DIMS);
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cprintf(RED,"file dimensions of y found %llu. Expected %d\n", chunk_dims[chunk_dims.size()-1], DEFAULT_CHUNK_Y_DIMS);
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std::cerr << "Error: Chunk dimensions could not be validated\n";
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return false;
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}
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cprintf(GREEN, "Chunk rank & dimensions validated.");
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return true;
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}
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bool HDF5File::OpenFrameIndexDataset() {
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// Get all the frame numbers
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// Open frame index dataset
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hid_t fi_dataset = H5Dopen2 (file, index_datasetname.c_str(), H5P_DEFAULT);
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if (fi_dataset < 0){
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cprintf (RED,"Could not open frame index dataset %s\n", index_datasetname.c_str());
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std::cerr << "Error: Could not open frame index dataset\n";
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return false;
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}
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hid_t fi_dataspace = H5Dget_space (fi_dataset);
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int fi_rank = H5Sget_simple_extent_ndims(fi_dataspace);
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std::vector<hsize_t> fi_dims(fi_rank);
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H5Sget_simple_extent_dims (fi_dataspace, fi_dims.data(), nullptr);
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std::cout << "Frame index dataset dimensions: (";
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for (size_t i = 0; i < fi_dims.size(); ++i) {
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std::cout << fi_dims[i];
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if (i < fi_dims.size() - 1) std::cout << ", ";
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}
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std::cout << ")\n";
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// validate size
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if (fi_dims[0] != file_dims[0]) {
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cprintf (RED,"Frame index dimensions of z found %llu. Expected %llu\n", fi_dims[0], file_dims[0]);
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std::cerr << "Error: Z dimension of frame index dataset does not align with z dimension of image dataset\n";
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H5Sclose (fi_dataspace);
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H5Dclose (fi_dataset);
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return false;
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}
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H5Sclose (fi_dataspace);
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// allocate frame index memory
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frame_index_list.resize(file_dims[0]);
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//read frame index values
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//Is u32 correct? I would think not. But I get a segmentation fault if I use u64.
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if (H5Dread (fi_dataset, H5T_STD_U32LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, frame_index_list.data()) < 0) {
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cprintf (RED,"Could not read frame index dataset %s\n", index_datasetname);
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std::cerr << "Error: Could not read frame index dataset\n";
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H5Dclose (fi_dataset);
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return false;
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}
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H5Dclose(fi_dataset);
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return true;
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}
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int HDF5File::OpenResources (char const*const fname, bool validate) {
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// Initialize
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//InitializeParameters();
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// Open File
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file = H5Fopen (fname, H5F_ACC_RDONLY, H5P_DEFAULT);
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if (file < 0) {
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cprintf(RED,"could not open hdf5 file\n");
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cprintf(RED,"Could not open hdf5 file\n");
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std::cerr << "Error: H5Fopen failed\n";
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return 0;
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}
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cprintf(BLUE, "Opened File: %s\n", fname);
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// Open Dataset
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dataset = H5Dopen2 (file, DATA_DATASETNAME, H5P_DEFAULT);
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dataset = H5Dopen2 (file, data_datasetname.c_str(), H5P_DEFAULT);
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if (dataset < 0){
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cprintf(RED,"could not open dataset\n");
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cprintf(RED,"Could not open dataset\n");
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std::cerr << "Error: H5Dopen2 failed\n";
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CloseResources ();
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return 0;
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}
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cprintf(BLUE, "Opened Dataset: %s\n", DATA_DATASETNAME);
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cprintf(BLUE, "Opened Dataset: %s\n", data_datasetname.c_str());
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// Create Dataspace
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dataspace = H5Dget_space (dataset);
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if (dataspace < 0){
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cprintf(RED,"could not open dataspace\n");
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cprintf(RED,"Could not open dataspace\n");
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std::cerr << "Error: H5Dget_space failed\n";
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CloseResources ();
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return 0;
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}
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// Get Dimensions
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int rank = H5Sget_simple_extent_dims (dataspace, file_dims, NULL);
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cprintf (BLUE, "Number of Images: %llu\n", file_dims[Z]);
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// validate file dimensions
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if (validate) {
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// validate rank
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if(rank != RANK) {
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cprintf(RED,"rank found %d. Expected %d\n", rank, RANK);
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CloseResources ();
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return 0;
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}
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// validate file dimensions of x and y
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if (file_dims[X] != DEFAULT_X_DIMS) {
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cprintf(RED,"file dimensions of x found %llu. Expected %d\n", file_dims[X], DEFAULT_X_DIMS);
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CloseResources ();
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return 0;
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}
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if (file_dims[Y] != DEFAULT_Y_DIMS) {
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cprintf(RED,"file dimensions of y found %llu. Expected %d\n", file_dims[Y], DEFAULT_Y_DIMS);
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CloseResources ();
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return 0;
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}
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cprintf(GREEN, "File rank & dimensions validated. "
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"Rank: %d, Dimensions: %llu x %llu x %llu\n",
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rank, file_dims[Z], file_dims[Y], file_dims[X]);
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}
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// Get layout
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hid_t cparms = H5Dget_create_plist(dataset);
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// validate chunk layout
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if (validate) {
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if (H5D_CHUNKED != H5Pget_layout (cparms)) {
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cprintf(RED,"not chunked data file\n");
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H5Pclose(cparms);
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CloseResources ();
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return 0;
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}
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cprintf(GREEN, "Chunk layout validated\n");
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}
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// Get Chunk Dimensions
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int rank_chunk = H5Pget_chunk (cparms, RANK, chunk_dims);
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// validate dimensions
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if (validate) {
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// validate rank
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if(rank_chunk != RANK) {
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cprintf(RED,"chunk rank found %d. Expected %d\n", rank, RANK);
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H5Pclose(cparms);
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CloseResources ();
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return 0;
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}
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// validate file dimensions of x, y and z
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if (chunk_dims[X] != DEFAULT_CHUNK_X_DIMS) {
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cprintf(RED,"chunk dimensions of x found %llu. Expected %d\n", chunk_dims[X], DEFAULT_CHUNK_X_DIMS);
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H5Pclose(cparms);
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CloseResources ();
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return 0;
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}
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if (chunk_dims[Y] != DEFAULT_CHUNK_Y_DIMS) {
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cprintf(RED,"chunk dimensions of y found %llu. Expected %d\n", chunk_dims[Y], DEFAULT_CHUNK_Y_DIMS);
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H5Pclose(cparms);
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CloseResources ();
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return 0;
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}
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/*if (chunk_dims[Z] != DEFAULT_CHUNK_Z_DIMS) {
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cprintf(RED,"chunk dimensions of z found %llu. Expected %d\n", chunk_dims[Z], DEFAULT_CHUNK_Z_DIMS);
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H5Pclose(cparms);
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CloseResources ();
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return 0;
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}*/
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cprintf(GREEN, "Chunk rank & dimensions validated. "
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"Rank: %d, Dimensions: %llu x %llu x %llu\n",
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rank_chunk, chunk_dims[Z], chunk_dims[Y], chunk_dims[X]);
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}
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H5Pclose (cparms);
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// allocate chunk memory
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//current_image = new uint16_t[chunk_dims[Z]*DEFAULT_CHUNK_Y_DIMS*DEFAULT_CHUNK_X_DIMS];
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//current_image = new uint16_t[DEFAULT_X_DIMS*DEFAULT_Y_DIMS];
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// Define memory space
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//memspace = H5Screate_simple (RANK, chunk_dims, NULL);
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// Get all the frame numbers
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// Open frame index dataset
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hid_t fi_dataset = H5Dopen2 (file, INDEX_DATASETNAME, H5P_DEFAULT);
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if (fi_dataset < 0){
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cprintf (RED,"could not open frame index dataset %s\n", INDEX_DATASETNAME);
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CloseResources ();
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InitializeDimensions();
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// Get chunk dimensions
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if (!ReadChunkDimensions()) {
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CloseResources();
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return 0;
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}
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// validate size of frame index dataset
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// validate file dimensions
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if (validate) {
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hsize_t fi_dims[2];
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hid_t fi_dataspace = H5Dget_space (fi_dataset);
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int fi_rank = H5Sget_simple_extent_dims (fi_dataspace, fi_dims, NULL);
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// validate rank
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if(fi_rank != 2) {
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cprintf(RED,"Frame index dataset rank found %d. Expected %d\n", fi_rank, 2);
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H5Sclose (fi_dataspace);
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H5Dclose (fi_dataset);
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CloseResources ();
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return 0;
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if ( !ValidateDimensions() || !ValidateChunkDimensions() ) {
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CloseResources();
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return 0;
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}
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// validate size
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if (fi_dims[Z] != file_dims[Z]) {
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cprintf (RED,"Frame index dimensions of z found %llu. Expected %llu\n", fi_dims[Z], file_dims[Z]);
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H5Sclose (fi_dataspace);
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H5Dclose (fi_dataset);
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CloseResources ();
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return 0;
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}
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H5Sclose (fi_dataspace);
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}
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// allocate frame index memory
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frame_index_list = new unsigned int[file_dims[Z]];
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//read frame index values
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//Is u32 correct? I would think not. But I get a segmentation fault if I use u64.
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if (H5Dread (fi_dataset, H5T_STD_U32LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, frame_index_list) < 0) {
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cprintf (RED,"Could not read frame index dataset %s\n", INDEX_DATASETNAME);
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H5Dclose (fi_dataset);
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CloseResources ();
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//Read frame indices
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if (!OpenFrameIndexDataset()) {
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CloseResources();
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return 0;
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}
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H5Dclose(fi_dataset);
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return 1;
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}
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@ -228,73 +230,179 @@ void HDF5File::CloseResources () {
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H5Fclose(file);
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file = -1;
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}
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//if (memspace >= 0) H5Sclose(memspace); // VH: I am getting memory leaks after recompilation
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}
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/*
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* Function takes uint16_t* argument to make explicit that the caller has to handle memory allocation and deallocation.
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* This is legacy caused by the structure with which the slsDetectorCalibration cluster finder is written.
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* Best practice for modern C++ would be to rewrite using smart pointers.
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* (Best practice for modern C++ would be using smart pointers.)
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*
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* Originially, this function took uint16_t** which may lead to memory management issues since image gets redirected
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* to point to current_image, which is owned by HDF5File.
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* (Good practice in classic C-style. HDF5File needs to clean up the resource at destruction.)
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*
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* \param image pointer to uint16_t, buffer which the image is read into. (Memory handled by caller!)
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* \param offset contains iFrame at [0] and storage cell number at [1],
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* depending on dimensionality of the dataset, the storage cell number may not be included.
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* Note that frame number (as read from file) may (likely) differ from frame index (in the dataset)!
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*/
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int HDF5File::ReadImage (uint16_t* image, int& iFrame) {
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/*
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* Originially, this function took uint16_t** but this may lead to memory management issues since image gets redirected
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* to point to current_image, which is owned by HDF5File.
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* (Usually, this would be good practice and classic C-style.)
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*/
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int HDF5File::ReadImage (uint16_t* image, std::vector<hsize_t>& offset ) {
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// no images in this frame
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if (frame_index_list[frame_offset[Z]] == 0) {
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cprintf (RED,"No images in this frame offset %llu\n", frame_offset[Z]);
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// Validate input arguments
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if (!image) {
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std::cerr << "Error: image buffer is null.\n";
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return -99;
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}
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if ( offset.size() != rank-2 ) {
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cprintf ( RED,"Offset vector must have size %llu. Found %llu\n", rank-2, offset.size() );
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std::cerr << "Error: Wrong offset vector size\n";
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CloseResources ();
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return -99;
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}
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// Initialize frame_offset
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if (frame_offset.empty())
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frame_offset.resize(rank,0);
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// Validate frame_offset index
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if (frame_offset[0] >= frame_index_list.size()) {
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std::cerr << "Error: frame_offset[0] out of bounds.\n";
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return -99;
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}
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// Check if images exist at the current frame offset
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if (frame_index_list[frame_offset[0]] == 0) {
|
||||
cprintf (RED,"No images at this frame offset %llu\n", frame_offset[0]);
|
||||
std::cerr << "Error: Framenumber 0 at this frame offset\n";
|
||||
CloseResources ();
|
||||
return -99;
|
||||
}
|
||||
|
||||
if (frame_offset[Z] == file_dims[Z]-1) {
|
||||
// Check if we reached the end of file
|
||||
// Compares that the offsets of frame and storage cell (Z and S) have reached the end of file
|
||||
// Excludes X and Y indices (of the image dataset) from the comparison
|
||||
if( std::equal( frame_offset.cbegin(), frame_offset.cend()-2, file_dims.cbegin() ) ) {
|
||||
printf("End of file reached\n");
|
||||
return -1;
|
||||
}
|
||||
/* //old
|
||||
if (frame_offset[0] == file_dims[0]-1) {
|
||||
printf("end of file\n");
|
||||
return -1;
|
||||
}
|
||||
*/
|
||||
|
||||
hsize_t frame_size[RANK] = {1, file_dims[X], file_dims[Y]};
|
||||
// Optional: Ensure dataset and dataspace are valid
|
||||
if (dataset < 0) {
|
||||
std::cerr << "Error: Invalid dataset ID.\n";
|
||||
return -99;
|
||||
}
|
||||
if (dataspace < 0) {
|
||||
std::cerr << "Error: Invalid dataspace.\n";
|
||||
return -99;
|
||||
}
|
||||
|
||||
// Define the size of the hyperslab to read
|
||||
std::vector<hsize_t> frame_size(rank, 1);
|
||||
std::copy(file_dims.begin() + rank-2, file_dims.end(), frame_size.begin() + rank-2);
|
||||
/*
|
||||
for ( int d=0; d < rank; ++d ) {
|
||||
if (d < rank-2)
|
||||
frame_size[d] = 1;
|
||||
if ( d >= rank-2 )
|
||||
frame_size[d] = file_dims[d];
|
||||
}
|
||||
*/
|
||||
|
||||
// Define memory space
|
||||
hid_t memspace = H5Screate_simple (RANK, frame_size, NULL);
|
||||
hid_t memspace = H5Screate_simple (rank, frame_size.data(), nullptr);
|
||||
if (memspace < 0) {
|
||||
std::cerr << "Error: Failed to create memory space for HDF5 read operation\n";
|
||||
CloseResources();
|
||||
return -99;
|
||||
}
|
||||
|
||||
// create hyperslab
|
||||
// Create hyperslab selection
|
||||
// This aligns dataspace such that we read the correct frame
|
||||
if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, frame_offset, NULL, frame_size, NULL) < 0 ) {
|
||||
cprintf (RED,"Could not create hyperslab for frame count %llu\n", frame_offset[Z]);
|
||||
CloseResources ();
|
||||
if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, frame_offset.data(), nullptr, frame_size.data(), nullptr) < 0 ) {
|
||||
cprintf (RED,"Could not create hyperslab for frame offset %s\n", vectorToString(frame_offset));
|
||||
std::cerr << "Error: Hyperslab creation failed for frame offset " << vectorToString(frame_offset) << "\n";
|
||||
CloseResources();
|
||||
H5Sclose(memspace);
|
||||
return -99;
|
||||
}
|
||||
|
||||
// read dataset into current_image
|
||||
if (H5Dread(dataset, H5T_STD_U16LE, memspace, dataspace, H5P_DEFAULT, image /*was 'current_image'*/) < 0 ) {
|
||||
cprintf (RED,"Could not read dataset for frame count %llu\n", frame_offset[Z]);
|
||||
// Read dataset into image buffer (previously read to current_image owned by HDF5File)
|
||||
if (H5Dread(dataset, H5T_STD_U16LE, memspace, dataspace, H5P_DEFAULT, image) < 0 ) {
|
||||
cprintf (RED,"Could not read dataset for frame offset %s\n", vectorToString(frame_offset));
|
||||
std::cerr << "Error: Reading of dataset failed for given start frame offset " << vectorToString(frame_offset) << "\n";
|
||||
CloseResources ();
|
||||
H5Sclose(memspace);
|
||||
return -99;
|
||||
}
|
||||
|
||||
// Clean up memory space
|
||||
H5Sclose(memspace);
|
||||
|
||||
//*image = current_image; //if uint16_t** is passed, HDF5File owns the resource image points to, which is potentially dangerous
|
||||
|
||||
// return frame number and then increment frame count number
|
||||
unsigned int retval = frame_index_list[frame_offset[Z]];
|
||||
iFrame = (int)frame_offset[Z];
|
||||
++frame_offset[Z];
|
||||
// Return frame number
|
||||
unsigned int retval = frame_index_list[frame_offset[0]];
|
||||
|
||||
// Pass updated frame offset value(s) via offset parameter vector
|
||||
std::copy_n(frame_offset.begin(), offset.size(), offset.begin());
|
||||
/*
|
||||
std::transform( offset.begin(), offset.end(), offset.begin(),
|
||||
[&, i = 0](size_t) mutable { return frame_offset[i++]; } );
|
||||
*/
|
||||
|
||||
// Increment frame offset correctly
|
||||
conditionalIncrement(frame_offset, file_dims[1]);
|
||||
//++frame_offset[0]; //old
|
||||
|
||||
return retval;
|
||||
}
|
||||
|
||||
|
||||
|
||||
void HDF5File::PrintCurrentImage () {
|
||||
void HDF5File::PrintCurrentImage (uint16_t* image) {
|
||||
printf("\n");
|
||||
printf("Frame %llu, Image: %d\n", frame_offset[Z]-1, frame_index_list[frame_offset[Z]-1]);
|
||||
printf("Frame %llu, Image: %d\n", frame_offset[0]-1, frame_index_list[frame_offset[0]-1]);
|
||||
|
||||
unsigned long long int size = file_dims[Y] * file_dims[X];
|
||||
for (unsigned int i = 0; i < size; ++i){
|
||||
printf("%u ", current_image[i]);
|
||||
if (!((i+1) % file_dims[X] ))
|
||||
hsize_t size = file_dims[rank-1] * file_dims[rank-2];
|
||||
for (hsize_t i = 0; i < size; ++i){
|
||||
printf("%u ", image[i]);
|
||||
if (!((i+1) % file_dims[rank-2] ))
|
||||
printf("\n\n");
|
||||
}
|
||||
printf("\n\n\n\n");
|
||||
}
|
||||
|
||||
/*
|
||||
* No class member helper functions
|
||||
*/
|
||||
std::string vectorToString(std::vector<hsize_t> const& v) {
|
||||
return fmt::format("({})", fmt::join(v, ", "));
|
||||
}
|
||||
|
||||
/*
|
||||
* increment frame offset (if s dimension exists, loop through all before incrementing z)
|
||||
* should also work if file_dims[1] is not s but x (in that case we ignore it)
|
||||
*/
|
||||
void conditionalIncrement(std::vector<hsize_t>& vec, int max_value) {
|
||||
|
||||
if (vec.size() < 3) {
|
||||
throw std::invalid_argument("Vector must have at least 3 elements.");
|
||||
}
|
||||
|
||||
// If vector has 4 elements, increment vec[1] first
|
||||
if (vec.size() == 4) {
|
||||
if (++vec[1] >= max_value) { //max_value is never reached!
|
||||
vec[1] = 0; // Reset and increment vec[0]
|
||||
++vec[0];
|
||||
}
|
||||
}
|
||||
// If vector has 3 elements, increment vec[0] directly
|
||||
else if (vec.size() == 3) {
|
||||
++vec[0];
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user