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https://github.com/slsdetectorgroup/slsDetectorPackage.git
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first draft
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291
slsDetectorCalibration/dataStructures/HDF5File.cpp
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291
slsDetectorCalibration/dataStructures/HDF5File.cpp
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#include "HDF5File.h"
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#include "ansi.h"
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#include <string.h>
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HDF5File::HDF5File () {
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//InitializeParameters();
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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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}
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int HDF5File::OpenResources (const char* 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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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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if (dataset < 0){
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cprintf(RED,"could not open dataset\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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// 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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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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return 0;
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}
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// validate size of frame index dataset
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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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}
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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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}
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H5Dclose(fi_dataset);
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return 1;
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}
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void HDF5File::CloseResources () {
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if (dataspace >=0 ) {
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H5Sclose(dataspace);
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dataspace = -1;
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}
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if (dataset >=0 ) {
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H5Dclose(dataset);
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dataset = -1;
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}
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if (file >=0 ) {
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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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int HDF5File::ReadImage (uint16_t** image, int& iFrame) {
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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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CloseResources ();
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return -99;
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}
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if (frame_offset[Z] == file_dims[Z]-1) {
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printf("end of file\n");
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return -1;
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}
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hsize_t frame_size[RANK] = {1, file_dims[X], file_dims[Y]};
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// Define memory space
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hid_t memspace = H5Screate_simple (RANK, frame_size, NULL);
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// create hyperslab
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// If I understand correctly, this puts dataspace such that we read the correct frame
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if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, frame_offset, NULL, frame_size, NULL) < 0 ) {
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cprintf (RED,"Could not create hyperslab for frame count %llu\n", frame_offset[Z]);
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CloseResources ();
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return -99;
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}
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// read dataset into current_image
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if (H5Dread(dataset, H5T_STD_U16LE, memspace, dataspace, H5P_DEFAULT, current_image) < 0 ) {
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cprintf (RED,"Could not read dataset for frame count %llu\n", frame_offset[Z]);
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CloseResources ();
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return -99;
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}
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*image = current_image;
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// return frame number and then increment frame count number
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unsigned int retval = frame_index_list[frame_offset[Z]];
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iFrame = (int)frame_offset[Z];
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++frame_offset[Z];
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return retval;
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}
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void HDF5File::PrintCurrentImage () {
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printf("\n");
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printf("Frame %llu, Image: %d\n", frame_offset[Z]-1, frame_index_list[frame_offset[Z]-1]);
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unsigned long long int size = file_dims[Y] * file_dims[X];
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for (unsigned int i = 0; i < size; ++i){
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printf("%u ", current_image[i]);
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if (!((i+1) % file_dims[X] ))
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printf("\n\n");
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}
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printf("\n\n\n\n");
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}
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