hdf5/examples/h5_chunk_read.c

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the COPYING file, which can be found at the root of the source code       *
 * distribution tree, or in https://www.hdfgroup.org/licenses.               *
 * If you do not have access to either file, you may request a copy from     *
 * help@hdfgroup.org.                                                        *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

/*
 *   This example shows how to read data from a chunked dataset.
 *   We will read from the file created by h5_extend_write.c
 */

#include "hdf5.h"

#define H5FILE_NAME "SDSextendible.h5"
#define DATASETNAME "ExtendibleArray"
#define RANK        2
#define RANKC       1
#define NX          10
#define NY          5

int
main(void)
{
    hid_t   file; /* handles */
    hid_t   dataset;
    hid_t   filespace;
    hid_t   memspace;
    hid_t   cparms;
    hsize_t dims[2]; /* dataset and chunk dimensions*/
    hsize_t chunk_dims[2];
    hsize_t col_dims[1];
    hsize_t count[2];
    hsize_t offset[2];

    herr_t status, status_n;

    int data_out[NX][NY]; /* buffer for dataset to be read */
    int chunk_out[2][5];  /* buffer for chunk to be read */
    int column[10];       /* buffer for column to be read */
    int rank, rank_chunk;
    int i, j;

    /*
     * Open the file and the dataset.
     */
    file    = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT);
    dataset = H5Dopen2(file, DATASETNAME, H5P_DEFAULT);

    /*
     * Get dataset rank and dimension.
     */

    filespace = H5Dget_space(dataset); /* Get filespace handle first. */
    rank      = H5Sget_simple_extent_ndims(filespace);
    status_n  = H5Sget_simple_extent_dims(filespace, dims, NULL);
    printf("dataset rank %d, dimensions %lu x %lu\n", rank, (unsigned long)(dims[0]),
           (unsigned long)(dims[1]));

    /*
     * Define the memory space to read dataset.
     */
    memspace = H5Screate_simple(RANK, dims, NULL);

    /*
     * Read dataset back and display.
     */
    status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, data_out);
    printf("\n");
    printf("Dataset: \n");
    for (j = 0; j < dims[0]; j++) {
        for (i = 0; i < dims[1]; i++)
            printf("%d ", data_out[j][i]);
        printf("\n");
    }

    /*
     * Close/release resources.
     */
    H5Sclose(memspace);

    /*
     *	    dataset rank 2, dimensions 10 x 5
     *	    chunk rank 2, dimensions 2 x 5

     *	    Dataset:
     *	    1 1 1 3 3
     *	    1 1 1 3 3
     *	    1 1 1 0 0
     *	    2 0 0 0 0
     *	    2 0 0 0 0
     *	    2 0 0 0 0
     *	    2 0 0 0 0
     *	    2 0 0 0 0
     *	    2 0 0 0 0
     *	    2 0 0 0 0
     */

    /*
     * Read the third column from the dataset.
     * First define memory dataspace, then define hyperslab
     * and read it into column array.
     */
    col_dims[0] = 10;
    memspace    = H5Screate_simple(RANKC, col_dims, NULL);

    /*
     * Define the column (hyperslab) to read.
     */
    offset[0] = 0;
    offset[1] = 2;
    count[0]  = 10;
    count[1]  = 1;
    status    = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);
    status    = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, column);
    printf("\n");
    printf("Third column: \n");
    for (i = 0; i < 10; i++) {
        printf("%d \n", column[i]);
    }

    /*
     * Close/release resources.
     */
    H5Sclose(memspace);

    /*
     *	    Third column:
     *	    1
     *	    1
     *	    1
     *	    0
     *	    0
     *	    0
     *	    0
     *	    0
     *	    0
     *	    0
     */

    /*
     * Get creation properties list.
     */
    cparms = H5Dget_create_plist(dataset); /* Get properties handle first. */

    if (H5D_CHUNKED == H5Pget_layout(cparms)) {

        /*
         * Get chunking information: rank and dimensions
         */
        rank_chunk = H5Pget_chunk(cparms, 2, chunk_dims);
        printf("chunk rank %d, dimensions %lu x %lu\n", rank_chunk, (unsigned long)(chunk_dims[0]),
               (unsigned long)(chunk_dims[1]));

        /*
         * Define the memory space to read a chunk.
         */
        memspace = H5Screate_simple(rank_chunk, chunk_dims, NULL);

        /*
         * Define chunk in the file (hyperslab) to read.
         */
        offset[0] = 2;
        offset[1] = 0;
        count[0]  = chunk_dims[0];
        count[1]  = chunk_dims[1];
        status    = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);

        /*
         * Read chunk back and display.
         */
        status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, chunk_out);
        printf("\n");
        printf("Chunk: \n");
        for (j = 0; j < chunk_dims[0]; j++) {
            for (i = 0; i < chunk_dims[1]; i++)
                printf("%d ", chunk_out[j][i]);
            printf("\n");
        }
        /*
         *	 Chunk:
         *	 1 1 1 0 0
         *	 2 0 0 0 0
         */

        /*
         * Close/release resources.
         */
        H5Sclose(memspace);
    }

    /*
     * Close/release resources.
     */
    H5Pclose(cparms);
    H5Dclose(dataset);
    H5Sclose(filespace);
    H5Fclose(file);

    return 0;
}