hdf5/examples/h5_chunk_read.c

/*  
 *   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 FILE        "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];
    hssize_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;
    hsize_t	i, j;
    

 
    /*
     * Open the file and the dataset.
     */
    file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
    dataset = H5Dopen(file, DATASETNAME);
 
    /*
     * 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]));

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

    /* 
     * Check if dataset is chunked.
     */
    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 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");
    }     

    /*
     *	    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]);
    }

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

    /*
     * 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.
     */
    H5Pclose(cparms);
    H5Dclose(dataset);
    H5Sclose(filespace);
    H5Sclose(memspace);
    H5Fclose(file);

    return 0;
}