Introduction to HDF5 
HDF5 User’s Guide 
HDF5 Reference Manual 
Other HDF5 documents and links 

Introduction to HDF5 -- Example Codes


Table of Contents
         1: Creating and writing a dataset
         2. Reading a hyperslab
         3. Writing selected data
         4. Working with compound datatypes
         5. Creating and writing an extendible
                  dataset
         6. Reading data
         7. Creating groups
            8. Writing and reading attributes
         9. Creating and writing references
                  to objects
         10. Reading references to objects
         11. Creating and writing references
                  to dataset regions
         12. Reading references to dataset
                  regions


Example 1: How to create a homogeneous multi-dimensional dataset and write it to a file.

This example creates a 2-dimensional HDF 5 dataset of little endian 32-bit integers.


/*  
 *  This example writes data to the HDF5 file.
 *  Data conversion is performed during write operation.  
 */
 
#include 

#define FILE        "SDS.h5"
#define DATASETNAME "IntArray" 
#define NX     5                      /* dataset dimensions */
#define NY     6
#define RANK   2

int
main (void)
{
    hid_t       file, dataset;         /* file and dataset handles */
    hid_t       datatype, dataspace;   /* handles */
    hsize_t     dimsf[2];              /* dataset dimensions */
    herr_t      status;                             
    int         data[NX][NY];          /* data to write */
    int         i, j;

    /* 
     * Data  and output buffer initialization. 
     */
    for (j = 0; j < NX; j++) {
	for (i = 0; i < NY; i++)
	    data[j][i] = i + j;
    }     
    /*
     * 0 1 2 3 4 5 
     * 1 2 3 4 5 6
     * 2 3 4 5 6 7
     * 3 4 5 6 7 8
     * 4 5 6 7 8 9
     */

    /*
     * Create a new file using H5F_ACC_TRUNC access,
     * default file creation properties, and default file
     * access properties.
     */
    file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    /*
     * Describe the size of the array and create the data space for fixed
     * size dataset. 
     */
    dimsf[0] = NX;
    dimsf[1] = NY;
    dataspace = H5Screate_simple(RANK, dimsf, NULL); 

    /* 
     * Define datatype for the data in the file.
     * We will store little endian INT numbers.
     */
    datatype = H5Tcopy(H5T_NATIVE_INT);
    status = H5Tset_order(datatype, H5T_ORDER_LE);

    /*
     * Create a new dataset within the file using defined dataspace and
     * datatype and default dataset creation properties.
     */
    dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace,
			H5P_DEFAULT);

    /*
     * Write the data to the dataset using default transfer properties.
     */
    status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
		      H5P_DEFAULT, data);

    /*
     * Close/release resources.
     */
    H5Sclose(dataspace);
    H5Tclose(datatype);
    H5Dclose(dataset);
    H5Fclose(file);
 
    return 0;
}     

 

(Return to TOC)  

Example 2. How to read a hyperslab from file into memory.

This example reads a hyperslab from a 2-d HDF5 dataset into a 3-d dataset in memory.


/*  
 *   This example reads hyperslab from the SDS.h5 file 
 *   created by h5_write.c program into two-dimensional
 *   plane of the three-dimensional array. 
 *   Information about dataset in the SDS.h5 file is obtained. 
 */
 
#include "hdf5.h"

#define FILE        "SDS.h5"
#define DATASETNAME "IntArray" 
#define NX_SUB  3           /* hyperslab dimensions */ 
#define NY_SUB  4 
#define NX 7           /* output buffer dimensions */ 
#define NY 7 
#define NZ  3 
#define RANK         2
#define RANK_OUT     3

int
main (void)
{
    hid_t       file, dataset;         /* handles */
    hid_t       datatype, dataspace;   
    hid_t       memspace; 
    H5T_class_t class;                 /* datatype class */
    H5T_order_t order;                 /* data order */
    size_t      size;                  /*
				        * size of the data element	       
				        * stored in file
				        */
    hsize_t     dimsm[3];              /* memory space dimensions */
    hsize_t     dims_out[2];           /* dataset dimensions */      
    herr_t      status;                             

    int         data_out[NX][NY][NZ ]; /* output buffer */
   
    hsize_t      count[2];              /* size of the hyperslab in the file */
    hsize_t      offset[2];             /* hyperslab offset in the file */
    hsize_t      count_out[3];          /* size of the hyperslab in memory */
    hsize_t      offset_out[3];         /* hyperslab offset in memory */
    int          i, j, k, status_n, rank;

    for (j = 0; j < NX; j++) {
	for (i = 0; i < NY; i++) {
	    for (k = 0; k < NZ ; k++)
		data_out[j][i][k] = 0;
	}
    } 
 
    /*
     * Open the file and the dataset.
     */
    file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
    dataset = H5Dopen(file, DATASETNAME);

    /*
     * Get datatype and dataspace handles and then query
     * dataset class, order, size, rank and dimensions.
     */
    datatype  = H5Dget_type(dataset);     /* datatype handle */ 
    class     = H5Tget_class(datatype);
    if (class == H5T_INTEGER) printf("Data set has INTEGER type \n");
    order     = H5Tget_order(datatype);
    if (order == H5T_ORDER_LE) printf("Little endian order \n");

    size  = H5Tget_size(datatype);
    printf(" Data size is %d \n", size);

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

    /* 
     * Define hyperslab in the dataset. 
     */
    offset[0] = 1;
    offset[1] = 2;
    count[0]  = NX_SUB;
    count[1]  = NY_SUB;
    status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, 
				 count, NULL);

    /*
     * Define the memory dataspace.
     */
    dimsm[0] = NX;
    dimsm[1] = NY;
    dimsm[2] = NZ ;
    memspace = H5Screate_simple(RANK_OUT,dimsm,NULL);   

    /* 
     * Define memory hyperslab. 
     */
    offset_out[0] = 3;
    offset_out[1] = 0;
    offset_out[2] = 0;
    count_out[0]  = NX_SUB;
    count_out[1]  = NY_SUB;
    count_out[2]  = 1;
    status = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, offset_out, NULL, 
				 count_out, NULL);

    /*
     * Read data from hyperslab in the file into the hyperslab in 
     * memory and display.
     */
    status = H5Dread(dataset, H5T_NATIVE_INT, memspace, dataspace,
		     H5P_DEFAULT, data_out);
    for (j = 0; j < NX; j++) {
	for (i = 0; i < NY; i++) printf("%d ", data_out[j][i][0]);
	printf("\n");
    }
    /*
     * 0 0 0 0 0 0 0
     * 0 0 0 0 0 0 0
     * 0 0 0 0 0 0 0
     * 3 4 5 6 0 0 0  
     * 4 5 6 7 0 0 0
     * 5 6 7 8 0 0 0
     * 0 0 0 0 0 0 0
     */

    /*
     * Close/release resources.
     */
    H5Tclose(datatype);
    H5Dclose(dataset);
    H5Sclose(dataspace);
    H5Sclose(memspace);
    H5Fclose(file);

    return 0;
}     

 

(Return to TOC)

Example 3. Writing selected data from memory to a file.

This example shows how to use the selection capabilities of HDF5 to write selected data to a file. It includes the examples discussed in the text.


/* 
 *  This program shows how the H5Sselect_hyperslab and H5Sselect_elements
 *  functions are used to write selected data from memory to the file.
 *  Program takes 48 elements from the linear buffer and writes them into
 *  the matrix using 3x2 blocks, (4,3) stride and (2,4) count. 
 *  Then four elements  of the matrix are overwritten with the new values and 
 *  file is closed. Program reopens the file and reads and displays the result.
 */ 
 
#include 

#define FILE "Select.h5"

#define MSPACE1_RANK     1          /* Rank of the first dataset in memory */
#define MSPACE1_DIM      50         /* Dataset size in memory */ 

#define MSPACE2_RANK     1          /* Rank of the second dataset in memory */ 
#define MSPACE2_DIM      4          /* Dataset size in memory */ 

#define FSPACE_RANK      2          /* Dataset rank as it is stored in the file */
#define FSPACE_DIM1      8          /* Dimension sizes of the dataset as it is
                                       stored in the file */
#define FSPACE_DIM2      12 

                                    /* We will read dataset back from the file
                                       to the dataset in memory with these
                                       dataspace parameters. */  
#define MSPACE_RANK      2
#define MSPACE_DIM1      8 
#define MSPACE_DIM2      12 

#define NPOINTS          4          /* Number of points that will be selected 
                                       and overwritten */ 
int main (void)
{

   hid_t   file, dataset;           /* File and dataset identifiers */
   hid_t   mid1, mid2, fid;         /* Dataspace identifiers */
   hsize_t dim1[] = {MSPACE1_DIM};  /* Dimension size of the first dataset 
                                       (in memory) */ 
   hsize_t dim2[] = {MSPACE2_DIM};  /* Dimension size of the second dataset
                                       (in memory */ 
   hsize_t fdim[] = {FSPACE_DIM1, FSPACE_DIM2}; 
                                    /* Dimension sizes of the dataset (on disk) */

   hsize_t start[2];  /* Start of hyperslab */
   hsize_t stride[2]; /* Stride of hyperslab */
   hsize_t count[2];  /* Block count */
   hsize_t block[2];  /* Block sizes */

   hsize_t coord[NPOINTS][FSPACE_RANK]; /* Array to store selected points 
                                            from the file dataspace */ 
   herr_t  ret;
   uint    i,j;
   int     matrix[MSPACE_DIM1][MSPACE_DIM2];
   int     vector[MSPACE1_DIM];
   int     values[] = {53, 59, 61, 67};  /* New values to be written */

   /*
    * Buffers' initialization.
    */
   vector[0] = vector[MSPACE1_DIM - 1] = -1;
   for (i = 1; i < MSPACE1_DIM - 1; i++) vector[i] = i;

   for (i = 0; i < MSPACE_DIM1; i++) {
       for (j = 0; j < MSPACE_DIM2; j++)
       matrix[i][j] = 0;
    }

    /*
     * Create a file.
     */
    file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    /* 
     * Create dataspace for the dataset in the file.
     */
    fid = H5Screate_simple(FSPACE_RANK, fdim, NULL);

    /*
     * Create dataset and write it into the file.
     */
    dataset = H5Dcreate(file, "Matrix in file", H5T_NATIVE_INT, fid, H5P_DEFAULT);
    ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, matrix);

    /*
     * Select hyperslab for the dataset in the file, using 3x2 blocks, 
     * (4,3) stride and (2,4) count starting at the position (0,1).
     */
    start[0]  = 0; start[1]  = 1;
    stride[0] = 4; stride[1] = 3;
    count[0]  = 2; count[1]  = 4;    
    block[0]  = 3; block[1]  = 2;
    ret = H5Sselect_hyperslab(fid, H5S_SELECT_SET, start, stride, count, block);

    /*
     * Create dataspace for the first dataset.
     */
    mid1 = H5Screate_simple(MSPACE1_RANK, dim1, NULL);

    /*
     * Select hyperslab. 
     * We will use 48 elements of the vector buffer starting at the second element.
     * Selected elements are 1 2 3 . . . 48
     */
    start[0]  = 1;
    stride[0] = 1;
    count[0]  = 48;
    block[0]  = 1;
    ret = H5Sselect_hyperslab(mid1, H5S_SELECT_SET, start, stride, count, block);
 
    /*
     * Write selection from the vector buffer to the dataset in the file.
     *
     * File dataset should look like this:       
     *                    0  1  2  0  3  4  0  5  6  0  7  8 
     *                    0  9 10  0 11 12  0 13 14  0 15 16
     *                    0 17 18  0 19 20  0 21 22  0 23 24
     *                    0  0  0  0  0  0  0  0  0  0  0  0
     *                    0 25 26  0 27 28  0 29 30  0 31 32
     *                    0 33 34  0 35 36  0 37 38  0 39 40
     *                    0 41 42  0 43 44  0 45 46  0 47 48
     *                    0  0  0  0  0  0  0  0  0  0  0  0
     */
     ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid1, fid, H5P_DEFAULT, vector);

    /*
     * Reset the selection for the file dataspace fid.
     */
    ret = H5Sselect_none(fid);

    /*
     * Create dataspace for the second dataset.
     */
    mid2 = H5Screate_simple(MSPACE2_RANK, dim2, NULL);

    /*
     * Select sequence of NPOINTS points in the file dataspace.
     */
    coord[0][0] = 0; coord[0][1] = 0;
    coord[1][0] = 3; coord[1][1] = 3;
    coord[2][0] = 3; coord[2][1] = 5;
    coord[3][0] = 5; coord[3][1] = 6;

    ret = H5Sselect_elements(fid, H5S_SELECT_SET, NPOINTS, 
                             (const hsize_t **)coord);

    /*
     * Write new selection of points to the dataset.
     */
    ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid2, fid, H5P_DEFAULT, values);   

    /*
     * File dataset should look like this:     
     *                   53  1  2  0  3  4  0  5  6  0  7  8 
     *                    0  9 10  0 11 12  0 13 14  0 15 16
     *                    0 17 18  0 19 20  0 21 22  0 23 24
     *                    0  0  0 59  0 61  0  0  0  0  0  0
     *                    0 25 26  0 27 28  0 29 30  0 31 32
     *                    0 33 34  0 35 36 67 37 38  0 39 40
     *                    0 41 42  0 43 44  0 45 46  0 47 48
     *                    0  0  0  0  0  0  0  0  0  0  0  0
     *                                        
     */
   
    /*
     * Close memory file and memory dataspaces.
     */
    ret = H5Sclose(mid1); 
    ret = H5Sclose(mid2); 
    ret = H5Sclose(fid); 
 
    /*
     * Close dataset.
     */
    ret = H5Dclose(dataset);

    /*
     * Close the file.
     */
    ret = H5Fclose(file);

    /*
     * Open the file.
     */
    file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);

    /*
     * Open the dataset.
     */
    dataset = dataset = H5Dopen(file,"Matrix in file");

    /*
     * Read data back to the buffer matrix.
     */
    ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
                  H5P_DEFAULT, matrix);

    /*
     * Display the result.
     */
    for (i=0; i < MSPACE_DIM1; i++) {
        for(j=0; j < MSPACE_DIM2; j++) printf("%3d  ", matrix[i][j]);
        printf("\n");
    }

    return 0;
}

 

(Return to TOC)

Example 4. Working with compound datatypes.

This example shows how to create a compound datatype, write an array which has the compound datatype to the file, and read back subsets of fields.


/*
 * This example shows how to create a compound datatype,
 * write an array which has the compound datatype to the file,
 * and read back fields' subsets.
 */

#include "hdf5.h"

#define FILE          "SDScompound.h5"
#define DATASETNAME   "ArrayOfStructures"
#define LENGTH        10
#define RANK          1

int
main(void)
{

    /* First structure  and dataset*/
    typedef struct s1_t {
	int    a;
	float  b;
	double c; 
    } s1_t;
    s1_t       s1[LENGTH];
    hid_t      s1_tid;     /* File datatype identifier */

    /* Second structure (subset of s1_t)  and dataset*/
    typedef struct s2_t {
	double c;
	int    a;
    } s2_t;
    s2_t       s2[LENGTH];
    hid_t      s2_tid;    /* Memory datatype handle */

    /* Third "structure" ( will be used to read float field of s1) */
    hid_t      s3_tid;   /* Memory datatype handle */
    float      s3[LENGTH];

    int        i;
    hid_t      file, dataset, space; /* Handles */
    herr_t     status;
    hsize_t    dim[] = {LENGTH};   /* Dataspace dimensions */


    /*
     * Initialize the data
     */
    for (i = 0; i< LENGTH; i++) {
        s1[i].a = i;
        s1[i].b = i*i;
        s1[i].c = 1./(i+1);
    }

    /*
     * Create the data space.
     */
    space = H5Screate_simple(RANK, dim, NULL);

    /*
     * Create the file.
     */
    file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    /*
     * Create the memory datatype. 
     */
    s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
    H5Tinsert(s1_tid, "a_name", HOFFSET(s1_t, a), H5T_NATIVE_INT);
    H5Tinsert(s1_tid, "c_name", HOFFSET(s1_t, c), H5T_NATIVE_DOUBLE);
    H5Tinsert(s1_tid, "b_name", HOFFSET(s1_t, b), H5T_NATIVE_FLOAT);

    /* 
     * Create the dataset.
     */
    dataset = H5Dcreate(file, DATASETNAME, s1_tid, space, H5P_DEFAULT);

    /*
     * Wtite data to the dataset; 
     */
    status = H5Dwrite(dataset, s1_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, s1);

    /*
     * Release resources
     */
    H5Tclose(s1_tid);
    H5Sclose(space);
    H5Dclose(dataset);
    H5Fclose(file);
 
    /*
     * Open the file and the dataset.
     */
    file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
 
    dataset = H5Dopen(file, DATASETNAME);

    /* 
     * Create a datatype for s2
     */
    s2_tid = H5Tcreate(H5T_COMPOUND, sizeof(s2_t));

    H5Tinsert(s2_tid, "c_name", HOFFSET(s2_t, c), H5T_NATIVE_DOUBLE);
    H5Tinsert(s2_tid, "a_name", HOFFSET(s2_t, a), H5T_NATIVE_INT);

    /*
     * Read two fields c and a from s1 dataset. Fields in the file
     * are found by their names "c_name" and "a_name".
     */
    status = H5Dread(dataset, s2_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, s2);

    /*
     * Display the fields
     */
    printf("\n");
    printf("Field c : \n");
    for( i = 0; i < LENGTH; i++) printf("%.4f ", s2[i].c);
    printf("\n");

    printf("\n");
    printf("Field a : \n");
    for( i = 0; i < LENGTH; i++) printf("%d ", s2[i].a);
    printf("\n");

    /* 
     * Create a datatype for s3.
     */
    s3_tid = H5Tcreate(H5T_COMPOUND, sizeof(float));

    status = H5Tinsert(s3_tid, "b_name", 0, H5T_NATIVE_FLOAT);

    /*
     * Read field b from s1 dataset. Field in the file is found by its name.
     */
    status = H5Dread(dataset, s3_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, s3);

    /*
     * Display the field
     */
    printf("\n");
    printf("Field b : \n");
    for( i = 0; i < LENGTH; i++) printf("%.4f ", s3[i]);
    printf("\n");

    /*
     * Release resources
     */
    H5Tclose(s2_tid);
    H5Tclose(s3_tid);
    H5Dclose(dataset);
    H5Fclose(file);

    return 0;
}

 

(Return to TOC)

Example 5. Creating and writing an extendible dataset.

This example shows how to create a 3x3 extendible dataset, to extend the dataset to 10x3, then to extend it again to 10x5.


/*  
 *   This example shows how to work with extendible dataset.
 *   In the current version of the library dataset MUST be
 *   chunked.
 *   
 */
 
#include "hdf5.h"

#define FILE        "SDSextendible.h5"
#define DATASETNAME "ExtendibleArray" 
#define RANK         2
#define NX     10
#define NY     5 

int
main (void)
{
    hid_t       file;                          /* handles */
    hid_t       dataspace, dataset;  
    hid_t       filespace;                   
    hid_t       cparms;                     
    hsize_t      dims[2]  = { 3, 3};            /*
						 * dataset dimensions				
						 * at the creation time
						 */
    hsize_t      dims1[2] = { 3, 3};            /* data1 dimensions */ 
    hsize_t      dims2[2] = { 7, 1};            /* data2 dimensions */  
    hsize_t      dims3[2] = { 2, 2};            /* data3 dimensions */ 

    hsize_t      maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
    hsize_t      chunk_dims[2] ={2, 5};
    hsize_t      size[2];
    hsize_t      offset[2];

    herr_t      status;                             

    int         data1[3][3] = { {1, 1, 1},       /* data to write */
				{1, 1, 1},
				{1, 1, 1} };      

    int         data2[7]    = { 2, 2, 2, 2, 2, 2, 2};

    int         data3[2][2] = { {3, 3},
				{3, 3} };

    /*
     * Create the data space with unlimited dimensions. 
     */
    dataspace = H5Screate_simple(RANK, dims, maxdims); 

    /*
     * Create a new file. If file exists its contents will be overwritten.
     */
    file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    /* 
     * Modify dataset creation properties, i.e. enable chunking.
     */
    cparms = H5Pcreate (H5P_DATASET_CREATE);
    status = H5Pset_chunk( cparms, RANK, chunk_dims);

    /*
     * Create a new dataset within the file using cparms
     * creation properties.
     */
    dataset = H5Dcreate(file, DATASETNAME, H5T_NATIVE_INT, dataspace,
			cparms);

    /*
     * Extend the dataset. This call assures that dataset is at least 3 x 3.
     */
    size[0]   = 3; 
    size[1]   = 3; 
    status = H5Dextend (dataset, size);

    /*
     * Select a hyperslab.
     */
    filespace = H5Dget_space (dataset);
    offset[0] = 0;
    offset[1] = 0;
    status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
				 dims1, NULL);  

    /*
     * Write the data to the hyperslab.
     */
    status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
		      H5P_DEFAULT, data1);

    /*
     * Extend the dataset. Dataset becomes 10 x 3.
     */
    dims[0]   = dims1[0] + dims2[0];
    size[0]   = dims[0];  
    size[1]   = dims[1]; 
    status = H5Dextend (dataset, size);

    /*
     * Select a hyperslab.
     */
    filespace = H5Dget_space (dataset);
    offset[0] = 3;
    offset[1] = 0;
    status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
				 dims2, NULL);  

    /*
     * Define memory space
     */
    dataspace = H5Screate_simple(RANK, dims2, NULL); 

    /*
     * Write the data to the hyperslab.
     */
    status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
		      H5P_DEFAULT, data2);

    /*
     * Extend the dataset. Dataset becomes 10 x 5.
     */
    dims[1]   = dims1[1] + dims3[1];
    size[0]   = dims[0];  
    size[1]   = dims[1]; 
    status = H5Dextend (dataset, size);

    /*
     * Select a hyperslab
     */
    filespace = H5Dget_space (dataset);
    offset[0] = 0;
    offset[1] = 3;
    status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, 
				 dims3, NULL);  

    /*
     * Define memory space.
     */
    dataspace = H5Screate_simple(RANK, dims3, NULL); 

    /*
     * Write the data to the hyperslab.
     */
    status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
		      H5P_DEFAULT, data3);

    /*
     * Resulting 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
     */
    /*
     * Close/release resources.
     */
    H5Dclose(dataset);
    H5Sclose(dataspace);
    H5Sclose(filespace);
    H5Fclose(file);

    return 0;
}     

 

(Return to TOC)

Example 6. Reading data.

This example shows how to read information the chunked dataset written by Example 5.


/*  
 *   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];
    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;
    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;
}

 

(Return to TOC)

Example 7. Creating groups.

This example shows how to create and access a group in an HDF5 file and to place a dataset within this group. It also illustrates the usage of the H5Giterate, H5Glink, and H5Gunlink functions.


/*
 * This example creates a group in the file and dataset in the group. 
 * Hard link to the group object is created and the dataset is accessed
 * under different names. 
 * Iterator function is used to find the object names in the root group.
 */ 


#include "hdf5.h"


#define FILE    "group.h5"
#define RANK    2

 
herr_t file_info(hid_t loc_id, const char *name, void *opdata);
                                     /* Operator function */
int
main(void)
{

    hid_t    file;
    hid_t    grp;
    hid_t    dataset, dataspace;
    hid_t    plist; 

    herr_t   status;
    hsize_t  dims[2];
    hsize_t  cdims[2];
 
    int      idx;

    /*
     * Create a file.
     */
    file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    /*
     * Create a group in the file. 
     */
    grp = H5Gcreate(file, "/Data", 0);

    /*
     * Create dataset "Compressed Data" in the group using absolute
     * name. Dataset creation property list is modified to use 
     * GZIP compression with the compression effort set to 6. 
     * Note that compression can be used only when dataset is chunked. 
     */
    dims[0] = 1000;
    dims[1] = 20;
    cdims[0] = 20;
    cdims[1] = 20;
    dataspace = H5Screate_simple(RANK, dims, NULL);
    plist     = H5Pcreate(H5P_DATASET_CREATE);
                H5Pset_chunk(plist, 2, cdims);
                H5Pset_deflate( plist, 6); 
    dataset = H5Dcreate(file, "/Data/Compressed_Data", H5T_NATIVE_INT, 
                        dataspace, plist); 
 
    /* 
     * Close the dataset and the file.
     */
    H5Sclose(dataspace);
    H5Dclose(dataset);
    H5Fclose(file);

    /*
     * Now reopen the file and group in the file. 
     */
    file = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT);
    grp  = H5Gopen(file, "Data");

    /* 
     * Access "Compressed_Data" dataset in the group. 
     */
    dataset = H5Dopen(grp, "Compressed_Data");
    if( dataset < 0) printf(" Dataset is not found. \n");
    printf("\"/Data/Compressed_Data\" dataset is open \n");

    /*
     * Close the dataset.
     */
    status = H5Dclose(dataset);

    /*
     * Create hard link to the Data group.
     */
    status = H5Glink(file, H5G_LINK_HARD, "Data", "Data_new");

    /* 
     * We can access "Compressed_Data" dataset using created
     * hard link "Data_new". 
     */
    dataset = H5Dopen(file, "/Data_new/Compressed_Data");
    if( dataset < 0) printf(" Dataset is not found. \n");
    printf("\"/Data_new/Compressed_Data\" dataset is open \n");

    /*
     * Close the dataset.
     */
    status = H5Dclose(dataset);

    /* 
     * Use iterator to see the names of the objects in the file
     * root directory.
     */
    idx = H5Giterate(file, "/", NULL, file_info, NULL);

    /*
     * Unlink  name "Data" and use iterator to see the names
     * of the objects in the file root direvtory.
     */
    if (H5Gunlink(file, "Data") < 0)  
      printf(" H5Gunlink failed \n");
    else  
      printf("\"Data\" is unlinked \n");

    idx = H5Giterate(file, "/", NULL, file_info, NULL);
    

    /*
     * Close the file.
     */
     
    status = H5Fclose(file);

    return 0;
}
/*
 * Operator function.
 */
herr_t
file_info(hid_t loc_id, const char *name, void *opdata)
{
    hid_t grp;
    /*
     * Open the group using its name.
     */
    grp = H5Gopen(loc_id, name);
 
    /*
     * Display group name.
     */
    printf("\n");
    printf("Name : ");
    puts(name);
    
    H5Gclose(grp);
    return 0;
 }

 

(Return to TOC)

Example 8. Writing and reading attributes.

This example shows how to create HDF5 attributes, to attach them to a dataset, and to read through all of the attributes of a dataset.


/* 
 *  This program illustrates the usage of the H5A Interface functions.
 *  It creates and writes a dataset, and then creates and writes array,
 *  scalar, and string attributes of the dataset. 
 *  Program reopens the file, attaches to the scalar attribute using
 *  attribute name and reads and displays its value. Then index of the
 *  third attribute is used to read and display attribute values.
 *  The H5Aiterate function is used to iterate through the dataset attributes,
 *  and display their names. The function is also reads and displays the values 
 *  of the array attribute. 
 */ 
 
#include 
#include 

#define FILE "Attributes.h5"

#define RANK  1   /* Rank and size of the dataset  */ 
#define SIZE  7

#define ARANK  2   /* Rank and dimension sizes of the first dataset attribute */
#define ADIM1  2
#define ADIM2  3 
#define ANAME  "Float attribute"      /* Name of the array attribute */
#define ANAMES "Character attribute" /* Name of the string attribute */

herr_t attr_info(hid_t loc_id, const char *name, void *opdata); 
                                     /* Operator function */

int 
main (void)
{

   hid_t   file, dataset;       /* File and dataset identifiers */
   
   hid_t   fid;                 /* Dataspace identifier */
   hid_t   attr1, attr2, attr3; /* Attribute identifiers */
   hid_t   attr;
   hid_t   aid1, aid2, aid3;    /* Attribute dataspace identifiers */ 
   hid_t   atype;               /* Attribute type */

   hsize_t fdim[] = {SIZE};
   hsize_t adim[] = {ADIM1, ADIM2};  /* Dimensions of the first attribute  */
   
   float matrix[ADIM1][ADIM2]; /* Attribute data */ 

   herr_t  ret;                /* Return value */
   uint    i,j;                /* Counters */
   int     idx;                /* Attribute index */
   char    string_out[80];     /* Buffer to read string attribute back */
   int     point_out;          /* Buffer to read scalar attribute back */

   /*
    * Data initialization.
    */
   int vector[] = {1, 2, 3, 4, 5, 6, 7};  /* Dataset data */
   int point = 1;                         /* Value of the scalar attribute */ 
   char string[] = "ABCD";                /* Value of the string attribute */

   
   for (i=0; i < ADIM1; i++) {            /* Values of the array attribute */
       for (j=0; j < ADIM2; j++)
       matrix[i][j] = -1.;
   }

   /*
    * Create a file.
    */
   file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

   /* 
    * Create the dataspace for the dataset in the file.
    */
   fid = H5Screate(H5S_SIMPLE);
   ret = H5Sset_extent_simple(fid, RANK, fdim, NULL);

   /*
    * Create the dataset in the file.
    */
   dataset = H5Dcreate(file, "Dataset", H5T_NATIVE_INT, fid, H5P_DEFAULT);

   /*
    * Write data to the dataset.
    */
   ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT, vector);

   /*
    * Create dataspace for the first attribute. 
    */
   aid1 = H5Screate(H5S_SIMPLE);
   ret  = H5Sset_extent_simple(aid1, ARANK, adim, NULL);

   /*
    * Create array attribute.
    */
   attr1 = H5Acreate(dataset, ANAME, H5T_NATIVE_FLOAT, aid1, H5P_DEFAULT);

   /*
    * Write array attribute.
    */
   ret = H5Awrite(attr1, H5T_NATIVE_FLOAT, matrix);

   /*
    * Create scalar attribute.
    */
   aid2  = H5Screate(H5S_SCALAR);
   attr2 = H5Acreate(dataset, "Integer attribute", H5T_NATIVE_INT, aid2,
                     H5P_DEFAULT);

   /*
    * Write scalar attribute.
    */
   ret = H5Awrite(attr2, H5T_NATIVE_INT, &point); 

   /*
    * Create string attribute.
    */
   aid3  = H5Screate(H5S_SCALAR);
   atype = H5Tcopy(H5T_C_S1);
           H5Tset_size(atype, 4);
   attr3 = H5Acreate(dataset, ANAMES, atype, aid3, H5P_DEFAULT);

   /*
    * Write string attribute.
    */
   ret = H5Awrite(attr3, atype, string); 

   /*
    * Close attribute and file dataspaces.
    */
   ret = H5Sclose(aid1); 
   ret = H5Sclose(aid2); 
   ret = H5Sclose(aid3); 
   ret = H5Sclose(fid); 

   /*
    * Close the attributes.
    */ 
   ret = H5Aclose(attr1);
   ret = H5Aclose(attr2);
   ret = H5Aclose(attr3);
 
   /*
    * Close the dataset.
    */
   ret = H5Dclose(dataset);

   /*
    * Close the file.
    */
   ret = H5Fclose(file);

   /*
    * Reopen the file.
    */
   file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);

   /*
    * Open the dataset.
    */
   dataset = H5Dopen(file,"Dataset");

   /*
    * Attach to the scalar attribute using attribute name, then read and 
    * display its value.
    */
   attr = H5Aopen_name(dataset,"Integer attribute");
   ret  = H5Aread(attr, H5T_NATIVE_INT, &point_out);
   printf("The value of the attribute \"Integer attribute\" is %d \n", point_out); 
   ret =  H5Aclose(attr);

   /*
    * Attach to the string attribute using its index, then read and display the value.
    */
   attr  = H5Aopen_idx(dataset, 2);
   atype = H5Tcopy(H5T_C_S1);
           H5Tset_size(atype, 4);
   ret   = H5Aread(attr, atype, string_out);
   printf("The value of the attribute with the index 2 is %s \n", string_out);
   ret   = H5Aclose(attr);
   ret   = H5Tclose(atype);

   /*
    * Get attribute info using iteration function. 
    */
   idx = H5Aiterate(dataset, NULL, attr_info, NULL);

   /*
    * Close the dataset and the file.
    */
   H5Dclose(dataset);
   H5Fclose(file);

   return 0;  
}

/*
 * Operator function.
 */
herr_t 
attr_info(hid_t loc_id, const char *name, void *opdata)
{
    hid_t attr, atype, aspace;  /* Attribute, datatype and dataspace identifiers */
    int   rank;
    hsize_t sdim[64]; 
    herr_t ret;
    int i;
    size_t npoints;             /* Number of elements in the array attribute. */ 
    float *float_array;         /* Pointer to the array attribute. */
    /*
     * Open the attribute using its name.
     */    
    attr = H5Aopen_name(loc_id, name);

    /*
     * Display attribute name.
     */
    printf("\n");
    printf("Name : ");
    puts(name);

    /* 
     * Get attribute datatype, dataspace, rank, and dimensions.
     */
    atype  = H5Aget_type(attr);
    aspace = H5Aget_space(attr);
    rank = H5Sget_simple_extent_ndims(aspace);
    ret = H5Sget_simple_extent_dims(aspace, sdim, NULL);

    /*
     *  Display rank and dimension sizes for the array attribute.
     */

    if(rank > 0) {
    printf("Rank : %d \n", rank); 
    printf("Dimension sizes : ");
    for (i=0; i< rank; i++) printf("%d ", (int)sdim[i]);
    printf("\n");
    }

    /*
     * Read array attribute and display its type and values.
     */

    if (H5T_FLOAT == H5Tget_class(atype)) {
    printf("Type : FLOAT \n"); 
    npoints = H5Sget_simple_extent_npoints(aspace);
    float_array = (float *)malloc(sizeof(float)*(int)npoints); 
    ret = H5Aread(attr, atype, float_array);
    printf("Values : ");
    for( i = 0; i < (int)npoints; i++) printf("%f ", float_array[i]); 
    printf("\n");
    free(float_array);
    }

    /*
     * Release all identifiers.
     */
    H5Tclose(atype);
    H5Sclose(aspace);
    H5Aclose(attr);

    return 0;
}

 

(Return to TOC)

Example 9. Creating and storing references to objects.

This example creates a group and two datasets and a named datatype in the group. References to these four objects are stored in the dataset in the root group.

#include <hdf5.h>

#define FILE1   "trefer1.h5"

/* 1-D dataset with fixed dimensions */
#define SPACE1_NAME  "Space1"
#define SPACE1_RANK	1
#define SPACE1_DIM1	4

/* 2-D dataset with fixed dimensions */
#define SPACE2_NAME  "Space2"
#define SPACE2_RANK	2
#define SPACE2_DIM1	10
#define SPACE2_DIM2	10

int 
main(void) {
    hid_t		fid1;		/* HDF5 File IDs		*/
    hid_t		dataset;	/* Dataset ID			*/
    hid_t		group;      /* Group ID             */
    hid_t		sid1;       /* Dataspace ID			*/
    hid_t		tid1;       /* Datatype ID			*/
    hsize_t		dims1[] = {SPACE1_DIM1};
    hobj_ref_t      *wbuf;      /* buffer to write to disk */
    int       *tu32;      /* Temporary pointer to int data */
    int        i;          /* counting variables */
    const char *write_comment="Foo!"; /* Comments for group */
    herr_t		ret;		/* Generic return value		*/

/* Compound datatype */
typedef struct s1_t {
    unsigned int a;
    unsigned int b;
    float c;
} s1_t;

    /* Allocate write buffers */
    wbuf=(hobj_ref_t *)malloc(sizeof(hobj_ref_t)*SPACE1_DIM1);
    tu32=malloc(sizeof(int)*SPACE1_DIM1);

    /* Create file */
    fid1 = H5Fcreate(FILE1, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    /* Create dataspace for datasets */
    sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);

    /* Create a group */
    group=H5Gcreate(fid1,"Group1",-1);

    /* Set group's comment */
    ret=H5Gset_comment(group,".",write_comment);

    /* Create a dataset (inside Group1) */
    dataset=H5Dcreate(group,"Dataset1",H5T_STD_U32LE,sid1,H5P_DEFAULT);

    for(i=0; i < SPACE1_DIM1; i++)
        tu32[i] = i*3;

    /* Write selection to disk */
    ret=H5Dwrite(dataset,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,tu32);

    /* Close Dataset */
    ret = H5Dclose(dataset);

    /* Create another dataset (inside Group1) */
    dataset=H5Dcreate(group,"Dataset2",H5T_NATIVE_UCHAR,sid1,H5P_DEFAULT);

    /* Close Dataset */
    ret = H5Dclose(dataset);

    /* Create a datatype to refer to */
    tid1 = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));

    /* Insert fields */
    ret=H5Tinsert (tid1, "a", HOFFSET(s1_t,a), H5T_NATIVE_INT);

    ret=H5Tinsert (tid1, "b", HOFFSET(s1_t,b), H5T_NATIVE_INT);

    ret=H5Tinsert (tid1, "c", HOFFSET(s1_t,c), H5T_NATIVE_FLOAT);

    /* Save datatype for later */
    ret=H5Tcommit (group, "Datatype1", tid1);

    /* Close datatype */
    ret = H5Tclose(tid1);

    /* Close group */
    ret = H5Gclose(group);

    /* Create a dataset to store references */
    dataset=H5Dcreate(fid1,"Dataset3",H5T_STD_REF_OBJ,sid1,H5P_DEFAULT);

    /* Create reference to dataset */
    ret = H5Rcreate(&wbuf[0],fid1,"/Group1/Dataset1",H5R_OBJECT,-1);

    /* Create reference to dataset */
    ret = H5Rcreate(&wbuf[1],fid1,"/Group1/Dataset2",H5R_OBJECT,-1);

    /* Create reference to group */
    ret = H5Rcreate(&wbuf[2],fid1,"/Group1",H5R_OBJECT,-1);

    /* Create reference to named datatype */
    ret = H5Rcreate(&wbuf[3],fid1,"/Group1/Datatype1",H5R_OBJECT,-1);

    /* Write selection to disk */
    ret=H5Dwrite(dataset,H5T_STD_REF_OBJ,H5S_ALL,H5S_ALL,H5P_DEFAULT,wbuf);

    /* Close disk dataspace */
    ret = H5Sclose(sid1);
    
    /* Close Dataset */
    ret = H5Dclose(dataset);

    /* Close file */
    ret = H5Fclose(fid1);
    free(wbuf);
    free(tu32);
    return 0;
}

 

(Return to TOC)

Example 10. Reading references to objects.

This example opens and reads dataset Dataset3 from the file created in Example 9. Then the program dereferences the references to dataset Dataset1, the group and the named datatype, and opens those objects. The program reads and displays the dataset's data, the group's comment, and the number of members of the compound datatype.

#include <stdlib.h>
#include <hdf5.h>

#define FILE1   "trefer1.h5"

/* dataset with fixed dimensions */
#define SPACE1_NAME  "Space1"
#define SPACE1_RANK	1
#define SPACE1_DIM1	4

int 
main(void)
{
    hid_t		fid1;		/* HDF5 File IDs		*/
    hid_t		dataset,	/* Dataset ID			*/
                dset2;      /* Dereferenced dataset ID */
    hid_t		group;      /* Group ID             */
    hid_t		sid1;       /* Dataspace ID			*/
    hid_t		tid1;       /* Datatype ID			*/
    hobj_ref_t      *rbuf;      /* buffer to read from disk */
    int                *tu32;      /* temp. buffer read from disk */
    int        i;          /* counting variables */
    char read_comment[10];
    herr_t		ret;		/* Generic return value		*/

    /* Allocate read buffers */
    rbuf = malloc(sizeof(hobj_ref_t)*SPACE1_DIM1);
    tu32 = malloc(sizeof(int)*SPACE1_DIM1);

    /* Open the file */
    fid1 = H5Fopen(FILE1, H5F_ACC_RDWR, H5P_DEFAULT);

    /* Open the dataset */
    dataset=H5Dopen(fid1,"/Dataset3");

    /* Read selection from disk */
    ret=H5Dread(dataset,H5T_STD_REF_OBJ,H5S_ALL,H5S_ALL,H5P_DEFAULT,rbuf);

    /* Open dataset object */
    dset2 = H5Rdereference(dataset,H5R_OBJECT,&rbuf[0]);

    /* Check information in referenced dataset */
    sid1 = H5Dget_space(dset2);

    ret=H5Sget_simple_extent_npoints(sid1);

    /* Read from disk */
    ret=H5Dread(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,tu32);
    printf("Dataset data : \n");
     for (i=0; i < SPACE1_DIM1 ; i++) printf (" %d ", tu32[i]);
    printf("\n");
    printf("\n");

    /* Close dereferenced Dataset */
    ret = H5Dclose(dset2);

    /* Open group object */
    group = H5Rdereference(dataset,H5R_OBJECT,&rbuf[2]);

    /* Get group's comment */
    ret=H5Gget_comment(group,".",10,read_comment);
    printf("Group comment is %s \n", read_comment);
    printf(" \n");
    /* Close group */
    ret = H5Gclose(group);

    /* Open datatype object */
    tid1 = H5Rdereference(dataset,H5R_OBJECT,&rbuf[3]);

    /* Verify correct datatype */
    {
        H5T_class_t tclass;

        tclass= H5Tget_class(tid1);
        if ((tclass == H5T_COMPOUND))
           printf ("Number of compound datatype members is %d \n", H5Tget_nmembers(tid1)); 
    printf(" \n");
    }

    /* Close datatype */
    ret = H5Tclose(tid1);

    /* Close Dataset */
    ret = H5Dclose(dataset);

    /* Close file */
    ret = H5Fclose(fid1);

    /* Free memory buffers */
    free(rbuf);
    free(tu32);
    return 0;
}   

 

(Return to TOC)

Example 11. Creating and writing a reference to a region.

This example creates a dataset in the file. Then it creates a dataset to store references to the dataset regions (selections). The first selection is a 6 x 6 hyperslab. The second selection is a point selection in the same dataset. References to both selections are created and stored in the buffer, and then written to the dataset in the file.
#include <stdlib.h>
#include <hdf5.h>

#define FILE2	"trefer2.h5"
#define SPACE1_NAME  "Space1"
#define SPACE1_RANK     1
#define SPACE1_DIM1     4

/* Dataset with fixed dimensions */
#define SPACE2_NAME  "Space2"
#define SPACE2_RANK	2
#define SPACE2_DIM1	10
#define SPACE2_DIM2	10

/* Element selection information */
#define POINT1_NPOINTS 10

int
main(void)
{
    hid_t	fid1;		/* HDF5 File IDs		*/
    hid_t	dset1,		/* Dataset ID			*/
                dset2;      /* Dereferenced dataset ID */
    hid_t	sid1,       /* Dataspace ID	#1		*/
                sid2;       /* Dataspace ID	#2		*/
    hsize_t	dims1[] = {SPACE1_DIM1},
            	dims2[] = {SPACE2_DIM1, SPACE2_DIM2};
    hsize_t	start[SPACE2_RANK];     /* Starting location of hyperslab */
    hsize_t	stride[SPACE2_RANK];    /* Stride of hyperslab */
    hsize_t	count[SPACE2_RANK];     /* Element count of hyperslab */
    hsize_t	block[SPACE2_RANK];     /* Block size of hyperslab */
    hsize_t	coord1[POINT1_NPOINTS][SPACE2_RANK]; 
                                    /* Coordinates for point selection */
    hdset_reg_ref_t      *wbuf;      /* buffer to write to disk */
    int     *dwbuf;      /* Buffer for writing numeric data to disk */
    int        i;          /* counting variables */
    herr_t		ret;		/* Generic return value		*/


    /* Allocate write & read buffers */
    wbuf=calloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1);
    dwbuf=malloc(sizeof(int)*SPACE2_DIM1*SPACE2_DIM2);

    /* Create file */
    fid1 = H5Fcreate(FILE2, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    /* Create dataspace for datasets */
    sid2 = H5Screate_simple(SPACE2_RANK, dims2, NULL);

    /* Create a dataset */
    dset2=H5Dcreate(fid1,"Dataset2",H5T_STD_U8LE,sid2,H5P_DEFAULT);

    for(i=0; i < SPACE2_DIM1*SPACE2_DIM2; i++)
        dwbuf[i]=i*3;

    /* Write selection to disk */
    ret=H5Dwrite(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,dwbuf);

    /* Close Dataset */
    ret = H5Dclose(dset2);

    /* Create dataspace for the reference dataset */
    sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);

    /* Create a dataset */
    dset1=H5Dcreate(fid1,"Dataset1",H5T_STD_REF_DSETREG,sid1,H5P_DEFAULT);

    /* Create references */

    /* Select 6x6 hyperslab for first reference */
    start[0]=2; start[1]=2;
    stride[0]=1; stride[1]=1;
    count[0]=6; count[1]=6;
    block[0]=1; block[1]=1;
    ret = H5Sselect_hyperslab(sid2,H5S_SELECT_SET,start,stride,count,block);

    /* Store first dataset region */
    ret = H5Rcreate(&wbuf[0],fid1,"/Dataset2",H5R_DATASET_REGION,sid2);

    /* Select sequence of ten points for second reference */
    coord1[0][0]=6; coord1[0][1]=9;
    coord1[1][0]=2; coord1[1][1]=2;
    coord1[2][0]=8; coord1[2][1]=4;
    coord1[3][0]=1; coord1[3][1]=6;
    coord1[4][0]=2; coord1[4][1]=8;
    coord1[5][0]=3; coord1[5][1]=2;
    coord1[6][0]=0; coord1[6][1]=4;
    coord1[7][0]=9; coord1[7][1]=0;
    coord1[8][0]=7; coord1[8][1]=1;
    coord1[9][0]=3; coord1[9][1]=3;
    ret = H5Sselect_elements(sid2,H5S_SELECT_SET,POINT1_NPOINTS,(const hsize_t **)coord1);

    /* Store second dataset region */
    ret = H5Rcreate(&wbuf[1],fid1,"/Dataset2",H5R_DATASET_REGION,sid2);

    /* Write selection to disk */
    ret=H5Dwrite(dset1,H5T_STD_REF_DSETREG,H5S_ALL,H5S_ALL,H5P_DEFAULT,wbuf);

    /* Close all objects */
    ret = H5Sclose(sid1);
    ret = H5Dclose(dset1);
    ret = H5Sclose(sid2);
    
    /* Close file */
    ret = H5Fclose(fid1);

    free(wbuf);
    free(dwbuf);
    return 0;
}   

 

(Return to TOC)

Example 12. Reading a reference to a region.

This example reads a dataset containing dataset region references. It reads data from the dereferenced dataset and displays the number of elements and raw data. Then it reads two selections: a hyperslab selection and a point selection. The program queries a number of points in the hyperslab and the coordinates and displays them. Then it queries a number of selected points and their coordinates and displays the information.
   
#include <stdlib.h>
#include <hdf5.h>

#define FILE2	"trefer2.h5"
#define NPOINTS 10
 
/* 1-D dataset with fixed dimensions */
#define SPACE1_NAME  "Space1"
#define SPACE1_RANK	1
#define SPACE1_DIM1	4

/* 2-D dataset with fixed dimensions */
#define SPACE2_NAME  "Space2"
#define SPACE2_RANK	2
#define SPACE2_DIM1	10
#define SPACE2_DIM2	10

int 
main(void)
{
    hid_t		fid1;		/* HDF5 File IDs		*/
    hid_t		dset1,	/* Dataset ID			*/
                dset2;      /* Dereferenced dataset ID */
    hid_t		sid1,       /* Dataspace ID	#1		*/
                sid2;       /* Dataspace ID	#2		*/
    hsize_t *   coords;             /* Coordinate buffer */
    hsize_t		low[SPACE2_RANK];   /* Selection bounds */
    hsize_t		high[SPACE2_RANK];     /* Selection bounds */
    hdset_reg_ref_t      *rbuf;      /* buffer to to read disk */
    int    *drbuf;      /* Buffer for reading numeric data from disk */
    int        i, j;          /* counting variables */
    herr_t		ret;		/* Generic return value		*/

    /* Output message about test being performed */

    /* Allocate write & read buffers */
    rbuf=malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1);
    drbuf=calloc(sizeof(int),SPACE2_DIM1*SPACE2_DIM2);

    /* Open the file */
    fid1 = H5Fopen(FILE2, H5F_ACC_RDWR, H5P_DEFAULT);

    /* Open the dataset */
    dset1=H5Dopen(fid1,"/Dataset1");

    /* Read selection from disk */
    ret=H5Dread(dset1,H5T_STD_REF_DSETREG,H5S_ALL,H5S_ALL,H5P_DEFAULT,rbuf);

    /* Try to open objects */
    dset2 = H5Rdereference(dset1,H5R_DATASET_REGION,&rbuf[0]);

    /* Check information in referenced dataset */
    sid1 = H5Dget_space(dset2);

    ret=H5Sget_simple_extent_npoints(sid1);
    printf(" Number of elements in the dataset is : %d\n",ret);

    /* Read from disk */
    ret=H5Dread(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,drbuf);

    for(i=0; i < SPACE2_DIM1; i++) {
        for (j=0; j < SPACE2_DIM2; j++) printf (" %d ", drbuf[i*SPACE2_DIM2+j]);
        printf("\n"); }

    /* Get the hyperslab selection */
    sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[0]);

    /* Verify correct hyperslab selected */
    ret = H5Sget_select_npoints(sid2);
    printf(" Number of elements in the hyperslab is : %d \n", ret);
    ret = H5Sget_select_hyper_nblocks(sid2);
    coords=malloc(ret*SPACE2_RANK*sizeof(hsize_t)*2); /* allocate space for the hyperslab blocks */
    ret = H5Sget_select_hyper_blocklist(sid2,0,ret,coords);
    printf(" Hyperslab coordinates are : \n");
    printf (" ( %lu , %lu ) ( %lu , %lu ) \n", \
(unsigned long)coords[0],(unsigned long)coords[1],(unsigned long)coords[2],(unsigned long)coords[3]); 
    free(coords);
    ret = H5Sget_select_bounds(sid2,low,high);

    /* Close region space */
    ret = H5Sclose(sid2);

    /* Get the element selection */
    sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[1]);

    /* Verify correct elements selected */
    ret = H5Sget_select_elem_npoints(sid2);
    printf(" Number of selected elements is : %d\n", ret);

    /* Allocate space for the element points */
    coords= malloc(ret*SPACE2_RANK*sizeof(hsize_t)); 
    ret = H5Sget_select_elem_pointlist(sid2,0,ret,coords);
    printf(" Coordinates of selected elements are : \n");
    for (i=0; i < 2*NPOINTS; i=i+2) 
         printf(" ( %lu , %lu ) \n", (unsigned long)coords[i],(unsigned long)coords[i+1]); 
          
    free(coords);
    ret = H5Sget_select_bounds(sid2,low,high);

    /* Close region space */
    ret = H5Sclose(sid2);

    /* Close first space */
    ret = H5Sclose(sid1);

    /* Close dereferenced Dataset */
    ret = H5Dclose(dset2);

    /* Close Dataset */
    ret = H5Dclose(dset1);

    /* Close file */
    ret = H5Fclose(fid1);

    /* Free memory buffers */
    free(rbuf);
    free(drbuf);
    return 0;
}   

 

(Return to TOC)


Introduction to HDF5 
HDF5 User’s Guide 
HDF5 Reference Manual 
Other HDF5 documents and links 

The HDF Group Help Desk:
Describes HDF5 Development Trunk, Release 1.11.x.
Highest current public release is HDF5 Release 1.8.x.
  Copyright by The HDF Group
and the Board of Trustees of the University of Illinois
Last modified: 3 August 2004