chunks.cpp

This example shows how to read data from a chunked dataset.

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * 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://support.hdfgroup.org/ftp/HDF5/releases.  *
 * 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 extend.cpp
 */

#ifdef OLD_HEADER_FILENAME
#include <iostream.h>
#else
#include <iostream>
#endif
using std::cout;
using std::endl;

#include <string>
#include "H5Cpp.h"
using namespace H5;

const H5std_string FILE_NAME( "SDSextendible.h5" );
const H5std_string DATASET_NAME( "ExtendibleArray" );
const int      NX = 10;
const int      NY = 5;
const int      RANK = 2;
const int      RANKC = 1;

int main (void)
{
    hsize_t i, j;

    // Try block to detect exceptions raised by any of the calls inside it
    try
    {
    /*
     * Turn off the auto-printing when failure occurs so that we can
     * handle the errors appropriately
     */
    Exception::dontPrint();

    /*
     * Open the file and the dataset.
     */
    H5File file( FILE_NAME, H5F_ACC_RDONLY );
    DataSet dataset = file.openDataSet( DATASET_NAME );

    /*
     * Get filespace for rank and dimension
     */
    DataSpace filespace = dataset.getSpace();

    /*
     * Get number of dimensions in the file dataspace
     */
    int rank = filespace.getSimpleExtentNdims();

    /*
     * Get and print the dimension sizes of the file dataspace
     */
    hsize_t dims[2];    // dataset dimensions
    rank = filespace.getSimpleExtentDims( dims );
    cout << "dataset rank = " << rank << ", dimensions "
         << (unsigned long)(dims[0]) << " x "
         << (unsigned long)(dims[1]) << endl;

    /*
     * Define the memory space to read dataset.
     */
    DataSpace mspace1(RANK, dims);

    /*
     * Read dataset back and display.
     */
    int data_out[NX][NY];  // buffer for dataset to be read
    dataset.read( data_out, PredType::NATIVE_INT, mspace1, filespace );

    cout << "\n";
    cout << "Dataset: \n";
    for (j = 0; j < dims[0]; j++)
    {
        for (i = 0; i < dims[1]; i++)
        cout << data_out[j][i] << " ";
        cout << endl;
    }

    /*
     *      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.
     */
    hsize_t col_dims[1];
    col_dims[0] = 10;
    DataSpace mspace2( RANKC, col_dims );

    /*
     * Define the column (hyperslab) to read.
     */
    hsize_t offset[2] = { 0, 2 };
    hsize_t  count[2] = { 10, 1 };
    int column[10];  // buffer for column to be read

    /*
     * Define hyperslab and read.
     */
    filespace.selectHyperslab( H5S_SELECT_SET, count, offset );
    dataset.read( column, PredType::NATIVE_INT, mspace2, filespace );

    cout << endl;
    cout << "Third column: " << endl;
    for (i = 0; i < 10; i++)
        cout << column[i] << endl;

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

    /*
     * Get creation properties list.
     */
    DSetCreatPropList cparms = dataset.getCreatePlist();

    /*
     * Check if dataset is chunked.
     */
    hsize_t chunk_dims[2];
    int     rank_chunk;
    if( H5D_CHUNKED == cparms.getLayout() )
    {
        /*
         * Get chunking information: rank and dimensions
         */
        rank_chunk = cparms.getChunk( 2, chunk_dims);
        cout << "chunk rank " << rank_chunk << "dimensions "
        << (unsigned long)(chunk_dims[0]) << " x "
        << (unsigned long)(chunk_dims[1]) << endl;

        /*
         * Define the memory space to read a chunk.
         */
        DataSpace mspace3( rank_chunk, chunk_dims );

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

        /*
         * Read chunk back and display.
         */
        int chunk_out[2][5];   // buffer for chunk to be read
        dataset.read( chunk_out, PredType::NATIVE_INT, mspace3, filespace );
        cout << endl;
        cout << "Chunk:" << endl;
        for (j = 0; j < chunk_dims[0]; j++)
        {
        for (i = 0; i < chunk_dims[1]; i++)
            cout << chunk_out[j][i] << " ";
        cout << endl;
        }
        /*
         *   Chunk:
         *   1 1 1 0 0
         *   2 0 0 0 0
         */
    }
    }  // end of try block

    // catch failure caused by the H5File operations
    catch( FileIException error )
    {
    error.printError();
    return -1;
    }

    // catch failure caused by the DataSet operations
    catch( DataSetIException error )
    {
    error.printError();
    return -1;
    }

    // catch failure caused by the DataSpace operations
    catch( DataSpaceIException error )
    {
    error.printError();
    return -1;
    }
    return 0;
}