HDF5 C++ API Reference Manual

 

 

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 files COPYING and Copyright.html.  COPYING can be found at the root   *
 * of the source code distribution tree; Copyright.html can be found at the  *
 * root level of an installed copy of the electronic HDF5 document set and   *
 * is linked from the top-level documents page.  It can also be found at     *
 * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
 * access to either file, you may request a copy from [email protected].     *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

/*
 *   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
#include <string>

#ifndef H5_NO_NAMESPACE
#ifndef H5_NO_STD
    using std::cout;
    using std::endl;
#endif  // H5_NO_STD
#endif

#include "H5Cpp.h"

#ifndef H5_NO_NAMESPACE
    using namespace H5;
#endif

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;
}

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