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     *
 * https://support.hdfgroup.org/HDF5/doc/Copyright.html.  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.C
 */

#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;

      /*
       * 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 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

      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
       */

      /*
       * 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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