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/*
* Copyright 2011 - 2018 ETH Zuerich, CISD and SIS.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package ch.systemsx.cisd.hdf5.examples;
import static ch.systemsx.cisd.hdf5.HDF5ArrayBlockParamsBuilder.slice;
import static ch.systemsx.cisd.hdf5.HDF5ArrayBlockParamsBuilder.blockIndex;
import static ch.systemsx.cisd.hdf5.MatrixUtils.dims;
import java.util.Random;
import org.apache.commons.lang3.ArrayUtils;
import ch.systemsx.cisd.base.mdarray.MDIntArray;
import ch.systemsx.cisd.hdf5.HDF5DataSet;
import ch.systemsx.cisd.hdf5.HDF5Factory;
import ch.systemsx.cisd.hdf5.HDF5MDDataBlock;
import ch.systemsx.cisd.hdf5.IHDF5Reader;
import ch.systemsx.cisd.hdf5.IHDF5Writer;
/**
* An example for block-wise reading and writing of an integer matrix. This can be used to read and
* write arrays and matrices that are too big to fit into memory. Only the block
*/
public class BlockwiseMatrixExample
{
public static void main(String[] args)
{
Random rng = new Random();
MDIntArray mydata = new MDIntArray(dims(10, 10));
// Write the integer matrix.
try (IHDF5Writer writer = HDF5Factory.open("largeimatrix.h5"))
{
// Define the block size as 10 x 10.
try (HDF5DataSet dataSet = writer.int32().createMDArrayAndOpen("mydata", dims(10, 10)))
{
// Write 5 x 7 blocks.
for (int bx = 0; bx < 5; ++bx)
{
for (int by = 0; by < 7; ++by)
{
fillMatrix(rng, mydata);
writer.int32().writeMDArray(dataSet, mydata, blockIndex(bx, by));
}
}
}
}
// Read the matrix in again, using the "natural" 10 x 10 blocks.
try (IHDF5Reader reader = HDF5Factory.openForReading("largeimatrix.h5"))
{
for (HDF5MDDataBlock<MDIntArray> block : reader.int32().getMDArrayNaturalBlocks("mydata"))
{
System.out.println(ArrayUtils.toString(block.getIndex()) + " -> "
+ block.getData().toString());
}
// Read a 1d sliced block of size 10 where the first index is fixed
System.out.println(reader.int32().readMDArray("mydata", slice(30, -1).block(10).index(4)));
}
}
static void fillMatrix(Random rng, MDIntArray mydata)
{
for (int i = 0; i < mydata.size(0); ++i)
{
for (int j = 0; j < mydata.size(1); ++j)
{
mydata.set(rng.nextInt(), i, j);
}
}
}
}
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