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/*
* Copyright 2007 - 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;
import java.io.File;
import java.util.BitSet;
import java.util.List;
import ch.systemsx.cisd.base.convert.NativeData;
import hdf.hdf5lib.HDFNativeData;
import hdf.hdf5lib.exceptions.HDF5LibraryException;
/**
* @author Bernd Rinn
*/
public class HDF5ReadTest
{
public static void main(String[] args)
{
try
{
IHDF5Reader reader = HDF5FactoryProvider.get().openForReading(new File("test.h5"));
System.out.println(reader.object().getGroupMemberPaths("/"));
describe(reader, "/Group1/MyBitSet", null);
describe(reader, "/Group1/MyDataSet", null);
byte[] bsb = reader.readAsByteArray("/Group1/MyBitSet");
long[] bsl = HDFNativeData.byteToLong(0, bsb.length / NativeData.LONG_SIZE, bsb);
System.out.println("length of /Group1/MyBitSet=" + bsl.length);
for (long l : bsl)
{
System.out.print(l + " ");
}
System.out.println();
BitSet bs = reader.readBitField("/Group1/MyBitSet");
System.out.println(bs);
System.out.println(reader.float64().getAttr("/", "version"));
List<String> members = reader.object().getGroupMemberPaths("/Group1");
for (String m : members)
{
System.out.println(" " + m);
}
listAttributes(reader, "/Group1");
listAttributes(reader, "/Group1/MyDataSet");
describe(reader, "/Group1/MyDataSet", "foo");
describe(reader, "/Group1", "active");
System.out.println(reader.bool().getAttr("/Group1", "active"));
System.out.println(reader.string().getAttr("/Group1/MyDataSet", "foo"));
System.out.println(reader.string().getAttr("/Group1/SubGroup1/MyDataSet", "foo"));
System.out.println(reader.float64().readMatrix("/Group1/MyDataSet")[1][0]);
System.out.println(reader.float32().readMatrix("/Group1/SubGroup1/MyDataSet")[1][2]);
System.out.println(reader.string().read("/Group1/MyString").length());
listAttributes(reader, "empty");
} catch (HDF5LibraryException ex)
{
System.err.println(ex.getHDF5ErrorStackAsString());
ex.printStackTrace();
}
}
private static void listAttributes(IHDF5Reader reader, String objectName)
{
final List<String> attributeNames = reader.object().getAttributeNames(objectName);
System.out.printf("Found %d attributes for object '%s':\n", attributeNames.size(),
objectName);
for (String a : attributeNames)
{
System.out.println(a);
}
}
private static void describe(IHDF5Reader reader, String objectName, String attributeNameOrNull)
{
HDF5DataSetInformation dsInfo;
HDF5DataTypeInformation dtInfo;
if (attributeNameOrNull == null)
{
dsInfo = reader.getDataSetInformation(objectName);
dtInfo = dsInfo.getTypeInformation();
} else
{
dsInfo = null;
dtInfo = reader.object().getAttributeInformation(objectName, attributeNameOrNull);
}
System.out.printf("%s%s, class=%s, elemSize=%d", objectName,
attributeNameOrNull != null ? "#" + attributeNameOrNull : "",
dtInfo.getDataClass(), dtInfo.getElementSize());
if (dsInfo != null)
{
System.out.printf(", rank=%d, scalar=%s, variant=%s\n", dsInfo.getRank(), Boolean
.toString(dsInfo.isScalar()), dsInfo.tryGetTypeVariant());
for (long dim : dsInfo.getDimensions())
{
System.out.println(" DIM " + dim);
}
} else
{
System.out.println();
}
}
}
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