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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 static hdf.hdf5lib.HDF5Constants.H5T_STRING;
import java.io.UnsupportedEncodingException;
import java.util.Iterator;
import hdf.hdf5lib.exceptions.HDF5JavaException;
import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters;
import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp;
import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry;
/**
* Implementation of {@link IHDF5OpaqueReader}
*
* @author Bernd Rinn
*/
public class HDF5OpaqueReader implements IHDF5OpaqueReader
{
private final HDF5BaseReader baseReader;
HDF5OpaqueReader(HDF5BaseReader baseReader)
{
assert baseReader != null;
this.baseReader = baseReader;
}
@Override
public String tryGetOpaqueTag(final String objectPath)
{
baseReader.checkOpen();
final ICallableWithCleanUp<String> readTagCallable = new ICallableWithCleanUp<String>()
{
@Override
public String call(ICleanUpRegistry registry)
{
final long dataSetId =
baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry);
final long dataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry);
return baseReader.h5.tryGetOpaqueTag(dataTypeId);
}
};
return baseReader.runner.call(readTagCallable);
}
@Override
public HDF5OpaqueType tryGetOpaqueType(final String objectPath)
{
baseReader.checkOpen();
final ICallableWithCleanUp<HDF5OpaqueType> readTagCallable =
new ICallableWithCleanUp<HDF5OpaqueType>()
{
@Override
public HDF5OpaqueType call(ICleanUpRegistry registry)
{
final long dataSetId =
baseReader.h5.openDataSet(baseReader.fileId, objectPath,
registry);
final long dataTypeId =
baseReader.h5.getDataTypeForDataSet(dataSetId,
baseReader.fileRegistry);
final String opaqueTagOrNull =
baseReader.h5.tryGetOpaqueTag(dataTypeId);
if (opaqueTagOrNull == null)
{
return null;
} else
{
return new HDF5OpaqueType(baseReader.fileId, dataTypeId,
opaqueTagOrNull, baseReader);
}
}
};
return baseReader.runner.call(readTagCallable);
}
@Override
public byte[] readArray(final String objectPath)
{
baseReader.checkOpen();
final ICallableWithCleanUp<byte[]> readCallable = new ICallableWithCleanUp<byte[]>()
{
@Override
public byte[] call(ICleanUpRegistry registry)
{
final long dataSetId =
baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry);
final DataSpaceParameters spaceParams =
baseReader.getSpaceParameters(dataSetId, registry);
final long nativeDataTypeId =
baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry);
final boolean isString =
(baseReader.h5.getClassType(nativeDataTypeId) == H5T_STRING);
byte[] data;
if (isString)
{
if (baseReader.h5.isVariableLengthString(nativeDataTypeId))
{
String[] value = new String[1];
baseReader.h5.readDataSetVL(dataSetId, nativeDataTypeId, value);
try
{
data = value[0].getBytes(CharacterEncoding.ASCII.getCharSetName());
} catch (UnsupportedEncodingException ex)
{
data = value[0].getBytes();
}
} else
{
final int size = baseReader.h5.getDataTypeSize(nativeDataTypeId);
data = new byte[size];
baseReader.h5.readDataSetNonNumeric(dataSetId, nativeDataTypeId, data);
}
} else
{
final int elementSize = baseReader.h5.getDataTypeSize(nativeDataTypeId);
data = new byte[spaceParams.blockSize * elementSize];
baseReader.h5.readDataSet(dataSetId, nativeDataTypeId,
spaceParams.memorySpaceId, spaceParams.dataSpaceId, data);
}
return data;
}
};
return baseReader.runner.call(readCallable);
}
@Override
public byte[] getArrayAttr(final String objectPath, final String attributeName)
{
baseReader.checkOpen();
final ICallableWithCleanUp<byte[]> readCallable = new ICallableWithCleanUp<byte[]>()
{
@Override
public byte[] call(ICleanUpRegistry registry)
{
final long objectId =
baseReader.h5.openObject(baseReader.fileId, objectPath, registry);
return baseReader.getAttributeAsByteArray(objectId, attributeName, registry);
}
};
return baseReader.runner.call(readCallable);
}
@Override
public byte[] readArrayBlock(final String objectPath, final int blockSize,
final long blockNumber) throws HDF5JavaException
{
baseReader.checkOpen();
final ICallableWithCleanUp<byte[]> readCallable = new ICallableWithCleanUp<byte[]>()
{
@Override
public byte[] call(ICleanUpRegistry registry)
{
final long dataSetId =
baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry);
final DataSpaceParameters spaceParams =
baseReader.getSpaceParameters(dataSetId, blockNumber * blockSize,
blockSize, registry);
final long nativeDataTypeId =
baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry);
checkNotAString(objectPath, nativeDataTypeId);
final int elementSize = baseReader.h5.getDataTypeSize(nativeDataTypeId);
final byte[] data = new byte[elementSize * spaceParams.blockSize];
baseReader.h5.readDataSet(dataSetId, nativeDataTypeId,
spaceParams.memorySpaceId, spaceParams.dataSpaceId, data);
return data;
}
};
return baseReader.runner.call(readCallable);
}
@Override
public byte[] readArrayBlockWithOffset(final String objectPath, final int blockSize,
final long offset) throws HDF5JavaException
{
baseReader.checkOpen();
final ICallableWithCleanUp<byte[]> readCallable = new ICallableWithCleanUp<byte[]>()
{
@Override
public byte[] call(ICleanUpRegistry registry)
{
final long dataSetId =
baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry);
final DataSpaceParameters spaceParams =
baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry);
final long nativeDataTypeId =
baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry);
checkNotAString(objectPath, nativeDataTypeId);
final int elementSize = baseReader.h5.getDataTypeSize(nativeDataTypeId);
final byte[] data = new byte[elementSize * spaceParams.blockSize];
baseReader.h5.readDataSet(dataSetId, nativeDataTypeId,
spaceParams.memorySpaceId, spaceParams.dataSpaceId, data);
return data;
}
};
return baseReader.runner.call(readCallable);
}
@Override
public int readArrayToBlockWithOffset(final String objectPath, final byte[] buffer,
final int blockSize, final long offset, final int memoryOffset)
throws HDF5JavaException
{
if (blockSize + memoryOffset > buffer.length)
{
throw new HDF5JavaException("Buffer not large enough for blockSize and memoryOffset");
}
baseReader.checkOpen();
final ICallableWithCleanUp<Integer> readCallable = new ICallableWithCleanUp<Integer>()
{
@Override
public Integer call(ICleanUpRegistry registry)
{
final long dataSetId =
baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry);
final DataSpaceParameters spaceParams =
baseReader.getSpaceParameters(dataSetId, memoryOffset, offset,
blockSize, registry);
final long nativeDataTypeId =
baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry);
checkNotAString(objectPath, nativeDataTypeId);
final int elementSize = baseReader.h5.getDataTypeSize(nativeDataTypeId);
if ((blockSize + memoryOffset) * elementSize > buffer.length)
{
throw new HDF5JavaException(
"Buffer not large enough for blockSize and memoryOffset");
}
baseReader.h5.readDataSet(dataSetId, nativeDataTypeId,
spaceParams.memorySpaceId, spaceParams.dataSpaceId, buffer);
return spaceParams.blockSize;
}
};
return baseReader.runner.call(readCallable);
}
@Override
public Iterable<HDF5DataBlock<byte[]>> getArrayNaturalBlocks(final String dataSetPath)
throws HDF5JavaException
{
final HDF5NaturalBlock1DParameters params =
new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath));
return new Iterable<HDF5DataBlock<byte[]>>()
{
@Override
public Iterator<HDF5DataBlock<byte[]>> iterator()
{
return new Iterator<HDF5DataBlock<byte[]>>()
{
final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index =
params.getNaturalBlockIndex();
@Override
public boolean hasNext()
{
return index.hasNext();
}
@Override
public HDF5DataBlock<byte[]> next()
{
final long offset = index.computeOffsetAndSizeGetOffset();
final byte[] block =
readArrayBlockWithOffset(dataSetPath,
index.getBlockSize(), offset);
return new HDF5DataBlock<byte[]>(block, index.getAndIncIndex(),
offset);
}
@Override
public void remove()
{
throw new UnsupportedOperationException();
}
};
}
};
}
private void checkNotAString(final String objectPath, final long nativeDataTypeId)
{
final boolean isString =
(baseReader.h5.getClassType(nativeDataTypeId) == H5T_STRING);
if (isString)
{
throw new HDF5JavaException(objectPath + " cannot be a String.");
}
}
}
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