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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_ARRAY;
import static hdf.hdf5lib.HDF5Constants.H5T_REFERENCE;
import static hdf.hdf5lib.HDF5Constants.H5T_STD_REF_OBJ;
import java.util.Iterator;
import hdf.hdf5lib.exceptions.HDF5JavaException;
import ch.systemsx.cisd.base.mdarray.MDAbstractArray;
import ch.systemsx.cisd.base.mdarray.MDArray;
import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters;
import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp;
import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry;
import hdf.hdf5lib.HDF5Constants;
/**
* A reader for HDF5 references.
*
* @author Bernd Rinn
*/
public class HDF5ReferenceReader implements IHDF5ReferenceReader
{
private final HDF5BaseReader baseReader;
HDF5ReferenceReader(HDF5BaseReader baseReader)
{
assert baseReader != null;
this.baseReader = baseReader;
}
// /////////////////////
// Specific
// /////////////////////
@Override
public String resolvePath(String reference)
{
assert reference != null;
baseReader.checkOpen();
if (reference.charAt(0) != '\0')
{
throw new HDF5JavaException(String.format("'%s' is not a reference.", reference));
}
return baseReader.h5.getReferencedObjectName(baseReader.fileId,
Long.parseLong(reference.substring(1)));
}
private String refToStr(long reference)
{
return '\0' + Long.toString(reference);
}
private String[] refToStr(long[] references)
{
final String[] result = new String[references.length];
for (int i = 0; i < references.length; ++i)
{
result[i] = '\0' + Long.toString(references[i]);
}
return result;
}
private void checkReference(final long dataTypeId, final String objectPath)
throws HDF5JavaException
{
final boolean isReference = (baseReader.h5.getClassType(dataTypeId) == H5T_REFERENCE);
if (isReference == false)
{
throw new HDF5JavaException("Dataset " + objectPath + " is not a reference.");
}
}
private void checkRank1(final int[] arrayDimensions, final String objectPath)
{
if (arrayDimensions.length != 1)
{
throw new HDF5JavaException("Dataset " + objectPath
+ ": array needs to be of rank 1, but is of rank " + arrayDimensions.length);
}
}
private void checkRank1(final long[] arrayDimensions, final String objectPath)
{
if (arrayDimensions.length != 1)
{
throw new HDF5JavaException("Dataset " + objectPath
+ ": array needs to be of rank 1, but is of rank " + arrayDimensions.length);
}
}
// /////////////////////
// Attributes
// /////////////////////
@Override
public String getAttr(final String objectPath, final String attributeName)
{
return getAttr(objectPath, attributeName, true);
}
@Override
public String getAttr(final String objectPath, final String attributeName,
final boolean resolveName)
{
assert objectPath != null;
assert attributeName != null;
baseReader.checkOpen();
final ICallableWithCleanUp<String> readRunnable = new ICallableWithCleanUp<String>()
{
@Override
public String call(ICleanUpRegistry registry)
{
final long objectId =
baseReader.h5.openObject(baseReader.fileId, objectPath, registry);
final long attributeId =
baseReader.h5.openAttribute(objectId, attributeName, registry);
final long dataTypeId =
baseReader.h5.getDataTypeForAttribute(attributeId, registry);
checkReference(dataTypeId, objectPath);
final long[] reference =
baseReader.h5.readAttributeAsLongArray(attributeId, dataTypeId, 1);
return resolveName ? baseReader.h5.getReferencedObjectName(attributeId,
reference[0]) : refToStr(reference[0]);
}
};
return baseReader.runner.call(readRunnable);
}
@Override
public String[] getArrayAttr(final String objectPath,
final String attributeName)
{
return getArrayAttr(objectPath, attributeName, true);
}
@Override
public String[] getArrayAttr(final String objectPath,
final String attributeName, final boolean resolveName)
{
assert objectPath != null;
assert attributeName != null;
baseReader.checkOpen();
final ICallableWithCleanUp<String[]> getAttributeRunnable =
new ICallableWithCleanUp<String[]>()
{
@Override
public String[] call(ICleanUpRegistry registry)
{
final long objectId =
baseReader.h5.openObject(baseReader.fileId, objectPath,
registry);
final long attributeId =
baseReader.h5.openAttribute(objectId, attributeName, registry);
final long attributeTypeId =
baseReader.h5.getDataTypeForAttribute(attributeId, registry);
final long memoryTypeId;
final int len;
if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY)
{
final long baseDataTypeId =
baseReader.h5.getBaseDataType(attributeTypeId, registry);
checkReference(baseDataTypeId, objectPath);
final int[] arrayDimensions =
baseReader.h5.getArrayDimensions(attributeTypeId);
checkRank1(arrayDimensions, objectPath);
len = arrayDimensions[0];
memoryTypeId =
baseReader.h5.createArrayType(H5T_STD_REF_OBJ, len,
registry);
} else
{
checkReference(attributeTypeId, objectPath);
final long[] arrayDimensions =
baseReader.h5.getDataDimensionsForAttribute(attributeId,
registry);
checkRank1(arrayDimensions, objectPath);
memoryTypeId = H5T_STD_REF_OBJ;
len = HDF5Utils.getOneDimensionalArraySize(arrayDimensions);
}
final long[] references =
baseReader.h5.readAttributeAsLongArray(attributeId,
memoryTypeId, len);
return resolveName ? baseReader.h5.getReferencedObjectNames(
attributeId, references) : refToStr(references);
}
};
return baseReader.runner.call(getAttributeRunnable);
}
@Override
public MDArray<String> getMDArrayAttr(final String objectPath,
final String attributeName)
{
return getMDArrayAttr(objectPath, attributeName, true);
}
@Override
public MDArray<String> getMDArrayAttr(final String objectPath,
final String attributeName, final boolean resolveName)
{
assert objectPath != null;
assert attributeName != null;
baseReader.checkOpen();
final ICallableWithCleanUp<MDArray<String>> getAttributeRunnable =
new ICallableWithCleanUp<MDArray<String>>()
{
@Override
public MDArray<String> call(ICleanUpRegistry registry)
{
try
{
final long objectId =
baseReader.h5.openObject(baseReader.fileId, objectPath,
registry);
final long attributeId =
baseReader.h5.openAttribute(objectId, attributeName,
registry);
final long attributeTypeId =
baseReader.h5
.getDataTypeForAttribute(attributeId, registry);
final long memoryTypeId;
final int[] arrayDimensions;
if (baseReader.h5.getClassType(attributeTypeId) == H5T_ARRAY)
{
final long baseDataTypeId =
baseReader.h5
.getBaseDataType(attributeTypeId, registry);
checkReference(baseDataTypeId, objectPath);
arrayDimensions =
baseReader.h5.getArrayDimensions(attributeTypeId);
memoryTypeId =
baseReader.h5.createArrayType(H5T_STD_REF_OBJ,
arrayDimensions, registry);
} else
{
checkReference(attributeTypeId, objectPath);
arrayDimensions =
MDAbstractArray.toInt(baseReader.h5
.getDataDimensionsForAttribute(attributeId,
registry));
memoryTypeId = H5T_STD_REF_OBJ;
}
final int len;
len = MDAbstractArray.getLength(arrayDimensions);
final long[] references =
baseReader.h5.readAttributeAsLongArray(attributeId,
memoryTypeId, len);
return new MDArray<String>(
resolveName ? baseReader.h5.getReferencedObjectNames(
attributeId, references) : refToStr(references),
arrayDimensions);
} catch (IllegalArgumentException ex)
{
throw new HDF5JavaException(ex.getMessage());
}
}
};
return baseReader.runner.call(getAttributeRunnable);
}
// /////////////////////
// Data Sets
// /////////////////////
@Override
public String read(final String objectPath)
{
return read(objectPath, true);
}
@Override
public String read(final String objectPath, final boolean resolveName)
{
assert objectPath != null;
baseReader.checkOpen();
final ICallableWithCleanUp<String> readRunnable = new ICallableWithCleanUp<String>()
{
@Override
public String call(ICleanUpRegistry registry)
{
final long dataSetId =
baseReader.h5.openObject(baseReader.fileId, objectPath, registry);
final long objectReferenceDataTypeId =
baseReader.h5.getDataTypeForDataSet(dataSetId, registry);
checkReference(objectReferenceDataTypeId, objectPath);
final long[] reference = new long[1];
baseReader.h5.readDataSet(dataSetId, objectReferenceDataTypeId, reference);
return resolveName ? baseReader.h5.getReferencedObjectName(dataSetId,
reference[0]) : refToStr(reference[0]);
}
};
return baseReader.runner.call(readRunnable);
}
@Override
public String[] readArray(final String objectPath)
{
return readArray(objectPath, true);
}
@Override
public String[] readArray(final String objectPath, final boolean resolveName)
{
assert objectPath != null;
baseReader.checkOpen();
final ICallableWithCleanUp<String[]> readCallable = 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);
final long[] references;
if (baseReader.h5.getClassType(dataTypeId) == H5T_REFERENCE)
{
final DataSpaceParameters spaceParams =
baseReader.getSpaceParameters(dataSetId, registry);
checkRank1(spaceParams.dimensions, objectPath);
references = new long[spaceParams.blockSize];
baseReader.h5.readDataSet(dataSetId, dataTypeId, spaceParams.memorySpaceId,
spaceParams.dataSpaceId, references);
} else if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY
&& baseReader.h5.getClassType(baseReader.h5.getBaseDataType(dataTypeId,
registry)) == H5T_REFERENCE)
{
final long spaceId = baseReader.h5.createScalarDataSpace();
final int[] dimensions = baseReader.h5.getArrayDimensions(dataTypeId);
checkRank1(dimensions, objectPath);
final int len = dimensions[0];
references = new long[len];
final long memoryTypeId =
baseReader.h5.createArrayType(H5T_STD_REF_OBJ, len, registry);
baseReader.h5.readDataSet(dataSetId, memoryTypeId, spaceId, spaceId,
references);
} else
{
throw new HDF5JavaException("Dataset " + objectPath
+ " is not a reference.");
}
return resolveName ? baseReader.h5.getReferencedObjectNames(baseReader.fileId,
references) : refToStr(references);
}
};
return baseReader.runner.call(readCallable);
}
@Override
public String[] readArrayBlock(final String objectPath, final int blockSize,
final long blockNumber)
{
return readArrayBlockWithOffset(objectPath, blockSize, blockNumber
* blockSize, true);
}
@Override
public String[] readArrayBlock(final String objectPath, final int blockSize,
final long blockNumber, final boolean resolveName)
{
return readArrayBlockWithOffset(objectPath, blockSize, blockNumber
* blockSize, resolveName);
}
@Override
public String[] readArrayBlockWithOffset(final String objectPath,
final int blockSize, final long offset)
{
return readArrayBlockWithOffset(objectPath, blockSize, offset, true);
}
@Override
public String[] readArrayBlockWithOffset(final String objectPath,
final int blockSize, final long offset, final boolean resolveName)
{
assert objectPath != null;
baseReader.checkOpen();
final ICallableWithCleanUp<String[]> readCallable = new ICallableWithCleanUp<String[]>()
{
@Override
public String[] call(ICleanUpRegistry registry)
{
final long dataSetId =
baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry);
final DataSpaceParameters spaceParams =
baseReader.getSpaceParameters(dataSetId, offset, blockSize, registry);
final long[] references = new long[spaceParams.blockSize];
baseReader.h5.readDataSet(dataSetId, H5T_STD_REF_OBJ,
spaceParams.memorySpaceId, spaceParams.dataSpaceId, references);
return resolveName ? baseReader.h5.getReferencedObjectNames(baseReader.fileId,
references) : refToStr(references);
}
};
return baseReader.runner.call(readCallable);
}
@Override
public MDArray<String> readMDArray(final String objectPath)
{
return readMDArray(objectPath, true);
}
@Override
public MDArray<String> readMDArray(final String objectPath,
final boolean resolveName)
{
assert objectPath != null;
baseReader.checkOpen();
final ICallableWithCleanUp<MDArray<String>> readCallable =
new ICallableWithCleanUp<MDArray<String>>()
{
@Override
public MDArray<String> call(ICleanUpRegistry registry)
{
final long dataSetId =
baseReader.h5.openDataSet(baseReader.fileId, objectPath,
registry);
final long dataTypeId =
baseReader.h5.getDataTypeForDataSet(dataSetId, registry);
final long[] references;
final int[] dimensions;
if (baseReader.h5.getClassType(dataTypeId) == H5T_REFERENCE)
{
final DataSpaceParameters spaceParams =
baseReader.getSpaceParameters(dataSetId, registry);
dimensions = MDAbstractArray.toInt(spaceParams.dimensions);
references = new long[spaceParams.blockSize];
baseReader.h5.readDataSet(dataSetId, dataTypeId,
spaceParams.memorySpaceId, spaceParams.dataSpaceId,
references);
} else if (baseReader.h5.getClassType(dataTypeId) == HDF5Constants.H5T_ARRAY
&& baseReader.h5.getClassType(baseReader.h5.getBaseDataType(
dataTypeId, registry)) == H5T_REFERENCE)
{
final long spaceId = baseReader.h5.createScalarDataSpace();
dimensions = baseReader.h5.getArrayDimensions(dataTypeId);
final int len = MDAbstractArray.getLength(dimensions);
references = new long[len];
final long memoryTypeId =
baseReader.h5.createArrayType(H5T_STD_REF_OBJ, len,
registry);
baseReader.h5.readDataSet(dataSetId, memoryTypeId, spaceId,
spaceId, references);
} else
{
throw new HDF5JavaException("Dataset " + objectPath
+ " is not a reference.");
}
final String[] referencedObjectNames =
resolveName ? baseReader.h5.getReferencedObjectNames(
baseReader.fileId, references) : refToStr(references);
return new MDArray<String>(referencedObjectNames, dimensions);
}
};
return baseReader.runner.call(readCallable);
}
@Override
public MDArray<String> readMDArrayBlock(final String objectPath,
final int[] blockDimensions, final long[] blockNumber)
{
return readMDArrayBlock(objectPath, blockDimensions, blockNumber, true);
}
@Override
public MDArray<String> readMDArrayBlock(final String objectPath,
final int[] blockDimensions, final long[] blockNumber, final boolean resolveName)
{
final long[] offset = new long[blockDimensions.length];
for (int i = 0; i < offset.length; ++i)
{
offset[i] = blockNumber[i] * blockDimensions[i];
}
return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset,
resolveName);
}
@Override
public MDArray<String> readMDArrayBlockWithOffset(final String objectPath,
final int[] blockDimensions, final long[] offset)
{
return readMDArrayBlockWithOffset(objectPath, blockDimensions, offset, true);
}
@Override
public MDArray<String> readMDArrayBlockWithOffset(final String objectPath,
final int[] blockDimensions, final long[] offset, final boolean resolveName)
{
assert objectPath != null;
assert blockDimensions != null;
assert offset != null;
baseReader.checkOpen();
final ICallableWithCleanUp<MDArray<String>> readCallable =
new ICallableWithCleanUp<MDArray<String>>()
{
@Override
public MDArray<String> call(ICleanUpRegistry registry)
{
final long dataSetId =
baseReader.h5.openDataSet(baseReader.fileId, objectPath,
registry);
final DataSpaceParameters spaceParams =
baseReader.getSpaceParameters(dataSetId, offset,
blockDimensions, registry);
final long[] referencesBlock = new long[spaceParams.blockSize];
baseReader.h5.readDataSet(dataSetId, H5T_STD_REF_OBJ,
spaceParams.memorySpaceId, spaceParams.dataSpaceId,
referencesBlock);
final String[] referencedObjectNamesBlock =
resolveName ? baseReader.h5.getReferencedObjectNames(
baseReader.fileId, referencesBlock)
: refToStr(referencesBlock);
return new MDArray<String>(referencedObjectNamesBlock, blockDimensions);
}
};
return baseReader.runner.call(readCallable);
}
@Override
public Iterable<HDF5DataBlock<String[]>> getArrayNaturalBlocks(
final String dataSetPath) throws HDF5JavaException
{
return getArrayNaturalBlocks(dataSetPath, true);
}
@Override
public Iterable<HDF5DataBlock<String[]>> getArrayNaturalBlocks(
final String dataSetPath, final boolean resolveName) throws HDF5JavaException
{
baseReader.checkOpen();
final HDF5NaturalBlock1DParameters params =
new HDF5NaturalBlock1DParameters(baseReader.getDataSetInformation(dataSetPath));
return new Iterable<HDF5DataBlock<String[]>>()
{
@Override
public Iterator<HDF5DataBlock<String[]>> iterator()
{
return new Iterator<HDF5DataBlock<String[]>>()
{
final HDF5NaturalBlock1DParameters.HDF5NaturalBlock1DIndex index =
params.getNaturalBlockIndex();
@Override
public boolean hasNext()
{
return index.hasNext();
}
@Override
public HDF5DataBlock<String[]> next()
{
final long offset = index.computeOffsetAndSizeGetOffset();
final String[] referencesBlock =
readArrayBlockWithOffset(dataSetPath,
index.getBlockSize(), offset, resolveName);
return new HDF5DataBlock<String[]>(referencesBlock,
index.getAndIncIndex(), offset);
}
@Override
public void remove()
{
throw new UnsupportedOperationException();
}
};
}
};
}
@Override
public Iterable<HDF5MDDataBlock<MDArray<String>>> getMDArrayNaturalBlocks(
final String dataSetPath)
{
return getMDArrayNaturalBlocks(dataSetPath, true);
}
@Override
public Iterable<HDF5MDDataBlock<MDArray<String>>> getMDArrayNaturalBlocks(
final String dataSetPath, final boolean resolveName)
{
baseReader.checkOpen();
final HDF5NaturalBlockMDParameters params =
new HDF5NaturalBlockMDParameters(baseReader.getDataSetInformation(dataSetPath));
return new Iterable<HDF5MDDataBlock<MDArray<String>>>()
{
@Override
public Iterator<HDF5MDDataBlock<MDArray<String>>> iterator()
{
return new Iterator<HDF5MDDataBlock<MDArray<String>>>()
{
final HDF5NaturalBlockMDParameters.HDF5NaturalBlockMDIndex index =
params.getNaturalBlockIndex();
@Override
public boolean hasNext()
{
return index.hasNext();
}
@Override
public HDF5MDDataBlock<MDArray<String>> next()
{
final long[] offset = index.computeOffsetAndSizeGetOffsetClone();
final MDArray<String> data =
readMDArrayBlockWithOffset(dataSetPath,
index.getBlockSize(), offset, resolveName);
return new HDF5MDDataBlock<MDArray<String>>(data,
index.getIndexClone(), offset);
}
@Override
public void remove()
{
throw new UnsupportedOperationException();
}
};
}
};
}
}
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