/* * 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_NATIVE_B64; import static hdf.hdf5lib.HDF5Constants.H5T_NATIVE_UINT64; import java.util.BitSet; import hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException; import hdf.hdf5lib.exceptions.HDF5JavaException; import ch.systemsx.cisd.base.mdarray.MDLongArray; import ch.systemsx.cisd.hdf5.HDF5BaseReader.DataSpaceParameters; import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp; import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry; /** * Implementation of {@link IHDF5BooleanReader}. * * @author Bernd Rinn */ public class HDF5BooleanReader implements IHDF5BooleanReader { private final HDF5BaseReader baseReader; HDF5BooleanReader(HDF5BaseReader baseReader) { assert baseReader != null; this.baseReader = baseReader; } // ///////////////////// // Attributes // ///////////////////// @Override public boolean getAttr(final String objectPath, final String attributeName) throws HDF5JavaException { assert objectPath != null; assert attributeName != null; baseReader.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Boolean call(ICleanUpRegistry registry) { final long objectId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry); final long attributeId = baseReader.h5.openAttribute(objectId, attributeName, registry); final long nativeDataTypeId = baseReader.h5.getNativeDataTypeForAttribute(attributeId, registry); byte[] data = baseReader.h5 .readAttributeAsByteArray(attributeId, nativeDataTypeId, 1); final Boolean value = baseReader.h5.tryGetBooleanValue(nativeDataTypeId, data[0]); if (value == null) { throw new HDF5JavaException("Attribute " + attributeName + " of path " + objectPath + " needs to be a Boolean."); } return value; } }; return baseReader.runner.call(writeRunnable); } // ///////////////////// // Data Sets // ///////////////////// @Override public boolean read(final String objectPath) throws HDF5JavaException { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp writeRunnable = new ICallableWithCleanUp() { @Override public Boolean call(ICleanUpRegistry registry) { final long dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final long nativeDataTypeId = baseReader.h5.getNativeDataTypeForDataSet(dataSetId, registry); final byte[] data = new byte[1]; baseReader.h5.readDataSet(dataSetId, nativeDataTypeId, data); final Boolean value = baseReader.h5.tryGetBooleanValue(nativeDataTypeId, data[0]); if (value == null) { throw new HDF5JavaException(objectPath + " needs to be a Boolean."); } return value; } }; return baseReader.runner.call(writeRunnable); } @Override public BitSet readBitField(final String objectPath) throws HDF5DatatypeInterfaceException { baseReader.checkOpen(); return BitSetConversionUtils.fromStorageForm(readBitFieldStorageForm(objectPath)); } private long[] readBitFieldStorageForm(final String objectPath) { assert objectPath != null; final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final long dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); final long[] data = new long[spaceParams.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_B64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public BitSet readBitFieldBlock(String objectPath, int blockSize, long blockNumber) { return readBitFieldBlockWithOffset(objectPath, blockSize, blockSize * blockNumber); } private long[] readBitFieldStorageForm(final String objectPath, final int blockSize, final long offset, final boolean nullWhenOutside) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public long[] call(ICleanUpRegistry registry) { final long dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParamsOrNull = baseReader.tryGetSpaceParameters(dataSetId, offset, blockSize, nullWhenOutside, registry); if (spaceParamsOrNull == null) { return null; } final long[] data = new long[spaceParamsOrNull.blockSize]; baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_B64, spaceParamsOrNull.memorySpaceId, spaceParamsOrNull.dataSpaceId, data); return data; } }; return baseReader.runner.call(readCallable); } @Override public BitSet readBitFieldBlockWithOffset(String objectPath, int blockSize, long offset) { baseReader.checkOpen(); return BitSetConversionUtils.fromStorageForm(readBitFieldStorageForm(objectPath, blockSize, offset, false)); } @Override public boolean isBitSet(String objectPath, int bitIndex) { final int wordIndex = BitSetConversionUtils.getWordIndex(bitIndex); final long[] storageFormOrNull = readBitFieldStorageForm(objectPath, 1, wordIndex, true); // If the bitIndex is outside of the bit field, we return false if (storageFormOrNull == null) { return false; } final long word = storageFormOrNull[0]; return (word & BitSetConversionUtils.getBitMaskInWord(bitIndex)) != 0; } @Override public BitSet[] readBitFieldArray(String objectPath) { baseReader.checkOpen(); return BitSetConversionUtils.fromStorageForm2D(readBitFieldArrayStorageForm(objectPath)); } private MDLongArray readBitFieldArrayStorageForm(final String objectPath) { assert objectPath != null; final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final long dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final DataSpaceParameters spaceParams = baseReader.getSpaceParameters(dataSetId, registry); checkDimensions2D(spaceParams.dimensions); final long[] data = new long[spaceParams.blockSize]; if (baseReader.isScaledBitField(dataSetId, registry)) { baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); } else { baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_B64, spaceParams.memorySpaceId, spaceParams.dataSpaceId, data); } return new MDLongArray(data, spaceParams.dimensions); } }; return baseReader.runner.call(readCallable); } @Override public BitSet[] readBitFieldArrayBlockWithOffset(String objectPath, int blockSize, long offset) { baseReader.checkOpen(); return BitSetConversionUtils.fromStorageForm2D(readBitFieldBlockStorageForm2D(objectPath, blockSize, offset, true)); } private MDLongArray readBitFieldBlockStorageForm2D(final String objectPath, final int blockSize, final long offset, final boolean nullWhenOutside) { assert objectPath != null; baseReader.checkOpen(); final ICallableWithCleanUp readCallable = new ICallableWithCleanUp() { @Override public MDLongArray call(ICleanUpRegistry registry) { final long dataSetId = baseReader.h5.openDataSet(baseReader.fileId, objectPath, registry); final long[] dimensions = baseReader.h5.getDataDimensions(dataSetId, registry); checkDimensions2D(dimensions); final int numberOfWords = dimToInt(dimensions[0]); final int[] blockDimensions = new int[] { numberOfWords, blockSize }; final DataSpaceParameters spaceParamsOrNull = baseReader.tryGetSpaceParameters(dataSetId, new long[] { 0, offset }, blockDimensions, nullWhenOutside, registry); if (spaceParamsOrNull == null) { return null; } final long[] data = new long[spaceParamsOrNull.blockSize]; if (baseReader.isScaledBitField(dataSetId, registry)) { baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_UINT64, spaceParamsOrNull.memorySpaceId, spaceParamsOrNull.dataSpaceId, data); } else { baseReader.h5.readDataSet(dataSetId, H5T_NATIVE_B64, spaceParamsOrNull.memorySpaceId, spaceParamsOrNull.dataSpaceId, data); } return new MDLongArray(data, blockDimensions); } }; return baseReader.runner.call(readCallable); } private static void checkDimensions2D(final long[] dimensions) { if (dimensions.length != 2) { throw new HDF5JavaException( "Array is supposed to be of rank 2, but is of rank " + dimensions.length); } } static int dimToInt(long longNumber) { final int intNumber = (int) longNumber; if (intNumber != longNumber) { throw new HDF5JavaException("Dimension " + longNumber + " out of bounds."); } return intNumber; } @Override public BitSet[] readBitFieldArrayBlock(String objectPath, int blockSize, long blockNumber) { return readBitFieldArrayBlockWithOffset(objectPath, blockSize, blockNumber * blockSize); } }