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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.util.BitSet;
//import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.base.mdarray.MDLongArray;
import hdf.hdf5lib.exceptions.HDF5JavaException;
/**
* Methods for converting {@link BitSet}s to a storage form suitable for storing in an HDF5 file.
* <p>
* <i>This is an internal API that should not be expected to be stable between releases!</i>
*
* @author Bernd Rinn
*/
public final class BitSetConversionUtils
{
private final static int ADDRESS_BITS_PER_WORD = 6;
private final static int BITS_PER_WORD = 1 << ADDRESS_BITS_PER_WORD;
private final static int BIT_INDEX_MASK = BITS_PER_WORD - 1;
public static BitSet fromStorageForm(final long[] serializedWordArray, int start, int length)
{
final BitSet result = new BitSet();
for (int wordIndex = 0; wordIndex < length; ++wordIndex)
{
final long word = serializedWordArray[start + wordIndex];
for (int bitInWord = 0; bitInWord < BITS_PER_WORD; ++bitInWord)
{
if ((word & 1L << bitInWord) != 0)
{
result.set(wordIndex << ADDRESS_BITS_PER_WORD | bitInWord);
}
}
}
return result;
}
public static BitSet fromStorageForm(final long[] serializedWordArray)
{
return fromStorageForm(serializedWordArray, 0, serializedWordArray.length);
}
public static BitSet[] fromStorageForm2D(final MDLongArray serializedWordArray)
{
if (serializedWordArray.rank() != 2)
{
throw new HDF5JavaException("Array is supposed to be of rank 2, but is of rank "
+ serializedWordArray.rank());
}
final int dimX = serializedWordArray.dimensions()[0];
final int dimY = serializedWordArray.dimensions()[1];
final BitSet[] result = new BitSet[dimY];
for (int i = 0; i < result.length; ++i)
{
result[i] = fromStorageForm(serializedWordArray.getAsFlatArray(), i * dimX, dimX);
}
return result;
}
public static long[] toStorageForm(final BitSet data)
{
final long[] words = new long[data.size() >> ADDRESS_BITS_PER_WORD];
for (int bitIndex = data.nextSetBit(0); bitIndex >= 0; bitIndex =
data.nextSetBit(bitIndex + 1))
{
final int wordIndex = getWordIndex(bitIndex);
words[wordIndex] |= getBitMaskInWord(bitIndex);
}
return words;
}
public static long[] toStorageForm(final BitSet data, final int numberOfWords)
{
final long[] words = new long[numberOfWords];
for (int bitIndex = data.nextSetBit(0); bitIndex >= 0; bitIndex =
data.nextSetBit(bitIndex + 1))
{
final int wordIndex = getWordIndex(bitIndex);
if (wordIndex >= words.length)
{
break;
}
words[wordIndex] |= getBitMaskInWord(bitIndex);
}
return words;
}
public static long[] toStorageForm(final BitSet[] data, int numberOfWords)
{
final long[] result = new long[data.length * numberOfWords];
int idx = 0;
for (BitSet bs : data)
{
System.arraycopy(toStorageForm(bs, numberOfWords), 0, result, idx, numberOfWords);
idx += numberOfWords;
}
return result;
}
/**
* Given a bit index return the word index containing it.
*/
public static int getWordIndex(final int bitIndex)
{
return bitIndex >> ADDRESS_BITS_PER_WORD;
}
/**
* Given a bit index, return a unit that masks that bit in its unit.
*/
public static long getBitMaskInWord(final int bitIndex)
{
return 1L << (bitIndex & BIT_INDEX_MASK);
}
static int getMaxLength(BitSet[] data)
{
int length = 0;
for (BitSet bs : data)
{
length = Math.max(length, bs.length());
}
return length;
}
}
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