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Blazegraph Modifications to the DSI utils. This are forked from version 1.10.0 under LGPLv2.1.
package it.unimi.dsi.compression;
/*
* DSI utilities
*
* Copyright (C) 2005-2009 Sebastiano Vigna
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by the Free
* Software Foundation; either version 2.1 of the License, or (at your option)
* any later version.
*
* This library is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
* for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
*/
import it.unimi.dsi.bits.BitVector;
import it.unimi.dsi.bits.LongArrayBitVector;
import java.io.Serializable;
import java.util.Arrays;
import cern.colt.Sorting;
import cern.colt.function.IntComparator;
/** An implementation of Huffman optimal prefix-free coding.
*
* A Huffman coder is built starting from an array of frequencies corresponding to each
* symbol. Frequency 0 symbols are allowed, but they will degrade the resulting code.
*
*
Instances of this class compute a canonical Huffman code
* (Eugene S. Schwartz and Bruce Kallick, “Generating a Canonical Prefix Encoding”, Commun. ACM 7(3), pages 166−169, 1964), which can
* by {@linkplain CanonicalFast64CodeWordDecoder quickly decoded using table lookups}.
* The construction uses the most efficient one-pass in-place codelength computation procedure
* described by Alistair Moffat and Jyrki Katajainen in “In-Place Calculation of Minimum-Redundancy Codes”,
* Algorithms and Data Structures, 4th International Workshop,
* number 955 in Lecture Notes in Computer Science, pages 393−402, Springer-Verlag, 1995.
*
*
We note by passing that this coded uses a {@link CanonicalFast64CodeWordDecoder}, which does not support codelengths above 64.
* However, since the worst case for codelengths is given by Fibonacci numbers, and frequencies are to be provided as integers,
* no codeword longer than the base-[(51/2 + 1)/2] logarithm of 51/2 · 231 (less than 47) will ever be generated.
*
*
Modifications
* -
* This class has been modified to define an alternative ctor which exposes the
* symbol[] in correlated order with the codeWord bitLength[] and the shortest
* code word in the generated canonical.
* -
* A method has been added to recreate the {@link PrefixCoder} from the
* shortest code word, the code word length[], and the symbol[].
*
*
* */
public class HuffmanCodec implements PrefixCodec, Serializable {
private static final boolean DEBUG = false;
private static final boolean ASSERTS = false;
private static final long serialVersionUID = 2L;
/** The number of symbols of this coder. */
public final int size;
/** The codewords for this coder. */
private final BitVector[] codeWord;
/** A cached singleton instance of the coder of this codec. */
private final Fast64CodeWordCoder coder;
/** A cached singleton instance of the decoder of this codec. */
private final CanonicalFast64CodeWordDecoder decoder;
/**
* Class encapsulates the data necessary to reconstruct a
* {@link CanonicalFast64CodeWordDecoder} or recreate the code.
*
* @author Bryan
* Thompson
* @version $Id: HuffmanCodec.java 2265 2009-10-26 12:51:06Z thompsonbry $
*/
public static class DecoderInputs {
private BitVector shortestCodeWord;
private int symbol[];
private int length[];
/**
* Ctor may be passed to {@link HuffmanCodec} to obtain the assigned
* length[] and symbol[] data and the shortest code word.
*/
public DecoderInputs() {
}
/**
* Ctor may be used to explicitly populate an instance with the caller's
* data.
*
* @param shortestCodeWord
* @param length
* @param symbol
*/
public DecoderInputs(final BitVector shortestCodeWord,
final int[] length, final int[] symbol) {
assert shortestCodeWord!=null;
assert length!=null;
assert symbol!=null;
assert length.length==symbol.length;
assert shortestCodeWord.size()==length[0];
this.shortestCodeWord = shortestCodeWord;
this.length = length;
this.symbol = symbol;
}
/**
* The shortest code word. Note that canonical huffman codes can be
* recreated from just length[0] and the shortest code word.
*/
public BitVector getShortestCodeWord() {
return shortestCodeWord;
}
/**
* Return the symbol[] in the permuted order used to construct the
* {@link CanonicalFast64CodeWordDecoder}. This information is
* transient.
*/
public int[] getSymbols() {
return symbol;
}
/**
* Return the codeWord bit lengths in the non-decreasing order used to
* construct the {@link CanonicalFast64CodeWordDecoder}. This information is
* transient.
*/
public int[] getLengths() {
return length;
}
}
/** Creates a new Huffman codec using the given vector of frequencies.
*
* @param frequency a vector of nonnnegative frequencies.
*/
public HuffmanCodec( final int[] frequency ) {
this(frequency, new DecoderInputs());
}
/**
* Creates a new Huffman codec using the given vector of frequencies.
*
* @param frequency
* a vector of non-negative frequencies.
* @param decoderInputs
* The inputs necessary to reconstruct a
* {@link CanonicalFast64CodeWordDecoder} will be set on this
* object.
*/
public HuffmanCodec( final int[] frequency, final DecoderInputs decoderInputs ) {
if(decoderInputs==null)
throw new IllegalArgumentException();
size = frequency.length;
if ( size == 0 || size == 1 ) {
codeWord = new BitVector[ size ];
if ( size == 1 ) codeWord[ 0 ] = LongArrayBitVector.getInstance();
coder = new Fast64CodeWordCoder( codeWord, new long[ size ] );
// Modified BBT 8/11/2009
// decoder = new CanonicalFast64CodeWordDecoder( new int[ size ], new int[ size ] );
decoderInputs.shortestCodeWord = LongArrayBitVector.getInstance().length( 0 );
decoderInputs.length = new int[size];
decoderInputs.symbol = new int[size];
decoder = new CanonicalFast64CodeWordDecoder( decoderInputs.length, decoderInputs.symbol );
return;
}
final long[] a = new long[ size ];
for( int i = size; i-- != 0; ) a[ i ] = frequency[ i ];
// Sort frequencies (this is the only n log n step).
Arrays.sort( a );
// The following lines are from Moffat & Katajainen sample code. Please refer to their paper.
// First pass, left to right, setting parent pointers.
a[ 0 ] += a[ 1 ];
int root = 0;
int leaf = 2;
for ( int next = 1; next < size - 1; next++ ) {
// Select first item for a pairing.
if ( leaf >= size || a[ root ] < a[ leaf ] ) {
a[ next ] = a[ root ];
a[ root++ ] = next;
}
else a[ next ] = a[ leaf++ ];
// Add on the second item.
if ( leaf >= size || ( root < next && a[ root ] < a[ leaf ] ) ) {
a[ next ] += a[ root ];
a[ root++ ] = next;
}
else a[ next ] += a[ leaf++ ];
}
// Second pass, right to left, setting internal depths.
a[ size - 2 ] = 0;
for ( int next = size - 3; next >= 0; next-- ) a[ next ] = a[ (int)a[ next ] ] + 1;
// Third pass, right to left, setting leaf depths.
int available = 1, used = 0, depth = 0;
root = size - 2;
int next = size - 1;
while ( available > 0 ) {
while ( root >= 0 && a[ root ] == depth ) {
used++;
root--;
}
while ( available > used ) {
a[ next-- ] = depth;
available--;
}
available = 2 * used;
depth++;
used = 0;
}
// Reverse the order of symbol lengths, and store them into an int array.
final int[] length = new int[ size ];
for( int i = size; i-- != 0; ) length[ i ] = (int)a[ size - 1 - i ];
// Sort symbols indices by decreasing frequencies (so symbols correspond to lengths).
final int[] symbol = new int[ size ];
for( int i = size; i-- != 0; ) symbol[ i ] = i;
Sorting.quickSort( symbol, 0, size, new IntComparator() {
public int compare( int x, int y ) {
return frequency[ y ] - frequency[ x ];
}
});
// Assign codewords (just for the coder--the decoder needs just the lengths).
int s = symbol[ 0 ];
int l = length[ 0 ];
long value = 0;
BitVector v;
codeWord = new BitVector[ size ];
final long[] longCodeWord = new long[ size ];
codeWord[ s ] = LongArrayBitVector.getInstance().length( l );
for( int i = 1; i < size; i++ ) {
s = symbol[ i ];
if ( length[ i ] == l ) value++;
else {
value++;
value <<= length[ i ] - l;
if ( ASSERTS ) assert length[ i ] > l;
l = length[ i ];
}
v = LongArrayBitVector.getInstance().length( l );
for( int j = l; j-- != 0; ) if ( ( 1L << j & value ) != 0 ) v.set( l - 1 - j );
codeWord[ s ] = v;
longCodeWord[ s ] = value;
}
coder = new Fast64CodeWordCoder( codeWord, longCodeWord );
// Modified BBT 8/11/2009
// decoder = new CanonicalFast64CodeWordDecoder( length, symbol );
decoderInputs.shortestCodeWord = codeWord[symbol[0]];
decoderInputs.length = length;
decoderInputs.symbol = symbol;
assert decoderInputs.shortestCodeWord.size() == length[0] : "shortestCodeWord="
+ decoderInputs.shortestCodeWord
+ ", but length[0]="
+ length[0];
decoder = new CanonicalFast64CodeWordDecoder( decoderInputs.length, decoderInputs.symbol);
if ( DEBUG ) {
final BitVector[] codeWord = codeWords();
System.err.println( "Codes: " );
for( int i = 0; i < size; i++ )
System.err.println( i + " (" + codeWord[ i ].size() + " bits): " + codeWord[ i ] );
long totFreq = 0;
for( int i = size; i-- != 0; ) totFreq += frequency[ i ];
long totBits = 0;
for( int i = size; i-- != 0; ) totBits += frequency[ i ] * codeWord[ i ].size();
System.err.println( "Compression: " + totBits + " / " + totFreq * Character.SIZE + " = " + (double)totBits/(totFreq * Character.SIZE) );
}
}
public CodeWordCoder coder() {
return coder;
}
public Decoder decoder() {
return decoder;
}
public int size() {
return size;
}
public BitVector[] codeWords() {
return coder.codeWords();
}
/**
* (Re-)constructs the canonical huffman code from the shortest code word,
* the non-decreasing bit lengths of each code word, and the permutation of
* the symbols corresponding to those bit lengths. This information is
* necessary and sufficient to reconstruct a canonical huffman code.
*
* @param decoderInputs
* This contains the necessary and sufficient information to
* recreate the {@link PrefixCoder}.
*
* @return A new {@link PrefixCoder} instance for the corresponding
* canonical huffman code.
*/
static public PrefixCoder newCoder(final DecoderInputs decoderInputs) {
return newCoder(decoderInputs.getShortestCodeWord(), decoderInputs
.getLengths(), decoderInputs.getSymbols());
}
/**
* (Re-)constructs the canonical huffman code from the shortest code word,
* the non-decreasing bit lengths of each code word, and the permutation of
* the symbols corresponding to those bit lengths. This information is
* necessary and sufficient to reconstruct a canonical huffman code.
*
* @param shortestCodeWord
* The code word with the shortest bit length.
* @param length
* The bit length of each code word in the non-decreasing order
* assigned when the code was generated. The length of this array
* is the #of symbols in the code.
* @param symbol
* The permutation of the symbols in the assigned when the
* canonical huffman code was generated. The length of this array
* is the #of symbols in the code.
*
* @return A new {@link PrefixCoder} instance for the corresponding
* canonical huffman code.
*
* @see DecoderInputs
*/
static public PrefixCoder newCoder(final BitVector shortestCodeWord,
final int[] length, final int[] symbol) {
if (shortestCodeWord == null)
throw new IllegalArgumentException();
if (shortestCodeWord.size() == 0)
throw new IllegalArgumentException();
if (length == null)
throw new IllegalArgumentException();
if (length.length == 0)
throw new IllegalArgumentException();
if (symbol == null)
throw new IllegalArgumentException();
if (symbol.length == 0)
throw new IllegalArgumentException();
final int size = length.length;
int s = symbol[ 0 ];
int l = length[ 0 ];
long value = 0;
BitVector v;
final BitVector[] codeWord = new BitVector[ size ];
final long[] longCodeWord = new long[ size ];
codeWord[ s ] = LongArrayBitVector.getInstance().length( l );
for( int i = 1; i < size; i++ ) {
s = symbol[ i ];
if ( length[ i ] == l ) value++;
else {
value++;
value <<= length[ i ] - l;
if ( ASSERTS ) assert length[ i ] > l;
l = length[ i ];
}
v = LongArrayBitVector.getInstance().length( l );
for( int j = l; j-- != 0; ) if ( ( 1L << j & value ) != 0 ) v.set( l - 1 - j );
codeWord[ s ] = v;
longCodeWord[ s ] = value;
}
return new Fast64CodeWordCoder(codeWord, longCodeWord);
}
}
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