gov.sandia.cognition.math.matrix.mtj.SparseVector Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of cognitive-foundry Show documentation
Show all versions of cognitive-foundry Show documentation
A single jar with all the Cognitive Foundry components.
/*
* File: SparseVector.java
* Authors: Kevin R. Dixon
* Company: Sandia National Laboratories
* Project: Cognitive Foundry
*
* Copyright February 21, 2006, Sandia Corporation. Under the terms of Contract
* DE-AC04-94AL85000, there is a non-exclusive license for use of this work by
* or on behalf of the U.S. Government. Export of this program may require a
* license from the United States Government. See CopyrightHistory.txt for
* complete details.
*
*/
package gov.sandia.cognition.math.matrix.mtj;
import gov.sandia.cognition.annotation.CodeReview;
import gov.sandia.cognition.math.matrix.SparseVectorFactory;
import gov.sandia.cognition.math.UnivariateScalarFunction;
import gov.sandia.cognition.math.matrix.Vector;
import gov.sandia.cognition.math.matrix.VectorEntry;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
/**
* A vector that only stores the nonzero elements, relies on MTJ's
* SparseVector. It has fast traversal by skipping nonzero elements but has slow
* indexing.
*
* @author Kevin R. Dixon
* @since 1.0
*/
@CodeReview(
reviewer="Justin Basilico",
date="2006-07-27",
changesNeeded=false,
comments="Looks good."
)
public class SparseVector
extends AbstractMTJVector
{
/**
* Creates a new instance of SparseVector with no initial size.
*
* @param numDimensions Maximum number of entries in the SparseVector.
*/
protected SparseVector(
final int numDimensions)
{
this(numDimensions, 0);
}
/**
* Creates a new instance of SparseVector with a specified initial size.
*
* @param numDimensions Maximum number of entries in the SparseVector.
* @param initialNonZeros Initial size of the SparseVector.
*/
protected SparseVector(
final int numDimensions,
final int initialNonZeros)
{
this(new no.uib.cipr.matrix.sparse.SparseVector(
numDimensions, initialNonZeros));
}
/**
* Creates a new copy of SparseVector.
*
* @param internalVector Internal MTJ-based vector to set into this.
*/
protected SparseVector(
final no.uib.cipr.matrix.sparse.SparseVector internalVector)
{
super(internalVector);
}
/**
* Creates a new copy of SparseVector.
*
* @param vector Vector to copy into this, will not be modified.
*/
protected SparseVector(
final Vector vector)
{
this(vector.getDimensionality());
for ( VectorEntry e : vector )
{
double value = e.getValue();
if ( value != 0.0 )
{
this.setElement(e.getIndex(), value);
}
}
}
@Override
public int getEntryCount()
{
return this.getInternalVector().getUsed();
}
/**
* Gets the number of elements used inside the sparse vector, equals the
* allocation size of the vector.
*
* @return The number of nonzero elements in the SparseVector.
*/
@Deprecated
public int getNumElementsUsed()
{
return this.getInternalVector().getUsed();
}
@Override
public void setElement(
final int index,
final double value)
{
// Only set a value in a SparseVector if it's different than what's
// in there already!
// (This is to prevent us from adding zeros into the SparseVector
// unnecessarily)
double existing = this.getElement( index );
if( existing != value )
{
super.setElement( index, value );
}
}
@Override
protected no.uib.cipr.matrix.sparse.SparseVector getInternalVector()
{
return (no.uib.cipr.matrix.sparse.SparseVector)
super.getInternalVector();
}
@Override
protected void setInternalVector(
final no.uib.cipr.matrix.Vector internalVector)
{
// Force it to be sparse.
this.setInternalVector((no.uib.cipr.matrix.sparse.SparseVector) internalVector);
}
/**
* Setter for the internal MTJ vector.
*
* @param internalVector Internal MTJ-based vector.
*/
protected void setInternalVector(
final no.uib.cipr.matrix.sparse.SparseVector internalVector)
{
super.setInternalVector(internalVector);
}
@Override
public double euclideanDistanceSquared(
final Vector other )
{
return this.minus( other ).norm2Squared();
}
@Override
public SparseRowMatrix outerProduct(
final AbstractMTJVector other)
{
int numRows = this.getDimensionality();
int numColumns = other.getDimensionality();
SparseRowMatrix result = new SparseRowMatrix(numRows, numColumns);
for ( VectorEntry e : this )
{
int i = e.getIndex();
for ( VectorEntry o : other )
{
int j = o.getIndex();
result.setElement(i, j, e.getValue() * o.getValue());
}
}
return result;
}
/**
* Prints the SparseVector in "Index: Value" format.
*
* @return String containing the representation of the SparseVector
*/
@Override
public String toString()
{
final StringBuffer result = new StringBuffer();
for ( VectorEntry e : this )
{
result.append("(" + e.getIndex() + "): " + e.getValue() + "\n");
}
return result.toString();
}
/**
* Compacts the SparseVector, getting rid of any zero'ed elements.
*/
public void compact()
{
this.getInternalVector().compact();
}
@Override
public SparseVector stack(
final Vector other)
{
int d1 = this.getDimensionality();
int d2 = other.getDimensionality();
SparseVector stacked = new SparseVector(d1 + d2);
for ( VectorEntry e : this )
{
stacked.setElement(e.getIndex(), e.getValue());
}
for ( VectorEntry e : other )
{
stacked.setElement(d1 + e.getIndex(), e.getValue());
}
return stacked;
}
@Override
public void transformNonZerosEquals(
final UnivariateScalarFunction function)
{
final no.uib.cipr.matrix.sparse.SparseVector internal = this.getInternalVector();
final double[] values = internal.getData();
final int used = internal.getUsed();
for (int i = 0; i < used; i++)
{
final double value = values[i];
if (value != 0.0)
{
values[i] = function.evaluate(value);
}
}
}
@Override
public void transformNonZerosEquals(
final IndexValueTransform function)
{
final no.uib.cipr.matrix.sparse.SparseVector internal = this.getInternalVector();
final int[] indices = internal.getRawIndex();
final double[] values = internal.getData();
final int used = internal.getUsed();
for (int i = 0; i < used; i++)
{
final double value = values[i];
if (value != 0.0)
{
values[i] = function.transform(indices[i], value);
}
}
}
@Override
public void forEachElement(
final IndexValueConsumer consumer)
{
// This is an optimized version of the method so that it doesn't end
// up doing a d * log(nnz) cost to iterate, even though it is a dense
// method.
final no.uib.cipr.matrix.sparse.SparseVector internal =
this.getInternalVector();
final int[] indices = internal.getRawIndex();
final double[] values = internal.getData();
final int used = internal.getUsed();
final int dimensionality = internal.size();
int i = 0;
int index = 0;
while (i < used && index < dimensionality)
{
final double value;
if (index < indices[i])
{
// Index is for a missing (zero) value.
value = 0.0;
}
else
{
// Get the value at the sparse index.
value = values[i];
i++;
}
consumer.consume(index, value);
index++;
}
// Passed the last used element fill in the rest in zeros.
while (index < dimensionality)
{
consumer.consume(index, 0.0);
index++;
}
}
@Override
public void forEachEntry(
final IndexValueConsumer consumer)
{
final no.uib.cipr.matrix.sparse.SparseVector internal = this.getInternalVector();
final int[] indices = internal.getRawIndex();
final double[] values = internal.getData();
final int used = internal.getUsed();
for (int i = 0; i < used; i++)
{
consumer.consume(indices[i], values[i]);
}
}
@Override
public void forEachNonZero(
final IndexValueConsumer consumer)
{
final no.uib.cipr.matrix.sparse.SparseVector internal = this.getInternalVector();
final int[] indices = internal.getRawIndex();
final double[] values = internal.getData();
final int used = internal.getUsed();
for (int i = 0; i < used; i++)
{
final double value = values[i];
if (value != 0.0)
{
consumer.consume(indices[i], value);
}
}
}
@Override
public boolean isSparse()
{
return true;
}
@Override
public double sum()
{
final double[] values = this.getInternalVector().getRawData();
double result = 0.0;
for (final double value : values)
{
result += value;
}
return result;
}
@Override
public double getMinValue()
{
double min = this.getEntryCount() < this.getDimensionality() ? 0.0 :
Double.POSITIVE_INFINITY;
for (final double value : this.getInternalVector().getRawData())
{
if (value < min)
{
min = value;
}
}
return min;
}
@Override
public double getMaxValue()
{
double max = this.getEntryCount() < this.getDimensionality() ? 0.0 :
Double.NEGATIVE_INFINITY;
for (final double value : this.getInternalVector().getRawData())
{
if (value > max)
{
max = value;
}
}
return max;
}
@Override
public int countNonZeros()
{
int result = 0;
for (final double value : this.getInternalVector().getRawData())
{
if (value != 0.0)
{
result++;
}
}
return result;
}
/**
* This method provides custom serialization for the class since the MTJ
* class does not implement Serializable.
*
* @param out The ObjectOutputStream to write this object to.
* @throws java.io.IOException If there is an error with the stream.
*/
private void writeObject(
ObjectOutputStream out)
throws IOException
{
// First compact the SparseVector
this.compact();
// Do the default stuff.
out.defaultWriteObject();
// Get all the data to write.
int dimensionality = this.getDimensionality();
int[] index = this.getInternalVector().getIndex();
double[] data = this.getInternalVector().getData();
// Manually serialize the super class.
out.writeObject( dimensionality );
out.writeObject( index );
out.writeObject( data );
}
@Override
public SparseVectorFactory getVectorFactory()
{
return SparseVectorFactoryMTJ.INSTANCE;
}
/**
* This method provides custom deserialization for the class since the MTJ
* class does not implement Serializable.
*
* @param in The ObjectInputStream to read the object from.
* @throws java.io.IOException If there is an error reading the object.
* @throws java.lang.ClassNotFoundException If a class cannot be found.
*/
private void readObject(
ObjectInputStream in)
throws IOException, ClassNotFoundException
{
// First do the default stuff.
in.defaultReadObject();
// Next read in the data.
int dimensionality = (Integer) in.readObject();
int[] index = (int[]) in.readObject();
double[] data = (double[]) in.readObject();
// Set the internal vector.
boolean deepCopy = false;
this.setInternalVector(
new no.uib.cipr.matrix.sparse.SparseVector(
dimensionality, index, data, deepCopy));
this.compact();
}
@Override
public SparseVector subVector(
final int minIndex,
final int maxIndex)
{
int M = maxIndex - minIndex + 1;
SparseVector subvector = new SparseVector( M );
for( int i = 0; i < M; i++ )
{
double value = this.getElement(i + minIndex);
if( value != 0.0 )
{
subvector.setElement( i, value );
}
}
return subvector;
}
}