/*
* File: DiagonalMatrixMTJ.java
* Authors: Kevin R. Dixon
* Company: Sandia National Laboratories
* Project: Cognitive Foundry
*
* Copyright Sep 19, 2008, 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.PublicationReference;
import gov.sandia.cognition.annotation.PublicationType;
import gov.sandia.cognition.math.ComplexNumber;
import gov.sandia.cognition.math.matrix.DiagonalMatrix;
import gov.sandia.cognition.math.matrix.Matrix;
import gov.sandia.cognition.math.matrix.MatrixFactory;
import gov.sandia.cognition.math.matrix.Vector;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.text.NumberFormat;
/**
* A diagonal matrix that wraps MTJ's BandMatrix class.
* @author Kevin R. Dixon
* @since 2.1
*/
@PublicationReference(
author="Bjorn-Ove Heimsund",
title="Matrix Toolkits for Java BandMatrix",
type=PublicationType.WebPage,
year=2006,
url="http://ressim.berlios.de/doc/no/uib/cipr/matrix/BandMatrix.html",
notes="This class wraps the BandMatrix class from Heimsund's MTJ package"
)
public class DiagonalMatrixMTJ
extends AbstractMTJMatrix
implements DiagonalMatrix
{
/**
* Creates a new instance of DiagonalMatrixMTJ
* @param dim
* Dimensionality of the square diagonal matrix
*/
protected DiagonalMatrixMTJ(
int dim )
{
super( new no.uib.cipr.matrix.BandMatrix( dim, 0, 0 ) );
}
/**
* Copy Constructor
* @param other DiagonalMatrixMTJ to copy
*/
protected DiagonalMatrixMTJ(
DiagonalMatrixMTJ other )
{
super( other.getInternalMatrix().copy() );
}
/**
* Creates a new instance of DiagonalMatrixMTJ
* @param diagonal
* Array of elements to set the diagonal to
*/
protected DiagonalMatrixMTJ(
double[] diagonal )
{
this( diagonal.length );
double[] actual = this.getDiagonal();
System.arraycopy(diagonal, 0, actual, 0, diagonal.length);
}
public int getDimensionality()
{
return this.getNumRows();
}
@Override
public no.uib.cipr.matrix.BandMatrix getInternalMatrix()
{
return (no.uib.cipr.matrix.BandMatrix) super.getInternalMatrix();
}
@Override
protected void setInternalMatrix(
no.uib.cipr.matrix.Matrix internalMatrix )
{
super.setInternalMatrix( (no.uib.cipr.matrix.BandMatrix) internalMatrix );
}
@Override
public AbstractMTJMatrix times(
AbstractMTJMatrix matrix )
{
this.assertMultiplicationDimensions(matrix);
final int M = this.getNumRows();
final int N = matrix.getNumColumns();
DenseMatrix retval = DenseMatrixFactoryMTJ.INSTANCE.createMatrix( M, N );
double[] diagonal = this.getDiagonal();
// The diagonal elements scale each row
for( int i = 0; i < M; i++ )
{
final double di = diagonal[i];
if( di != 0.0 )
{
for( int j = 0; j < N; j++ )
{
double vij = matrix.getElement( i, j );
if( vij != 0.0 )
{
retval.setElement( i, j, di*vij );
}
}
}
}
return retval;
}
@Override
public DiagonalMatrixMTJ times(
DiagonalMatrix matrix)
{
DiagonalMatrixMTJ clone = (DiagonalMatrixMTJ) this.clone();
clone.timesEquals(matrix);
return clone;
}
@Override
public void timesEquals(
DiagonalMatrix matrix)
{
if( !this.checkSameDimensions(matrix) )
{
throw new IllegalArgumentException( "Matrix must be the same size as this" );
}
final int M = this.getDimensionality();
// The diagonal elements scale each row
for( int i = 0; i < M; i++ )
{
final double d1i = this.getElement(i);
final double d2j = matrix.getElement(i);
final double v = d1i * d2j;
this.setElement(i, v);
}
}
@Override
public AbstractMTJVector times(
AbstractMTJVector vector )
{
final int M = this.getDimensionality();
if( M != vector.getDimensionality() )
{
throw new IllegalArgumentException(
"Number of Columns != vector.getDimensionality()" );
}
double[] diagonal = this.getDiagonal();
double[] retval = new double[ diagonal.length ];
for( int i = 0; i < M; i++ )
{
final double v2 = diagonal[i];
if( v2 != 0.0 )
{
final double v1 = vector.getElement( i );
if( v1 != 0.0 )
{
retval[i] = v1*v2;
}
}
}
return DenseVectorFactoryMTJ.INSTANCE.copyArray( retval );
}
@Override
public DiagonalMatrixMTJ dotTimes(
Matrix matrix )
{
DiagonalMatrixMTJ clone = (DiagonalMatrixMTJ) this.clone();
clone.dotTimesEquals( matrix );
return clone;
}
@Override
public void dotTimesEquals(
AbstractMTJMatrix matrix )
{
this.assertSameDimensions( matrix );
int M = this.getDimensionality();
double[] diagonal = this.getDiagonal();
for( int i = 0; i < M; i++ )
{
diagonal[i] *= matrix.getElement( i, i );
}
}
@Override
public boolean isSquare()
{
return true;
}
@Override
public boolean isSymmetric()
{
return true;
}
@Override
public boolean isSymmetric(
double effectiveZero )
{
return true;
}
@Override
public ComplexNumber logDeterminant()
{
// The diagonal elements (for either LU or QR) will be REAL, but
// they may be negative. The logarithm of a negative number is
// the logarithm of the absolute value of the number, with an
// imaginary part of PI. The exponential is all that matters, so
// the log-determinant is equivalent, MODULO PI (3.14...), so
// we just toggle this sign bit.
double logsum = 0.0;
int sign = 1;
double[] diagonal = this.getDiagonal();
for (int i = 0; i < diagonal.length; i++)
{
double eigenvalue = diagonal[i];
if (eigenvalue < 0.0)
{
sign = -sign;
logsum += Math.log(-eigenvalue);
}
else
{
logsum += Math.log(eigenvalue);
}
}
return new ComplexNumber(logsum, (sign < 0) ? Math.PI : 0.0);
}
@Override
public double normFrobenius()
{
double[] diagonal = this.getDiagonal();
double sum = 0.0;
for( int i = 0; i < diagonal.length; i++ )
{
double v = diagonal[i];
sum += v*v;
}
return Math.sqrt( sum );
}
@Override
public int rank(
double effectiveZero )
{
int rank = 0;
double[] diagonal = this.getDiagonal();
int M = diagonal.length;
for( int i = 0; i < M; i++ )
{
if( Math.abs( diagonal[i] ) > effectiveZero )
{
rank++;
}
}
return rank;
}
@Override
public Vector solve(
AbstractMTJVector b )
{
DiagonalMatrixMTJ pinvA = this.pseudoInverse();
return pinvA.times( b );
}
@Override
public Matrix solve(
Matrix B )
{
DiagonalMatrixMTJ pinvA = this.pseudoInverse();
return pinvA.times( B );
}
@Override
public Vector solve(
Vector b )
{
DiagonalMatrixMTJ pinvA = this.pseudoInverse();
return pinvA.times( b );
}
public SparseMatrix getSubMatrix(
int minRow,
int maxRow,
int minColumn,
int maxColumn )
{
int numRows = maxRow - minRow + 1;
if (numRows <= 0)
{
throw new IllegalArgumentException( "minRow " + minRow +
" >= maxRow " + maxRow );
}
int numColumns = maxColumn - minColumn + 1;
if (numColumns <= 0)
{
throw new IllegalArgumentException( "minCol " + minColumn +
" >= maxCol " + maxColumn );
}
SparseMatrix submatrix =
SparseMatrixFactoryMTJ.INSTANCE.createMatrix( numRows, numColumns );
this.getSubMatrixInto(
minRow, maxRow, minColumn, maxColumn, submatrix );
return submatrix;
}
public DiagonalMatrixMTJ transpose()
{
return this;
}
/**
* Gets the data along the diagonal
* @return
* Diagonal data
*/
public double[] getDiagonal()
{
return this.getInternalMatrix().getData();
}
@Override
public DiagonalMatrixMTJ pseudoInverse()
{
return this.pseudoInverse( 0.0 );
}
public DiagonalMatrixMTJ pseudoInverse(
double effectiveZero )
{
double[] diagonal = this.getDiagonal();
int M = diagonal.length;
double[] retval = new double[ M ];
for( int i = 0; i < M; i++ )
{
double di = diagonal[i];
if( Math.abs( di ) <= effectiveZero )
{
retval[i] = 0.0;
}
else
{
retval[i] = 1.0 / di;
}
}
return new DiagonalMatrixMTJ( retval );
}
@Override
public DiagonalMatrixMTJ inverse()
{
return this.pseudoInverse();
}
@Override
public boolean isSparse()
{
return true;
}
@Override
public int getEntryCount()
{
return this.getInternalMatrix().getData().length;
}
public Vector getColumn(
int columnIndex )
{
int M = this.getDimensionality();
Vector column = SparseVectorFactoryMTJ.getDefault().createVector( M );
column.setElement( columnIndex, this.getElement( columnIndex, columnIndex ) );
return column;
}
public Vector getRow(
int rowIndex )
{
int N = this.getDimensionality();
Vector row = SparseVectorFactoryMTJ.getDefault().createVector( N );
row.setElement( rowIndex, this.getElement( rowIndex, rowIndex ) );
return row;
}
@Override
public double getElement(
int rowIndex,
int columnIndex )
{
if( rowIndex != columnIndex )
{
return 0.0;
}
else
{
return this.getElement( rowIndex );
}
}
@Override
public void setElement(
int rowIndex,
int columnIndex,
double value )
{
if( rowIndex != columnIndex )
{
if( value != 0.0 )
{
throw new IllegalArgumentException(
"Can only set diagonal elements in a DiagonalMatrix!" );
}
}
else
{
this.setElement( rowIndex, value );
}
}
public double getElement(
int index )
{
double[] diagonal = this.getDiagonal();
return diagonal[index];
}
public void setElement(
int index,
double value )
{
double[] diagonal = this.getDiagonal();
diagonal[index] = value;
}
@Override
public DenseVector convertToVector()
{
return DenseVectorFactoryMTJ.INSTANCE.copyArray( this.getDiagonal() );
}
@Override
public void convertFromVector(
Vector parameters )
{
if( this.getNumRows() != parameters.getDimensionality() )
{
throw new IllegalArgumentException(
"Wrong number of parameters!" );
}
double[] diagonal = this.getDiagonal();
for( int i = 0; i < diagonal.length; i++ )
{
diagonal[i] = parameters.getElement( i );
}
}
@Override
public String toString()
{
int M = this.getDimensionality();
StringBuilder retval = new StringBuilder( M * 10 );
retval.append( "(" + M + "x" + M + "), diagonal:" );
for( int i = 0; i < M; i++ )
{
retval.append( " " + this.getElement( i ) );
}
return retval.toString();
}
public String toString(
final NumberFormat format)
{
final int d = this.getDimensionality();
final StringBuilder result = new StringBuilder(d * 5);
result.append("(" + d + "x" + d + "), diagonal:");
for (int i = 0; i < d; i++)
{
result.append(" " + format.format(this.getElement(i)));
}
return result.toString();
}
/**
* Writes a DenseMatrix out to a serialized file
* @param out output stream to which the DenseMatrix will be written
* @throws java.io.IOException On bad write
*/
private void writeObject(
ObjectOutputStream out )
throws IOException
{
out.defaultWriteObject();
//manually serialize superclass
int numDiagonal = this.getDimensionality();
double[] diag = new double[numDiagonal];
for( int i = 0; i < numDiagonal; i++ )
{
diag[i] = this.getElement(i);
}
out.writeObject( diag );
}
/**
* Reads in a serialized class from the specified stream
* @param in stream from which to read the DenseMatrix
* @throws java.io.IOException On bad read
* @throws java.lang.ClassNotFoundException if next object isn't DenseMatrix
*/
private void readObject(
ObjectInputStream in )
throws IOException, ClassNotFoundException
{
in.defaultReadObject();
double[] diag = (double[]) in.readObject();
this.setInternalMatrix( new no.uib.cipr.matrix.BandMatrix( diag.length, 0, 0 ) );
System.arraycopy(diag, 0, this.getDiagonal(), 0, diag.length);
}
@Override
public MatrixFactory<?> getMatrixFactory()
{
return SparseMatrixFactoryMTJ.INSTANCE;
}
}