org.openimaj.math.matrix.similarity

Class SimilarityMatrix

java.lang.Object

Jama.Matrix

org.openimaj.math.matrix.ReadWriteableMatrix

org.openimaj.math.matrix.similarity.SimilarityMatrix

All Implemented Interfaces:

Serializable, Cloneable, Readable, ReadableASCII, ReadableBinary, ReadWriteable, Writeable, WriteableASCII, WriteableBinary

public class SimilarityMatrix
extends ReadWriteableMatrix
implements ReadWriteable

A similarity matrix is a square matrix with an associated index. It can be used to store all the similarities across a set of objects.

Author:

Jonathon Hare (jsh2@ecs.soton.ac.uk)

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected String[]	index

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SimilarityMatrix() Construct an empty similarity matrix.
	SimilarityMatrix(int size) Construct a similarity matrix with the given size and allocate the index accordingly.
	SimilarityMatrix(String[] index) Construct a similarity matrix with the given index and set the matrix size based on the index length.
	SimilarityMatrix(String[] index, double[][] data) Construct a similarity matrix based on the given index and matrix data.
	SimilarityMatrix(String[] index, Jama.Matrix data) Construct a similarity matrix based on the given index and matrix.

Method Summary

Modifier and Type	Method and Description
String	asciiHeader() Header for ascii input.
byte[]	binaryHeader() Header for binary input.
SimilarityMatrix	clone()
SimilarityMatrix	copy()
String[]	getIndex() Get the index
String	getIndexValue(int i) Get a value from the index
int	indexOf(String value) Get the offset in the index for a given value
SimilarityMatrix	process(SimilarityMatrixProcessor proc) Process a copy of this similarity matrix with the given processor and return the copy.
SimilarityMatrix	processInplace(SimilarityMatrixProcessor proc) Process this matrix with the given processor.
void	readASCII(Scanner in) Read internal state from in.
void	readBinary(DataInput in) Read internal state from in.
void	setIndexValue(int i, String value) Set the value of the index at a given offset
String	toString()
org.jgrapht.UndirectedGraph<String,org.jgrapht.graph.DefaultEdge>	toUndirectedUnweightedGraph(double threshold) Convert the similarity matrix to an unweighted, undirected graph representation.
void	writeASCII(PrintWriter out) Write the content of this as ascii to out.
void	writeBinary(DataOutput out) Write the content of this as binary to out.

Methods inherited from class org.openimaj.math.matrix.ReadWriteableMatrix

setData

Methods inherited from class Jama.Matrix

arrayLeftDivide, arrayLeftDivideEquals, arrayRightDivide, arrayRightDivideEquals, arrayTimes, arrayTimesEquals, chol, cond, constructWithCopy, det, eig, get, getArray, getArrayCopy, getColumnDimension, getColumnPackedCopy, getMatrix, getMatrix, getMatrix, getMatrix, getRowDimension, getRowPackedCopy, identity, inverse, lu, minus, minusEquals, norm1, norm2, normF, normInf, plus, plusEquals, print, print, print, print, qr, random, rank, read, set, setMatrix, setMatrix, setMatrix, setMatrix, solve, solveTranspose, svd, times, times, timesEquals, trace, transpose, uminus

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

index

protected String[] index

Constructor Detail

SimilarityMatrix

protected SimilarityMatrix()

Construct an empty similarity matrix. Only for IOUtils use.

SimilarityMatrix

public SimilarityMatrix(int size)

Construct a similarity matrix with the given size and allocate the index accordingly.

Parameters:

size - the size of the matrix

SimilarityMatrix

public SimilarityMatrix(String[] index)

Construct a similarity matrix with the given index and set the matrix size based on the index length.

Parameters:

index - the index.

SimilarityMatrix

public SimilarityMatrix(String[] index,
                        Jama.Matrix data)

Construct a similarity matrix based on the given index and matrix. The matrix must be square and its dimensions must be the same as the index length.

Parameters:

index - the index

data - the matrix

SimilarityMatrix

public SimilarityMatrix(String[] index,
                        double[][] data)

Construct a similarity matrix based on the given index and matrix data. The matrix data must be square and its dimensions must be the same as the index length.

Parameters:

index - the index

data - the matrix data

Method Detail

indexOf

public int indexOf(String value)

Get the offset in the index for a given value

Parameters:

value - the value

Returns:

the index

setIndexValue

public void setIndexValue(int i,
                          String value)

Set the value of the index at a given offset

Parameters:

i - the offset

value - the value

getIndexValue

public String getIndexValue(int i)

Get a value from the index

Parameters:

i - the offset into the index

Returns:

the value

getIndex

public String[] getIndex()

Get the index

Returns:

the index

readASCII

public void readASCII(Scanner in)
               throws IOException

Description copied from interface: ReadableASCII

Read internal state from in.

Specified by:

readASCII in interface ReadableASCII

Overrides:

readASCII in class ReadWriteableMatrix

Parameters:

in - source to read from.

Throws:

IOException - an error reading input

asciiHeader

public String asciiHeader()

Description copied from interface: ReadableASCII

Header for ascii input. Will be automatically read by IOUtils when using readASCII().

Specified by:

asciiHeader in interface ReadableASCII

Specified by:

asciiHeader in interface WriteableASCII

Overrides:

asciiHeader in class ReadWriteableMatrix

Returns:

header

readBinary

public void readBinary(DataInput in)
                throws IOException

Description copied from interface: ReadableBinary

Read internal state from in.

Specified by:

readBinary in interface ReadableBinary

Overrides:

readBinary in class ReadWriteableMatrix

Parameters:

in - source to read from.

Throws:

IOException - an error reading input

binaryHeader

public byte[] binaryHeader()

Description copied from interface: ReadableBinary

Header for binary input. Will be automatically read by IOUtils when using readBinary().

Specified by:

binaryHeader in interface ReadableBinary

Specified by:

binaryHeader in interface WriteableBinary

Overrides:

binaryHeader in class ReadWriteableMatrix

Returns:

header

writeASCII

public void writeASCII(PrintWriter out)
                throws IOException

Description copied from interface: WriteableASCII

Write the content of this as ascii to out.

Specified by:

writeASCII in interface WriteableASCII

Overrides:

writeASCII in class ReadWriteableMatrix

Parameters:

out - sink to write to

Throws:

IOException - an error writing to out

writeBinary

public void writeBinary(DataOutput out)
                 throws IOException

Description copied from interface: WriteableBinary

Write the content of this as binary to out.

Specified by:

writeBinary in interface WriteableBinary

Overrides:

writeBinary in class ReadWriteableMatrix

Parameters:

out - sink to write to

Throws:

IOException - an error writing to out

toUndirectedUnweightedGraph

public org.jgrapht.UndirectedGraph<String,org.jgrapht.graph.DefaultEdge> toUndirectedUnweightedGraph(double threshold)

Convert the similarity matrix to an unweighted, undirected graph representation. A threshold is used to determine if edges should be created. If the value at [r][c] is bigger than the threshold, then an edge will be created between the vertices represented by index[r] and index[c].

Parameters:

threshold - the threshold

Returns:

the graph

copy

public SimilarityMatrix copy()

Overrides:

copy in class Jama.Matrix

clone

public SimilarityMatrix clone()

Overrides:

clone in class Jama.Matrix

process

public SimilarityMatrix process(SimilarityMatrixProcessor proc)

Process a copy of this similarity matrix with the given processor and return the copy.

Parameters:

proc - the processor

Returns:

a processed copy of this matrix

processInplace

public SimilarityMatrix processInplace(SimilarityMatrixProcessor proc)

Process this matrix with the given processor.

Parameters:

proc - the processor

Returns:

this.

toString

public String toString()

Overrides:

toString in class Object