endrov.flowColocalization
Class ColocCoefficients

java.lang.Object
  endrov.flowColocalization.ColocCoefficients

public class ColocCoefficients
extends java.lang.Object

Colocalization calculation. Assumes two images X and Y. Add all pixels, then retrieve the statistics.

Pixels<=0 are considered background when calculating Manders coefficient

Definitions: http://support.svi.nl/wiki/ColocalizationTheory Interesting pseuodo-code for improved numerical instability exists at: http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient

Field Summary

int	n
double	sumX
double	sumXcoloc
double	sumXminusY2
double	sumXX
double	sumXY
double	sumY
double	sumYcoloc
double	sumYY

Constructor Summary

ColocCoefficients()

Method Summary

void	add(double[] arrX, double[] arrY) Compare several pixels
void	add(double x, double y) Compare one pixel
void	add(float[] arrX, float[] arrY) Compare several pixels
void	add(int[] arrX, int[] arrY) Compare several pixels
void	fromXML(org.jdom.Element e)
double	getCovXY() Covariance(X,Y)
double	getKX() kX=k1
double	getKY() kY=k2
double	getL2()
double	getMandersX() Mander coefficient X (=index 1)
double	getMandersY() Mander coefficient Y (=index 2)
double	getPearson() Pearsons coefficient
double	getPearsonMean0() Pearsons coefficient, assume mean=0
double	getVarX() Variance of X
double	getVarY() Variance of Y
static void	main(java.lang.String[] args)
void	toXML(org.jdom.Element e)

Methods inherited from class java.lang.Object

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

Field Detail

sumX

public double sumX

sumXX

public double sumXX

sumY

public double sumY

sumYY

public double sumYY

sumXY

public double sumXY

sumXminusY2

public double sumXminusY2

sumXcoloc

public double sumXcoloc

sumYcoloc

public double sumYcoloc

n

public int n

Constructor Detail

ColocCoefficients

public ColocCoefficients()

Method Detail

add

public void add(int[] arrX,
                int[] arrY)

Compare several pixels

add

public void add(double[] arrX,
                double[] arrY)

Compare several pixels

add

public void add(float[] arrX,
                float[] arrY)

Compare several pixels

add

public void add(double x,
                double y)

Compare one pixel

getVarX

public double getVarX()

Variance of X

getVarY

public double getVarY()

Variance of Y

getCovXY

public double getCovXY()

Covariance(X,Y)

getPearson

public double getPearson()

Pearsons coefficient

getPearsonMean0

public double getPearsonMean0()

Pearsons coefficient, assume mean=0

getKX

public double getKX()

kX=k1

getKY

public double getKY()

kY=k2

getMandersX

public double getMandersX()

Mander coefficient X (=index 1)

getMandersY

public double getMandersY()

Mander coefficient Y (=index 2)

getL2

public double getL2()

main

public static void main(java.lang.String[] args)

toXML

public void toXML(org.jdom.Element e)

fromXML

public void fromXML(org.jdom.Element e)
             throws org.jdom.DataConversionException

Throws:

org.jdom.DataConversionException