de.gsi.math.fitter

Class NonLinearRegressionFitter2

java.lang.Object

de.gsi.math.fitter.NonLinearRegressionFitter2

Deprecated.

need to fix the n-dimensional handling - do not use (yet)

@Deprecated
public class NonLinearRegressionFitter2
extends Object

Non-linear regression class Nelder & Mead simplex algorithm being the primary back-bone of this implementation initial implementation based on the package provided by: Michael Thomas Flanagan at www.ee.ucl.ac.uk/~mflanaga, appears in all copies The code has been cleaned up and adapted to support true MxN multi-dimensional fits

Author:

rstein

Field Summary

Fields

Modifier and Type	Field and Description
protected double[]	best Deprecated.
protected double[]	bestSd Deprecated.
protected double	cCoeff Deprecated.
protected double	chiSquare Deprecated.
protected int	constraintMethod Deprecated.
protected double[]	constraints Deprecated.
protected double	constraintTolerance Deprecated.
protected double[][]	corrCoeff Deprecated.
protected double[][]	covar Deprecated.
protected int	degreesOfFreedom Deprecated.
protected double	delta Deprecated.
protected double	dStep Deprecated.
protected double	eCoeff Deprecated.
protected boolean[]	fixed Deprecated.
protected double	fMin Deprecated.
protected double[]	fscale Deprecated.
protected double	fTol Deprecated.
protected double[][]	grad Deprecated.
protected static double	histTol Deprecated.
protected boolean	ignoreDofFcheck Deprecated.
protected boolean	invertFlag Deprecated.
protected int	konvge Deprecated.
protected int	kRestart Deprecated.
protected double	lastSSnoConstraint Deprecated.
protected boolean	linNonLin Deprecated.
protected int	maxConstraintIndex Deprecated.
protected int	minTest Deprecated.
protected boolean	multipleY Deprecated.
protected int	nConstraints Deprecated.
protected int	nData Deprecated.
protected boolean	nFactorOption Deprecated.
protected int	nIter Deprecated.
protected boolean	nlrStatus Deprecated.
protected int	nMax Deprecated.
protected int	nSumConstraints Deprecated.
protected int	nTerms Deprecated.
protected int	nYarrays Deprecated.
protected ArrayList<Object>	penalties Deprecated.
protected boolean	penalty Deprecated.
protected int[]	penaltyCheck Deprecated.
protected int[]	penaltyParam Deprecated.
protected double	penaltyWeight Deprecated.
protected boolean	posVarFlag Deprecated.
protected double[]	pseudoSd Deprecated.
protected double[]	pValues Deprecated.
protected double	rCoeff Deprecated.
protected double	reducedChiSquare Deprecated.
protected VoxelArrayND	residual Deprecated.
protected VoxelArrayND	residualW Deprecated.
protected int	scaleOpt Deprecated.
protected double	simplexSd Deprecated.
protected double[]	startH Deprecated.
protected boolean	statFlag Deprecated.
protected double[]	step Deprecated.
protected double[]	sumConstraints Deprecated.
protected double	sumOfSquares Deprecated.
protected ArrayList<Object>	sumPenalties Deprecated.
protected boolean	sumPenalty Deprecated.
protected int[]	sumPenaltyCheck Deprecated.
protected int[]	sumPenaltyNumber Deprecated.
protected int[][]	sumPenaltyParam Deprecated.
protected double[][]	sumPlusOrMinus Deprecated.
protected boolean	trueFreq Deprecated.
protected double[]	tValues Deprecated.
protected double[]	values Deprecated.
protected VoxelArrayND	weight Deprecated.
protected int	weightFlag Deprecated.
protected boolean	weightOpt Deprecated.
protected VoxelArrayND	xData Deprecated.
protected VoxelArrayND	yCalc Deprecated.
protected VoxelArrayND	yData Deprecated.
protected boolean	zeroCheck Deprecated.

Constructor Summary

Constructors

Constructor and Description
NonLinearRegressionFitter2(double[] xData, double[] yData, double[] weight) Deprecated. Constructor with data with x as 1D array and weights provided
NonLinearRegressionFitter2(VoxelArrayND xData, VoxelArrayND yData, VoxelArrayND weights) Deprecated. Constructor with data with x as 1D array and weights provided

Method Summary

Modifier and Type	Method and Description
void	addConstraint(int[] paramIndices, double[] plusOrMinus, int conDir, double constraint) Deprecated.
void	addConstraint(int[] paramIndices, int[] plusOrMinus, int conDir, double constraint) Deprecated.
void	addConstraint(int paramIndex, int conDir, double constraint) Deprecated.
protected VoxelArrayND	checkForZeroWeights(VoxelArrayND weights) Deprecated. Check entered weights for zeros.
void	checkZeroNeg(double[] xx, double[] yy, double[] ww) Deprecated.
double[]	getBestEstimates() Deprecated.
double[]	getBestEstimatesErrors() Deprecated.
double[]	getbestestimatesStandardDeviations() Deprecated.
double[]	getBestEstimatesStandardDeviations() Deprecated.
double	getChiSquare() Deprecated.
double	getchiSquareProb() Deprecated.
double[]	getCoeff() Deprecated.
double[]	getCoeffSd() Deprecated.
double[]	getCoeffVar() Deprecated.
double[][]	getCorrCoeffMatrix() Deprecated.
double[][]	getCovMatrix() Deprecated.
double	getDegFree() Deprecated.
double	getDelta() Deprecated.
double[][]	getGrad() Deprecated.
boolean	getInversionCheck() Deprecated.
int	getMinTest() Deprecated.
int	getNiter() Deprecated.
boolean	getNlrStatus() Deprecated.
int	getNmax() Deprecated.
double	getNMcontract() Deprecated.
double	getNMextend() Deprecated.
double	getNMreflect() Deprecated.
int	getNrestarts() Deprecated.
int	getNrestartsMax() Deprecated.
boolean	getPosVarCheck() Deprecated.
double[]	getPseudoErrors() Deprecated.
double[]	getPseudoSd() Deprecated.
double[]	getPvalues() Deprecated.
double	getReducedChiSquare() Deprecated.
double[]	getResiduals() Deprecated.
double[]	getScale() Deprecated.
double	getSimplexSd() Deprecated.
double	getSumOfSquares() Deprecated.
double	getTolerance() Deprecated.
boolean	getTrueFreq() Deprecated.
double[]	getTvalues() Deprecated.
double[]	getWeightedResiduals() Deprecated.
double[]	getXdata() Deprecated. Get the input x values
double[]	getYcalc() Deprecated.
double[]	getYdata() Deprecated. Get the inputed y values
protected static double	halfWidth(double[] xData, double[] yData) Deprecated.
static double[][]	histogramBins(double[] data, double binWidth, double binZero) Deprecated.
static double[][]	histogramBins(double[] data, double binWidth, double binZero, double binUpper) Deprecated.
void	ignoreDofFcheck() Deprecated.
protected void	nelderMead(Object regFun, double[] start, double[] step, double fTol, int nMax) Deprecated. Nelder and Mead Simplex Simplex Non-linear Regression
protected int	pseudoLinearStats(Object regFun) Deprecated. apply linear statistics to a non-linear regression
void	removeConstraints() Deprecated.
void	setConstraintTolerance(double tolerance) Deprecated.
void	setData(double[] xData, double[] yData, double[] weights) Deprecated.
void	setData(VoxelArrayND xData, VoxelArrayND yData, VoxelArrayND weights) Deprecated.
void	setDelta(double delta) Deprecated.
void	setMinTest(int n) Deprecated.
void	setNmax(int nmax) Deprecated.
void	setNMcontract(double con) Deprecated.
void	setNMextend(double ext) Deprecated.
void	setNMreflect(double refl) Deprecated.
void	setNrestartsMax(int nrs) Deprecated.
void	setScale(double[] sc) Deprecated.
void	setScale(int n) Deprecated.
void	setTolerance(double tol) Deprecated.
void	setTrueFreq(boolean trFr) Deprecated.
protected static boolean	setTrueFreqWeights(VoxelArrayND yData, VoxelArrayND weight) Deprecated.
void	simplex(Function1D g, double[] start) Deprecated.
void	simplex(Function1D g, double[] start, double fTol) Deprecated.
void	simplex(Function1D g, double[] start, double[] step) Deprecated.
void	simplex(Function1D g, double[] start, double[] step, double fTol) Deprecated.
void	simplex(Function1D g, double[] start, double[] step, double fTol, int nMax) Deprecated.
void	simplex(Function1D g, double[] start, double[] step, int nMax) Deprecated.
void	simplex(Function1D g, double[] start, double fTol, int nMax) Deprecated.
void	simplex(Function1D g, double[] start, int nMax) Deprecated.
void	simplex2(FunctionND g, double[] start) Deprecated.
void	simplex2(FunctionND g, double[] start, double fTol) Deprecated.
void	simplex2(FunctionND g, double[] start, double[] step) Deprecated.
void	simplex2(FunctionND g, double[] start, double[] step, double fTol) Deprecated.
void	simplex2(FunctionND g, double[] start, double[] step, double fTol, int nMax) Deprecated.
void	simplex2(FunctionND g, double[] start, double[] step, int nMax) Deprecated.
void	simplex2(FunctionND g, double[] start, double fTol, int nMax) Deprecated.
void	simplex2(FunctionND g, double[] start, int nMax) Deprecated.
protected static void	sort(double[] x, double[] y, double[] w) Deprecated.
protected double	sumSquares(Object regFun, double[] testParameter) Deprecated. Calculate the sum of squares of the residuals for non-linear regression

Methods inherited from class java.lang.Object

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

Field Detail

histTol

protected static double histTol

Deprecated.

nData

protected int nData

Deprecated.

nYarrays

protected int nYarrays

Deprecated.

nTerms

protected int nTerms

Deprecated.

degreesOfFreedom

protected int degreesOfFreedom

Deprecated.

xData

protected VoxelArrayND xData

Deprecated.

yData

protected VoxelArrayND yData

Deprecated.

yCalc

protected VoxelArrayND yCalc

Deprecated.

weight

protected VoxelArrayND weight

Deprecated.

residual

protected VoxelArrayND residual

Deprecated.

residualW

protected VoxelArrayND residualW

Deprecated.

weightOpt

protected boolean weightOpt

Deprecated.

weightFlag

protected int weightFlag

Deprecated.

best

protected double[] best

Deprecated.

bestSd

protected double[] bestSd

Deprecated.

pseudoSd

protected double[] pseudoSd

Deprecated.

tValues

protected double[] tValues

Deprecated.

pValues

protected double[] pValues

Deprecated.

chiSquare

protected double chiSquare

Deprecated.

reducedChiSquare

protected double reducedChiSquare

Deprecated.

sumOfSquares

protected double sumOfSquares

Deprecated.

lastSSnoConstraint

protected double lastSSnoConstraint

Deprecated.

covar

protected double[][] covar

Deprecated.

corrCoeff

protected double[][] corrCoeff

Deprecated.

linNonLin

protected boolean linNonLin

Deprecated.

trueFreq

protected boolean trueFreq

Deprecated.

nlrStatus

protected boolean nlrStatus

Deprecated.

scaleOpt

protected int scaleOpt

Deprecated.

fscale

protected double[] fscale

Deprecated.

zeroCheck

protected boolean zeroCheck

Deprecated.

penalty

protected boolean penalty

Deprecated.

sumPenalty

protected boolean sumPenalty

Deprecated.

nConstraints

protected int nConstraints

Deprecated.

nSumConstraints

protected int nSumConstraints

Deprecated.

maxConstraintIndex

protected int maxConstraintIndex

Deprecated.

constraintTolerance

protected double constraintTolerance

Deprecated.

penalties

protected ArrayList<Object> penalties

Deprecated.

sumPenalties

protected ArrayList<Object> sumPenalties

Deprecated.

penaltyCheck

protected int[] penaltyCheck

Deprecated.

sumPenaltyCheck

protected int[] sumPenaltyCheck

Deprecated.

penaltyWeight

protected double penaltyWeight

Deprecated.

penaltyParam

protected int[] penaltyParam

Deprecated.

sumPenaltyParam

protected int[][] sumPenaltyParam

Deprecated.

sumPlusOrMinus

protected double[][] sumPlusOrMinus

Deprecated.

sumPenaltyNumber

protected int[] sumPenaltyNumber

Deprecated.

constraints

protected double[] constraints

Deprecated.

sumConstraints

protected double[] sumConstraints

Deprecated.

constraintMethod

protected int constraintMethod

Deprecated.

nMax

protected int nMax

Deprecated.

nIter

protected int nIter

Deprecated.

konvge

protected int konvge

Deprecated.

kRestart

protected int kRestart

Deprecated.

fMin

protected double fMin

Deprecated.

fTol

protected double fTol

Deprecated.

rCoeff

protected double rCoeff

Deprecated.

eCoeff

protected double eCoeff

Deprecated.

cCoeff

protected double cCoeff

Deprecated.

startH

protected double[] startH

Deprecated.

step

protected double[] step

Deprecated.

dStep

protected double dStep

Deprecated.

grad

protected double[][] grad

Deprecated.

delta

protected double delta

Deprecated.

invertFlag

protected boolean invertFlag

Deprecated.

posVarFlag

protected boolean posVarFlag

Deprecated.

minTest

protected int minTest

Deprecated.

simplexSd

protected double simplexSd

Deprecated.

statFlag

protected boolean statFlag

Deprecated.

multipleY

protected boolean multipleY

Deprecated.

values

protected double[] values

Deprecated.

fixed

protected boolean[] fixed

Deprecated.

ignoreDofFcheck

protected boolean ignoreDofFcheck

Deprecated.

nFactorOption

protected boolean nFactorOption

Deprecated.

Constructor Detail

NonLinearRegressionFitter2

public NonLinearRegressionFitter2(double[] xData,
                                  double[] yData,
                                  double[] weight)

Deprecated.

Constructor with data with x as 1D array and weights provided

Parameters:

xData - x coordinate of input data

yData - y coordinate of input data

weight - weighting vector

NonLinearRegressionFitter2

public NonLinearRegressionFitter2(VoxelArrayND xData,
                                  VoxelArrayND yData,
                                  VoxelArrayND weights)

Deprecated.

Constructor with data with x as 1D array and weights provided

Parameters:

xData - x coordinate of input data

yData - y coordinate of input data

weights - weighting vector

Method Detail

addConstraint

public void addConstraint(int paramIndex,
                          int conDir,
                          double constraint)

Deprecated.

addConstraint

public void addConstraint(int[] paramIndices,
                          double[] plusOrMinus,
                          int conDir,
                          double constraint)

Deprecated.

addConstraint

public void addConstraint(int[] paramIndices,
                          int[] plusOrMinus,
                          int conDir,
                          double constraint)

Deprecated.

checkForZeroWeights

protected VoxelArrayND checkForZeroWeights(VoxelArrayND weights)

Deprecated.

Check entered weights for zeros. If more than 40% are zero or less than zero, all weights replaced by unity If less than 40% are zero or less than zero, the zero or negative weights are replaced by the average of their nearest neighbours

Parameters:

weights - weighting vector

Returns:

the regularised weight vector

checkZeroNeg

public void checkZeroNeg(double[] xx,
                         double[] yy,
                         double[] ww)

Deprecated.

getBestEstimates

public double[] getBestEstimates()

Deprecated.

getBestEstimatesErrors

public double[] getBestEstimatesErrors()

Deprecated.

getbestestimatesStandardDeviations

public double[] getbestestimatesStandardDeviations()

Deprecated.

getBestEstimatesStandardDeviations

public double[] getBestEstimatesStandardDeviations()

Deprecated.

getChiSquare

public double getChiSquare()

Deprecated.

getchiSquareProb

public double getchiSquareProb()

Deprecated.

getCoeff

public double[] getCoeff()

Deprecated.

getCoeffSd

public double[] getCoeffSd()

Deprecated.

getCoeffVar

public double[] getCoeffVar()

Deprecated.

getCorrCoeffMatrix

public double[][] getCorrCoeffMatrix()

Deprecated.

getCovMatrix

public double[][] getCovMatrix()

Deprecated.

getDegFree

public double getDegFree()

Deprecated.

getDelta

public double getDelta()

Deprecated.

getGrad

public double[][] getGrad()

Deprecated.

getInversionCheck

public boolean getInversionCheck()

Deprecated.

getMinTest

public int getMinTest()

Deprecated.

getNiter

public int getNiter()

Deprecated.

getNlrStatus

public boolean getNlrStatus()

Deprecated.

getNmax

public int getNmax()

Deprecated.

getNMcontract

public double getNMcontract()

Deprecated.

getNMextend

public double getNMextend()

Deprecated.

getNMreflect

public double getNMreflect()

Deprecated.

getNrestarts

public int getNrestarts()

Deprecated.

getNrestartsMax

public int getNrestartsMax()

Deprecated.

getPosVarCheck

public boolean getPosVarCheck()

Deprecated.

getPseudoErrors

public double[] getPseudoErrors()

Deprecated.

getPseudoSd

public double[] getPseudoSd()

Deprecated.

getPvalues

public double[] getPvalues()

Deprecated.

getReducedChiSquare

public double getReducedChiSquare()

Deprecated.

getResiduals

public double[] getResiduals()

Deprecated.

getScale

public double[] getScale()

Deprecated.

getSimplexSd

public double getSimplexSd()

Deprecated.

getSumOfSquares

public double getSumOfSquares()

Deprecated.

getTolerance

public double getTolerance()

Deprecated.

getTrueFreq

public boolean getTrueFreq()

Deprecated.

getTvalues

public double[] getTvalues()

Deprecated.

getWeightedResiduals

public double[] getWeightedResiduals()

Deprecated.

getXdata

public double[] getXdata()

Deprecated.

Get the input x values

Returns:

array with x coordinates

getYcalc

public double[] getYcalc()

Deprecated.

getYdata

public double[] getYdata()

Deprecated.

Get the inputed y values

Returns:

array with input y coordinates

ignoreDofFcheck

public void ignoreDofFcheck()

Deprecated.

nelderMead

protected void nelderMead(Object regFun,
                          double[] start,
                          double[] step,
                          double fTol,
                          int nMax)

Deprecated.

Nelder and Mead Simplex Simplex Non-linear Regression

Parameters:

regFun - test function

start - initial parameter values

step - initial parameter step size

fTol - regression tolerance

nMax - maximum number of iterations

pseudoLinearStats

protected int pseudoLinearStats(Object regFun)

Deprecated.

apply linear statistics to a non-linear regression

Parameters:

regFun - test function

Returns:

0 if method fully successful; -1 posVarFlag or invertFlag is false; -2 posVarFlag and invertFlag are false

removeConstraints

public void removeConstraints()

Deprecated.

setConstraintTolerance

public void setConstraintTolerance(double tolerance)

Deprecated.

setData

public void setData(double[] xData,
                    double[] yData,
                    double[] weights)

Deprecated.

setData

public void setData(VoxelArrayND xData,
                    VoxelArrayND yData,
                    VoxelArrayND weights)

Deprecated.

setDelta

public void setDelta(double delta)

Deprecated.

setMinTest

public void setMinTest(int n)

Deprecated.

setNmax

public void setNmax(int nmax)

Deprecated.

setNMcontract

public void setNMcontract(double con)

Deprecated.

setNMextend

public void setNMextend(double ext)

Deprecated.

setNMreflect

public void setNMreflect(double refl)

Deprecated.

setNrestartsMax

public void setNrestartsMax(int nrs)

Deprecated.

setScale

public void setScale(double[] sc)

Deprecated.

setScale

public void setScale(int n)

Deprecated.

setTolerance

public void setTolerance(double tol)

Deprecated.

setTrueFreq

public void setTrueFreq(boolean trFr)

Deprecated.

simplex

public void simplex(Function1D g,
                    double[] start)

Deprecated.

simplex

public void simplex(Function1D g,
                    double[] start,
                    double fTol)

Deprecated.

simplex

public void simplex(Function1D g,
                    double[] start,
                    double fTol,
                    int nMax)

Deprecated.

simplex

public void simplex(Function1D g,
                    double[] start,
                    double[] step)

Deprecated.

simplex

public void simplex(Function1D g,
                    double[] start,
                    double[] step,
                    double fTol)

Deprecated.

simplex

public void simplex(Function1D g,
                    double[] start,
                    double[] step,
                    double fTol,
                    int nMax)

Deprecated.

simplex

public void simplex(Function1D g,
                    double[] start,
                    double[] step,
                    int nMax)

Deprecated.

simplex

public void simplex(Function1D g,
                    double[] start,
                    int nMax)

Deprecated.

simplex2

public void simplex2(FunctionND g,
                     double[] start)

Deprecated.

simplex2

public void simplex2(FunctionND g,
                     double[] start,
                     double fTol)

Deprecated.

simplex2

public void simplex2(FunctionND g,
                     double[] start,
                     double fTol,
                     int nMax)

Deprecated.

simplex2

public void simplex2(FunctionND g,
                     double[] start,
                     double[] step)

Deprecated.

simplex2

public void simplex2(FunctionND g,
                     double[] start,
                     double[] step,
                     double fTol)

Deprecated.

simplex2

public void simplex2(FunctionND g,
                     double[] start,
                     double[] step,
                     double fTol,
                     int nMax)

Deprecated.

simplex2

public void simplex2(FunctionND g,
                     double[] start,
                     double[] step,
                     int nMax)

Deprecated.

simplex2

public void simplex2(FunctionND g,
                     double[] start,
                     int nMax)

Deprecated.

sumSquares

protected double sumSquares(Object regFun,
                            double[] testParameter)

Deprecated.

Calculate the sum of squares of the residuals for non-linear regression

Parameters:

regFun - test function

testParameter - test parameter

Returns:

the sum of all square values

halfWidth

protected static double halfWidth(double[] xData,
                                  double[] yData)

Deprecated.

histogramBins

public static double[][] histogramBins(double[] data,
                                       double binWidth,
                                       double binZero)

Deprecated.

histogramBins

public static double[][] histogramBins(double[] data,
                                       double binWidth,
                                       double binZero,
                                       double binUpper)

Deprecated.

setTrueFreqWeights

protected static boolean setTrueFreqWeights(VoxelArrayND yData,
                                            VoxelArrayND weight)

Deprecated.

sort

protected static void sort(double[] x,
                           double[] y,
                           double[] w)

Deprecated.