Package gov.nih.mipav.model.algorithms

Class AlgorithmMultiExponentialFitting

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmMultiExponentialFitting

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmMultiExponentialFitting
extends AlgorithmBase

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private double[][]	adub
private double	chiSquared
private double	convrg
private double[][]	ddse
private double	delta
private double[]	deltap
private double[]	deltat
private double[][]	df
private double[][]	dfcapl
private double[][]	dgfl
private double	dgride
private double	dgridf
private double[]	dtoler
private double[][]	e
private double	enphi
private int	evarCalled
private double[][]	f
private boolean	failed
private boolean	fatalProblem
private boolean[][]	ffail
private double[]	fhat
private double	fhatmx
private double	gestl
private double[][]	gf
private double	gfstl
private double[][]	gse
private int	ibase
private int	iter
private int	iwt
private int	iwtsgn
private int	jgeadd
private int	jlamp1
private double[][][]	lamf
private double[][]	lamnmx
private double[]	lamst
private int	mdima
private int	minter
private int	mlammx
private int	mtry
private int	n
private int[][]	nbinom
private int	nf
private int[]	nftry
private int[]	ngrid2
private int	nint
private int	nintmx	This is a port of the Fortran program discrete.for version 2B (December, 1990) written by Stephen Provencher, PhD.
private int	nlammx
private boolean	nobase
private boolean	nonneg
private int[]	nperg2
private int[]	nt
private int[]	nvgrid
private double[]	palpha
private double[]	params
private double[]	pcerr
private boolean[]	pivalp
private double[]	plam
private double[]	plmtry
private boolean	plotrs
private double	precis
private boolean	prfinl
private boolean	prprel
private boolean	pry
private boolean	regint
private boolean	repeat
private double[][]	se
private double[]	sfde
private boolean	showDebug
private double[]	sigmap
private double	sigyy
private double[]	sqrtw
private int	status
private double	sumwt
private double	sumwty
private double[]	t
private double[]	tend
private double[]	trbase
private double[]	tstart
private double[]	var
private int	varfCalled
private double	varmin
private double[]	vgrid2
private boolean	wted
private double[]	y
private double[]	ylyfit
private double[]	zero

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
AlgorithmMultiExponentialFitting()
AlgorithmMultiExponentialFitting(int nlammx, int iwt, int mtry, boolean regint, boolean nobase, boolean nonneg, boolean showDebug, boolean pry, boolean prprel, boolean prfinl, boolean plotrs, boolean repeat, int n, double[] t, int nint, double[] tstart, double[] tend, int[] nt, double[] y, double[] sqrtw)

Method Summary

Modifier and Type	Method	Description
private void	anlerr(int jlam, int nlin, int itype, boolean inter, boolean prlsq)
private void	etheor(double plambd, boolean invert, boolean wted, double[] se, double[] dse, double[] ddse, double[] sye, boolean doe, boolean doye)
private void	evar(double[] q, int jlam, double[] var, boolean invert, boolean[] allpiv, double[] ylydum, int nlin, double varg, int ntry, boolean inter, int[] ierror)
private double	expsma(double s)
private void	fanlyz()
void	finalize()	Prepares this class for destruction.
private double	fisher(double fs, int nu1, int nu2)
double	getChiSquared()
double[]	getParameters()
int	getStatus()
private void	lstsqr(double[] lamst, int jlam, boolean rawdat, int n, int nlin, int routineCalled, int itype, boolean split, boolean inter, boolean prlsq)
private void	pivot(double[][] adub, int mdima, int np, boolean onlyin, boolean invert, boolean constr, double pmin, double pmax, double[] p, double[] dtoler, double[] deltap, boolean[] allpiv, double[] qg, boolean[] piv, int jlam, double[] qmax, int[] ierror)
private void	pivot1(double[][] adub, int mdima, int npp, int lpiv)
private void	residu(int jlam, boolean plot, double[] puncor, double[][][] asave)
void	runAlgorithm()	starts the algorithm.
void	selfTest()
private void	varf(double[] q, int jlam, double[] var, boolean invert, boolean[] allpiv, double[] ylyfit, int nlin, double varg, int ntry, boolean intdum, int[] ierror)
private void	weight(boolean finalVar)
private void	yanlyz()

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

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

Field Details

nintmx

private int nintmx

This is a port of the Fortran program discrete.for version 2B (December, 1990) written by Stephen Provencher, PhD. The README.txt file has: DISCLAIMER: This software and its documentation are free and come "as is" with absolutely no guarantee and no support. Applications: Analysis of multi-exponential decay data. Running in hundreds of laboratories on a wide variety of computers. Methods: Fully automatic: no starting estimates needed for the number of exponentials or for their parameters; Modified Gauss-Newton least squares, with intensive searches from many starting points to find the global optimum; Methods in the references below are used to get starting estimates and to speed up the analysis: References: I) S.W. Provencher: A Fourier Method for the Analysis of Exponential Decay Curves, Biophysical Journal, Vol. 16, pp. 27-41 (1976). II)S.W. Provencher: An eigenfunction expansion method for the analysis of exponential decay curves. J. Chem. Phys. 64, pp. 2772-2777. (1976). III)S.W. Provencher invalid input: '&' R.H. Vogel: Information loss with transform methods in system identification: A new set of transforms with high information content. Math. Biosci. 50, pp. 251-262 (1980). IV)S.W. Provencher invalid input: '&' R.H. Vogel: Regularization techniques for inverse problems in molecular biology in: Numerical Treatment of Inverse Problems in Differential and Integral Equations, eds. P. Deuflhard invalid input: '&' E. Hairer (Birkhauser, Boston, 1983), pp. 304-319. This program is used for the automatic analysis of multicomponent exponential decay for up to 9 components. Download the Users Manual and other essential documentation from http://S-provencher.com. The data is represented by y[k] = sum from j = 0 to nlambda of alpha[j]*exp(-lambda[j] * t[k]), k = 1, 2, ..., n, with nlambda varied from 1 to nlammx with nlammx invalid input: '<'= mlammx = 9. Provision can be make for an unknown baseline component alpha[0] with lambda[0] = 0. It is completely automatic in that only the raw data y[k] and t[k] are input; no potentially biased initial guesses at alpha[j], lambda[j], or even the number of terms nlambda are needed or even allowed. There is no need to normalize any of the input data like tstart, tend, t, y, or sqrtw. However, the number 1.0E20 has been used throughout the program to represent an infinitely large number and hence nothing should get larger than 1.0E20. Since some of the values are squared and summed over n, it is best to choose units so that all input values are between 1.0E-9 and 1.0E6 in absolute value. runAlgorithm calls routines weight, fanlyz, yanlyz which in turn call lstSqr, evar, varf, etheor, pivot, pivot1, anlerr, fisher, residu.

mlammx

private int mlammx

convrg

private double convrg

ngrid2

private int[] ngrid2

minter

private int minter

sigmap

private double[] sigmap

precis

private double precis

nlammx

private int nlammx

iwt

private int iwt

mtry

private int mtry

regint

private boolean regint

nobase

private boolean nobase

nonneg

private boolean nonneg

showDebug

private boolean showDebug

pry

private boolean pry

prprel

private boolean prprel

prfinl

private boolean prfinl

plotrs

private boolean plotrs

repeat

private boolean repeat

fatalProblem

private boolean fatalProblem

n

private int n

t

private double[] t

nint

private int nint

tstart

private double[] tstart

tend

private double[] tend

nt

private int[] nt

y

private double[] y

sqrtw

private double[] sqrtw

ylyfit

private double[] ylyfit

e

private double[][] e

gse

private double[][] gse

deltat

private double[] deltat

evarCalled

private int evarCalled

varfCalled

private int varfCalled

trbase

private double[] trbase

gf

private double[][] gf

dgfl

private double[][] dgfl

dgridf

private double dgridf

gfstl

private double gfstl

fhat

private double[] fhat

varmin

private double varmin

sumwty

private double sumwty

sumwt

private double sumwt

zero

private double[] zero

dgride

private double dgride

gestl

private double gestl

var

private double[] var

palpha

private double[] palpha

plam

private double[] plam

se

private double[][] se

plmtry

private double[] plmtry

deltap

private double[] deltap

dfcapl

private double[][] dfcapl

sfde

private double[] sfde

adub

private double[][] adub

ddse

private double[][] ddse

dtoler

private double[] dtoler

f

private double[][] f

df

private double[][] df

delta

private double delta

fhatmx

private double fhatmx

lamst

private double[] lamst

lamf

private double[][][] lamf

lamnmx

private double[][] lamnmx

sigyy

private double sigyy

enphi

private double enphi

pcerr

private double[] pcerr

vgrid2

private double[] vgrid2

jgeadd

private int jgeadd

nbinom

private int[][] nbinom

nvgrid

private int[] nvgrid

nperg2

private int[] nperg2

mdima

private int mdima

ibase

private int ibase

iwtsgn

private int iwtsgn

nf

private int nf

iter

private int iter

jlamp1

private int jlamp1

nftry

private int[] nftry

failed

private boolean failed

wted

private boolean wted

ffail

private boolean[][] ffail

pivalp

private boolean[] pivalp

params

private double[] params

chiSquared

private double chiSquared

status

private int status

Constructor Details

AlgorithmMultiExponentialFitting

public AlgorithmMultiExponentialFitting(int nlammx,
 int iwt,
 int mtry,
 boolean regint,
 boolean nobase,
 boolean nonneg,
 boolean showDebug,
 boolean pry,
 boolean prprel,
 boolean prfinl,
 boolean plotrs,
 boolean repeat,
 int n,
 double[] t,
 int nint,
 double[] tstart,
 double[] tend,
 int[] nt,
 double[] y,
 double[] sqrtw)

AlgorithmMultiExponentialFitting

public AlgorithmMultiExponentialFitting()

Method Details

selfTest

public void selfTest()

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

getParameters

public double[] getParameters()

getChiSquared

public double getChiSquared()

getStatus

public int getStatus()

runAlgorithm

public void runAlgorithm()

starts the algorithm.

Specified by:

runAlgorithm in class AlgorithmBase

weight

private void weight(boolean finalVar)

lstsqr

private void lstsqr(double[] lamst,
 int jlam,
 boolean rawdat,
 int n,
 int nlin,
 int routineCalled,
 int itype,
 boolean split,
 boolean inter,
 boolean prlsq)

pivot

private void pivot(double[][] adub,
 int mdima,
 int np,
 boolean onlyin,
 boolean invert,
 boolean constr,
 double pmin,
 double pmax,
 double[] p,
 double[] dtoler,
 double[] deltap,
 boolean[] allpiv,
 double[] qg,
 boolean[] piv,
 int jlam,
 double[] qmax,
 int[] ierror)

pivot1

private void pivot1(double[][] adub,
 int mdima,
 int npp,
 int lpiv)

evar

private void evar(double[] q,
 int jlam,
 double[] var,
 boolean invert,
 boolean[] allpiv,
 double[] ylydum,
 int nlin,
 double varg,
 int ntry,
 boolean inter,
 int[] ierror)

varf

private void varf(double[] q,
 int jlam,
 double[] var,
 boolean invert,
 boolean[] allpiv,
 double[] ylyfit,
 int nlin,
 double varg,
 int ntry,
 boolean intdum,
 int[] ierror)

anlerr

private void anlerr(int jlam,
 int nlin,
 int itype,
 boolean inter,
 boolean prlsq)

etheor

private void etheor(double plambd,
 boolean invert,
 boolean wted,
 double[] se,
 double[] dse,
 double[] ddse,
 double[] sye,
 boolean doe,
 boolean doye)

expsma

private double expsma(double s)

fanlyz

private void fanlyz()

yanlyz

private void yanlyz()

fisher

private double fisher(double fs,
 int nu1,
 int nu2)

residu

private void residu(int jlam,
 boolean plot,
 double[] puncor,
 double[][][] asave)