java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmTimeFitting

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmTimeFitting
extends AlgorithmBase
```

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`(package private) class`	`AlgorithmTimeFitting.FitExponential`
`(package private) class`	`AlgorithmTimeFitting.FitGaussian`
`(package private) class`	`AlgorithmTimeFitting.FitLaplace`
`(package private) class`	`AlgorithmTimeFitting.FitLine`
`(package private) class`	`AlgorithmTimeFitting.FitLorentz`
`(package private) class`	`AlgorithmTimeFitting.FitMultiExponential`
`(package private) class`	`AlgorithmTimeFitting.FitRayleigh`
`class`	`AlgorithmTimeFitting.fittingTask`

Nested classes/interfaces inherited from class java.lang.Thread
java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private java.lang.String`	`altTimeTag`
`private int`	`barMarker`
`private java.util.BitSet`	`bitMask`
`private double[]`	`destArray`
`private int[]`	`destExitStatusArray`
`private int[]`	`exitStatus`
`private ModelImage`	`exitStatusImage`
`private static int`	`EXPONENTIAL_FIT`
`private boolean`	`findInitialFromData`
`private int`	`functionFit`
`private static int`	`GAUSSIAN_FIT`
`private double[]`	`highBounds`
`private int`	`i`
`private double[]`	`initial`
`private static int`	`LAPLACE_FIT`
`private static int`	`LINEAR_FIT`
`private static int`	`LORENTZ_FIT`
`private double[]`	`lowBounds`
`private static int`	`MULTIEXPONENTIAL_FIT`	From Exponential analysis in physical phenomena by Andrei A.
`private int`	`numVariables`
`private int`	`oldBarMarker`
`private double[]`	`paramAverage`
`private int[]`	`paramInf`
`private double[]`	`paramMax`
`private double[]`	`paramMin`
`private int[]`	`paramNaN`
`private double[]`	`paramTotal`
`private int`	`processors`
`private static int`	`RAYLEIGH_FIT`
`private double[]`	`srcArray`
`private int`	`tDim`
`private double[]`	`timeVals`	A vector of center times for each volume
`private boolean`	`useAltTimeTag`
`private boolean[]`	`useBounds`
`private boolean`	`useLog`
`private int`	`validVoxels`
`private int`	`volSize`
`private long`	`voxelsProcessed`
`private boolean`	`wholeImage`
`private int`	`xDim`
`private int`	`yDim`
`private int`	`zDim`

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
`AlgorithmTimeFitting(ModelImage destImage, ModelImage srcImage, ModelImage exitStatusImage, boolean useLog, int functionFit, int numVariables, boolean findInitialFromData, double[] initial, boolean[] useBounds, double[] lowBounds, double[] highBounds)`	Creates a new AlgorithmTimeFitting object.
`AlgorithmTimeFitting(ModelImage destImage, ModelImage srcImage, ModelImage exitStatusImage, boolean useLog, int functionFit, int numVariables, boolean findInitialFromData, double[] initial, boolean[] useBounds, double[] lowBounds, double[] highBounds, boolean useAltTimeTag, java.lang.String altTimeTag)`	Creates a new AlgorithmTimeFitting object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for destruction.
`void`	`input(double[] y_array, int i)`
`void`	`output(double[] params, int i, int status, double chi_squared)`
`void`	`runAlgorithm()`	starts the algorithm.

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, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - LINEAR_FIT
```
private static final int LINEAR_FIT
```
    See Also:
    
    Constant Field Values
  - EXPONENTIAL_FIT
```
private static final int EXPONENTIAL_FIT
```
    See Also:
    
    Constant Field Values
  - GAUSSIAN_FIT
```
private static final int GAUSSIAN_FIT
```
    See Also:
    
    Constant Field Values
  - LAPLACE_FIT
```
private static final int LAPLACE_FIT
```
    See Also:
    
    Constant Field Values
  - LORENTZ_FIT
```
private static final int LORENTZ_FIT
```
    See Also:
    
    Constant Field Values
  - MULTIEXPONENTIAL_FIT
```
private static final int MULTIEXPONENTIAL_FIT
```
    From Exponential analysis in physical phenomena by Andrei A. Istratov and Oleg F. Vyvenko: Note that for a multiexponential fit nonlinear least squares analysis as used here can handle nonzero baseline offsets. However, for nonlinear least squares initial guesses are needed for the values of unknown decay parameters and, if these initial guesses are poor, the iteration may converge to a local minimum rather than to the absolute minimum. With Prony's method the baseline offset should be removed first. The differentiation of transients only allows the exponent time constants to be determined. It does not allow the amplitudes by which the exponents are multiplied to be determined. Also experimental transients are noisy, and large errors would result from their numerical differentiation. The method of modulating functions does not enable one to determine the amplitude of the transients and is not tolerant to nonzero baseline offsets. The integration method allows one to determine the baseline. However, the solution is more stable and exact if the baseline is subtracted from the raw signal before the analysis. For the integration method, on computed two-component decays with tau1/tau2 = 2.5 the reliable separation of components is impossible if the SNR is less than 30. For tau1/tau2, two components can be separated for a SNR of about 10. When two-component analysis is performed with a baseline determination the mean error of the calculated time constants increases by a factor of about 3-10. Before the method of moments can be applied, the baseline offset must be removed from the data. The Laplace-Pade approximation is not applicable to decays containing baseline offset. Tolerance of the method to baseline offsets may be very important, depending on whether a baseline offset can be encountered in the experiment. Few of the discussed techniques are tolerable of nonzero baseline offsets. Such commonly used methods as Prony's or method of moments will provide wrong results or even crash if a decay contains an offset. Unfortunately, algorithms for extrapolation of baseline offsets are poorly developed and are not always sufficiently exact. Therefore, we would recommend algorithms that do not require baseline corrections and can accommodate transients with a baseline. Taking into account stability for wide range changes in parameters and insensitivity to baseline offsets, the authors select nonlinear least squares as the best fitting method for multiexponential fits. Fitting routines are only accurate if the number of components is correct and the initial approximation is close to the true solution. A way to obtain this initial approximation is to extract it from a spectroscopic method, as was done by Provencher and Mazzola et al.
    
    See Also:
    
    Constant Field Values
  - RAYLEIGH_FIT
```
private static final int RAYLEIGH_FIT
```
    See Also:
    
    Constant Field Values
  - timeVals
```
private double[] timeVals
```
    A vector of center times for each volume
  - srcArray
```
private double[] srcArray
```
  - i
```
private int i
```
  - xDim
```
private int xDim
```
  - yDim
```
private int yDim
```
  - zDim
```
private int zDim
```
  - tDim
```
private int tDim
```
  - volSize
```
private int volSize
```
  - findInitialFromData
```
private boolean findInitialFromData
```
  - initial
```
private double[] initial
```
  - useBounds
```
private boolean[] useBounds
```
  - lowBounds
```
private double[] lowBounds
```
  - highBounds
```
private double[] highBounds
```
  - exitStatus
```
private int[] exitStatus
```
  - paramNaN
```
private int[] paramNaN
```
  - paramInf
```
private int[] paramInf
```
  - paramMin
```
private double[] paramMin
```
  - paramMax
```
private double[] paramMax
```
  - paramTotal
```
private double[] paramTotal
```
  - paramAverage
```
private double[] paramAverage
```
  - processors
```
private int processors
```
  - destArray
```
private double[] destArray
```
  - destExitStatusArray
```
private int[] destExitStatusArray
```
  - voxelsProcessed
```
private long voxelsProcessed
```
  - barMarker
```
private int barMarker
```
  - oldBarMarker
```
private int oldBarMarker
```
  - bitMask
```
private java.util.BitSet bitMask
```
  - validVoxels
```
private int validVoxels
```
  - wholeImage
```
private boolean wholeImage
```
  - exitStatusImage
```
private ModelImage exitStatusImage
```
  - useLog
```
private boolean useLog
```
  - functionFit
```
private int functionFit
```
  - numVariables
```
private int numVariables
```
  - useAltTimeTag
```
private boolean useAltTimeTag
```
  - altTimeTag
```
private java.lang.String altTimeTag
```
- Constructor Detail
  - AlgorithmTimeFitting
```
public AlgorithmTimeFitting(ModelImage destImage,
                            ModelImage srcImage,
                            ModelImage exitStatusImage,
                            boolean useLog,
                            int functionFit,
                            int numVariables,
                            boolean findInitialFromData,
                            double[] initial,
                            boolean[] useBounds,
                            double[] lowBounds,
                            double[] highBounds)
```
    Creates a new AlgorithmTimeFitting object.
  - AlgorithmTimeFitting
```
public AlgorithmTimeFitting(ModelImage destImage,
                            ModelImage srcImage,
                            ModelImage exitStatusImage,
                            boolean useLog,
                            int functionFit,
                            int numVariables,
                            boolean findInitialFromData,
                            double[] initial,
                            boolean[] useBounds,
                            double[] lowBounds,
                            double[] highBounds,
                            boolean useAltTimeTag,
                            java.lang.String altTimeTag)
```
    Creates a new AlgorithmTimeFitting object.
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - runAlgorithm
```
public void runAlgorithm()
```
    starts the algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - input
```
public void input(double[] y_array,
                  int i)
```
  - output
```
public void output(double[] params,
                   int i,
                   int status,
                   double chi_squared)
```

Class AlgorithmTimeFitting

Nested Class Summary

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

Field Summary

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

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

LINEAR_FIT

EXPONENTIAL_FIT

GAUSSIAN_FIT

LAPLACE_FIT

LORENTZ_FIT

MULTIEXPONENTIAL_FIT

RAYLEIGH_FIT

timeVals

srcArray

i

xDim

yDim

zDim

tDim

volSize

findInitialFromData

initial

useBounds

lowBounds

highBounds

exitStatus

paramNaN

paramInf

paramMin

paramMax

paramTotal

paramAverage

processors

destArray

destExitStatusArray

voxelsProcessed

barMarker

oldBarMarker

bitMask

validVoxels

wholeImage

exitStatusImage

useLog

functionFit

numVariables

useAltTimeTag

altTimeTag

Constructor Detail

AlgorithmTimeFitting

AlgorithmTimeFitting

Method Detail

finalize

runAlgorithm

input

output