CurveFitter (LOCI Javadocs 0-SNAPSHOT API)

java.lang.Object
- loci.slim.fit.CurveFitter

All Implemented Interfaces:

ICurveFitter

Direct Known Subclasses:

GACurveFitter, LMCurveFitter
```
public abstract class CurveFitter
extends Object
implements ICurveFitter
```
Base class for curve fitting algorithms.

Author:

Eric Kjellman

Field Summary

Fields
Modifier and Type	Field and Description
`protected int`	`components`
`protected double`	`currentRCSE`
`protected int[]`	`curveData`
`protected double[][]`	`curveEstimate`
`protected boolean[][]`	`curveFixed`
`protected static boolean`	`DEBUG`
`protected int`	`firstIndex`
`protected int`	`lastIndex`

Constructor Summary

Constructors
Constructor and Description

CurveFitter()

Constructors
Constructor and Description
`CurveFitter()`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`estimate()` Initializes the curve fitter with a starting curve estimate.
`double`	`getChiSquaredError()` Returns the Chi Squared Error of the current curve estimate.
`double`	`getChiSquaredError(double[][] estCurve)`
`int`	`getComponentCount()` Returns the number of exponentials to be fitted.
`double[][]`	`getCurve()` Returns the current curve estimate.
`int[]`	`getData()` Gets the data to be used to generate curve estimates.
`double[]`	`getEstimates(double[][] estimate)`
`int`	`getFirst()`
`boolean[][]`	`getFixed()` For each parameter, gets whether it should be fixed at the current value, or allowed to iterate toward an optimal value.
`abstract int`	`getIterations()` Returns the number of iterations so far.
`int`	`getLast()`
`double`	`getReducedChiSquaredError()` Returns the Reduced Chi Squared Error of the current curve estimate This is based on the number of dataPoints in data and the number of exponentials in setComponentCount.
`double`	`getReducedChiSquaredError(double[][] estCurve)`
`abstract void`	`iterate()` iterate() runs through one iteration of whatever curve fitting technique this curve fitter uses.
`void`	`setComponentCount(int numExp)` Sets how many exponentials are expected to be fitted.
`void`	`setCurve(double[][] curve)` Sets the current curve estimate, useful if information about the curve is already known.
`void`	`setData(int[] data)` Sets the data to be used to generate curve estimates.
`void`	`setData(int[] data, int first, int last)`
`void`	`setFixed(boolean[][] fixed)` For each parameter, sets whether it should be fixed at the current value, or allowed to iterate toward an optimal value.

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

- Field Detail
  - DEBUG
```
protected static final boolean DEBUG
```
    See Also:
    
    Constant Field Values
  - components
```
protected int components
```
  - curveData
```
protected int[] curveData
```
  - curveEstimate
```
protected double[][] curveEstimate
```
  - curveFixed
```
protected boolean[][] curveFixed
```
  - firstIndex
```
protected int firstIndex
```
  - lastIndex
```
protected int lastIndex
```
  - currentRCSE
```
protected double currentRCSE
```
- Constructor Detail
  - CurveFitter
```
public CurveFitter()
```
- Method Detail
  - iterate
```
public abstract void iterate()
```
    iterate() runs through one iteration of whatever curve fitting technique this curve fitter uses. This will generally update the information returned by getCurve and getChiSquaredError.
    
    Specified by:
    
    iterate in interface ICurveFitter
  - getIterations
```
public abstract int getIterations()
```
    Returns the number of iterations so far.
    
    Specified by:
    
    getIterations in interface ICurveFitter
  - getChiSquaredError
```
public double getChiSquaredError()
```
    Returns the Chi Squared Error of the current curve estimate.
    
    Specified by:
    
    getChiSquaredError in interface ICurveFitter
  - getChiSquaredError
```
public double getChiSquaredError(double[][] estCurve)
```
    Specified by:
    
    getChiSquaredError in interface ICurveFitter
  - getReducedChiSquaredError
```
public double getReducedChiSquaredError()
```
    Returns the Reduced Chi Squared Error of the current curve estimate This is based on the number of dataPoints in data and the number of exponentials in setComponentCount.
    
    Specified by:
    
    getReducedChiSquaredError in interface ICurveFitter
  - getReducedChiSquaredError
```
public double getReducedChiSquaredError(double[][] estCurve)
```
    Specified by:
    
    getReducedChiSquaredError in interface ICurveFitter
  - getEstimates
```
public double[] getEstimates(double[][] estimate)
```
    Specified by:
    
    getEstimates in interface ICurveFitter
  - setData
```
public void setData(int[] data)
```
    Sets the data to be used to generate curve estimates. Single dimension of data... time values are index, since we can assume that the dataPoints are evenly spaced.
    
    Specified by:
    
    setData in interface ICurveFitter
  - setData
```
public void setData(int[] data,
                    int first,
                    int last)
```
    Specified by:
    
    setData in interface ICurveFitter
  - getData
```
public int[] getData()
```
    Gets the data to be used to generate curve estimates. Single dimension of data... time values are index, since we can assume that the dataPoints are evenly spaced.
    
    Specified by:
    
    getData in interface ICurveFitter
  - getFirst
```
public int getFirst()
```
    Specified by:
    
    getFirst in interface ICurveFitter
  - getLast
```
public int getLast()
```
    Specified by:
    
    getLast in interface ICurveFitter
  - setComponentCount
```
public void setComponentCount(int numExp)
```
    Sets how many exponentials are expected to be fitted. Currently, more than 2 is not supported.
    
    Specified by:
    
    setComponentCount in interface ICurveFitter
  - getComponentCount
```
public int getComponentCount()
```
    Returns the number of exponentials to be fitted.
    
    Specified by:
    
    getComponentCount in interface ICurveFitter
  - setFixed
```
public void setFixed(boolean[][] fixed)
```
    Description copied from interface: ICurveFitter
    
    For each parameter, sets whether it should be fixed at the current value, or allowed to iterate toward an optimal value.
    
    Specified by:
    
    setFixed in interface ICurveFitter
  - getFixed
```
public boolean[][] getFixed()
```
    Description copied from interface: ICurveFitter
    
    For each parameter, gets whether it should be fixed at the current value, or allowed to iterate toward an optimal value.
    
    Specified by:
    
    getFixed in interface ICurveFitter
  - estimate
```
public void estimate()
```
    Initializes the curve fitter with a starting curve estimate.
    
    Specified by:
    
    estimate in interface ICurveFitter
  - getCurve
```
public double[][] getCurve()
```
    Returns the current curve estimate. Return size is expected to be [components][3] For each exponential of the form ae^-bt+c, [][0] is a, [1] is b, [2] is c.
    
    Specified by:
    
    getCurve in interface ICurveFitter
  - setCurve
```
public void setCurve(double[][] curve)
```
    Sets the current curve estimate, useful if information about the curve is already known. See getCurve for information about the array to pass.
    
    Specified by:
    
    setCurve in interface ICurveFitter

Class CurveFitter

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEBUG

components

curveData

curveEstimate

curveFixed

firstIndex

lastIndex

currentRCSE

Constructor Detail

CurveFitter

Method Detail

iterate

getIterations

getChiSquaredError

getChiSquaredError

getReducedChiSquaredError

getReducedChiSquaredError

getEstimates

setData

setData

getData

getFirst

getLast

setComponentCount

getComponentCount

setFixed

getFixed

estimate

getCurve

setCurve