de.mpg.biochem.mars.image

Class PeakFitter<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>

java.lang.Object

de.mpg.biochem.mars.image.PeakFitter<T>

public class PeakFitter<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
extends java.lang.Object

The PeakFitter determines the subpixel location of peaks with a symmetric gaussian function that include a baseline parameter. LevenbergMarquardt is used for optimization. The final double array resulting from fitting has the following assignments: p[0] = Baseline p[1] = Height p[2] = X p[3] = Y p[4] = Sigma with the same order for the associated error double array e.

Constructor Summary

Constructors

Constructor and Description
PeakFitter()
PeakFitter(boolean[] vary)
PeakFitter(boolean[] vary, double allowable_error)

Method Summary

Modifier and Type	Method and Description
void	fitPeak(net.imglib2.RandomAccessible<T> img, double[] p, double[] e, java.awt.Rectangle roi)
void	fitPeak(net.imglib2.RandomAccessible<T> img, double[] p, double[] e, java.awt.Rectangle roi, boolean findNegativePeaks)
void	fitPeak(net.imglib2.RandomAccessible<T> img, double[] p, double[] e, java.awt.Rectangle roi, double fitRegionThreshold, boolean findNegativePeaks)

Methods inherited from class java.lang.Object

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

Constructor Detail

PeakFitter

public PeakFitter()

PeakFitter

public PeakFitter(boolean[] vary)

PeakFitter

public PeakFitter(boolean[] vary,
                  double allowable_error)

Method Detail

fitPeak

public void fitPeak(net.imglib2.RandomAccessible<T> img,
                    double[] p,
                    double[] e,
                    java.awt.Rectangle roi)

fitPeak

public void fitPeak(net.imglib2.RandomAccessible<T> img,
                    double[] p,
                    double[] e,
                    java.awt.Rectangle roi,
                    boolean findNegativePeaks)

fitPeak

public void fitPeak(net.imglib2.RandomAccessible<T> img,
                    double[] p,
                    double[] e,
                    java.awt.Rectangle roi,
                    double fitRegionThreshold,
                    boolean findNegativePeaks)