de.mpg.biochem.mars.image

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

java.lang.Object

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

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

Constructor Summary

Constructors

Constructor and Description
DNAFinder(net.imagej.ops.OpService opService)

Method Summary

Modifier and Type	Method and Description
java.util.List<DNASegment>	findDNAs(net.imglib2.RandomAccessibleInterval<T> img, net.imglib2.Interval interval, int theT, int numThreads)
java.util.List<DNASegment>	findDNAs(net.imglib2.RandomAccessibleInterval<T> img, net.imglib2.roi.IterableRegion<net.imglib2.type.logic.BoolType> iterableRegion, int theT)
java.util.List<DNASegment>	findDNAs(net.imglib2.RandomAccessibleInterval<T> img, net.imglib2.roi.IterableRegion<net.imglib2.type.logic.BoolType> iterableRegion, int theT, int numThreads)
java.util.List<DNASegment>	findDNAs(net.imglib2.RandomAccessibleInterval<T> img, java.util.List<net.imglib2.roi.IterableRegion<net.imglib2.type.logic.BoolType>> iterableRegions, int theT)
java.util.List<DNASegment>	findDNAs(net.imglib2.RandomAccessibleInterval<T> img, java.util.List<net.imglib2.roi.IterableRegion<net.imglib2.type.logic.BoolType>> iterableRegions, int theT, int numThreads)
boolean	getFilterByMedianIntensity()
boolean	getFilterByVariance()
boolean	getFit()
int	getFitRadius()
boolean	getFitSecondOrder()
double	getGaussianSigma()
int	getMedianIntensityLowerBound()
int	getMinimumDistance()
int	getOptimalDNALength()
double	getThreshold()
int	getVarianceUpperBound()
int	getXDNAEndSearchRadius()
int	getYDNAEndSearchRadius()
void	setDogFilterRadius(double dogFilterRadius)
void	setFilterByMedianIntensity(boolean medianIntensityFilter)
void	setFilterByVariance(boolean varianceFilter)
void	setFit(boolean fit)
void	setFitRadius(int fitRadius)
void	setFitSecondOrder(boolean fitSecondOrder)
void	setGaussianSigma(double gaussSigma)
void	setMedianIntensityLowerBound(int medianIntensityLowerBound)
void	setMinimumDistance(int minimumDistance)
void	setOptimalDNALength(int optimalDNALength)
void	setThreshold(double threshold)
void	setUseDogFiler(boolean useDogFilter)
void	setVarianceUpperBound(int varianceUpperBound)
void	setXDNAEndSearchRadius(int xDNAEndSearchRadius)
void	setYDNAEndSearchRadius(int yDNAEndSearchRadius)

Methods inherited from class java.lang.Object

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

Constructor Detail

DNAFinder

public DNAFinder(net.imagej.ops.OpService opService)

Method Detail

findDNAs

public java.util.List<DNASegment> findDNAs(net.imglib2.RandomAccessibleInterval<T> img,
                                           net.imglib2.roi.IterableRegion<net.imglib2.type.logic.BoolType> iterableRegion,
                                           int theT)

findDNAs

public java.util.List<DNASegment> findDNAs(net.imglib2.RandomAccessibleInterval<T> img,
                                           net.imglib2.roi.IterableRegion<net.imglib2.type.logic.BoolType> iterableRegion,
                                           int theT,
                                           int numThreads)

findDNAs

public java.util.List<DNASegment> findDNAs(net.imglib2.RandomAccessibleInterval<T> img,
                                           java.util.List<net.imglib2.roi.IterableRegion<net.imglib2.type.logic.BoolType>> iterableRegions,
                                           int theT)

findDNAs

public java.util.List<DNASegment> findDNAs(net.imglib2.RandomAccessibleInterval<T> img,
                                           java.util.List<net.imglib2.roi.IterableRegion<net.imglib2.type.logic.BoolType>> iterableRegions,
                                           int theT,
                                           int numThreads)

findDNAs

public java.util.List<DNASegment> findDNAs(net.imglib2.RandomAccessibleInterval<T> img,
                                           net.imglib2.Interval interval,
                                           int theT,
                                           int numThreads)

setGaussianSigma

public void setGaussianSigma(double gaussSigma)

getGaussianSigma

public double getGaussianSigma()

setUseDogFiler

public void setUseDogFiler(boolean useDogFilter)

setDogFilterRadius

public void setDogFilterRadius(double dogFilterRadius)

setThreshold

public void setThreshold(double threshold)

getThreshold

public double getThreshold()

setMinimumDistance

public void setMinimumDistance(int minimumDistance)

getMinimumDistance

public int getMinimumDistance()

setOptimalDNALength

public void setOptimalDNALength(int optimalDNALength)

getOptimalDNALength

public int getOptimalDNALength()

setYDNAEndSearchRadius

public void setYDNAEndSearchRadius(int yDNAEndSearchRadius)

getYDNAEndSearchRadius

public int getYDNAEndSearchRadius()

setXDNAEndSearchRadius

public void setXDNAEndSearchRadius(int xDNAEndSearchRadius)

getXDNAEndSearchRadius

public int getXDNAEndSearchRadius()

setFilterByVariance

public void setFilterByVariance(boolean varianceFilter)

getFilterByVariance

public boolean getFilterByVariance()

getVarianceUpperBound

public int getVarianceUpperBound()

setVarianceUpperBound

public void setVarianceUpperBound(int varianceUpperBound)

setFilterByMedianIntensity

public void setFilterByMedianIntensity(boolean medianIntensityFilter)

getFilterByMedianIntensity

public boolean getFilterByMedianIntensity()

setMedianIntensityLowerBound

public void setMedianIntensityLowerBound(int medianIntensityLowerBound)

getMedianIntensityLowerBound

public int getMedianIntensityLowerBound()

setFit

public void setFit(boolean fit)

getFit

public boolean getFit()

setFitSecondOrder

public void setFitSecondOrder(boolean fitSecondOrder)

getFitSecondOrder

public boolean getFitSecondOrder()

setFitRadius

public void setFitRadius(int fitRadius)

getFitRadius

public int getFitRadius()