utils

Class ImageOperations

java.lang.Object

utils.ImageOperations

public class ImageOperations
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static double	SIGMA_TO_FWHM

Method Summary

Modifier and Type	Method and Description
ij.ImagePlus	discoidalFilter(ij.ImagePlus imp) Discoidal filter all images in the given stack.
ij.process.ImageProcessor	discoidalFilter(ij.process.ImageProcessor ip) The discoidal filter is used to amplify peaks in an image.
java.util.ArrayList<ij.gui.PointRoi>	findPeaks(ij.ImagePlus imp)
java.util.ArrayList<java.awt.Point>	findPeaks(ij.process.ImageProcessor ip) Find all the peaks in an image.
ij.measure.ResultsTable	fitPeaks(ij.ImagePlus imp)
ij.measure.ResultsTable	fitPeaks(ij.process.ImageProcessor ip)
ij.measure.ResultsTable	fitPeaks(ij.measure.ResultsTable table, ij.ImagePlus imp)
ij.measure.ResultsTable	fitPeaks(ij.measure.ResultsTable table, ij.process.ImageProcessor ip)
int	getFitRadius()
double	getFwhm()
int	getInnerRadius()
static ImageOperations	getInstance()
double	getMagnification()
double[]	getMaxError()
int	getMinimumDistance()
int	getOuterRadius()
double	getThreshold()
boolean	isUseDiscoidalFilter()
boolean	isUseStandardDeviation()
static double	normalDistribution(double x, double y, double sigmaX, double sigmaY)
ij.ImagePlus	reconstruction(ij.measure.ResultsTable table)
ij.ImagePlus	reconstruction(ij.measure.ResultsTable table, int x0, int y0, int x1, int y1)
void	setFitRadius(int fitRadius)
void	setFwhm(double fwhm)
void	setInnerRadius(int innerRadius)
void	setMagnification(double magnification)
void	setMaxError(double[] maxError)
void	setMinimumDistance(int minimumDistance)
void	setOuterRadius(int outerRadius)
void	setThreshold(double threshold)
void	setUseDiscoidalFilter(boolean useDiscoidalFilter)
void	setUseStandardDeviation(boolean useStandardDeviation)
boolean	showDialog()

Methods inherited from class java.lang.Object

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

Field Detail

SIGMA_TO_FWHM

public static final double SIGMA_TO_FWHM

Method Detail

getInstance

public static ImageOperations getInstance()

discoidalFilter

public ij.process.ImageProcessor discoidalFilter(ij.process.ImageProcessor ip)

The discoidal filter is used to amplify peaks in an image. It works by taking two circles: an inner circle and an outer circle. For each pixel the filter calculates the mean pixel value of all pixels that lie inside the inner circle minus the mean pixel value of all pixels that lie on the outer circle. When a pixel belong to a peak the difference between the mean pixel value of all pixels on the outer circle and the the mean pixel value of all pixels inside the inner circle will be huge (i.e. peaks will be amplified).

Parameters:

ip - image processor that will be filtered. The given image processor will be changed after calling this method!

Returns:

the filtered image (same as the given parameter)

discoidalFilter

public ij.ImagePlus discoidalFilter(ij.ImagePlus imp)

Discoidal filter all images in the given stack.

Parameters:

imp - The image that needs to be filtered. The given image will be changed after calling this method!

Returns:

the same image as the given parameter

findPeaks

public java.util.ArrayList<java.awt.Point> findPeaks(ij.process.ImageProcessor ip)

Find all the peaks in an image. This method first filters for peak (if useDiscoidalFilter is set). As a second step this method searches for the pixel with the maximum intensity. The position of this 'maximum pixel' is stored and then the second largest pixel value is searched for. This process continues until the found maximum pixel value is below the given threshold value.

Parameters:

ip - the ip

Returns:

the array list

findPeaks

public java.util.ArrayList<ij.gui.PointRoi> findPeaks(ij.ImagePlus imp)

fitPeaks

public ij.measure.ResultsTable fitPeaks(ij.measure.ResultsTable table,
                                        ij.process.ImageProcessor ip)

fitPeaks

public ij.measure.ResultsTable fitPeaks(ij.process.ImageProcessor ip)

fitPeaks

public ij.measure.ResultsTable fitPeaks(ij.measure.ResultsTable table,
                                        ij.ImagePlus imp)

fitPeaks

public ij.measure.ResultsTable fitPeaks(ij.ImagePlus imp)

normalDistribution

public static double normalDistribution(double x,
                                        double y,
                                        double sigmaX,
                                        double sigmaY)

reconstruction

public ij.ImagePlus reconstruction(ij.measure.ResultsTable table)

reconstruction

public ij.ImagePlus reconstruction(ij.measure.ResultsTable table,
                                   int x0,
                                   int y0,
                                   int x1,
                                   int y1)

showDialog

public boolean showDialog()

isUseDiscoidalFilter

public boolean isUseDiscoidalFilter()

setUseDiscoidalFilter

public void setUseDiscoidalFilter(boolean useDiscoidalFilter)

getInnerRadius

public int getInnerRadius()

setInnerRadius

public void setInnerRadius(int innerRadius)

getOuterRadius

public int getOuterRadius()

setOuterRadius

public void setOuterRadius(int outerRadius)

getThreshold

public double getThreshold()

setThreshold

public void setThreshold(double threshold)

isUseStandardDeviation

public boolean isUseStandardDeviation()

setUseStandardDeviation

public void setUseStandardDeviation(boolean useStandardDeviation)

getMinimumDistance

public int getMinimumDistance()

setMinimumDistance

public void setMinimumDistance(int minimumDistance)

getFitRadius

public int getFitRadius()

setFitRadius

public void setFitRadius(int fitRadius)

getFwhm

public double getFwhm()

setFwhm

public void setFwhm(double fwhm)

getMagnification

public double getMagnification()

setMagnification

public void setMagnification(double magnification)

getMaxError

public double[] getMaxError()

setMaxError

public void setMaxError(double[] maxError)