analysis

Class PeakFinder

java.lang.Object

analysis.PeakFinder

All Implemented Interfaces:

ij.gui.DialogListener, ij.plugin.filter.ExtendedPlugInFilter, ij.plugin.filter.PlugInFilter

public class PeakFinder
extends java.lang.Object
implements ij.plugin.filter.ExtendedPlugInFilter, ij.gui.DialogListener

The Class PeakFinder.

Field Summary

Fields inherited from interface ij.plugin.filter.ExtendedPlugInFilter

KEEP_PREVIEW

Fields inherited from interface ij.plugin.filter.PlugInFilter

CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, KEEP_THRESHOLD, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, PARALLELIZE_IMAGES, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

Constructors

Constructor and Description
PeakFinder() Instantiates a new peak finder.
PeakFinder(boolean useDiscoidalAveraging, DiscoidalAveragingFilter filter, double threshold, double thresholdValue, int minimumDistance) Instantiates a new peak finder.
PeakFinder(boolean b, DiscoidalAveragingFilter filter, java.lang.String SNR_THRESHOLD, java.lang.String INTENSITY_THRESHOLD, java.lang.String DISTANCE_BETWEEN_PEAKS) Instantiates a new peak finder.

Method Summary

Modifier and Type	Method and Description
boolean	dialogItemChanged(ij.gui.GenericDialog dialog, java.awt.AWTEvent e) Dialog item changed.
java.util.ArrayList<java.awt.Point>	findPeaks(ij.process.ImageProcessor ip) Find peaks.
ij.plugin.frame.RoiManager	getROIManager() Gets the ROI manager.
void	run(ij.ImagePlus imp) Run.
void	run(ij.process.ImageProcessor ip) Run.
void	setNPasses(int n) Sets the n passes.
int	setup(java.lang.String arg, ij.ImagePlus imp) Setup.
int	showDialog(ij.ImagePlus imp, java.lang.String arg, ij.plugin.filter.PlugInFilterRunner pfr) Show dialog.

Methods inherited from class java.lang.Object

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

Constructor Detail

PeakFinder

public PeakFinder()

Instantiates a new peak finder.

PeakFinder

public PeakFinder(boolean useDiscoidalAveraging,
                  DiscoidalAveragingFilter filter,
                  double threshold,
                  double thresholdValue,
                  int minimumDistance)

Instantiates a new peak finder.

Parameters:

useDiscoidalAveraging - the use discoidal averaging

filter - the filter

threshold - the threshold

thresholdValue - the threshold value

minimumDistance - the minimum distance

PeakFinder

public PeakFinder(boolean b,
                  DiscoidalAveragingFilter filter,
                  java.lang.String SNR_THRESHOLD,
                  java.lang.String INTENSITY_THRESHOLD,
                  java.lang.String DISTANCE_BETWEEN_PEAKS)

Instantiates a new peak finder.

Parameters:

b - the b

filter - the filter

SNR_THRESHOLD - the snr threshold

INTENSITY_THRESHOLD - the intensity threshold

DISTANCE_BETWEEN_PEAKS - the distance between peaks

Method Detail

getROIManager

public ij.plugin.frame.RoiManager getROIManager()

Gets the ROI manager.

Returns:

the ROI manager

run

public void run(ij.ImagePlus imp)

Run.

Parameters:

imp - the imp

run

public void run(ij.process.ImageProcessor ip)

Run.

Specified by:

run in interface ij.plugin.filter.PlugInFilter

Parameters:

ip - the ip

findPeaks

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

Find peaks.

Parameters:

ip - the ip

Returns:

the array list

setup

public int setup(java.lang.String arg,
                 ij.ImagePlus imp)

Setup.

Specified by:

setup in interface ij.plugin.filter.PlugInFilter

Parameters:

arg - the arg

imp - the imp

Returns:

the int

setNPasses

public void setNPasses(int n)

Sets the n passes.

Specified by:

setNPasses in interface ij.plugin.filter.ExtendedPlugInFilter

Parameters:

n - the new n passes

showDialog

public int showDialog(ij.ImagePlus imp,
                      java.lang.String arg,
                      ij.plugin.filter.PlugInFilterRunner pfr)

Show dialog.

Specified by:

showDialog in interface ij.plugin.filter.ExtendedPlugInFilter

Parameters:

imp - the imp

arg - the arg

pfr - the pfr

Returns:

the int

dialogItemChanged

public boolean dialogItemChanged(ij.gui.GenericDialog dialog,
                                 java.awt.AWTEvent e)

Dialog item changed.

Specified by:

dialogItemChanged in interface ij.gui.DialogListener

Parameters:

dialog - the dialog

e - the e

Returns:

true, if successful