Class FindPeaks

java.lang.Object

FindPeaks

All Implemented Interfaces:

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

public class FindPeaks
extends java.lang.Object
implements ij.plugin.filter.PlugInFilter, ij.gui.DialogListener

ImageJ plugin to find peaks (maxima) in vertical sections of a z-stack

Author:

thomasbraschler

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	doFiltering Octave's findpeak function works in two parts: primary peak detection, and then filtering according to various criteria to reject local maxima that do not satisfy the quality criteria This variable indicates whether this filtering step should be done (true) or not (false)
protected ij.ImagePlus	imp Holds a reference to the primary ImagePlus object associated with this plugin
protected ij.process.ImageProcessor	ip image processor at the time of starting the analysis
static double	maxW Maximum width, in pixels, in the z-direction.
static double	minD Minimal distance, in pixels, in the z-direction.
static double	minH Minimum height, in intensity units, above the background level.
static double	minW Minimal width, in pixels, in the z-direction.
static double	peak_fraction Expected fraction of pixels above the threshold to be set and thus to be eligible for being a peak

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
FindPeaks()

Method Summary

Modifier and Type	Method and Description
boolean	dialogItemChanged(ij.gui.GenericDialog gd, java.awt.AWTEvent e) Read the peak_fraction, minD, doFiltering, minW, maxW and minH parameters from the dialog
boolean	doDialog() Displays the dialog with the various findPeaks options
int[]	findPeaksInSection(int x, int y) Finds the indexes of the peaks in the z-Profile at a given xy position
int[]	getStackSection(int x, int y) Get the pixel values along the z direction in a stack, at a horizontal location specified by x and y
void	run(ij.process.ImageProcessor theIp) Displays the dialog for setting the custom options.
int	setup(java.lang.String arg, ij.ImagePlus imp) Indicate that we need greyscale images and also that the original image is not changed ( a new output image is generated instead)

Methods inherited from class java.lang.Object

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

Field Detail

imp

protected ij.ImagePlus imp

Holds a reference to the primary ImagePlus object associated with this plugin

ip

protected ij.process.ImageProcessor ip

image processor at the time of starting the analysis

peak_fraction

public static double peak_fraction

Expected fraction of pixels above the threshold to be set and thus to be eligible for being a peak

minD

public static double minD

Minimal distance, in pixels, in the z-direction. This is the minD argument to the Octave function findPeaks

minW

public static double minW

Minimal width, in pixels, in the z-direction. This is the minW argument to the Octave function findPeaks

maxW

public static double maxW

Maximum width, in pixels, in the z-direction. This is the maxW argument to the Octave function findPeaks

minH

public static double minH

Minimum height, in intensity units, above the background level. This is the minH of the Octave function findPeaks, but is interpreted as being the difference to background

doFiltering

public static boolean doFiltering

Octave's findpeak function works in two parts: primary peak detection, and then filtering according to various criteria to reject local maxima that do not satisfy the quality criteria This variable indicates whether this filtering step should be done (true) or not (false)

Constructor Detail

FindPeaks

public FindPeaks()

Method Detail

dialogItemChanged

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

Read the peak_fraction, minD, doFiltering, minW, maxW and minH parameters from the dialog

Specified by:

dialogItemChanged in interface ij.gui.DialogListener

setup

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

Indicate that we need greyscale images and also that the original image is not changed ( a new output image is generated instead)

Specified by:

setup in interface ij.plugin.filter.PlugInFilter

getStackSection

public int[] getStackSection(int x,
                             int y)

Get the pixel values along the z direction in a stack, at a horizontal location specified by x and y

Parameters:

x - x-position in pixel units, 0-based (ImageJ standard)

y - y-position in pixel units, 0-based (ImageJ standard)

Returns:

Pixel values along the z-profile

run

public void run(ij.process.ImageProcessor theIp)

Displays the dialog for setting the custom options. Then finds the temporal peaks with these options for each xy pixel position. Output: creates and shows a new stack with identical dimensions to the stack analyzed, where non-peak pixels are black (0) and peak pixels white (255)

Specified by:

run in interface ij.plugin.filter.PlugInFilter

findPeaksInSection

public int[] findPeaksInSection(int x,
                                int y)

Finds the indexes of the peaks in the z-Profile at a given xy position

Parameters:

x - x-position in pixel units, 0-based (ImageJ standard)

y - y-position in pixel units, 0-based (ImageJ standard)

Returns:

Array of peak positions (pixel units, 0-based) in the z-profile

doDialog

public boolean doDialog()

Displays the dialog with the various findPeaks options

Returns:

true upon success, false otherwise (including user cancel)