ij.plugin.filter
Class MaximumFinder

java.lang.Object
  ij.plugin.filter.MaximumFinder

All Implemented Interfaces:

DialogListener, ExtendedPlugInFilter, PlugInFilter

public class MaximumFinder

extends java.lang.Object

implements ExtendedPlugInFilter, DialogListener

This ImageJ plug-in filter creates a mask where the local maxima of the current image are marked (255; unmarked pixels 0). The plug-in can also create watershed-segmented particles (assume a landscape of inverted heights: maxima of the images are now water sinks. For each point in the image, the sink that the water goes to determines which particle it belongs to. Pixels with a level below the lower threshold can be left unprocessed. This plugin works with ROIs, including non-rectangular ROIs. Since this plug-in creates a separate output image it processes only single images or slices, no stacks. version 09-Nov-2006 Michael Schmid version 21-Nov-2006 Wayne Rasband. Adds "Display Point Selection" option and "Count" output type. version 28-May-2007 Michael Schmid. Preview added, bugfix: minima of calibrated images, uses Arrays.sort (Java2 required)

Field Summary

static int	COUNT Do not create an image, just count maxima and add count to Results table
static int	IN_TOLERANCE Output type all points around the maximum within the tolerance
static int	POINT_SELECTION Do not create image, only mark points
static int	SEGMENTED Output type watershed-segmented image
static int	SINGLE_POINTS Output type single points

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, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

MaximumFinder()

Method Summary

boolean	dialogItemChanged(GenericDialog gd, java.awt.AWTEvent e) Read the parameters (during preview or after showing the dialog)
ByteProcessor	findMaxima(ImageProcessor ip, double tolerance, double threshold, int outputType, boolean excludeOnEdges, boolean isEDM) Here the processing is done: Find the maxima of an image (does not find minima)
void	run(ImageProcessor ip) The plugin is inferred from ImageJ by this method
void	setNPasses(int nPasses) unused method required by interface ExtendedPlugInFilter
int	setup(java.lang.String arg, ImagePlus imp) Method to return types supported
int	showDialog(ImagePlus imp, java.lang.String command, PlugInFilterRunner pfr) This method is called after setup(arg, imp) unless the DONE flag has been set.

Methods inherited from class java.lang.Object

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

Field Detail

SINGLE_POINTS

public static final int SINGLE_POINTS

Output type single points

See Also:

Constant Field Values

IN_TOLERANCE

public static final int IN_TOLERANCE

Output type all points around the maximum within the tolerance

See Also:

Constant Field Values

SEGMENTED

public static final int SEGMENTED

Output type watershed-segmented image

See Also:

Constant Field Values

POINT_SELECTION

public static final int POINT_SELECTION

Do not create image, only mark points

See Also:

Constant Field Values

COUNT

public static final int COUNT

Do not create an image, just count maxima and add count to Results table

See Also:

Constant Field Values

Constructor Detail

MaximumFinder

public MaximumFinder()

Method Detail

setup

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

Method to return types supported

Specified by:

setup in interface PlugInFilter

Parameters:

arg - Not used by this plugin-filter

imp - The image to be filtered

Returns:

Code describing supported formats etc. (see ij.plugin.filter.PlugInFilter & ExtendedPlugInFilter)

showDialog

public int showDialog(ImagePlus imp,
                      java.lang.String command,
                      PlugInFilterRunner pfr)

Description copied from interface: ExtendedPlugInFilter

This method is called after setup(arg, imp) unless the DONE flag has been set.

Specified by:

showDialog in interface ExtendedPlugInFilter

Parameters:

imp - The active image already passed in the setup(arg, imp) call. It will be null, however, if the NO_IMAGE_REQUIRED flag has been set.

command - The command that has led to the invocation of the plugin-filter. Useful as a title for the dialog.

pfr - The PlugInFilterRunner calling this plugin-filter. It can be passed to a GenericDialog by addPreviewCheckbox to enable preview by calling the run(ip) method of this plugin-filter. pfr can be also used later for calling back the PlugInFilterRunner, e.g., to obtain the slice number currently processed by run(ip).

Returns:

The method should return a combination (bitwise OR) of the flags specified in interfaces PlugInFilter and ExtendedPlugInFilter.

dialogItemChanged

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

Read the parameters (during preview or after showing the dialog)

Specified by:

dialogItemChanged in interface DialogListener

Parameters:

e - The event that has been generated by the user action in the dialog. Note that e is null if the dialogItemChanged method is called after the user has pressed the OK button or if the GenericDialog has read its parameters from a macro.

gd - A reference to the GenericDialog.

Returns:

Should be true if the dialog input is valid. False disables the OK button and preview (if any).

setNPasses

public void setNPasses(int nPasses)

unused method required by interface ExtendedPlugInFilter

Specified by:

setNPasses in interface ExtendedPlugInFilter

run

public void run(ImageProcessor ip)

The plugin is inferred from ImageJ by this method

Specified by:

run in interface PlugInFilter

Parameters:

ip - The image where maxima (or minima) should be found

findMaxima

public ByteProcessor findMaxima(ImageProcessor ip,
                                double tolerance,
                                double threshold,
                                int outputType,
                                boolean excludeOnEdges,
                                boolean isEDM)

Here the processing is done: Find the maxima of an image (does not find minima)

Parameters:

ip - The input image

tolerance - Height tolerance: maxima are accepted only if protruding more than this value from the ridge to a higher maximum

threshold - minimum height of a maximum (uncalibrated); for no minimum height set it to ImageProcessor.NO_THRESHOLD

outputType - What to mark in output image: SINGLE_POINTS, MAXIMA_EXACT, IN_TOLERANCE or SEGMENTED

excludeOnEdges - Whether to exclude edge maxima

isEDM - Whether the image is a 16-bit Euclidian Distance Map

Returns:

A new byteProcessor with a normal (uninverted) LUT where the marked points are set to 255 (Background 0). Pixels outside of the roi of the input ip are not set. Returns null if outputType does not require an output or if cancelled.