ij.plugin.filter
Class ParticleAnalyzer

java.lang.Object
  ij.plugin.filter.ParticleAnalyzer

All Implemented Interfaces:

Measurements, PlugInFilter

public class ParticleAnalyzer
extends Object
implements PlugInFilter, Measurements

Implements ImageJ's Analyze Particles command.

        for each line do
                for each pixel in this line do
                        if the pixel value is "inside" the threshold range then
                                trace the edge to mark the object
                                do the measurement
                                fill the object with a color outside the threshold range
                        else
                                continue the scan
        

Field Summary

static int	ADD_TO_MANAGER Add particles to ROI Manager.
protected boolean	addToManager
protected Analyzer	analyzer
protected static int	BARE_OUTLINES
static int	CLEAR_WORKSHEET Clear ImageJ console before starting.
static int	DISPLAY_SUMMARY Display a summary.
protected boolean	displaySummary
protected static int	ELLIPSES
static int	EXCLUDE_EDGE_PARTICLES Do not measure particles touching edge of image.
protected boolean	excludeEdgeParticles
protected boolean	floodFill
static int	FOUR_CONNECTED Use 4-connected particle tracing.
protected ImagePlus	imp
static int	IN_SITU_SHOW Replace original image with masks.
static int	INCLUDE_HOLES Flood fill to ignore interior holes.
protected boolean	inSituShow
protected static int	MASKS
protected static int	NOTHING
protected static int	OUTLINES
protected static int	OVERLAY_MASKS
protected static int	OVERLAY_OUTLINES
protected boolean	processStack
static int	RECORD_STARTS Record starting coordinates so outline can be recreated later using doWand(x,y).
protected boolean	recordStarts
protected boolean	resetCounter
protected static int	ROI_MASKS
protected ResultsTable	rt
static int	SHOW_MASKS Display image containing binary masks of measured particles.
static int	SHOW_NONE Do not display particle outline image.
static int	SHOW_OUTLINES Display image containing outlines of measured particles.
static int	SHOW_OVERLAY_MASKS Display filled particle as an overlay.
static int	SHOW_OVERLAY_OUTLINES Display particle outlines as an overlay.
static int	SHOW_PROGRESS Display a progress bar.
static int	SHOW_RESULTS Display results in the ImageJ console.
static int	SHOW_ROI_MASKS Display image containing grayscales masks that identify measured particles.
static int	SHOW_SUMMARY Obsolete, replaced by DISPLAY_SUMMARY
protected boolean	showProgress
protected boolean	showResults
protected boolean	showSizeDistribution
protected int	slice
protected static int	staticShowChoice

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

Fields inherited from interface ij.measure.Measurements

ADD_TO_OVERLAY, AREA, AREA_FRACTION, CENTER_OF_MASS, CENTROID, CIRCULARITY, ELLIPSE, FERET, INTEGRATED_DENSITY, INVERT_Y, KURTOSIS, LABELS, LIMIT, MAX_STANDARDS, MEAN, MEDIAN, MIN_MAX, MODE, PERIMETER, RECT, SCIENTIFIC_NOTATION, SHAPE_DESCRIPTORS, SKEWNESS, SLICE, STACK_POSITION, STD_DEV

Constructor Summary

ParticleAnalyzer()
Default constructor

ParticleAnalyzer(int options, int measurements, ResultsTable rt, double minSize, double maxSize)
Constructs a ParticleAnalyzer using the default min and max circularity values (0 and 1).

ParticleAnalyzer(int options, int measurements, ResultsTable rt, double minSize, double maxSize, double minCirc, double maxCirc)
Constructs a ParticleAnalyzer.

Method Summary

boolean	analyze(ImagePlus imp) Performs particle analysis on the specified image.
boolean	analyze(ImagePlus imp, ImageProcessor ip) Performs particle analysis on the specified ImagePlus and ImageProcessor.
protected void	drawParticle(ImageProcessor drawIP, Roi roi, ImageStatistics stats, ImageProcessor mask) Draws a selected particle in a separate image.
ImagePlus	getOutputImage() Returns the "Outlines", "Masks", "Elipses" or "Count Masks" image, or null if "Nothing" is selected in the "Show:" menu.
void	run(ImageProcessor ip) Filters use this method to process the image.
static void	savePreferences(Properties prefs) Called once when ImageJ quits.
protected void	saveResults(ImageStatistics stats, Roi roi) Saves statistics for one particle in a results table.
static void	setFontColor(String color) Sets the color ("blue", "black", etc.) of the font used to label outlines in the next particle analyzer instance.
static void	setFontSize(int size) Sets the size of the font used to label outlines in the next particle analyzer instance.
void	setHideOutputImage(boolean hideOutputImage) Set 'hideOutputImage' true to not display the "Show:" image.
static void	setLineWidth(int width) Sets the outline line width for the next ParticleAnalyzer instance.
static void	setResultsTable(ResultsTable rt) Sets the ResultsTable to be used by the next ParticleAnalyzer instance.
static void	setRoiManager(RoiManager manager) Sets the RoiManager to be used by the next ParticleAnalyzer instance.
int	setup(String arg, ImagePlus imp) This method is called once when the filter is loaded.
boolean	showDialog() Displays a modal options dialog.

Methods inherited from class java.lang.Object

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

Field Detail

SHOW_RESULTS

public static final int SHOW_RESULTS

Display results in the ImageJ console.

See Also:

Constant Field Values

SHOW_SUMMARY

public static final int SHOW_SUMMARY

Obsolete, replaced by DISPLAY_SUMMARY

See Also:

Constant Field Values

SHOW_OUTLINES

public static final int SHOW_OUTLINES

Display image containing outlines of measured particles.

See Also:

Constant Field Values

EXCLUDE_EDGE_PARTICLES

public static final int EXCLUDE_EDGE_PARTICLES

Do not measure particles touching edge of image.

See Also:

Constant Field Values

SHOW_ROI_MASKS

public static final int SHOW_ROI_MASKS

Display image containing grayscales masks that identify measured particles.

See Also:

Constant Field Values

SHOW_PROGRESS

public static final int SHOW_PROGRESS

Display a progress bar.

See Also:

Constant Field Values

CLEAR_WORKSHEET

public static final int CLEAR_WORKSHEET

Clear ImageJ console before starting.

See Also:

Constant Field Values

RECORD_STARTS

public static final int RECORD_STARTS

Record starting coordinates so outline can be recreated later using doWand(x,y).

See Also:

Constant Field Values

DISPLAY_SUMMARY

public static final int DISPLAY_SUMMARY

Display a summary.

See Also:

Constant Field Values

SHOW_NONE

public static final int SHOW_NONE

Do not display particle outline image.

See Also:

Constant Field Values

INCLUDE_HOLES

public static final int INCLUDE_HOLES

Flood fill to ignore interior holes.

See Also:

Constant Field Values

ADD_TO_MANAGER

public static final int ADD_TO_MANAGER

Add particles to ROI Manager.

See Also:

Constant Field Values

SHOW_MASKS

public static final int SHOW_MASKS

Display image containing binary masks of measured particles.

See Also:

Constant Field Values

FOUR_CONNECTED

public static final int FOUR_CONNECTED

Use 4-connected particle tracing.

See Also:

Constant Field Values

IN_SITU_SHOW

public static final int IN_SITU_SHOW

Replace original image with masks.

See Also:

Constant Field Values

SHOW_OVERLAY_OUTLINES

public static final int SHOW_OVERLAY_OUTLINES

Display particle outlines as an overlay.

See Also:

Constant Field Values

SHOW_OVERLAY_MASKS

public static final int SHOW_OVERLAY_MASKS

Display filled particle as an overlay.

See Also:

Constant Field Values

NOTHING

protected static final int NOTHING

See Also:

Constant Field Values

OUTLINES

protected static final int OUTLINES

See Also:

Constant Field Values

BARE_OUTLINES

protected static final int BARE_OUTLINES

See Also:

Constant Field Values

ELLIPSES

protected static final int ELLIPSES

See Also:

Constant Field Values

MASKS

protected static final int MASKS

See Also:

Constant Field Values

ROI_MASKS

protected static final int ROI_MASKS

See Also:

Constant Field Values

OVERLAY_OUTLINES

protected static final int OVERLAY_OUTLINES

See Also:

Constant Field Values

OVERLAY_MASKS

protected static final int OVERLAY_MASKS

See Also:

Constant Field Values

staticShowChoice

protected static int staticShowChoice

imp

protected ImagePlus imp

rt

protected ResultsTable rt

analyzer

protected Analyzer analyzer

slice

protected int slice

processStack

protected boolean processStack

showResults

protected boolean showResults

excludeEdgeParticles

protected boolean excludeEdgeParticles

showSizeDistribution

protected boolean showSizeDistribution

resetCounter

protected boolean resetCounter

showProgress

protected boolean showProgress

recordStarts

protected boolean recordStarts

displaySummary

protected boolean displaySummary

floodFill

protected boolean floodFill

addToManager

protected boolean addToManager

inSituShow

protected boolean inSituShow

Constructor Detail

ParticleAnalyzer

public ParticleAnalyzer(int options,
                        int measurements,
                        ResultsTable rt,
                        double minSize,
                        double maxSize,
                        double minCirc,
                        double maxCirc)

Constructs a ParticleAnalyzer.

Parameters:

options - a flag word created by Oring SHOW_RESULTS, EXCLUDE_EDGE_PARTICLES, etc.

measurements - a flag word created by ORing constants defined in the Measurements interface

rt - a ResultsTable where the measurements will be stored

minSize - the smallest particle size in pixels

maxSize - the largest particle size in pixels

minCirc - minimum circularity

maxCirc - maximum circularity

ParticleAnalyzer

public ParticleAnalyzer(int options,
                        int measurements,
                        ResultsTable rt,
                        double minSize,
                        double maxSize)

Constructs a ParticleAnalyzer using the default min and max circularity values (0 and 1).

ParticleAnalyzer

public ParticleAnalyzer()

Default constructor

Method Detail

setup

public int setup(String arg,
                 ImagePlus imp)

Description copied from interface: PlugInFilter

This method is called once when the filter is loaded. 'arg', which may be blank, is the argument specified for this plugin in IJ_Props.txt or in the plugins.config file of a jar archive containing the plugin. 'imp' is the currently active image. This method should return a flag word that specifies the filters capabilities.

For Plugin-filters specifying the PlugInFilter.FINAL_PROCESSING flag, the setup method will be called again, this time with arg = "final" after all other processing is done.

Specified by:

setup in interface PlugInFilter

run

public void run(ImageProcessor ip)

Description copied from interface: PlugInFilter

Filters use this method to process the image. If the PlugInFilter.DOES_STACKS flag was set, it is called for each slice in a stack. With PlugInFilter.CONVERT_TO_FLOAT, the filter is called with the image data converted to a FloatProcessor (3 times per image for RGB images). ImageJ will lock the image before calling this method and unlock it when the filter is finished. For PlugInFilters specifying the PlugInFilter.NO_IMAGE_REQUIRED flag and not the PlugInFilter.DONE flag, run(ip) is called once with the argument null.

Specified by:

run in interface PlugInFilter

showDialog

public boolean showDialog()

Displays a modal options dialog.

analyze

public boolean analyze(ImagePlus imp)

Performs particle analysis on the specified image. Returns false if there is an error.

analyze

public boolean analyze(ImagePlus imp,
                       ImageProcessor ip)

Performs particle analysis on the specified ImagePlus and ImageProcessor. Returns false if there is an error.

saveResults

protected void saveResults(ImageStatistics stats,
                           Roi roi)

Saves statistics for one particle in a results table. This is a method subclasses may want to override.

drawParticle

protected void drawParticle(ImageProcessor drawIP,
                            Roi roi,
                            ImageStatistics stats,
                            ImageProcessor mask)

Draws a selected particle in a separate image. This is another method subclasses may want to override.

getOutputImage

public ImagePlus getOutputImage()

Returns the "Outlines", "Masks", "Elipses" or "Count Masks" image, or null if "Nothing" is selected in the "Show:" menu.

setHideOutputImage

public void setHideOutputImage(boolean hideOutputImage)

Set 'hideOutputImage' true to not display the "Show:" image.

setFontSize

public static void setFontSize(int size)

Sets the size of the font used to label outlines in the next particle analyzer instance.

setFontColor

public static void setFontColor(String color)

Sets the color ("blue", "black", etc.) of the font used to label outlines in the next particle analyzer instance.

setLineWidth

public static void setLineWidth(int width)

Sets the outline line width for the next ParticleAnalyzer instance.

setRoiManager

public static void setRoiManager(RoiManager manager)

Sets the RoiManager to be used by the next ParticleAnalyzer instance. There is a JavaScript example at http://imagej.nih.gov/ij/macros/js/HiddenRoiManager.js

setResultsTable

public static void setResultsTable(ResultsTable rt)

Sets the ResultsTable to be used by the next ParticleAnalyzer instance.

savePreferences

public static void savePreferences(Properties prefs)

Called once when ImageJ quits.