ParticleAnalyzer (ImageJ API)

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

Fields
Modifier and Type	Field	Description
`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 "Results" window 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.measure.Measurements
ADD_TO_OVERLAY, ALL_STATS, AREA, AREA_FRACTION, CENTER_OF_MASS, CENTROID, CIRCULARITY, ELLIPSE, FERET, INTEGRATED_DENSITY, INVERT_Y, KURTOSIS, LABELS, LIMIT, MAX_STANDARDS, MEAN, MEDIAN, MIN_MAX, MODE, NaN_EMPTY_CELLS, PERIMETER, RECT, SCIENTIFIC_NOTATION, SHAPE_DESCRIPTORS, SKEWNESS, SLICE, STACK_POSITION, STD_DEV

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	Description
`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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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 "Results" window 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 can 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.

Class ParticleAnalyzer

Field Summary

Fields inherited from interface ij.measure.Measurements

Fields inherited from interface ij.plugin.filter.PlugInFilter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SHOW_RESULTS

SHOW_SUMMARY

SHOW_OUTLINES

EXCLUDE_EDGE_PARTICLES

SHOW_ROI_MASKS

SHOW_PROGRESS

CLEAR_WORKSHEET

RECORD_STARTS

DISPLAY_SUMMARY

SHOW_NONE

INCLUDE_HOLES

ADD_TO_MANAGER

SHOW_MASKS

FOUR_CONNECTED

IN_SITU_SHOW

SHOW_OVERLAY_OUTLINES

SHOW_OVERLAY_MASKS

NOTHING

OUTLINES

BARE_OUTLINES

ELLIPSES

MASKS

ROI_MASKS

OVERLAY_OUTLINES

OVERLAY_MASKS

staticShowChoice

imp

rt

analyzer

slice

processStack

showResults

excludeEdgeParticles

showSizeDistribution

resetCounter

showProgress

recordStarts

displaySummary

floodFill

addToManager

inSituShow

Constructor Detail

ParticleAnalyzer

ParticleAnalyzer

ParticleAnalyzer

Method Detail

setup

run

showDialog

analyze

analyze

saveResults

drawParticle

getOutputImage

setHideOutputImage

setFontSize

setFontColor

setLineWidth

setRoiManager

setResultsTable

savePreferences