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, NO_UNDO_RESET, 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

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.
`static void`	`setSummaryTable(ResultsTable rt)`	Sets the ResultsTable to be used by the next ParticleAnalyzer instance for the summary.
`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 Details
- 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 Details
- 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 Details
- 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.
- setSummaryTable
  
  public static void setSummaryTable(ResultsTable rt)
  
  Sets the ResultsTable to be used by the next ParticleAnalyzer instance for the summary.
- 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 Details

Constructor Details

Method Details