edu.jhu.tmaj.beans.masks.results
Class ParticleAnalyzer2

java.lang.Object
  edu.jhu.tmaj.beans.masks.results.ParticleAnalyzer2

All Implemented Interfaces:

ij.measure.Measurements, ij.plugin.filter.PlugInFilter

public class ParticleAnalyzer2
extends java.lang.Object
implements ij.plugin.filter.PlugInFilter, ij.measure.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 Analyzer2	analyzer
(package private) static int	BYTE
static int	CLEAR_WORKSHEET Clear ImageJ console before starting.
(package private) int	counter
(package private) static double	DEFAULT_MAX_SIZE
(package private) static double	DEFAULT_MIN_SIZE
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
(package private) static int	FLOAT
protected boolean	floodFill
static int	FOUR_CONNECTED Use 4-connected particle tracing.
protected ij.ImagePlus	imp
static int	INCLUDE_HOLES Flood fill to ignore interior holes.
protected static int	MASKS
protected static int	NOTHING
(package private) static java.lang.String	OPTIONS
protected static int	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
(package private) static int	RGB
protected static int	ROI_MASKS
protected ij.measure.ResultsTable	rt
(package private) static int	SHORT
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_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
protected static int	showChoice
protected boolean	showProgress
protected boolean	showResults
protected boolean	showSizeDistribution
protected int	slice

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_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Fields inherited from interface ij.measure.Measurements

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

ParticleAnalyzer2()
Default constructor

ParticleAnalyzer2(int options, int measurements, ij.measure.ResultsTable rt, double minSize, double maxSize)
Constructs a ParticleAnalyzer using the default min and max circularity values (0 and 1).

ParticleAnalyzer2(int options, int measurements, ij.measure.ResultsTable rt, double minSize, double maxSize, double minCirc, double maxCirc)
Constructs a ParticleAnalyzer.

Method Summary

(package private) java.lang.String	addMeans(java.lang.String line, int start)
boolean	analyze(ij.ImagePlus imp) Performs particle analysis on the specified image.
boolean	analyze(ij.ImagePlus imp, ij.process.ImageProcessor ip) Performs particle analysis on the specified ImagePlus and ImageProcessor.
(package private) void	analyzeParticle(int x, int y, ij.ImagePlus imp, ij.process.ImageProcessor ip)
(package private) void	drawEllipse(ij.process.ImageProcessor ip, ij.process.ImageStatistics stats, int count)
(package private) void	drawFilledParticle(ij.process.ImageProcessor ip, ij.gui.Roi roi, ij.process.ImageProcessor mask)
(package private) void	drawOutline(ij.process.ImageProcessor ip, ij.gui.Roi roi, int count)
protected void	drawParticle(ij.process.ImageProcessor drawIP, ij.gui.Roi roi, ij.process.ImageStatistics stats, ij.process.ImageProcessor mask) Draws a selected particle in a separate image.
(package private) void	drawRoiFilledParticle(ij.process.ImageProcessor ip, ij.gui.Roi roi, ij.process.ImageProcessor mask, int count)
(package private) boolean	eraseOutsideRoi(ij.process.ImageProcessor ip, java.awt.Rectangle r, ij.process.ImageProcessor mask)
(package private) int	getColumnID(java.lang.String name)
ij.ImagePlus	getOutputImage() Returns the "Outlines", "Masks", "Elipses" or "Count Masks" image, or null if "Nothing" is selected in the "Show:" menu.
(package private) ij.process.ImageStatistics	getStatistics(ij.process.ImageProcessor ip, int mOptions, ij.measure.Calibration cal)
(package private) void	makeCustomLut()
(package private) java.lang.String	n(double n)
void	run(ij.process.ImageProcessor ip)
static void	savePreferences(java.util.Properties prefs) Called once when ImageJ quits.
protected void	saveResults(ij.process.ImageStatistics stats, ij.gui.Roi roi) Saves statistics for one particle in a results table.
void	setHideOutputImage(boolean hideOutputImage) Set 'hideOutputImage' true to not display the "Show:" image.
(package private) boolean	setThresholdLevels(ij.ImagePlus imp, ij.process.ImageProcessor ip)
int	setup(java.lang.String arg, ij.ImagePlus imp)
boolean	showDialog() Displays a modal options dialog.
(package private) void	showResults()
(package private) boolean	updateMacroOptions()
(package private) void	updateSliceSummary()

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

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

OPTIONS

static final java.lang.String OPTIONS

See Also:

Constant Field Values

BYTE

static final int BYTE

See Also:

Constant Field Values

SHORT

static final int SHORT

See Also:

Constant Field Values

FLOAT

static final int FLOAT

See Also:

Constant Field Values

RGB

static final int RGB

See Also:

Constant Field Values

DEFAULT_MIN_SIZE

static final double DEFAULT_MIN_SIZE

See Also:

Constant Field Values

DEFAULT_MAX_SIZE

static final double DEFAULT_MAX_SIZE

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

MASKS

protected static final int MASKS

See Also:

Constant Field Values

ELLIPSES

protected static final int ELLIPSES

See Also:

Constant Field Values

ROI_MASKS

protected static final int ROI_MASKS

See Also:

Constant Field Values

showChoice

protected static int showChoice

imp

protected ij.ImagePlus imp

rt

protected ij.measure.ResultsTable rt

analyzer

protected Analyzer2 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

counter

int counter

Constructor Detail

ParticleAnalyzer2

public ParticleAnalyzer2(int options,
                         int measurements,
                         ij.measure.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

ParticleAnalyzer2

public ParticleAnalyzer2(int options,
                         int measurements,
                         ij.measure.ResultsTable rt,
                         double minSize,
                         double maxSize)

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

ParticleAnalyzer2

public ParticleAnalyzer2()

Default constructor

Method Detail

setup

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

Specified by:

setup in interface ij.plugin.filter.PlugInFilter

run

public void run(ij.process.ImageProcessor ip)

Specified by:

run in interface ij.plugin.filter.PlugInFilter

showDialog

public boolean showDialog()

Displays a modal options dialog.

updateMacroOptions

boolean updateMacroOptions()

analyze

public boolean analyze(ij.ImagePlus imp)

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

analyze

public boolean analyze(ij.ImagePlus imp,
                       ij.process.ImageProcessor ip)

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

updateSliceSummary

void updateSliceSummary()

addMeans

java.lang.String addMeans(java.lang.String line,
                          int start)

n

java.lang.String n(double n)

eraseOutsideRoi

boolean eraseOutsideRoi(ij.process.ImageProcessor ip,
                        java.awt.Rectangle r,
                        ij.process.ImageProcessor mask)

setThresholdLevels

boolean setThresholdLevels(ij.ImagePlus imp,
                           ij.process.ImageProcessor ip)

analyzeParticle

void analyzeParticle(int x,
                     int y,
                     ij.ImagePlus imp,
                     ij.process.ImageProcessor ip)

getStatistics

ij.process.ImageStatistics getStatistics(ij.process.ImageProcessor ip,
                                         int mOptions,
                                         ij.measure.Calibration cal)

saveResults

protected void saveResults(ij.process.ImageStatistics stats,
                           ij.gui.Roi roi)

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

drawParticle

protected void drawParticle(ij.process.ImageProcessor drawIP,
                            ij.gui.Roi roi,
                            ij.process.ImageStatistics stats,
                            ij.process.ImageProcessor mask)

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

drawFilledParticle

void drawFilledParticle(ij.process.ImageProcessor ip,
                        ij.gui.Roi roi,
                        ij.process.ImageProcessor mask)

drawOutline

void drawOutline(ij.process.ImageProcessor ip,
                 ij.gui.Roi roi,
                 int count)

drawEllipse

void drawEllipse(ij.process.ImageProcessor ip,
                 ij.process.ImageStatistics stats,
                 int count)

drawRoiFilledParticle

void drawRoiFilledParticle(ij.process.ImageProcessor ip,
                           ij.gui.Roi roi,
                           ij.process.ImageProcessor mask,
                           int count)

showResults

void showResults()

getOutputImage

public ij.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.

getColumnID

int getColumnID(java.lang.String name)

makeCustomLut

void makeCustomLut()

savePreferences

public static void savePreferences(java.util.Properties prefs)

Called once when ImageJ quits.