edu.jhu.tmaj.beans.masks.results
Class Analyzer2

java.lang.Object
  edu.jhu.tmaj.beans.masks.results.Analyzer2

All Implemented Interfaces:

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

public class Analyzer2
extends java.lang.Object
implements ij.plugin.filter.PlugInFilter, ij.measure.Measurements

This plugin implements ImageJ's Analyze/Measure and Analyze/Set Measurements commands.

Field Summary

static java.awt.Color	darkBlue
(package private) static int	firstParticle
(package private) static int	lastParticle
static int	markWidth
static int	precision

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

Analyzer2()

Analyzer2(ij.ImagePlus imp)
Constructs a new Analyzer using the specified ImagePlus object and the current measurement options and default results table.

Analyzer2(ij.ImagePlus imp, int measurements, ij.measure.ResultsTable rt)
Construct a new Analyzer using an ImagePlus object and private measurement options and results table.

Method Summary

void	displayResults() Writes the last row in the system results table to the Results window.
(package private) void	doSetDialog()
(package private) double	getArea(java.awt.Polygon p)
static int	getCounter() Returns the current measurement count.
(package private) java.lang.String	getFileName()
static int	getMeasurements()
static int	getPrecision() Returns the number of digits displayed to the right of decimal point.
static ij.ImagePlus	getRedirectImage(ij.ImagePlus currentImage)
(package private) ij.process.ImageStatistics	getRedirectStats(int measurements, ij.gui.Roi roi)
static ij.measure.ResultsTable	getResultsTable() Returns the default results table.
static float[]	getUMeans() Returns an array containing the first 20 uncalibrated means.
(package private) void	incrementCounter()
static boolean	isRedirectImage() Returns true if an image is selected in the "Redirect To:" popup menu of the Analyze/Set Measurements dialog box.
void	measure() Measures the image or selection and adds the results to the default results table.
(package private) void	measureAngle(ij.gui.Roi roi)
(package private) void	measureLength(ij.gui.Roi roi)
(package private) void	measurePoint(ij.gui.Roi roi)
java.lang.String	n(double n) Converts a number to a formatted string with a tab at the end.
(package private) boolean	reset()
static boolean	resetCounter() Sets the measurement counter to zero.
void	run(ij.process.ImageProcessor ip)
(package private) void	savePoints(ij.gui.Roi roi)
static void	savePreferences(java.util.Properties prefs) Called once when ImageJ quits.
void	saveResults(ij.process.ImageStatistics stats, ij.gui.Roi roi) Saves the measurements specified in the "Set Measurements" dialog, or by calling setMeasurements(), in the default results table.
static void	setDefaultHeadings() Sets the default headings ("Area", "Mean", etc.).
static void	setMeasurement(int option, boolean state) Sets the specified system-wide measurement option.
static void	setMeasurements(int measurements) Sets the system-wide measurement options.
static void	setOption(java.lang.String option, boolean b)
(package private) void	setOptions(ij.gui.GenericDialog gd)
static void	setPrecision(int decimalPlaces) Sets the number of digits displayed to the right of decimal point.
static void	setRedirectImage(ij.ImagePlus imagePlus)
static void	setResultsTable(ij.measure.ResultsTable rt)
static void	setUnsavedMeasurements(boolean b)
int	setup(java.lang.String arg, ij.ImagePlus imp)
void	summarize()
(package private) void	summarizeAreas()
void	updateHeadings() Redisplays the results table.
static double	updateY(double y, int imageHeight) Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.
static int	updateY(int y, int imageHeight) Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.

Methods inherited from class java.lang.Object

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

Field Detail

darkBlue

public static java.awt.Color darkBlue

markWidth

public static int markWidth

precision

public static int precision

firstParticle

static int firstParticle

lastParticle

static int lastParticle

Constructor Detail

Analyzer2

public Analyzer2()

Analyzer2

public Analyzer2(ij.ImagePlus imp)

Constructs a new Analyzer using the specified ImagePlus object and the current measurement options and default results table.

Analyzer2

public Analyzer2(ij.ImagePlus imp,
                 int measurements,
                 ij.measure.ResultsTable rt)

Construct a new Analyzer using an ImagePlus object and private measurement options and results table.

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

doSetDialog

void doSetDialog()

setOptions

void setOptions(ij.gui.GenericDialog gd)

measure

public void measure()

Measures the image or selection and adds the results to the default results table.

reset

boolean reset()

setRedirectImage

public static void setRedirectImage(ij.ImagePlus imagePlus)

getRedirectImage

public static ij.ImagePlus getRedirectImage(ij.ImagePlus currentImage)

isRedirectImage

public static boolean isRedirectImage()

Returns true if an image is selected in the "Redirect To:" popup menu of the Analyze/Set Measurements dialog box.

getRedirectStats

ij.process.ImageStatistics getRedirectStats(int measurements,
                                            ij.gui.Roi roi)

measurePoint

void measurePoint(ij.gui.Roi roi)

measureAngle

void measureAngle(ij.gui.Roi roi)

measureLength

void measureLength(ij.gui.Roi roi)

saveResults

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

Saves the measurements specified in the "Set Measurements" dialog, or by calling setMeasurements(), in the default results table.

getArea

final double getArea(java.awt.Polygon p)

savePoints

void savePoints(ij.gui.Roi roi)

getFileName

java.lang.String getFileName()

displayResults

public void displayResults()

Writes the last row in the system results table to the Results window.

updateHeadings

public void updateHeadings()

Redisplays the results table.

n

public java.lang.String n(double n)

Converts a number to a formatted string with a tab at the end.

incrementCounter

void incrementCounter()

summarize

public void summarize()

summarizeAreas

void summarizeAreas()

getCounter

public static int getCounter()

Returns the current measurement count.

resetCounter

public static boolean resetCounter()

Sets the measurement counter to zero. Displays a dialog that allows the user to save any existing measurements. Returns false if the user cancels the dialog.

setUnsavedMeasurements

public static void setUnsavedMeasurements(boolean b)

getMeasurements

public static int getMeasurements()

setMeasurements

public static void setMeasurements(int measurements)

Sets the system-wide measurement options.

setMeasurement

public static void setMeasurement(int option,
                                  boolean state)

Sets the specified system-wide measurement option.

savePreferences

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

Called once when ImageJ quits.

getUMeans

public static float[] getUMeans()

Returns an array containing the first 20 uncalibrated means.

getResultsTable

public static ij.measure.ResultsTable getResultsTable()

Returns the default results table. This table should only be displayed in a the "Results" window.

getPrecision

public static int getPrecision()

Returns the number of digits displayed to the right of decimal point.

setPrecision

public static void setPrecision(int decimalPlaces)

Sets the number of digits displayed to the right of decimal point.

updateY

public static int updateY(int y,
                          int imageHeight)

Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.

updateY

public static double updateY(double y,
                             int imageHeight)

Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.

setDefaultHeadings

public static void setDefaultHeadings()

Sets the default headings ("Area", "Mean", etc.).

setOption

public static void setOption(java.lang.String option,
                             boolean b)

setResultsTable

public static void setResultsTable(ij.measure.ResultsTable rt)