theba.core.math.EDM Class Reference

List of all members.

Public Member Functions
void	run (short[] pixels, int width, int height)
void	makeEDM (short[] pixels, int width, int height)
void	findUltimatePoints (ImageProcessor ip)
Package Functions
void	setValue (int offset, int rowsize, short[] image16)
void	setEdgeValue (int offset, int rowsize, short[] image16, int x, int y, int xmax, int ymax)
void	convertToBytes (int width, int height, short[] image16, byte[] image8)
void	filterEDM (ImageProcessor edm, boolean smooth)
int	get (int x, int y, byte[] pixels, int width, int height)
void	makeCoordinateArrays (ImageProcessor edm)
void	doWatershed (ImageProcessor ip1)
int[]	makeFateTable ()
void	processLevel (int level, int pass, ImageProcessor ip1, ImageProcessor ip2, int[] table)
void	postProcess (ImageProcessor ip)
Package Attributes
ImagePlus	imp
String	arg
int	maxEDM
short[]	xCoordinate
short[]	yCoordinate
int[]	levelStart
int[]	levelOffset
int[]	histogram
int	slice
int	count
boolean	watershed
ImageWindow	win
boolean	canceled
ImageStack	movie
boolean	debug = IJ.debugMode
boolean	invertImage
Static Package Attributes
static boolean	whiteBackground = true

Detailed Description

This plugin implements the Euclidean Distance Map (EDM), Ultimate Eroded Points and Watershed commands in the Process/Binary submenu.

Definition at line 13 of file EDM.java.

Member Function Documentation

void theba.core.math.EDM.convertToBytes	(	int	width,
		int	height,
		short[]	image16,
		byte[]	image8
	)			`[package]`

Definition at line 309 of file EDM.java.

References theba.core.math.EDM.maxEDM.

void theba.core.math.EDM.doWatershed ( ImageProcessor ip1 ) [package]

Definition at line 533 of file EDM.java.

References theba.core.math.EDM.canceled, theba.core.math.EDM.count, theba.core.math.EDM.debug, theba.core.math.EDM.makeFateTable(), theba.core.math.EDM.maxEDM, theba.core.math.EDM.movie, theba.core.math.EDM.postProcess(), theba.core.math.EDM.processLevel(), and theba.core.math.EDM.win.

void theba.core.math.EDM.filterEDM	(	ImageProcessor	edm,
		boolean	smooth
	)			`[package]`

Definition at line 418 of file EDM.java.

Referenced by theba.core.math.EDM.findUltimatePoints().

void theba.core.math.EDM.findUltimatePoints ( ImageProcessor ip )

Finds peaks in the EDM that contain pixels equal to or greater than all of their neighbors.

Definition at line 332 of file EDM.java.

References theba.core.math.EDM.count, theba.core.math.EDM.debug, theba.core.math.EDM.filterEDM(), theba.core.math.EDM.histogram, theba.core.math.EDM.levelStart, theba.core.math.EDM.makeCoordinateArrays(), theba.core.math.EDM.maxEDM, theba.core.math.EDM.movie, theba.core.math.EDM.watershed, theba.core.math.EDM.xCoordinate, and theba.core.math.EDM.yCoordinate.

int theba.core.math.EDM.get	(	int	x,
		int	y,
		byte[]	pixels,
		int	width,
		int	height
	)			`[package]`

Definition at line 473 of file EDM.java.

void theba.core.math.EDM.makeCoordinateArrays ( ImageProcessor edm ) [package]

Generates the xy coordinate arrays that allow pixels at each level to be accessed directly without searching through the entire image. This method, suggested by Stein Roervik (stein@kjemi.unit.no), greatly speeds up the watershed segmentation routine.

Definition at line 491 of file EDM.java.

References theba.core.math.EDM.histogram, theba.core.math.EDM.levelOffset, theba.core.math.EDM.levelStart, theba.core.math.EDM.maxEDM, theba.core.math.EDM.xCoordinate, and theba.core.math.EDM.yCoordinate.

Referenced by theba.core.math.EDM.findUltimatePoints().

void theba.core.math.EDM.makeEDM	(	short[]	pixels,
		int	width,
		int	height
	)

Converts a binary image into a grayscale Euclidean Distance Map (EDM). Each foreground (black) pixel in the binary image is assigned a value equal to its distance from the nearest background (white) pixel. Uses the two-pass EDM algorithm from the "Image Processing Handbook" by John Russ.

Definition at line 59 of file EDM.java.

References theba.core.math.EDM.setEdgeValue(), and theba.core.math.EDM.setValue().

Referenced by theba.core.math.EDM.run().

int [] theba.core.math.EDM.makeFateTable ( ) [package]

Definition at line 564 of file EDM.java.

Referenced by theba.core.math.EDM.doWatershed().

void theba.core.math.EDM.postProcess ( ImageProcessor ip ) [package]

Definition at line 662 of file EDM.java.

Referenced by theba.core.math.EDM.doWatershed().