theba.trackers.HHTracker Class Reference

List of all members.

Classes
class	FindAllCandidatesAction
class	FindCandidatesAction
Public Member Functions
void	track ()
	HHTracker (ThebaGUI f)
void	setup ()
float	checkReg (int xp, int yp, final short[] input)
void	findCandidates (int slice)
LinkedList	getFibers ()
boolean	isReserved (short val)
void	mouseClicked (Point3D p)
boolean	removeCrack (int slice, short[] lumen)
void	removeStuff (int slice, short[] lumen)
void	selectSeed (Point e)
void	setFibers (LinkedList fibers)
void	traceWalls ()
void	reset ()
void	stop ()
Static Public Member Functions
static void	dilate3d_toWhite (Stack voxels, long[] counts)
Static Package Functions
static final short	max (short x, short y)
Package Attributes
boolean	seedStillValid = true

Detailed Description

This class represents a java-version of the HH-approach described in the Thesis

Author:: jensbw; perchrh

Definition at line 44 of file HHTracker.java.

Constructor & Destructor Documentation

theba.trackers.HHTracker.HHTracker ( ThebaGUI f )

Definition at line 196 of file HHTracker.java.

Member Function Documentation

float theba.trackers.HHTracker.checkReg	(	int	xp,
		int	yp,
		final short[]	input
	)

Definition at line 360 of file HHTracker.java.

Referenced by theba.trackers.HHTracker.removeStuff().

static void theba.trackers.HHTracker.dilate3d_toWhite	(	Stack	voxels,
		long[]	counts
	)			`[static]`

Dilates a 3d volume using the elementary 6-connected structure element

Parameters:

voxels

Definition at line 242 of file HHTracker.java.

References theba.core.Tracker.control, theba.core.Stack.getDepth(), theba.core.Stack.getHeight(), theba.core.gui.ThebaGUI.getInstance(), theba.core.Stack.getSlice(), theba.core.Stack.getWidth(), theba.trackers.HHTracker.max(), and theba.core.gui.ThebaGUI.setProgress().

void theba.trackers.HHTracker.findCandidates ( int slice )

Returns a centered point in a region marked by search data.

Parameters:

	searchmask
	data

Returns:

Definition at line 427 of file HHTracker.java.

Referenced by theba.trackers.HHTracker.setup().

LinkedList theba.trackers.HHTracker.getFibers ( )

Definition at line 515 of file HHTracker.java.

boolean theba.trackers.HHTracker.isReserved ( short val )

Definition at line 519 of file HHTracker.java.

Referenced by theba.trackers.HHTracker.traceWalls().

static final short theba.trackers.HHTracker.max	(	short	x,
		short	y
	)			`[static, package]`

Definition at line 231 of file HHTracker.java.

Referenced by theba.trackers.HHTracker.dilate3d_toWhite().

void theba.trackers.HHTracker.mouseClicked ( Point3D p ) [virtual]

Implements theba.core.Tracker.

Definition at line 526 of file HHTracker.java.

References theba.trackers.HHTracker.selectSeed(), theba.core.math.Point3D.x, and theba.core.math.Point3D.y.

boolean theba.trackers.HHTracker.removeCrack	(	int	slice,
		short[]	lumen
	)

Definition at line 531 of file HHTracker.java.

References theba.trackers.HHTracker.seedStillValid.

Referenced by theba.trackers.HHTracker.track().

void theba.trackers.HHTracker.removeStuff	(	int	slice,
		short[]	lumen
	)

Definition at line 578 of file HHTracker.java.

References theba.trackers.HHTracker.checkReg(), theba.core.LumenCandidate.getSize(), theba.core.Tracker.log, theba.core.math.Point3D.x, and theba.core.math.Point3D.y.

Referenced by theba.trackers.HHTracker.track().

void theba.trackers.HHTracker.reset ( ) [virtual]

Implements theba.core.Tracker.

Definition at line 1064 of file HHTracker.java.

void theba.trackers.HHTracker.selectSeed ( Point e )

Definition at line 631 of file HHTracker.java.

Referenced by theba.trackers.HHTracker.mouseClicked().

void theba.trackers.HHTracker.setFibers ( LinkedList fibers )

Definition at line 669 of file HHTracker.java.

void theba.trackers.HHTracker.setup ( ) [virtual]

Implements theba.core.Tracker.

Definition at line 201 of file HHTracker.java.

References theba.core.gui.ThebaGUI.addMenuItem(), theba.core.gui.ThebaGUI.addMenuSeparator(), theba.core.gui.ThebaGUI.addToolbarButton(), theba.core.Tracker.control, theba.trackers.HHTracker.findCandidates(), and theba.trackers.HHTracker.track().

void theba.trackers.HHTracker.stop ( ) [virtual]

Implements theba.core.Tracker.

Definition at line 1068 of file HHTracker.java.

void theba.trackers.HHTracker.traceWalls ( )

This function uses tracked lumens to track the walls around the lumens. Theory of operation: First, extract all lumens from the image. Then extract all the disjoint regions that make up each lumen. Merge the two largest regions of each lumen by tracing a path between them. Create an Euclidean distance map of image+lumens. Do watershed segmentation of the inverse of this map with background pixels set to background. For all lumens, join watershed regions that touches the lumen.

Definition at line 684 of file HHTracker.java.

References theba.core.io.SliceWriter.flush(), theba.core.Lumen.getBounds(), theba.core.Lumen.getDistanceMap(), theba.core.Lumen.getId(), theba.core.Lumen.getLumenMask(), theba.core.math.DistancePath.getPath(), theba.trackers.HHTracker.isReserved(), theba.core.Tracker.keepTracking, theba.core.FiberSlice.lumendata, and theba.core.io.SliceWriter.putSlice().