theba.trackers.BackTracker Class Reference

List of all members.

Classes

class  AutosegmentAction
class  FindAllCandidatesAction
class  FindCandidatesAction

Public Member Functions

 BackTracker (ThebaGUI f)
void setup ()
void autoSegment ()
float checkReg (int xp, int yp, final short[] input)
void dispose ()
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 reset ()
void selectSeed (Point e)
void setFibers (LinkedList fibers)
void traceWalls ()
void track ()
void stop ()

Static Public Member Functions

static void dilate3d_toWhite (Stack voxels)

Static Package Functions

static final short max (short x, short y)

Package Attributes

PrintStream neuralOut
boolean seedStillValid = true

Detailed Description

Definition at line 39 of file BackTracker.java.


Constructor & Destructor Documentation

theba.trackers.BackTracker.BackTracker ( ThebaGUI  f  ) 

Definition at line 91 of file BackTracker.java.


Member Function Documentation

void theba.trackers.BackTracker.autoSegment (  ) 
float theba.trackers.BackTracker.checkReg ( int  xp,
int  yp,
final short[]  input 
)
static void theba.trackers.BackTracker.dilate3d_toWhite ( Stack  voxels  )  [static]
void theba.trackers.BackTracker.dispose (  ) 

Definition at line 355 of file BackTracker.java.

References theba.trackers.BackTracker.neuralOut.

void theba.trackers.BackTracker.findCandidates ( int  slice  ) 
LinkedList theba.trackers.BackTracker.getFibers (  ) 

Definition at line 449 of file BackTracker.java.

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

Definition at line 453 of file BackTracker.java.

References theba.core.gui.ThebaGUI.INVALID.

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

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

Definition at line 168 of file BackTracker.java.

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

void theba.trackers.BackTracker.mouseClicked ( Point3D  p  )  [virtual]
boolean theba.trackers.BackTracker.removeCrack ( int  slice,
short[]  lumen 
)
void theba.trackers.BackTracker.removeStuff ( int  slice,
short[]  lumen 
)
void theba.trackers.BackTracker.reset (  )  [virtual]

Implements theba.core.Tracker.

Definition at line 578 of file BackTracker.java.

void theba.trackers.BackTracker.selectSeed ( Point  e  ) 
void theba.trackers.BackTracker.setFibers ( LinkedList  fibers  ) 

Definition at line 625 of file BackTracker.java.

void theba.trackers.BackTracker.setup (  )  [virtual]
void theba.trackers.BackTracker.stop (  )  [virtual]

Implements theba.core.Tracker.

Definition at line 1107 of file BackTracker.java.

void theba.trackers.BackTracker.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 640 of file BackTracker.java.

References theba.core.gui.ThebaGUI.addChannel(), theba.core.gui.ThebaGUI.clearChannels(), theba.core.io.SliceWriter.flush(), theba.core.Lumen.getBounds(), theba.core.Stack.getDepth(), theba.core.Lumen.getDistanceMap(), theba.core.Stack.getHeight(), theba.core.Lumen.getId(), theba.core.Lumen.getLumenMask(), theba.core.math.DistancePath.getPath(), theba.core.gui.ThebaGUI.getSlice(), theba.core.gui.ThebaGUI.getStack(), theba.core.Stack.getWidth(), theba.core.gui.ThebaGUI.INVALID, theba.trackers.BackTracker.isReserved(), theba.core.Tracker.keepTracking, theba.core.FiberSlice.lumendata, theba.core.io.SliceWriter.putSlice(), theba.core.gui.ThebaGUI.updateImage(), and theba.core.gui.ThebaGUI.updateSlice().

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

void theba.trackers.BackTracker.track (  )  [virtual]

Member Data Documentation

PrintStream theba.trackers.BackTracker.neuralOut [package]

The documentation for this class was generated from the following file:

Generated on Fri Nov 13 08:57:08 2009 for Theba by  doxygen 1.6.1