Classes | |
class | AutosegmentAction |
class | FindAllCandidatesAction |
class | FindCandidatesAction |
Public Member Functions | |
void | track () |
FiberTracker (ThebaGUI f) | |
void | setup () |
void | autoSegment () |
float | checkReg (int xp, int yp, final short[] input) |
void | findCandidates (int slice) |
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 | 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 |
This class represents the methods suggested for composite fiber-segmentation in our thesis
Definition at line 39 of file FiberTracker.java.
theba.trackers.FiberTracker.FiberTracker | ( | ThebaGUI | f | ) |
Definition at line 180 of file FiberTracker.java.
void theba.trackers.FiberTracker.autoSegment | ( | ) |
Definition at line 221 of file FiberTracker.java.
References theba.core.Tracker.control, theba.trackers.FiberTracker.findCandidates(), theba.core.gui.ThebaGUI.flipVolume(), theba.core.Stack.getDepth(), theba.core.gui.ThebaGUI.getStack(), and theba.trackers.FiberTracker.track().
float theba.trackers.FiberTracker.checkReg | ( | int | xp, | |
int | yp, | |||
final short[] | input | |||
) |
Definition at line 399 of file FiberTracker.java.
Referenced by theba.trackers.FiberTracker.removeStuff().
static void theba.trackers.FiberTracker.dilate3d_toWhite | ( | Stack | voxels, | |
long[] | counts | |||
) | [static] |
Dilates a 3d volume using the elementary 6-connected structure element
voxels |
Definition at line 250 of file FiberTracker.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.FiberTracker.max(), and theba.core.gui.ThebaGUI.setProgress().
void theba.trackers.FiberTracker.findCandidates | ( | int | slice | ) |
Returns a centered point in a region marked by search data.
searchmask | ||
data |
Definition at line 466 of file FiberTracker.java.
Referenced by theba.trackers.FiberTracker.autoSegment(), and theba.trackers.FiberTracker.setup().
boolean theba.trackers.FiberTracker.isReserved | ( | short | val | ) |
Definition at line 564 of file FiberTracker.java.
static final short theba.trackers.FiberTracker.max | ( | short | x, | |
short | y | |||
) | [static, package] |
Definition at line 239 of file FiberTracker.java.
Referenced by theba.trackers.FiberTracker.dilate3d_toWhite().
void theba.trackers.FiberTracker.mouseClicked | ( | Point3D | p | ) | [virtual] |
Implements theba.core.Tracker.
Definition at line 571 of file FiberTracker.java.
References theba.trackers.FiberTracker.selectSeed(), theba.core.math.Point3D.x, and theba.core.math.Point3D.y.
boolean theba.trackers.FiberTracker.removeCrack | ( | int | slice, | |
short[] | lumen | |||
) |
Definition at line 576 of file FiberTracker.java.
References theba.trackers.FiberTracker.seedStillValid.
Referenced by theba.trackers.FiberTracker.track().
void theba.trackers.FiberTracker.removeStuff | ( | int | slice, | |
short[] | lumen | |||
) |
Counts the number of lumen regions and orders them by size. Only the largest region is kept, unless the two largest regions are comparable in size indicating a lumen split.
Definition at line 633 of file FiberTracker.java.
References theba.trackers.FiberTracker.checkReg(), theba.core.LumenCandidate.getSize(), theba.core.Tracker.log, theba.core.math.Point3D.x, and theba.core.math.Point3D.y.
Referenced by theba.trackers.FiberTracker.track().
void theba.trackers.FiberTracker.reset | ( | ) | [virtual] |
Implements theba.core.Tracker.
Definition at line 792 of file FiberTracker.java.
void theba.trackers.FiberTracker.selectSeed | ( | Point | e | ) |
Definition at line 683 of file FiberTracker.java.
Referenced by theba.trackers.FiberTracker.mouseClicked().
void theba.trackers.FiberTracker.setup | ( | ) | [virtual] |
Implements theba.core.Tracker.
Definition at line 185 of file FiberTracker.java.
References theba.core.gui.ThebaGUI.addMenuItem(), theba.core.gui.ThebaGUI.addMenuSeparator(), theba.core.gui.ThebaGUI.addToolbarButton(), theba.core.Tracker.control, theba.trackers.FiberTracker.findCandidates(), and theba.trackers.FiberTracker.track().
void theba.trackers.FiberTracker.stop | ( | ) | [virtual] |
Implements theba.core.Tracker.
Definition at line 796 of file FiberTracker.java.
void theba.trackers.FiberTracker.track | ( | ) | [virtual] |
This is the code executed to track all currently selected seeds
Implements theba.core.Tracker.
Definition at line 68 of file FiberTracker.java.
References theba.core.Tracker.control, theba.core.Stack.getDepth(), theba.core.Stack.getHeight(), theba.core.gui.ThebaGUI.getNewFiberId(), theba.core.gui.ThebaGUI.getPreferences(), theba.core.gui.ThebaGUI.getSlice(), theba.core.gui.ThebaGUI.getStack(), theba.core.Stack.getWidth(), theba.core.gui.ThebaGUI.INVALID, theba.core.Tracker.keepTracking, theba.core.Tracker.log, theba.core.gui.ThebaGUI.MAX_FIBERS, theba.core.gui.ThebaGUI.releaseFiberId(), theba.trackers.FiberTracker.removeCrack(), theba.trackers.FiberTracker.removeStuff(), theba.trackers.FiberTracker.seedStillValid, theba.core.gui.ThebaGUI.setProgress(), theba.core.gui.ThebaGUI.setProgressComplete(), theba.core.gui.ThebaGUI.showImage(), theba.core.gui.ThebaGUI.showResults(), theba.core.gui.ThebaGUI.updateImage(), theba.core.math.Point3D.x, theba.core.math.Point3D.y, and theba.core.math.Point3D.z.
Referenced by theba.trackers.FiberTracker.autoSegment(), and theba.trackers.FiberTracker.setup().
boolean theba.trackers.FiberTracker.seedStillValid = true [package] |
Definition at line 48 of file FiberTracker.java.
Referenced by theba.trackers.FiberTracker.removeCrack(), and theba.trackers.FiberTracker.track().