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 |
Definition at line 39 of file BackTracker.java.
theba.trackers.BackTracker.BackTracker | ( | ThebaGUI | f | ) |
Definition at line 91 of file BackTracker.java.
void theba.trackers.BackTracker.autoSegment | ( | ) |
Definition at line 144 of file BackTracker.java.
References theba.core.Tracker.control, theba.trackers.BackTracker.findCandidates(), theba.core.gui.ThebaGUI.flipVolume(), theba.core.Stack.getDepth(), theba.core.gui.ThebaGUI.getStack(), and theba.trackers.BackTracker.track().
float theba.trackers.BackTracker.checkReg | ( | int | xp, | |
int | yp, | |||
final short[] | input | |||
) |
Definition at line 295 of file BackTracker.java.
References theba.core.Stack.getHeight(), theba.core.gui.ThebaGUI.getStack(), and theba.core.Stack.getWidth().
Referenced by theba.trackers.BackTracker.removeStuff().
static void theba.trackers.BackTracker.dilate3d_toWhite | ( | Stack | voxels | ) | [static] |
Dilates a 3d volume using the elementary 6-connected structure element
voxels |
Definition at line 179 of file BackTracker.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.BackTracker.max(), and theba.core.gui.ThebaGUI.setProgress().
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 | ) |
Returns a centered point in a region marked by search data.
searchmask | ||
data |
Definition at line 367 of file BackTracker.java.
References theba.core.Stack.getHeight(), theba.core.gui.ThebaGUI.getSlice(), theba.core.gui.ThebaGUI.getStack(), theba.core.Stack.getWidth(), theba.core.gui.ThebaGUI.setLabel(), and theba.core.gui.ThebaGUI.showImage().
Referenced by theba.trackers.BackTracker.autoSegment(), and theba.trackers.BackTracker.setup().
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] |
Implements theba.core.Tracker.
Definition at line 460 of file BackTracker.java.
References theba.trackers.BackTracker.selectSeed(), theba.core.math.Point3D.x, and theba.core.math.Point3D.y.
boolean theba.trackers.BackTracker.removeCrack | ( | int | slice, | |
short[] | lumen | |||
) |
Definition at line 465 of file BackTracker.java.
References theba.core.Stack.getDepth(), theba.core.Stack.getHeight(), theba.core.gui.ThebaGUI.getPreferences(), theba.core.gui.ThebaGUI.getSlice(), theba.core.gui.ThebaGUI.getStack(), theba.core.Stack.getWidth(), and theba.trackers.BackTracker.seedStillValid.
Referenced by theba.trackers.BackTracker.track().
void theba.trackers.BackTracker.removeStuff | ( | int | slice, | |
short[] | lumen | |||
) |
Definition at line 519 of file BackTracker.java.
References theba.trackers.BackTracker.checkReg(), theba.core.Stack.getHeight(), theba.core.LumenCandidate.getSize(), theba.core.gui.ThebaGUI.getSlice(), theba.core.gui.ThebaGUI.getStack(), theba.core.Stack.getWidth(), theba.core.Tracker.log, theba.core.math.Point3D.x, and theba.core.math.Point3D.y.
Referenced by theba.trackers.BackTracker.track().
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 | ) |
Definition at line 583 of file BackTracker.java.
References theba.core.gui.ThebaGUI.currentSlice(), theba.core.gui.ThebaGUI.getCurrentPixels(), theba.core.Stack.getHeight(), theba.core.gui.ThebaGUI.getStack(), theba.core.Stack.getWidth(), theba.core.gui.ThebaGUI.showImage(), and theba.core.gui.ThebaGUI.updateImage().
Referenced by theba.trackers.BackTracker.mouseClicked().
void theba.trackers.BackTracker.setFibers | ( | LinkedList | fibers | ) |
Definition at line 625 of file BackTracker.java.
void theba.trackers.BackTracker.setup | ( | ) | [virtual] |
Implements theba.core.Tracker.
Definition at line 96 of file BackTracker.java.
References theba.core.gui.ThebaGUI.addMenuItem(), theba.core.gui.ThebaGUI.addMenuSeparator(), theba.core.gui.ThebaGUI.addToolbarButton(), theba.core.Tracker.control, theba.trackers.BackTracker.findCandidates(), theba.trackers.BackTracker.neuralOut, theba.trackers.BackTracker.traceWalls(), and theba.trackers.BackTracker.track().
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] |
Implements theba.core.Tracker.
Definition at line 889 of file BackTracker.java.
References 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.Tracker.keepTracking, theba.core.Tracker.log, theba.core.gui.ThebaGUI.MAX_FIBERS, theba.core.Tracker.paused, theba.trackers.BackTracker.removeCrack(), theba.trackers.BackTracker.removeStuff(), theba.trackers.BackTracker.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.BackTracker.autoSegment(), and theba.trackers.BackTracker.setup().
PrintStream theba.trackers.BackTracker.neuralOut [package] |
Definition at line 48 of file BackTracker.java.
Referenced by theba.trackers.BackTracker.dispose(), and theba.trackers.BackTracker.setup().
boolean theba.trackers.BackTracker.seedStillValid = true [package] |
Definition at line 50 of file BackTracker.java.
Referenced by theba.trackers.BackTracker.removeCrack(), and theba.trackers.BackTracker.track().