deformablemesh.track

Class FrameToFrameDisplacement

java.lang.Object

deformablemesh.track.FrameToFrameDisplacement

public class FrameToFrameDisplacement
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
double	JI_CUTOFF

Constructor Summary

Constructors

Constructor and Description
FrameToFrameDisplacement(int frame) Creates a frame to frame displacement with the starting frame provided.

Method Summary

Modifier and Type	Method and Description
static double[][]	boundingBoxJaccardIndexMatrix(List<DeformableMesh3D> one, List<DeformableMesh3D> two)
void	calculateCenterOfMass(List<Track> tracks) Calculates the center of mass based on the provided tracks.
static double[]	centerOfMass(List<DeformableMesh3D> meshes)
static double[][]	displacements(List<DeformableMesh3D> A, List<DeformableMesh3D> B, double[] aToB)
static ij.ImagePlus	generateMosaicImage(List<DeformableMesh3D> meshes)
UndoableActions	getPerform() Creates an undoable action based on the tracking result.
static List<deformablemesh.track.FrameToFrameDisplacement.Mapping>	jaccardIndex(List<DeformableMesh3D> one, List<DeformableMesh3D> two) Finds the jaccardIndexMatrix between the two lists of meshes.
static double[][]	jaccardIndexMatrix(List<DeformableMesh3D> one, List<DeformableMesh3D> two)
static void	main(String[] args)
static void	print2DMatrix(double[][] ji)
List<deformablemesh.track.FrameToFrameDisplacement.Mapping>	processJaccardIndexMap(List<DeformableMesh3D> m1, List<DeformableMesh3D> m2)
List<double[]>	processJaccardIndexMatrix(List<DeformableMesh3D> m1, List<DeformableMesh3D> m2)
static FrameToFrameDisplacement	trackAvailableFrameForward(SegmentationController controller) Takes the current set tracks, find tracks that are available in the current frame, and the set of tracks that are available in the next frame, then attempts to link them.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

JI_CUTOFF

public double JI_CUTOFF

Constructor Detail

FrameToFrameDisplacement

public FrameToFrameDisplacement(int frame)

Creates a frame to frame displacement with the starting frame provided.

Parameters:

frame -

Method Detail

trackAvailableFrameForward

public static FrameToFrameDisplacement trackAvailableFrameForward(SegmentationController controller)

Takes the current set tracks, find tracks that are available in the current frame, and the set of tracks that are available in the next frame, then attempts to link them.

Parameters:

tracks - full collection of tracks that will be filtered and linked

frame - starting frame for tracking.

Returns:

A frame to frame displacement with tracking prepared.

getPerform

public UndoableActions getPerform()

Creates an undoable action based on the tracking result.

Returns:

perform will create two track lists, one that represents the current state and one that represents the previous list. It will also create a list of track data for each track that gets modified. A before list and an after list. undo sets the controller to have the previous track list and all of the modified tracks will have their original track data set. redo sets the controller to have the updated track list and all of the modified tracks will have their updated track data set.

calculateCenterOfMass

public void calculateCenterOfMass(List<Track> tracks)

Calculates the center of mass based on the provided tracks.

Parameters:

tracks -

centerOfMass

public static double[] centerOfMass(List<DeformableMesh3D> meshes)

processJaccardIndexMatrix

public List<double[]> processJaccardIndexMatrix(List<DeformableMesh3D> m1,
                                                List<DeformableMesh3D> m2)

processJaccardIndexMap

public List<deformablemesh.track.FrameToFrameDisplacement.Mapping> processJaccardIndexMap(List<DeformableMesh3D> m1,
                                                                                          List<DeformableMesh3D> m2)

main

public static void main(String[] args)
                 throws IOException

Throws:

IOException

displacements

public static double[][] displacements(List<DeformableMesh3D> A,
                                       List<DeformableMesh3D> B,
                                       double[] aToB)

generateMosaicImage

public static ij.ImagePlus generateMosaicImage(List<DeformableMesh3D> meshes)

jaccardIndexMatrix

public static double[][] jaccardIndexMatrix(List<DeformableMesh3D> one,
                                            List<DeformableMesh3D> two)

boundingBoxJaccardIndexMatrix

public static double[][] boundingBoxJaccardIndexMatrix(List<DeformableMesh3D> one,
                                                       List<DeformableMesh3D> two)

jaccardIndex

public static List<deformablemesh.track.FrameToFrameDisplacement.Mapping> jaccardIndex(List<DeformableMesh3D> one,
                                                                                       List<DeformableMesh3D> two)

Finds the jaccardIndexMatrix between the two lists of meshes. Finds the maximum jaccard index value for all of the meshes in one, . for each mesh in list one and maps it to a mesh in .

Parameters:

one - List of meshes to be tracked from.

two - List of meshes to be tracked too.

Returns:

a list of mappings the same length as one

print2DMatrix

public static void print2DMatrix(double[][] ji)