de.unihalle.informatik.MiToBo.topology

Class MTBTopologicalNumber

java.lang.Object

de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber

Direct Known Subclasses:

MTBTopologicalNumber2D

public abstract class MTBTopologicalNumber
extends Object

An abstract class to compute topological numbers given a neighborhood.

See Han, X. and Xu, C. and Prince, J.L., A topology preserving level set method for geometric deformable models}, PAMI, pages 755-768, 2003
for definitions and notation.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private class	MTBTopologicalNumber.PixelIndexIterator
class	MTBTopologicalNumber.PixelOffsetIterator
static class	MTBTopologicalNumber.Point3D This class is used as a light weight 3D point implementation

Field Summary

Fields

Modifier and Type	Field and Description
protected ArrayList<MTBTopologicalNumber.Point3D>[]	coordinatesNeighborNeighbors For each neighbor in the neighborhood this collection holds coordinates of all other pixels in the neighborhood which are connected to the neighbor under consideration with regard the the neighborhood definition.
protected ArrayList<MTBTopologicalNumber.Point3D>[][][]	coordinatesNeighborNeighborsByCoord As this array gives for each neighbor in the neighborhood coordinates of its neighbors (i.e. neighborneighbors).
protected MTBTopologicalNumber.Point3D[]	coordinatesNeighbors For each neighbor in the neighborhood this gives their coordinates in a 3x3x3 array center around the current pixel (of which the neighborhood is represented).
protected static boolean	debug debug flag
protected int	dimension Dimension of image
protected float	maxDist Maximal distance of points within the neighborhood to current pixel, i.e. the pixel which neighborhood we are considering
protected ArrayList<MTBTopologicalNumber.Point3D>[]	offsetsNeighborNeighbors As for the neighbors this collection is in analogy to coordinatesNeighborNeighbors and gives for each neighborneighbor the offset instead of coordinates.
protected MTBTopologicalNumber.Point3D[]	offsetsNeighbors In analogy to coordinatesNeighbors this array hold the offsets of the neighbors.
protected int	sizeNeighborhood The size of the neighborhood, i.e. numbers of pixels in the neighborhood
protected boolean[][][]	X 8- or 26 neighbors of the current pixel used to determine topological numbers represented as an 3x3x3 array center around the current pixel.

Constructor Summary

Constructors

Constructor and Description
MTBTopologicalNumber()

Method Summary

Modifier and Type	Method and Description
protected abstract void	computeN() Derive N_n^k from X, see Han et al.
ArrayList<MTBTopologicalNumber.Point3D>	getCoordinatesNeighborNeighbors(int z, int y, int x)
float	getMaxDist()
int	getSizeNeighborhood()
protected boolean	hasOneCC() Checks if the neighborhood represented in X has exactly one connected component of entries set to true using the neighborhood definition as as represented in the neighborhood arrays of the class.
Iterator<MTBTopologicalNumber.Point3D>	iterator() Returns a iterator for the coordinatesNeighbors in the order as defined
Iterator<MTBTopologicalNumber.Point3D>	iteratorOffsets() Returns a iterator for the pixelOffsets in the order as defined
void	print() Print information of this class to stdout
abstract boolean	topoNumberIsOne(int[][][] nbClasses3D, int c) Check if topological for the class c is one in the neighborhood nbClassess3D.
boolean	topoNumberIsOne(MTBSegmentationInterface segmentation, int x, int y, int z, int c) Check if topological for the class c is one in the pixel with coordinate (x,y,z) in the segmentation object segmentation.
private void	visitCC(int z, int y, int x) Visit (x,y,z): reset the corresponding entry in X to false and recursively visit all neighbors of (x,y,z) in X.

Methods inherited from class java.lang.Object

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

Field Detail

debug

protected static boolean debug

debug flag

sizeNeighborhood

protected int sizeNeighborhood

The size of the neighborhood, i.e. numbers of pixels in the neighborhood

maxDist

protected float maxDist

Maximal distance of points within the neighborhood to current pixel, i.e. the pixel which neighborhood we are considering

dimension

protected int dimension

Dimension of image

coordinatesNeighbors

protected MTBTopologicalNumber.Point3D[] coordinatesNeighbors

For each neighbor in the neighborhood this gives their coordinates in a 3x3x3 array center around the current pixel (of which the neighborhood is represented). The coordinates of this current pixel are (1,1,1). The order of the neighbors is define in the class extending this abstract super class.

offsetsNeighbors

protected MTBTopologicalNumber.Point3D[] offsetsNeighbors

In analogy to coordinatesNeighbors this array hold the offsets of the neighbors. Each offset may also be considered as the coordinates of a neighbor in a a 3x3x3 array center around the current pixel where the coordinates of this current pixel are (0,0,0).

The order of neighbors within the array are the same as for coordinatesNeighbors.

coordinatesNeighborNeighbors

protected ArrayList<MTBTopologicalNumber.Point3D>[] coordinatesNeighborNeighbors

For each neighbor in the neighborhood this collection holds coordinates of all other pixels in the neighborhood which are connected to the neighbor under consideration with regard the the neighborhood definition. (These are called neighborneighbors subsequently.) Coordinates are as for neighbors in a a 3x3x3 array center around the current pixel The order of neighbors within the array are the same as for coordinatesNeighbors while the order of neighborneighbors in the collection is arbitrary.

coordinatesNeighborNeighborsByCoord

protected ArrayList<MTBTopologicalNumber.Point3D>[][][] coordinatesNeighborNeighborsByCoord

As this array gives for each neighbor in the neighborhood coordinates of its neighbors (i.e. neighborneighbors). Coordinates are as for neighbors in a a 3x3x3 array center around the current pixel However the collections of neighborneighbors are not indexed by the order of the neighbors but by the coordinate of each neighbor within an 3x3x3 array, coordinatesNeighbors.

offsetsNeighborNeighbors

protected ArrayList<MTBTopologicalNumber.Point3D>[] offsetsNeighborNeighbors

As for the neighbors this collection is in analogy to coordinatesNeighborNeighbors and gives for each neighborneighbor the offset instead of coordinates.

X

protected boolean[][][] X

8- or 26 neighbors of the current pixel used to determine topological numbers represented as an 3x3x3 array center around the current pixel. Memory layout is nbClasses3D[z][y][x].

First it is assigned to the array X of Han et al, i.e.: An entry is true if class in neighborhood is equal to the class under consideration, false otherwise.

Subsequently to the array N_n^k

And finally altered to compute number of components.

This array is recycled for efficiency.

Constructor Detail

MTBTopologicalNumber

public MTBTopologicalNumber()

Method Detail

topoNumberIsOne

public abstract boolean topoNumberIsOne(int[][][] nbClasses3D,
                                        int c)

Check if topological for the class c is one in the neighborhood nbClassess3D. Specifically, all pixels in nbClasses3D with equal values to c are considered as elements of X, the rest as not in X.

nbClassess3D is a 3D volume of size 3x3x3 where the current pixel is located in the center, i.e. with coordinates (1,1,1). Memory layout is nbClasses3D[z][y][x]. The values give the classes or phases to which the pixels belong to.

Neighborhood definitions are define in derived sub classes. If this is a 2D neighborhood, only the z=0 slice of nbClasses3D will be considered and accessed.

topoNumberIsOne

public boolean topoNumberIsOne(MTBSegmentationInterface segmentation,
                               int x,
                               int y,
                               int z,
                               int c)

Check if topological for the class c is one in the pixel with coordinate (x,y,z) in the segmentation object segmentation. Specifically, all pixels in neighborhood with equal values to c are considered as elements of X, the rest as not in X.

Neighborhood definitions are define in derived sub classes.

If this segmentation is 2D a 2D topology is to be used

TODO: conceive how to handle invalid pixels

computeN

protected abstract void computeN()

Derive N_n^k from X, see Han et al. This method works destructive on X (for efficiency), that is upon return X contains N_n^k, which is a subset of X. n and k are define in derived sub classes.

hasOneCC

protected boolean hasOneCC()

Checks if the neighborhood represented in X has exactly one connected component of entries set to true using the neighborhood definition as as represented in the neighborhood arrays of the class.

visitCC

private void visitCC(int z,
                     int y,
                     int x)

Visit (x,y,z): reset the corresponding entry in X to false and recursively visit all neighbors of (x,y,z) in X.

print

public void print()

Print information of this class to stdout

iterator

public Iterator<MTBTopologicalNumber.Point3D> iterator()

Returns a iterator for the coordinatesNeighbors in the order as defined

iteratorOffsets

public Iterator<MTBTopologicalNumber.Point3D> iteratorOffsets()

Returns a iterator for the pixelOffsets in the order as defined

getSizeNeighborhood

public int getSizeNeighborhood()

Returns:

the sizeNeighborhood

getMaxDist

public float getMaxDist()

Returns:

the maxDist

getCoordinatesNeighborNeighbors

public ArrayList<MTBTopologicalNumber.Point3D> getCoordinatesNeighborNeighbors(int z,
                                                                               int y,
                                                                               int x)

Returns:

the coordinatesNeighborNeighbors