de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE

Class MTBLevelsetMembership

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDData

de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership

public class MTBLevelsetMembership
extends de.unihalle.informatik.Alida.operator.ALDData

A class to hold a level set function where only the membership to a phase is required and represented. Background pixels gets phase BG_PHASE, object phases start with BG_PHASE+1. The implementation asserts that all phases > BG_PHASE are indeed object phases. Value INVALID_PHASE is reserved for invalid pixels.

Field Summary

Fields

Modifier and Type	Field and Description
static short	BG_PHASE Level set function value to represent the background phase
static short	INVALID_PHASE Level set function value to represent invalid pixels
static int	MAX_ALLOWED_NUM_PHASES Maximal number of phases which may be represented including background phase.
private int	numPhases
private short[][][]	phi
private int[]	sizePhases
private int	sizeX
private int	sizeY
private int	sizeZ
private int	sumSizeObject

Constructor Summary

Constructors

Constructor and Description
MTBLevelsetMembership(int sizeX, int sizeY, int sizeZ) Constructs a two phase level set function which is initialized with a circle or sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
MTBLevelsetMembership(int sizeX, int sizeY, int sizeZ, MTBImage invalidImg) Constructs a two phase level set function which is initialiazed with a circle or sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
MTBLevelsetMembership(int sizeX, int sizeY, int sizeZ, MTBImage img, int threshold, MTBImage invalidImg) Creates a two phase level set function from an image via thresholding.
MTBLevelsetMembership(int sizeX, int sizeY, MTBRegion2DSet regions, MTBImage invalidImg, boolean multiphase) Constructor for given size which is initialized from a MTBRegion2DSet for a 2D level set function.
MTBLevelsetMembership(int sizeX, int sizeY, Vector<MTBRegion2D> regions, MTBImage invalidImg, boolean multiphase) Constructor for given size which is initialized from a list of 2D regions for a 2D level set function.
MTBLevelsetMembership(MTBImage initLabelImg, MTBImage invalidImg) Constructor for a two phase level set function from a label image.
MTBLevelsetMembership(MTBImage initLabelImg, MTBImage invalidImg, boolean multiphase) Constructor for a level set function from a label image.
MTBLevelsetMembership(MTBLevelsetMembership phi) Creates a copy of phi.

Method Summary

Modifier and Type	Method and Description
void	changePhase(int x, int y, int z, short phase) Change a pixel/voxel to a new phase.
void	changePhase(int x, int y, short phase) Change a pixel to a new phase.
MTBImageShort	getMTBImage() Creates a bi-level MTBImageShort of the level set function.
MTBImageShort	getMTBImageLabel() Creates a MTBImageShort of the level set function.
int	getNumPhases() Return .e. number phases.
short	getPhase(int x, int y) Return phase for a pixel/voxel, z coordinate defaults to zero
short	getPhase(int x, int y, int z) Return phase for a pixel/voxel
short	getPhaseCheckXY(int x, int y) Return phase for a pixel checking limits of all coordinates.
short	getPhaseCheckXYZ(int x, int y, int z) Return phase for a pixel/voxel checking limits of all coordinates.
int	getPixelInside() Return number of pixels of all object phases.
int	getPixelOutside() Return number of pixels of background phase.
int	getSizePhase(short phase) Return the size, i.e. number of pixel/voxels of a phase.
int	getSizeX() Return X size of the level set function.
int	getSizeY() Return Y size of the level set function.
int	getSizeZ() Return Z size of the level set function.
private void	initFromLabels(MTBImage initLabelImg, MTBImage invalidImg, boolean multiphase) Helper for constructors from a label image.
private void	initLevelset(MTBImage invalidImg) Helper to initialize a two phase level set function of size as given by invalidImg with a circle/sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
private void	initLevelset(MTBImage img, int threshold, MTBImage invalidImg) Initialize a two phase level set function by thresholding an image.
boolean	isValid(MTBImage invalidImg, int x, int y, int z) returns true, if pixel/voxel is valid.
String	toString() Return a string representation.

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDData

cloneProperties, getLocation, getProperty, getPropertyKeys, print, setLocation, setProperty

Methods inherited from class java.lang.Object

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

Field Detail

BG_PHASE

public static final short BG_PHASE

Level set function value to represent the background phase

See Also:

Constant Field Values

INVALID_PHASE

public static final short INVALID_PHASE

Level set function value to represent invalid pixels

See Also:

Constant Field Values

MAX_ALLOWED_NUM_PHASES

public static final int MAX_ALLOWED_NUM_PHASES

Maximal number of phases which may be represented including background phase.

See Also:

Constant Field Values

phi

private short[][][] phi

sumSizeObject

private int sumSizeObject

sizePhases

private int[] sizePhases

sizeX

private final int sizeX

sizeY

private final int sizeY

sizeZ

private final int sizeZ

numPhases

private int numPhases

Constructor Detail

MTBLevelsetMembership

public MTBLevelsetMembership(int sizeX,
                             int sizeY,
                             int sizeZ)

Constructs a two phase level set function which is initialized with a circle or sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.

Parameters:

sizeX -

sizeY -

sizeZ -

MTBLevelsetMembership

public MTBLevelsetMembership(int sizeX,
                             int sizeY,
                             int sizeZ,
                             MTBImage invalidImg)

Constructs a two phase level set function which is initialiazed with a circle or sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.

If invalidImg is non null, than pixels <> zero in invalidImg are invalid

Parameters:

sizeX -

sizeY -

sizeZ -

invalidImg -

MTBLevelsetMembership

public MTBLevelsetMembership(int sizeX,
                             int sizeY,
                             int sizeZ,
                             MTBImage img,
                             int threshold,
                             MTBImage invalidImg)

Creates a two phase level set function from an image via thresholding. All pixels with intensities greater equal the threshold constitute the object phase, other pixels the background.

If invalidImg is non null, than pixels <> zero in invalidImg are invalid

Parameters:

sizeX -

sizeY -

sizeZ -

img - Images tp be thresholded

threshold - All pixels with intensities greater equal are object pixels

invalidImg -

MTBLevelsetMembership

public MTBLevelsetMembership(MTBLevelsetMembership phi)

Creates a copy of phi.

Parameters:

phi - levelset function to copy

MTBLevelsetMembership

public MTBLevelsetMembership(int sizeX,
                             int sizeY,
                             Vector<MTBRegion2D> regions,
                             MTBImage invalidImg,
                             boolean multiphase)

Constructor for given size which is initialized from a list of 2D regions for a 2D level set function. If multiphase is true, then each region yields on phase thus the number of regions determines the the number of phases. If multiphase is false, exactly one object phase is populated from all regions.

If invalidImg is non null, than pixels <> zero in invalidImg are invalid

Parameters:

sizeX -

sizeY -

regions - Vector of regions to initialize from

invalidImg - pixels which are non zero are assumed invalid

multiphase - if true create one phase for each region, otherwise two phases

MTBLevelsetMembership

public MTBLevelsetMembership(int sizeX,
                             int sizeY,
                             MTBRegion2DSet regions,
                             MTBImage invalidImg,
                             boolean multiphase)

Constructor for given size which is initialized from a MTBRegion2DSet for a 2D level set function. If multiphase is true, each region yields on phase thus the number of regions determines the the number of phases. If multiphase is true, then each region yields on phase thus the number of regions determines the the number of phases. If mutliphase is false, exactly one object phase is populated from all regions. If invalidImg is non null, than pixels <> zero in invalidImg are invalid

Parameters:

sizeX -

sizeY -

regions - Region2D set to initialize from

invalidImg - pixels which are non zero are assumed invalid

multiphase - if true create one phase for each region, otherwise two phases

MTBLevelsetMembership

public MTBLevelsetMembership(MTBImage initLabelImg,
                             MTBImage invalidImg)

Constructor for a two phase level set function from a label image. Label zero is interpreted as background, everything else as foreground, e.g. the only object phase. If invalidImg is non null, than pixels <> zero in invalidImg are invalid

Parameters:

initLabelImg - Label image for initialization

invalidImg - Image indicating invalid pixels with values <> 0

MTBLevelsetMembership

public MTBLevelsetMembership(MTBImage initLabelImg,
                             MTBImage invalidImg,
                             boolean multiphase)

Constructor for a level set function from a label image. if multiphase is true, then a multi phase level set function is created, where labels ared interpreted as phases (a label of zero indeicated background). Otherwise a two phase level set function is created, where all non zero labels are interpreted as foreground.

If invalidImg is non null, than pixels <> zero in invalidImg are invalid

Parameters:

initLabelImg - Label image for initialization

invalidImg - Image indicating invalid pixels with values <> 0

Method Detail

initFromLabels

private void initFromLabels(MTBImage initLabelImg,
                            MTBImage invalidImg,
                            boolean multiphase)

Helper for constructors from a label image. If multiphase is true, then a multi phase level set function is created, where labels are interpreted as phases (a label of zero indicates background). The set of occurring in the label image are mapped to a contiguous interval of phases (starting with BG_PHASE). The label 0 is mapped to BG_PHASE

Otherwise a two phase level set function is created, where all non zero labels are interpreted as foreground.

If invalidImg is non null, than pixels <> zero in invalidImg are invalid

Parameters:

initLabelImg - Label image for initialization

invalidImg - Image indicating invalid pixels with values <> 0

multiphase - Construct multi or two phase level set function iff true or false, resp.

initLevelset

private void initLevelset(MTBImage invalidImg)

Helper to initialize a two phase level set function of size as given by invalidImg with a circle/sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.

If invalidImg is non null, than pixels <> zero in invalidImg are invalid

initLevelset

private void initLevelset(MTBImage img,
                          int threshold,
                          MTBImage invalidImg)

Initialize a two phase level set function by thresholding an image. All pixels with intensities greater equal the threshold constitute the object phase, other pixels the background.

If invalidImg is non null, than pixels <> zero in invalidImg are invalid

Parameters:

threshold -

threshold - All pixels with intensities greater equal are object pixels

invalidImg -

changePhase

public void changePhase(int x,
                        int y,
                        int z,
                        short phase)

Change a pixel/voxel to a new phase. Note: validity of phase is NOT checked.

Parameters:

x -

y -

z -

phase -

changePhase

public void changePhase(int x,
                        int y,
                        short phase)

Change a pixel to a new phase. Note: validity of phase is NOT checked.

Parameters:

x -

y -

phase -

getPhase

public short getPhase(int x,
                      int y,
                      int z)

Return phase for a pixel/voxel

Parameters:

x -

y -

z -

getPhaseCheckXYZ

public short getPhaseCheckXYZ(int x,
                              int y,
                              int z)

Return phase for a pixel/voxel checking limits of all coordinates. If coordinates are invalid, INVALID_PHASE is returned.

Parameters:

x -

y -

z -

Returns:

phase

getPhase

public short getPhase(int x,
                      int y)

Return phase for a pixel/voxel, z coordinate defaults to zero

Parameters:

x -

y -

getPhaseCheckXY

public short getPhaseCheckXY(int x,
                             int y)

Return phase for a pixel checking limits of all coordinates. If coordinates are invalid, INVALID_PHASE is returned.

Parameters:

x -

y -

Returns:

phase

getMTBImage

public MTBImageShort getMTBImage()

Creates a bi-level MTBImageShort of the level set function. Background and invalid pixels get intensity 0, object pixels intensity 255.

Returns:

MTBImage

getMTBImageLabel

public MTBImageShort getMTBImageLabel()

Creates a MTBImageShort of the level set function. Background and invalid pixels get value 0, the object phases get values starting with 1

Returns:

MTBImageShort

getPixelInside

public int getPixelInside()

Return number of pixels of all object phases.

getPixelOutside

public int getPixelOutside()

Return number of pixels of background phase.

getSizeX

public int getSizeX()

Return X size of the level set function.

getSizeY

public int getSizeY()

Return Y size of the level set function.

getSizeZ

public int getSizeZ()

Return Z size of the level set function.

getSizePhase

public int getSizePhase(short phase)

Return the size, i.e. number of pixel/voxels of a phase.

getNumPhases

public int getNumPhases()

Return .e. number phases.

toString

public String toString()

Return a string representation.

Overrides:

toString in class Object

isValid

public boolean isValid(MTBImage invalidImg,
                       int x,
                       int y,
                       int z)

returns true, if pixel/voxel is valid. Valid pixels are define as zero pixels (i.e. invalid pixels are marks with phase not equal to zero

Parameters:

invalidImg -

x -

y -

z -