Package gov.nih.mipav.model.algorithms.levelset

Class LseEvolve3

java.lang.Object

gov.nih.mipav.model.algorithms.levelset.LsePdeFilter

gov.nih.mipav.model.algorithms.levelset.LsePdeFilter3

gov.nih.mipav.model.algorithms.levelset.LseEvolve3

Direct Known Subclasses:

LseGeodesicActiveContour3, LseShapeDetection3, LseThreshold3

public abstract class LseEvolve3
extends LsePdeFilter3

The abstract base class for level-set evolution of 3D images. It is based on PDEs that are solved numerically using finite-difference approximations.

Version:

0.1 November 7, 2006

Author:

David Eberly

Field Summary

Fields

Modifier and Type	Field	Description
protected float[][]	m_aafD2	The second-order derivatives of the current pixel.
protected float[]	m_afAdvection	The advection for the current pixel.
protected float[]	m_afD1	The first-order derivatives of the current pixel.
protected float[]	m_afD1Bwd	Backward finite-difference approximations to the first-order derivatives of the current pixel.
protected float[]	m_afD1Fwd	Forward finite-difference approximations to the first-order derivatives of the current pixel.
protected float	m_fD0	The image value of the current pixel.
protected float	m_fGradMagSqr	The squared magnitude of the gradient vector for the current pixel.
protected LseParameters	m_kParameters	The parameters associated with level-set evolution.

Fields inherited from class gov.nih.mipav.model.algorithms.levelset.LsePdeFilter3

m_aaabMask, m_aaafDst, m_aaafSrc, m_fFourthInvDxDy, m_fFourthInvDxDz, m_fFourthInvDyDz, m_fHalfInvDx, m_fHalfInvDy, m_fHalfInvDz, m_fInvDx, m_fInvDxDx, m_fInvDy, m_fInvDyDy, m_fInvDz, m_fInvDzDz, m_fUmmm, m_fUmmp, m_fUmmz, m_fUmpm, m_fUmpp, m_fUmpz, m_fUmzm, m_fUmzp, m_fUmzz, m_fUpmm, m_fUpmp, m_fUpmz, m_fUppm, m_fUppp, m_fUppz, m_fUpzm, m_fUpzp, m_fUpzz, m_fUzmm, m_fUzmp, m_fUzmz, m_fUzpm, m_fUzpp, m_fUzpz, m_fUzzm, m_fUzzp, m_fUzzz, m_fXSpacing, m_fYSpacing, m_fZSpacing, m_iXBound, m_iYBound, m_iZBound

Fields inherited from class gov.nih.mipav.model.algorithms.levelset.LsePdeFilter

m_eScaleType, m_fBorderValue, m_fMin, m_fOffset, m_fScale, m_fTimeStep, m_iQuantity, NONE, PRESERVE_ZERO, SYMMETRIC, UNIT

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	LseEvolve3(int iXBound, int iYBound, int iZBound, float fXSpacing, float fYSpacing, float fZSpacing, float[] afData, boolean[] abMask, float fBorderValue, int eScaleType)	Create a new level-set evolver for 3D images.

Method Summary

Modifier and Type	Method	Description
protected float[]	computeAdvection(int iX, int iY, int iZ)	Override this function to implement the desired advection for your level-set evolver.
protected final float	computeCurvature(int iX, int iY, int iZ)	Compute the product of length and mean curvature at the voxel (x,y,z).
protected float	computeCurvatureSpeed(int iX, int iY, int iZ)	Override this function to implement the desired curvature speed for your level-set evolver.
protected final float	computeFunction(int iX, int iY, int iZ)	Evolution support.
protected float	computeLaplacianSpeed(int iX, int iY, int iZ)	Override this function to implement the desired Laplacian speed for your level-set evolver.
protected float	computePropagationSpeed(int iX, int iY, int iZ)	Override this function to implement the desired propagation speed for your level-set evolver.
final LseParameters	getParameters()	Get the current level-set evolution parameters.
protected void	onPreUpdate()	The override of LsePdeFilter3.onPreUpdate.
protected void	onUpdate(int iX, int iY, int iZ)	The override of LsePdeFilter3.onUpdate.

Methods inherited from class gov.nih.mipav.model.algorithms.levelset.LsePdeFilter3

assignDirichletImageBorder, assignDirichletMaskBorder, assignNeumannImageBorder, assignNeumannMaskBorder, getMask, getU, getUx, getUxx, getUxy, getUxz, getUy, getUyy, getUyz, getUz, getUzz, getXBound, getXSpacing, getYBound, getYSpacing, getZBound, getZSpacing, lookUp27, lookUp7, onPostUpdate, onUpdate

Methods inherited from class gov.nih.mipav.model.algorithms.levelset.LsePdeFilter

getBorderValue, getQuantity, getScaleType, getTimeStep, setTimeStep, update

Methods inherited from class java.lang.Object

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

Field Details

m_kParameters

protected LseParameters m_kParameters

The parameters associated with level-set evolution.

m_fD0

protected float m_fD0

The image value of the current pixel.

m_afD1

protected float[] m_afD1

The first-order derivatives of the current pixel.

m_aafD2

protected float[][] m_aafD2

The second-order derivatives of the current pixel.

m_afD1Fwd

protected float[] m_afD1Fwd

Forward finite-difference approximations to the first-order derivatives of the current pixel.

m_afD1Bwd

protected float[] m_afD1Bwd

Backward finite-difference approximations to the first-order derivatives of the current pixel.

m_fGradMagSqr

protected float m_fGradMagSqr

The squared magnitude of the gradient vector for the current pixel.

m_afAdvection

protected float[] m_afAdvection

The advection for the current pixel.

Constructor Details

LseEvolve3

protected LseEvolve3(int iXBound,
 int iYBound,
 int iZBound,
 float fXSpacing,
 float fYSpacing,
 float fZSpacing,
 float[] afData,
 boolean[] abMask,
 float fBorderValue,
 int eScaleType)

Create a new level-set evolver for 3D images.

Parameters:

iXBound - The x-bound of the image.

iYBound - The y-bound of the image.

iZBound - The z-bound of the image.

fXSpacing - The x-spacing of the image.

fYSpacing - The y-spacing of the image.

fZSpacing - The z-spacing of the image.

afData - The image elements, stored in lexicographical order.

abMask - The image mask, stored in lexicographical order. A voxel value is processed by the PDE solver only when the mask value is false.

fBorderValue - Specifies how to handle the image value. When set to Float.MAX_VALUE, Neumann conditions are in use, in which case zero-valued derivatives are assumed on the image border. Otherwise, Dirichlet conditions are used, in which case the image is assumed to be constant on the border with value specified by fBorderValue.

eScaleType - The type of scaling to apply to the input image. The choices are NONE, UNIT, SYMMETRIC, or PRESERVE_ZERO.

Method Details

getParameters

public final LseParameters getParameters()

Get the current level-set evolution parameters.

Returns:

The current level-set evolution parameters.

computeFunction

protected final float computeFunction(int iX,
 int iY,
 int iZ)

Evolution support. ComputeTimeStep() is called each time before ComputeFunction() is called. The function ComputeCurvature() actually computes k*L, where k is the mean curvature and L is the length of the gradient vector. The resulting quantity is

k*L = (Uxx*(Uy*Uy+Uz*Uz) + Uyy*(Ux*Ux+Uz*Uz) + Uzz*(Ux*Ux+Uy*Uy) - 2*(Uxy*Ux*Uy + Uxz*Ux*Uz + Uyz*Uy*Uz))/(Ux*Ux+Uy*Uy+Uz*Uz)

where Ux, Uy, and Uz are first-order partial derivatives and Uxx, Uxy, Uxz, Uyy, Uyz, and Uzz are second-order partial derivatives.

Parameters:

iX - The x-coordinate of the voxel.

iY - The y-coordinate of the voxel.

iZ - The z-coordinate of the voxel.

Returns:

The value of the right-hand side of the PDE that governs the level-set evolution.

computeCurvature

protected final float computeCurvature(int iX,
 int iY,
 int iZ)

Compute the product of length and mean curvature at the voxel (x,y,z).

Parameters:

iX - The x-coordinate of the voxel.

iY - The y-coordinate of the voxel.

iZ - The z-coordinate of the voxel.

Returns:

The product of length and curvature at the voxel.

computeAdvection

protected float[] computeAdvection(int iX,
 int iY,
 int iZ)

Override this function to implement the desired advection for your level-set evolver.

Parameters:

iX - The x-coordinate of the voxel.

iY - The y-coordinate of the voxel.

iZ - The z-coordinate of the voxel.

Returns:

The advection at the voxel.

computePropagationSpeed

protected float computePropagationSpeed(int iX,
 int iY,
 int iZ)

Override this function to implement the desired propagation speed for your level-set evolver.

Parameters:

iX - The x-coordinate of the voxel.

iY - The y-coordinate of the voxel.

iZ - The z-coordinate of the voxel.

Returns:

The propagation speed at the voxel.

computeCurvatureSpeed

protected float computeCurvatureSpeed(int iX,
 int iY,
 int iZ)

Override this function to implement the desired curvature speed for your level-set evolver.

Parameters:

iX - The x-coordinate of the voxel.

iY - The y-coordinate of the voxel.

iZ - The z-coordinate of the voxel.

Returns:

The curvature speed at the voxel.

computeLaplacianSpeed

protected float computeLaplacianSpeed(int iX,
 int iY,
 int iZ)

Override this function to implement the desired Laplacian speed for your level-set evolver.

Parameters:

iX - The x-coordinate of the voxel.

iY - The y-coordinate of the voxel.

iZ - The z-coordinate of the voxel.

Returns:

The Laplacian speed at the voxel.

onPreUpdate

protected void onPreUpdate()

The override of LsePdeFilter3.onPreUpdate. This is where ComputeTimeStep is called.

Overrides:

onPreUpdate in class LsePdeFilter3

onUpdate

protected void onUpdate(int iX,
 int iY,
 int iZ)

The override of LsePdeFilter3.onUpdate. This is where ComputeFunction is called.

Specified by:

onUpdate in class LsePdeFilter3

Parameters:

iX - The x-coordinate of the voxel.

iY - The y-coordinate of the voxel.

iZ - The z-coordinate of the voxel.