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

Class LseThreshold3

java.lang.Object

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

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

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

gov.nih.mipav.model.algorithms.levelset.LseThreshold3

public class LseThreshold3
extends LseEvolve3

A level-set evolver for 3D images. The PDE to be solved numerically for I(x,t) is:

dI/dt = -b*P(x)*|grad(I)| + c*F(x)*K(x,t)*|grad(I)|, t > 0
I(x,0) = I0(x)

where the feature image is typically

F(x) = 1/(1+|grad(convolve(G,I0))|) or F(x) = exp(-|grad(convolve(G,I0))|)

where G(x,t) is the Gaussian kernel and where K(x,t) is the curvature of I(x,t). The propagation image, P(x), is computed from the feature image, F(x), as follows. A lower threshold L and an upper threshold U are selected by the user; then

P(x) = F(x) - L, if F(x) invalid input: '<' (U+L)/2

P(x) = U - F(x), if F(x) >= (U+L)/2

The constant b is the propagation weight and the constant c is the curvature weight.

Version:

0.1 November 7, 2006

Author:

David Eberly

Field Summary

Fields

Modifier and Type	Field	Description
protected float[][][]	m_aaafFeature	The feature image to control the segmentation.
protected float[][][]	m_aaafPropagation	The propagation image to control the segmentation.
protected float	m_fZeroTolerance	The threshold below which the feature image values are clamped to this tolerance.

Fields inherited from class gov.nih.mipav.model.algorithms.levelset.LseEvolve3

m_aafD2, m_afAdvection, m_afD1, m_afD1Bwd, m_afD1Fwd, m_fD0, m_fGradMagSqr, m_kParameters

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

Constructor	Description
LseThreshold3(int iXBound, int iYBound, int iZBound, float fXSpacing, float fYSpacing, float fZSpacing, float[] afData, boolean[] abMask, float fBorderValue, int eScaleType, float[] afFeature, float fLowerThreshold, float fUpperThreshold, float fPropagationWeight, float fCurvatureWeight)	Create a new level-set evolver for 2D images.

Method Summary

Modifier and Type	Method	Description
protected float	computeCurvatureSpeed(int iX, int iY, int iZ)	Compute the curvature speed at voxel (x,y,z).
protected float	computePropagationSpeed(int iX, int iY, int iZ)	Compute the propagation speed at voxel (x,y,z).

Methods inherited from class gov.nih.mipav.model.algorithms.levelset.LseEvolve3

computeAdvection, computeCurvature, computeFunction, computeLaplacianSpeed, getParameters, onPreUpdate, 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_fZeroTolerance

protected float m_fZeroTolerance

The threshold below which the feature image values are clamped to this tolerance. The value is hard-coded as 1e-06.

m_aaafFeature

protected float[][][] m_aaafFeature

The feature image to control the segmentation.

m_aaafPropagation

protected float[][][] m_aaafPropagation

The propagation image to control the segmentation.

Constructor Details

LseThreshold3

public LseThreshold3(int iXBound,
 int iYBound,
 int iZBound,
 float fXSpacing,
 float fYSpacing,
 float fZSpacing,
 float[] afData,
 boolean[] abMask,
 float fBorderValue,
 int eScaleType,
 float[] afFeature,
 float fLowerThreshold,
 float fUpperThreshold,
 float fPropagationWeight,
 float fCurvatureWeight)

Create a new level-set evolver for 2D 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 pixel 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.

afFeature - The feature image to control the evolution.

fLowerThreshold - The lower threshold L used in computing P(x).

fUpperThreshold - The lower threshold U used in computing P(x).

fPropagationWeight - The propagation coefficient 'b' in the PDE that controls the evolution.

fCurvatureWeight - The curvature coefficient 'c' in the PDE that controls the evolution.

Method Details

computePropagationSpeed

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

Compute the propagation speed at voxel (x,y,z). In this evolver, the propagation speed is obtained simply by a lookup into the feature image.

Overrides:

computePropagationSpeed in class LseEvolve3

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)

Compute the curvature speed at voxel (x,y,z). In this evolver, the curvature speed is obtained simply by a lookup into the feature image.

Overrides:

computeCurvatureSpeed in class LseEvolve3

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.