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

Class LseGradientAnisotropic3

java.lang.Object

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

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

gov.nih.mipav.model.algorithms.levelset.LseGradientAnisotropic3

public class LseGradientAnisotropic3
extends LsePdeFilter3

This class implements the gradient anistropic curvature flow filter for 3D images using a finite-difference-based solver for the partial differential equation:

du/dt = divergence(exp(-0.5*|grad(u)|^2/(k^2*average(|grad(u)|^2))*grad(u))

where u(x,y,z,t) is the evolved image at time t, du/dt is the time derivative of u, and grad(u) is the gradient of u with respect to the spatial variables. The value k is a used-selected parameter and may be thought of as a local curvature parameter. The notation divergence(Q) = Q0_x + Q1_y + Q2_z, the sum of first-order derivatives of the vector-valued function Q = (Q0,Q1).

Version:

0.1 November 7, 2006

Author:

David Eberly

Field Summary

Fields

Modifier and Type	Field	Description
private float	m_fK	The local curvature parameter, call it k.
private float	m_fMHalfParam	-0.5/(k^2*average(|grad(u)|^2))
private float	m_fParam	1/(k^2*average(|grad(u)|^2))

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
LseGradientAnisotropic3(int iXBound, int iYBound, int iZBound, float fXSpacing, float fYSpacing, float fZSpacing, float[] afData, boolean[] abMask, float fBorderValue, int eScaleType, float fK)	Creates a new LseCurvatureFlow3 object.

Method Summary

Modifier and Type	Method	Description
protected void	computeParam()	Compute the average gradient magnitude squared for the current image u(x,y,t).
protected void	onPreUpdate()	The function onPreUpdate was abstractly defined in the LsePdeFilter base class.
protected void	onUpdate(int iX, int iY, int iZ)	The per-voxel update function of the PDE solver.

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_fK

private float m_fK

The local curvature parameter, call it k.

m_fParam

private float m_fParam

1/(k^2*average(|grad(u)|^2))

m_fMHalfParam

private float m_fMHalfParam

-0.5/(k^2*average(|grad(u)|^2))

Constructor Details

LseGradientAnisotropic3

public LseGradientAnisotropic3(int iXBound,
 int iYBound,
 int iZBound,
 float fXSpacing,
 float fYSpacing,
 float fZSpacing,
 float[] afData,
 boolean[] abMask,
 float fBorderValue,
 int eScaleType,
 float fK)

Creates a new LseCurvatureFlow3 object.

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.

fK - The local curvature parameter in the exponential term of the PDE.

Method Details

computeParam

protected void computeParam()

Compute the average gradient magnitude squared for the current image u(x,y,t). The terms p = 1/(k*k*average(|grad(u)|^2) and -0.5*p are computed once and used in the per-pixel update in the PDE solver.

onPreUpdate

protected void onPreUpdate()

The function onPreUpdate was abstractly defined in the LsePdeFilter base class. It is called before any per-pixel updates. In this class, the parameters in the exponential term of the PDE are precomputed for use by the onUpdate() function.

Overrides:

onPreUpdate in class LsePdeFilter3

onUpdate

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

The per-voxel update function of the PDE solver.

Specified by:

onUpdate in class LsePdeFilter3

Parameters:

iX - The x-value of the voxel to be updated.

iY - The y-value of the voxel to be updated.

iZ - The z-value of the voxel to be updated.