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

All Methods Instance Methods Concrete Methods
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 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 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.
`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 Detail
  - 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 Detail
  - 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 Detail
  - 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.

Class LseEvolve3

Field Summary

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

Field Detail

m_kParameters

m_fD0

m_afD1

m_aafD2

m_afD1Fwd

m_afD1Bwd

m_fGradMagSqr

m_afAdvection

Constructor Detail

LseEvolve3

Method Detail

getParameters

computeFunction

computeCurvature

computeAdvection

computePropagationSpeed

computeCurvatureSpeed

computeLaplacianSpeed

onPreUpdate

onUpdate