java.lang.Object
- gov.nih.mipav.model.algorithms.levelset.LsePdeFilter
- - gov.nih.mipav.model.algorithms.levelset.LsePdeFilter3

Direct Known Subclasses:

LseCurvatureFlow3, LseEvolve3, LseGaussianBlur3, LseGradientAnisotropic3
```
public abstract class LsePdeFilter3
extends LsePdeFilter
```
The abstract base class for finite-difference-based solvers for partial differential equations in 3D. This system exists to support level-set evolution for image segmentation.

The internal 3D data and mask images are copies of the inputs to the constructor but padded with a 1-voxel thick border to support filtering on the image boundary. These images are of size (xbound+2)-by-(ybound+2)-by-(zbound+2). The inputs (x,y,z) to access the data and mask avlues are constrained to 0 <= x < xbound, 0 <= y < ybound, and 0 <= z < zbound. The correct lookups into the padded arrays are handled internally.

Version:

0.1 November 7, 2006

Author:

David Eberly

Field Summary

Fields
Modifier and Type	Field	Description
`protected boolean[][][]`	`m_aaabMask`	Voxels may be masked out so that the PDE solver does not process them.
`protected float[][][]`	`m_aaafDst`	Successive iterations of the PDE solver toggle between two buffers.
`protected float[][][]`	`m_aaafSrc`	Successive iterations of the PDE solver toggle between two buffers.
`protected float`	`m_fFourthInvDxDy`	invFourthDxDy = 1/(4dxdy)
`protected float`	`m_fFourthInvDxDz`	invFourthDxDz = 1/(4dxdz)
`protected float`	`m_fFourthInvDyDz`	invFourthDyDz = 1/(4dydz)
`protected float`	`m_fHalfInvDx`	halfInvDx = 1/(2*dx)
`protected float`	`m_fHalfInvDy`	halfInvDy = 1/(2*dy)
`protected float`	`m_fHalfInvDz`	halfInvDz = 1/(2*dz)
`protected float`	`m_fInvDx`	invDx = 1/dx
`protected float`	`m_fInvDxDx`	invDxDx = 1/(dx*dx)
`protected float`	`m_fInvDy`	invDy = 1/dy
`protected float`	`m_fInvDyDy`	invDyDy = 1/(dy*dy)
`protected float`	`m_fInvDz`	invDz = 1/dz
`protected float`	`m_fInvDzDz`	invDzDz = 1/(dz*dz)
`protected float`	`m_fUmmm`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUmmp`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUmmz`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUmpm`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUmpp`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUmpz`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUmzm`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUmzp`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUmzz`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUpmm`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUpmp`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUpmz`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUppm`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUppp`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUppz`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUpzm`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUpzp`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUpzz`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUzmm`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUzmp`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUzmz`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUzpm`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUzpp`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUzpz`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUzzm`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUzzp`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fUzzz`	Temporary storage for 3x3x3 neighborhood.
`protected float`	`m_fXSpacing`	The x-spacing of the image, call it dx.
`protected float`	`m_fYSpacing`	The y-spacing of the image, call it dy.
`protected float`	`m_fZSpacing`	The z-spacing of the image, call it dz.
`protected int`	`m_iXBound`	The x-bound of the image.
`protected int`	`m_iYBound`	The y-bound of the image.
`protected int`	`m_iZBound`	The z-bound of the image.

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`	`LsePdeFilter3(int iXBound, int iYBound, int iZBound, float fXSpacing, float fYSpacing, float fZSpacing, float[] afData, boolean[] abMask, float fBorderValue, int eScaleType)`	Create a new PDE filter object for 3D images.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`assignDirichletImageBorder()`	Assign values to the 1-voxel-thick image border.
`protected void`	`assignDirichletMaskBorder()`	Assign values to the 1-voxel-thick borders that surround unmasked regions.
`protected void`	`assignNeumannImageBorder()`	Assign values to the 1-voxel-thick image border.
`protected void`	`assignNeumannMaskBorder()`	Assign values to the 1-voxel-thick borders that surround unmasked regions.
`boolean`	`getMask(int iX, int iY, int iZ)`	Get the mask value at voxel (x,y,z).
`float`	`getU(int iX, int iY, int iZ)`	Get the image value at voxel (x,y,z), call it u(x,y,z).
`float`	`getUx(int iX, int iY, int iZ)`	Get the first-order x-derivative of the image value at voxel (x,y,z), call it u_x(x,y,z).
`float`	`getUxx(int iX, int iY, int iZ)`	Get the second-order x-derivative of the image value at voxel (x,y,z), call it u_xx(x,y,z).
`float`	`getUxy(int iX, int iY, int iZ)`	Get the second-order xy-mixed-derivative of the image value at voxel (x,y,z), call it u_xy(x,y,z).
`float`	`getUxz(int iX, int iY, int iZ)`	Get the second-order xz-mixed-derivative of the image value at voxel (x,y,z), call it u_xz(x,y,z).
`float`	`getUy(int iX, int iY, int iZ)`	Get the first-order y-derivative of the image value at voxel (x,y,z), call it u_y(x,y,z).
`float`	`getUyy(int iX, int iY, int iZ)`	Get the second-order y-derivative of the image value at voxel (x,y,z), call it u_yy(x,y,z).
`float`	`getUyz(int iX, int iY, int iZ)`	Get the second-order yz-mixed-derivative of the image value at voxel (x,y,z), call it u_yz(x,y,z).
`float`	`getUz(int iX, int iY, int iZ)`	Get the first-order z-derivative of the image value at voxel (x,y,z), call it u_z(x,y,z).
`float`	`getUzz(int iX, int iY, int iZ)`	Get the second-order z-derivative of the image value at voxel (x,y,z), call it u_zz(x,y,z).
`int`	`getXBound()`	Get the x-bound for the image.
`float`	`getXSpacing()`	Get the x-spacing for the image.
`int`	`getYBound()`	Get the y-bound for the image.
`float`	`getYSpacing()`	Get the y-spacing for the image.
`int`	`getZBound()`	Get the z-bound for the image.
`float`	`getZSpacing()`	Get the z-spacing for the image.
`protected void`	`lookUp27(int iX, int iY, int iZ)`	Copy the source data to temporary storage in order to avoid redundant array accesses.
`protected void`	`lookUp7(int iX, int iY, int iZ)`	Copy the source data to temporary storage in order to avoid redundant array accesses.
`protected void`	`onPostUpdate()`	Swap the buffers for the next pass of the PDE solver.
`protected void`	`onPreUpdate()`	Recompute the boundary values when Neumann conditions are in effect.
`protected void`	`onUpdate()`	Iterate over all the voxels and call onUpdate(x,y,z) for each voxel that is not masked out.
`protected abstract void`	`onUpdate(int iX, int iY, int iZ)`	An abstract function that allows per-voxel processing by the PDE solver.

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_iXBound
```
protected int m_iXBound
```
    The x-bound of the image.
  - m_iYBound
```
protected int m_iYBound
```
    The y-bound of the image.
  - m_iZBound
```
protected int m_iZBound
```
    The z-bound of the image.
  - m_fXSpacing
```
protected float m_fXSpacing
```
    The x-spacing of the image, call it dx.
  - m_fYSpacing
```
protected float m_fYSpacing
```
    The y-spacing of the image, call it dy.
  - m_fZSpacing
```
protected float m_fZSpacing
```
    The z-spacing of the image, call it dz.
  - m_fInvDx
```
protected float m_fInvDx
```
    invDx = 1/dx
  - m_fInvDy
```
protected float m_fInvDy
```
    invDy = 1/dy
  - m_fInvDz
```
protected float m_fInvDz
```
    invDz = 1/dz
  - m_fHalfInvDx
```
protected float m_fHalfInvDx
```
    halfInvDx = 1/(2*dx)
  - m_fHalfInvDy
```
protected float m_fHalfInvDy
```
    halfInvDy = 1/(2*dy)
  - m_fHalfInvDz
```
protected float m_fHalfInvDz
```
    halfInvDz = 1/(2*dz)
  - m_fInvDxDx
```
protected float m_fInvDxDx
```
    invDxDx = 1/(dx*dx)
  - m_fFourthInvDxDy
```
protected float m_fFourthInvDxDy
```
    invFourthDxDy = 1/(4*dx*dy)
  - m_fFourthInvDxDz
```
protected float m_fFourthInvDxDz
```
    invFourthDxDz = 1/(4*dx*dz)
  - m_fInvDyDy
```
protected float m_fInvDyDy
```
    invDyDy = 1/(dy*dy)
  - m_fFourthInvDyDz
```
protected float m_fFourthInvDyDz
```
    invFourthDyDz = 1/(4*dy*dz)
  - m_fInvDzDz
```
protected float m_fInvDzDz
```
    invDzDz = 1/(dz*dz)
  - m_fUmmm
```
protected float m_fUmmm
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzmm
```
protected float m_fUzmm
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUpmm
```
protected float m_fUpmm
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUmzm
```
protected float m_fUmzm
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzzm
```
protected float m_fUzzm
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUpzm
```
protected float m_fUpzm
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUmpm
```
protected float m_fUmpm
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzpm
```
protected float m_fUzpm
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUppm
```
protected float m_fUppm
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUmmz
```
protected float m_fUmmz
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzmz
```
protected float m_fUzmz
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUpmz
```
protected float m_fUpmz
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUmzz
```
protected float m_fUmzz
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzzz
```
protected float m_fUzzz
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUpzz
```
protected float m_fUpzz
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUmpz
```
protected float m_fUmpz
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzpz
```
protected float m_fUzpz
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUppz
```
protected float m_fUppz
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUmmp
```
protected float m_fUmmp
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzmp
```
protected float m_fUzmp
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUpmp
```
protected float m_fUpmp
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUmzp
```
protected float m_fUmzp
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzzp
```
protected float m_fUzzp
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUpzp
```
protected float m_fUpzp
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUmpp
```
protected float m_fUmpp
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzpp
```
protected float m_fUzpp
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUppp
```
protected float m_fUppp
```
    Temporary storage for 3x3x3 neighborhood. In the notation m_fUijk, the i, j, and k indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_aaafSrc
```
protected float[][][] m_aaafSrc
```
    Successive iterations of the PDE solver toggle between two buffers. This is the source buffer, which is the input to the solver.
  - m_aaafDst
```
protected float[][][] m_aaafDst
```
    Successive iterations of the PDE solver toggle between two buffers. This is the destination buffer, which is the output of the solver.
  - m_aaabMask
```
protected boolean[][][] m_aaabMask
```
    Voxels may be masked out so that the PDE solver does not process them. This is useful for filtering only those voxels in a subimage.
- Constructor Detail
  - LsePdeFilter3
```
protected LsePdeFilter3(int iXBound,
                        int iYBound,
                        int iZBound,
                        float fXSpacing,
                        float fYSpacing,
                        float fZSpacing,
                        float[] afData,
                        boolean[] abMask,
                        float fBorderValue,
                        int eScaleType)
```
    Create a new PDE filter object 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
  - getXBound
```
public final int getXBound()
```
    Get the x-bound for the image.
    
    Returns:
    
    The x-bound for the image.
  - getYBound
```
public final int getYBound()
```
    Get the y-bound for the image.
    
    Returns:
    
    The y-bound for the image.
  - getZBound
```
public final int getZBound()
```
    Get the z-bound for the image.
    
    Returns:
    
    The z-bound for the image.
  - getXSpacing
```
public final float getXSpacing()
```
    Get the x-spacing for the image.
    
    Returns:
    
    The x-spacing for the image.
  - getYSpacing
```
public final float getYSpacing()
```
    Get the y-spacing for the image.
    
    Returns:
    
    The y-spacing for the image.
  - getZSpacing
```
public final float getZSpacing()
```
    Get the z-spacing for the image.
    
    Returns:
    
    The z-spacing for the image.
  - getU
```
public final float getU(int iX,
                        int iY,
                        int iZ)
```
    Get the image value at voxel (x,y,z), call it u(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 image value, u(x,y,z).
  - getUx
```
public final float getUx(int iX,
                         int iY,
                         int iZ)
```
    Get the first-order x-derivative of the image value at voxel (x,y,z), call it u_x(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 x-derivative of the image value, u_x(x,y,z).
  - getUy
```
public final float getUy(int iX,
                         int iY,
                         int iZ)
```
    Get the first-order y-derivative of the image value at voxel (x,y,z), call it u_y(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 y-derivative of the image value, u_y(x,y,z).
  - getUz
```
public final float getUz(int iX,
                         int iY,
                         int iZ)
```
    Get the first-order z-derivative of the image value at voxel (x,y,z), call it u_z(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 z-derivative of the image value, u_z(x,y,z).
  - getUxx
```
public final float getUxx(int iX,
                          int iY,
                          int iZ)
```
    Get the second-order x-derivative of the image value at voxel (x,y,z), call it u_xx(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 xx-derivative of the image value, u_xx(x,y).
  - getUxy
```
public final float getUxy(int iX,
                          int iY,
                          int iZ)
```
    Get the second-order xy-mixed-derivative of the image value at voxel (x,y,z), call it u_xy(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 xy-derivative of the image value, u_xy(x,y,z).
  - getUxz
```
public final float getUxz(int iX,
                          int iY,
                          int iZ)
```
    Get the second-order xz-mixed-derivative of the image value at voxel (x,y,z), call it u_xz(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 xz-derivative of the image value, u_xz(x,y,z).
  - getUyy
```
public final float getUyy(int iX,
                          int iY,
                          int iZ)
```
    Get the second-order y-derivative of the image value at voxel (x,y,z), call it u_yy(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 yy-derivative of the image value, u_yy(x,y).
  - getUyz
```
public final float getUyz(int iX,
                          int iY,
                          int iZ)
```
    Get the second-order yz-mixed-derivative of the image value at voxel (x,y,z), call it u_yz(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 yz-derivative of the image value, u_yz(x,y,z).
  - getUzz
```
public final float getUzz(int iX,
                          int iY,
                          int iZ)
```
    Get the second-order z-derivative of the image value at voxel (x,y,z), call it u_zz(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 zz-derivative of the image value, u_zz(x,y).
  - getMask
```
public final boolean getMask(int iX,
                             int iY,
                             int iZ)
```
    Get the mask value at 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 mask value at voxel (x,y,z). Its value is true when that pixel should not be processed by the PDE solver.
  - assignDirichletImageBorder
```
protected void assignDirichletImageBorder()
```
    Assign values to the 1-voxel-thick image border. The border value has been specified during object construction.
  - assignNeumannImageBorder
```
protected void assignNeumannImageBorder()
```
    Assign values to the 1-voxel-thick image border. The border values are chosen so that the first-order image derivatives at the border pixels are zero. Thus, the border values are duplicates of the adjacent image values.
  - assignDirichletMaskBorder
```
protected void assignDirichletMaskBorder()
```
    Assign values to the 1-voxel-thick borders that surround unmasked regions. The border value has been specified during object construction.
  - assignNeumannMaskBorder
```
protected void assignNeumannMaskBorder()
```
    Assign values to the 1-voxel-thick borders that surround unmasked regions. The border values are chosen so that the first-order image derivatives at the border voxels are zero. Thus, the border values are duplicates of the adjacent image values.
  - onPreUpdate
```
protected void onPreUpdate()
```
    Recompute the boundary values when Neumann conditions are in effect. If a derived class overrides this, it must call the base-class onPreUpdate first.
    
    Specified by:
    
    onPreUpdate in class LsePdeFilter
  - onUpdate
```
protected void onUpdate()
```
    Iterate over all the voxels and call onUpdate(x,y,z) for each voxel that is not masked out.
    
    Specified by:
    
    onUpdate in class LsePdeFilter
  - onPostUpdate
```
protected void onPostUpdate()
```
    Swap the buffers for the next pass of the PDE solver. If a derived class overrides this, it must call the base-class onPostUpdate last.
    
    Specified by:
    
    onPostUpdate in class LsePdeFilter
  - onUpdate
```
protected abstract void onUpdate(int iX,
                                 int iY,
                                 int iZ)
```
    An abstract function that allows per-voxel processing by the PDE solver. The voxel (x,y,z) must be in padded coordinates, namely, 1 <= x <= xbound, 1 <= y <= ybound, and 1 <= z <= zbound.
    
    Parameters:
    
    iX - The x-coordinate of the voxel.
    
    iY - The y-coordinate of the voxel.
    
    iZ - The z-coordinate of the voxel.
  - lookUp7
```
protected void lookUp7(int iX,
                       int iY,
                       int iZ)
```
    Copy the source data to temporary storage in order to avoid redundant array accesses. The copy involves the 7 voxels (x,y,z), (x+1,y,z), (x-1,y,z), (x,y+1,z), (x,y-1,z), (x,y,z+1), and (x,y,z-1).
  - lookUp27
```
protected void lookUp27(int iX,
                        int iY,
                        int iZ)
```
    Copy the source data to temporary storage in order to avoid redundant array accesses. The copy involves the 27 pixels in the 3x3x3 neighborhood of (x,y,z).

Class LsePdeFilter3

Field Summary

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.LsePdeFilter

Methods inherited from class java.lang.Object

Field Detail

m_iXBound

m_iYBound

m_iZBound

m_fXSpacing

m_fYSpacing

m_fZSpacing

m_fInvDx

m_fInvDy

m_fInvDz

m_fHalfInvDx

m_fHalfInvDy

m_fHalfInvDz

m_fInvDxDx

m_fFourthInvDxDy

m_fFourthInvDxDz

m_fInvDyDy

m_fFourthInvDyDz

m_fInvDzDz

m_fUmmm

m_fUzmm

m_fUpmm

m_fUmzm

m_fUzzm

m_fUpzm

m_fUmpm

m_fUzpm

m_fUppm

m_fUmmz

m_fUzmz

m_fUpmz

m_fUmzz

m_fUzzz

m_fUpzz

m_fUmpz

m_fUzpz

m_fUppz

m_fUmmp

m_fUzmp

m_fUpmp

m_fUmzp

m_fUzzp

m_fUpzp

m_fUmpp

m_fUzpp

m_fUppp

m_aaafSrc

m_aaafDst

m_aaabMask

Constructor Detail

LsePdeFilter3

Method Detail

getXBound

getYBound

getZBound

getXSpacing

getYSpacing

getZSpacing

getU

getUx

getUy

getUz

getUxx

getUxy

getUxz

getUyy

getUyz

getUzz

getMask

assignDirichletImageBorder

assignNeumannImageBorder

assignDirichletMaskBorder

assignNeumannMaskBorder