java.lang.Object
- gov.nih.mipav.model.algorithms.levelset.LsePdeFilter
- - gov.nih.mipav.model.algorithms.levelset.LsePdeFilter2

Direct Known Subclasses:

LseCurvatureFlow2, LseEvolve2, LseGaussianBlur2, LseGradientAnisotropic2
```
public abstract class LsePdeFilter2
extends LsePdeFilter
```
The abstract base class for finite-difference-based solvers for partial differential equations in 2D. This system exists to support level-set evolution for image segmentation.

The internal 2D data and mask images are copies of the inputs to the constructor but padded with a 1-pixel thick border to support filtering on the image boundary. These images are of size (xbound+2)-by-(ybound+2). The inputs (x,y) to access the data and mask avlues are constrained to 0 <= x < xbound and 0 <= y < ybound. 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_aabMask`	Pixels may be masked out so that the PDE solver does not process them.
`protected float[][]`	`m_aafDst`	Successive iterations of the PDE solver toggle between two buffers.
`protected float[][]`	`m_aafSrc`	Successive iterations of the PDE solver toggle between two buffers.
`protected float`	`m_fFourthInvDxDy`	invFourthDxDy = 1/(4dxdy)
`protected float`	`m_fHalfInvDx`	halfInvDx = 1/(2*dx)
`protected float`	`m_fHalfInvDy`	halfInvDy = 1/(2*dy)
`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_fUmm`	Temporary storage for 3x3 neighborhood.
`protected float`	`m_fUmp`	Temporary storage for 3x3 neighborhood.
`protected float`	`m_fUmz`	Temporary storage for 3x3 neighborhood.
`protected float`	`m_fUpm`	Temporary storage for 3x3 neighborhood.
`protected float`	`m_fUpp`	Temporary storage for 3x3 neighborhood.
`protected float`	`m_fUpz`	Temporary storage for 3x3 neighborhood.
`protected float`	`m_fUzm`	Temporary storage for 3x3 neighborhood.
`protected float`	`m_fUzp`	Temporary storage for 3x3 neighborhood.
`protected float`	`m_fUzz`	Temporary storage for 3x3 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 int`	`m_iXBound`	The x-bound of the image.
`protected int`	`m_iYBound`	The y-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`	`LsePdeFilter2(int iXBound, int iYBound, float fXSpacing, float fYSpacing, float[] afData, boolean[] abMask, float fBorderValue, int eScaleType)`	Create a new PDE filter object for 2D images.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`assignDirichletImageBorder()`	Assign values to the 1-pixel-thick image border.
`protected void`	`assignDirichletMaskBorder()`	Assign values to the 1-pixel-thick borders that surround unmasked regions.
`protected void`	`assignNeumannImageBorder()`	Assign values to the 1-pixel-thick image border.
`protected void`	`assignNeumannMaskBorder()`	Assign values to the 1-pixel-thick borders that surround unmasked regions.
`boolean`	`getMask(int iX, int iY)`	Get the mask value at pixel (x,y).
`float`	`getU(int iX, int iY)`	Get the image value at pixel (x,y), call it u(x,y).
`float`	`getUx(int iX, int iY)`	Get the first-order x-derivative of the image value at pixel (x,y), call it u_x(x,y).
`float`	`getUxx(int iX, int iY)`	Get the second-order x-derivative of the image value at pixel (x,y), call it u_xx(x,y).
`float`	`getUxy(int iX, int iY)`	Get the second-order mixed-derivative of the image value at pixel (x,y), call it u_xy(x,y).
`float`	`getUy(int iX, int iY)`	Get the first-order y-derivative of the image value at pixel (x,y), call it u_y(x,y).
`float`	`getUyy(int iX, int iY)`	Get the second-order y-derivative of the image value at pixel (x,y), call it u_yy(x,y).
`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.
`protected void`	`lookUp5(int iX, int iY)`	Copy the source data to temporary storage in order to avoid redundant array accesses.
`protected void`	`lookUp9(int iX, int iY)`	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 pixels and call onUpdate(x,y) for each pixel that is not masked out.
`protected abstract void`	`onUpdate(int iX, int iY)`	An abstract function that allows per-pixel 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_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_fInvDx
```
protected float m_fInvDx
```
    invDx = 1/dx
  - m_fInvDy
```
protected float m_fInvDy
```
    invDy = 1/dy
  - m_fHalfInvDx
```
protected float m_fHalfInvDx
```
    halfInvDx = 1/(2*dx)
  - m_fHalfInvDy
```
protected float m_fHalfInvDy
```
    halfInvDy = 1/(2*dy)
  - m_fInvDxDx
```
protected float m_fInvDxDx
```
    invDxDx = 1/(dx*dx)
  - m_fFourthInvDxDy
```
protected float m_fFourthInvDxDy
```
    invFourthDxDy = 1/(4*dx*dy)
  - m_fInvDyDy
```
protected float m_fInvDyDy
```
    invDyDy = 1/(dy*dy)
  - m_fUmm
```
protected float m_fUmm
```
    Temporary storage for 3x3 neighborhood. In the notation m_fUij, the i and j indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzm
```
protected float m_fUzm
```
    Temporary storage for 3x3 neighborhood. In the notation m_fUij, the i and j indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUpm
```
protected float m_fUpm
```
    Temporary storage for 3x3 neighborhood. In the notation m_fUij, the i and j indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUmz
```
protected float m_fUmz
```
    Temporary storage for 3x3 neighborhood. In the notation m_fUij, the i and j indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzz
```
protected float m_fUzz
```
    Temporary storage for 3x3 neighborhood. In the notation m_fUij, the i and j indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUpz
```
protected float m_fUpz
```
    Temporary storage for 3x3 neighborhood. In the notation m_fUij, the i and j indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUmp
```
protected float m_fUmp
```
    Temporary storage for 3x3 neighborhood. In the notation m_fUij, the i and j indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUzp
```
protected float m_fUzp
```
    Temporary storage for 3x3 neighborhood. In the notation m_fUij, the i and j indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_fUpp
```
protected float m_fUpp
```
    Temporary storage for 3x3 neighborhood. In the notation m_fUij, the i and j indices are in {m,z,p}, referring to subtract 1 (m), no change (z), or add 1 (p) to the appropriate index.
  - m_aafSrc
```
protected float[][] m_aafSrc
```
    Successive iterations of the PDE solver toggle between two buffers. This is the source buffer, which is the input to the solver.
  - m_aafDst
```
protected float[][] m_aafDst
```
    Successive iterations of the PDE solver toggle between two buffers. This is the destination buffer, which is the output of the solver.
  - m_aabMask
```
protected boolean[][] m_aabMask
```
    Pixels may be masked out so that the PDE solver does not process them. This is useful for filtering only those pixels in a subimage.
- Constructor Detail
  - LsePdeFilter2
```
protected LsePdeFilter2(int iXBound,
                        int iYBound,
                        float fXSpacing,
                        float fYSpacing,
                        float[] afData,
                        boolean[] abMask,
                        float fBorderValue,
                        int eScaleType)
```
    Create a new PDE filter object for 2D images.
    
    Parameters:
    
    iXBound - The x-bound of the image.
    
    iYBound - The y-bound of the image.
    
    fXSpacing - The x-spacing of the image.
    
    fYSpacing - The y-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.
- 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.
  - 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.
  - getU
```
public final float getU(int iX,
                        int iY)
```
    Get the image value at pixel (x,y), call it u(x,y).
    
    Parameters:
    
    iX - The x-coordinate of the pixel.
    
    iY - The y-coordinate of the pixel.
    
    Returns:
    
    The image value, u(x,y).
  - getUx
```
public final float getUx(int iX,
                         int iY)
```
    Get the first-order x-derivative of the image value at pixel (x,y), call it u_x(x,y).
    
    Parameters:
    
    iX - The x-coordinate of the pixel.
    
    iY - The y-coordinate of the pixel.
    
    Returns:
    
    The x-derivative of the image value, u_x(x,y).
  - getUy
```
public final float getUy(int iX,
                         int iY)
```
    Get the first-order y-derivative of the image value at pixel (x,y), call it u_y(x,y).
    
    Parameters:
    
    iX - The x-coordinate of the pixel.
    
    iY - The y-coordinate of the pixel.
    
    Returns:
    
    The y-derivative of the image value, u_y(x,y).
  - getUxx
```
public final float getUxx(int iX,
                          int iY)
```
    Get the second-order x-derivative of the image value at pixel (x,y), call it u_xx(x,y).
    
    Parameters:
    
    iX - The x-coordinate of the pixel.
    
    iY - The y-coordinate of the pixel.
    
    Returns:
    
    The xx-derivative of the image value, u_xx(x,y).
  - getUxy
```
public final float getUxy(int iX,
                          int iY)
```
    Get the second-order mixed-derivative of the image value at pixel (x,y), call it u_xy(x,y).
    
    Parameters:
    
    iX - The x-coordinate of the pixel.
    
    iY - The y-coordinate of the pixel.
    
    Returns:
    
    The xy-derivative of the image value, u_xy(x,y).
  - getUyy
```
public final float getUyy(int iX,
                          int iY)
```
    Get the second-order y-derivative of the image value at pixel (x,y), call it u_yy(x,y).
    
    Parameters:
    
    iX - The x-coordinate of the pixel.
    
    iY - The y-coordinate of the pixel.
    
    Returns:
    
    The yy-derivative of the image value, u_xx(x,y).
  - getMask
```
public final boolean getMask(int iX,
                             int iY)
```
    Get the mask value at pixel (x,y).
    
    Parameters:
    
    iX - The x-coordinate of the pixel.
    
    iY - The y-coordinate of the pixel.
    
    Returns:
    
    The mask value at pixel (x,y). Its value is true when that pixel should not be processed by the PDE solver.
  - assignDirichletImageBorder
```
protected void assignDirichletImageBorder()
```
    Assign values to the 1-pixel-thick image border. The border value has been specified during object construction.
  - assignNeumannImageBorder
```
protected void assignNeumannImageBorder()
```
    Assign values to the 1-pixel-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-pixel-thick borders that surround unmasked regions. The border value has been specified during object construction.
  - assignNeumannMaskBorder
```
protected void assignNeumannMaskBorder()
```
    Assign values to the 1-pixel-thick borders that surround unmasked regions. 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.
  - 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 pixels and call onUpdate(x,y) for each pixel 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)
```
    An abstract function that allows per-pixel processing by the PDE solver. The pixel (x,y) must be in padded coordinates, namely, 1 <= x <= xbound and 1 <= y <= ybound.
    
    Parameters:
    
    iX - The x-coordinate of the pixel.
    
    iY - The y-coordinate of the pixel.
  - lookUp5
```
protected void lookUp5(int iX,
                       int iY)
```
    Copy the source data to temporary storage in order to avoid redundant array accesses. The copy involves the 5 pixels (x,y), (x+1,y), (x-1,y), (x,y+1), and (x,y-1).
  - lookUp9
```
protected void lookUp9(int iX,
                       int iY)
```
    Copy the source data to temporary storage in order to avoid redundant array accesses. The copy involves the 9 pixels in the 3x3 neighborhood of (x,y).

Class LsePdeFilter2

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_fXSpacing

m_fYSpacing

m_fInvDx

m_fInvDy

m_fHalfInvDx

m_fHalfInvDy

m_fInvDxDx

m_fFourthInvDxDy

m_fInvDyDy

m_fUmm

m_fUzm

m_fUpm

m_fUmz

m_fUzz

m_fUpz

m_fUmp

m_fUzp

m_fUpp

m_aafSrc

m_aafDst

m_aabMask

Constructor Detail

LsePdeFilter2

Method Detail

getXBound

getYBound

getXSpacing

getYSpacing

getU

getUx

getUy

getUxx

getUxy

getUyy

getMask

assignDirichletImageBorder

assignNeumannImageBorder

assignDirichletMaskBorder

assignNeumannMaskBorder

onPreUpdate

onUpdate

onPostUpdate

onUpdate

lookUp5

lookUp9