MTBLevelsetFunctionPDE (mitobo 2.5 API)

java.lang.Object
- de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
- - de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE

All Implemented Interfaces:

MTBSegmentationInterface, Cloneable
```
public class MTBLevelsetFunctionPDE
extends MTBLevelsetFunctionDerivable
implements Cloneable
```
Class representing a 3-dimensional level set function.
The representation includes two classes with labels 0 and 1. Label 0 refers to the background including all pixels in the level set function's domain where the value of the function is smaller than zero. Class 1, i.e. the foreground phase of the level set function, is linked to all pixels in the domain with function values larger than zero.
The levelset function can be transformed into a signed-distance function.

Author:

Martin Scharm, Michael Schneider, Birgit Moeller

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`protected class`	`MTBLevelsetFunctionPDE.SortedList<EType>` A genric class representing a sorted list
`protected class`	`MTBLevelsetFunctionPDE.SortedListElement<EType>` internal representation of elements

Nested classes/interfaces inherited from interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
MTBSegmentationInterface.SegmentationDimension

Field Summary

Fields
Modifier and Type	Field and Description
`protected int`	`borderDist` Safety distance along image borders.
`private boolean`	`DEFAULT_FALL_BACK`
`protected int`	`depth` Depth of the input image and levelset function.
`protected int`	`height` Height of the input image and levelset function.
`private double[][]`	`helperArray` 2D array of first two levelset dimension used for visualization
`static double`	`MAX_VALUE` Constant used in SDF calculations.
`protected ArrayList<MTBPoint3D>`	`narrow` Pixels in narrow-band.
`protected double[][][]`	`phi` The level set function.
`protected HashMap<MTBPoint3D,MTBPoint3D>`	`predecessors` Map of precursors on contour for each pixel in narrow-band.
`protected boolean[][][]`	`visible` Visibility array.
`protected int`	`width` Width of the input image and levelset function.

Constructor Summary

Constructors
Constructor and Description
`MTBLevelsetFunctionPDE(boolean nb_diag, int w, int h, int d)` create a new levelsetfunction, setting a default handle for derivations on borders
`MTBLevelsetFunctionPDE(boolean nb_diag, int w, int h, int d, boolean default_fallback)` create a new levelsetfunction, setting a default handle for derivations on borders
`MTBLevelsetFunctionPDE(int w, int h, int d)` Create a new levelset function.
`MTBLevelsetFunctionPDE(int w, int h, int d, boolean default_fallback)` create a new levelsetfunction, setting a default handle for derivations on borders
`MTBLevelsetFunctionPDE(int w, int h, int d, int border)` Constructor to init empty function with safety border.
`MTBLevelsetFunctionPDE(int w, int h, int d, MTBSegmentationInterface seg, boolean default_fallback)` Constructor to build a level set function from a segmentation object.
`MTBLevelsetFunctionPDE(int w, int h, int d, MTBSegmentationInterface seg, boolean default_fallback, int border)` Constructor to build a level set function from a segmentation object.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`double`	`backwardDifferencing_X(int x, int y, int z)` retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
`double`	`backwardDifferencing_X(int x, int y, int z, boolean fallback)` retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
`double`	`backwardDifferencing_Y(int x, int y, int z)` retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
`double`	`backwardDifferencing_Y(int x, int y, int z, boolean fallback)` retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
`double`	`backwardDifferencing_Z(int x, int y, int z)` retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
`double`	`backwardDifferencing_Z(int x, int y, int z, boolean fallback)` retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
`MTBLevelsetFunctionPDE`	`clone()` generate a clone of this object
`void`	`copyTo(MTBLevelsetFunctionPDE two)` copy this object to another one
`boolean`	`equals(MTBLevelsetFunctionPDE ls2d)` are these two LevelSets equal?
`double`	`forwardDifferencing_X(int x, int y, int z, boolean fallback)` retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
`double`	`forwardDifferencing_Y(int x, int y, int z, boolean fallback)` retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
`double`	`forwardDifferencing_Z(int x, int y, int z, boolean fallback)` retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
`double`	`get(int x, int y, int z)` get the value of this function at the position of the predecessor of ( x, y, z )
`MTBImageByte`	`getBinaryMask()` Get a binary mask of the represented segmentation.
`int`	`getClass(int x, int y)` Returns the class label of position (x,y).
`int`	`getClass(int x, int y, int z)` Returns the class label of position (x,y,z).
`double`	`getCurvature(int x, int y, int z)` compute the curvature at at nearest contourpoint to (x,y,z) if x or y are not in the boundaries it returns 0 if z is not in the boundaries it returns the 2d cuvature
`double`	`getDerivativeX(int x, int y, int z)` retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
`double`	`getDerivativeXX(int x, int y, int z)` computes the the derivation in x direction 2 times at nearest contourpoint to (x,y,z)
`double`	`getDerivativeXY(int x, int y, int z)` computes the the derivation in x and y direction at nearest contourpoint to (x,y,z)
`double`	`getDerivativeXZ(int x, int y, int z)` computes the the derivation in x and z direction at nearest contourpoint to (x,y,z)
`double`	`getDerivativeY(int x, int y, int z)` retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
`double`	`getDerivativeYY(int x, int y, int z)` computes the the derivation in y direction 2 times at nearest contourpoint to (x,y,z)
`double`	`getDerivativeYZ(int x, int y, int z)` computes the the derivation in y and z direction at nearest contourpoint to (x,y,z)
`double`	`getDerivativeZ(int x, int y, int z)` retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
`double`	`getDerivativeZZ(int x, int y, int z)` computes the the derivation in z direction 2 times at nearest contourpoint to (x,y,z)
`MTBSegmentationInterface.SegmentationDimension`	`getDimension()` Returns the dimension of the segmentation.
`double`	`getForegroundSum()`
`MTBImage`	`getMask(int class_)` Gets the mask of the specified class (0 Background, 255 Foreground)
`int`	`getMaxLabel()` Returns the maximal label used in the segmentation representation.
`Iterator<MTBPoint3D>`	`getNarrowIterator()` get an iterator through narrow band
`int`	`getNumberOfClasses()` Returns the number of classes represented by the segmentation.
`MTBImageRGB`	`getPhiColorImage2D(MTBImageRGB targetImg)` Get visualization of current level set function in red-blue color map.
`MTBImageShort`	`getPhiImage()` Get visualization of current level set function.
`MTBPoint3D`	`getPredecessorOnContour(int x, int y, int z)` gets the value of the nearest contourpoint to point (x,y,z)
`int`	`getSizeX()` Get width of level set function.
`int`	`getSizeY()` Get height of level set function.
`int`	`getSizeZ()` Get depth of level set function.
`double`	`getWeight(int x, int y)` Returns the pixel weight of position (x,y).
`double`	`getWeight(int x, int y, int z)` Returns the pixel weight of position (x,y,z).
`boolean`	`isVisible(int x, int y)` True, if position (x,y) is visible.
`boolean`	`isVisible(int x, int y, int z)` is this pixel visible?
`void`	`set(int x, int y, int z, double value)` assign a value to the matrix at position ( x, y, z )
`void`	`setClass(int x, int y, int c)` Deprecated.
`void`	`setClass(int x, int y, int z, int c)` Deprecated.
`void`	`setInvisible(int x, int y)` Set position (x,y) invisible.
`void`	`setInvisible(int x, int y, int z)` Set position (x,y,z) invisible.
`boolean`	`setVisible(boolean[][][] mask)` Set visibility of positions.
`void`	`setVisible(int x, int y)` Set position (x,y) visible.
`void`	`setVisible(int x, int y, int z)` Set position (x,y,z) visible.
`void`	`setWeight(int x, int y, double c)` Sets the pixel weight of position (x,y) to c.
`void`	`setWeight(int x, int y, int z, double c)` Sets the pixel weight of position (x,y,z) to c.
`private double`	`sgnSum(int x, int y, int z)` Computes scaled sign in neighborhood.
`void`	`signDistance(double b)` Transform function into signed distance function.
`private void`	`signedExpandation(MTBLevelsetFunctionPDE.SortedList<MTBPoint3D> slist, double maximum, double toAdd)` Expand signed distances around zero-level.
`boolean`	`valid(int x, int y, int z)` is this pixel valid?

Methods inherited from class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
nearZero, sgn

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - MAX_VALUE
```
public static final double MAX_VALUE
```
    Constant used in SDF calculations.
    
    See Also:
    
    Constant Field Values
  - phi
```
protected double[][][] phi
```
    The level set function.
  - visible
```
protected boolean[][][] visible
```
    Visibility array.
  - height
```
protected int height
```
    Height of the input image and levelset function.
  - width
```
protected int width
```
    Width of the input image and levelset function.
  - depth
```
protected int depth
```
    Depth of the input image and levelset function.
  - borderDist
```
protected int borderDist
```
    Safety distance along image borders.
    Pixels closer to border than this distance are ignored in calculations.
  - narrow
```
protected ArrayList<MTBPoint3D> narrow
```
    Pixels in narrow-band.
    The array is updated on transforming the function into a SDF.
  - predecessors
```
protected HashMap<MTBPoint3D,MTBPoint3D> predecessors
```
    Map of precursors on contour for each pixel in narrow-band.
    The map is updated on transforming the function into a SDF.
  - helperArray
```
private double[][] helperArray
```
    2D array of first two levelset dimension used for visualization
  - DEFAULT_FALL_BACK
```
private boolean DEFAULT_FALL_BACK
```
- Constructor Detail
  - MTBLevelsetFunctionPDE
```
public MTBLevelsetFunctionPDE(int w,
                              int h,
                              int d)
```
    Create a new levelset function.
    The default handle for calculations of derivatives along borders is set to fall back to other methods to calculate the derivatives.
    
    Parameters:
    
    w - Width of function.
    
    h - Height of function.
    
    d - Depth of function.
  - MTBLevelsetFunctionPDE
```
public MTBLevelsetFunctionPDE(int w,
                              int h,
                              int d,
                              int border)
```
    Constructor to init empty function with safety border.
    
    Parameters:
    
    w - Width of levelset function (x-size).
    
    h - Height of levelset function (y-size).
    
    d - Depth of levelset function (z-size).
    
    border - Width of border to ignore in calculations.
  - MTBLevelsetFunctionPDE
```
public MTBLevelsetFunctionPDE(int w,
                              int h,
                              int d,
                              boolean default_fallback)
```
    create a new levelsetfunction, setting a default handle for derivations on borders
    
    Parameters:
    
    w - length of function
    
    h - height of function
    
    d - depth of function
    
    default_fallback - default strategy for border, true -> fall back, false -> cancel with NaN
  - MTBLevelsetFunctionPDE
```
public MTBLevelsetFunctionPDE(boolean nb_diag,
                              int w,
                              int h,
                              int d)
```
    create a new levelsetfunction, setting a default handle for derivations on borders
    
    Parameters:
    
    width - length of function
    
    height - height of function
    
    depth - depth of function false -> cancel with NaN
  - MTBLevelsetFunctionPDE
```
public MTBLevelsetFunctionPDE(boolean nb_diag,
                              int w,
                              int h,
                              int d,
                              boolean default_fallback)
```
    create a new levelsetfunction, setting a default handle for derivations on borders
    
    Parameters:
    
    width - length of function
    
    height - height of function
    
    depth - depth of function
    
    default_fallback - default strategy for border, true -> fall back, false -> cancel with NaN
  - MTBLevelsetFunctionPDE
```
public MTBLevelsetFunctionPDE(int w,
                              int h,
                              int d,
                              MTBSegmentationInterface seg,
                              boolean default_fallback)
```
    Constructor to build a level set function from a segmentation object.
    The level set function is initialized with value -1 for the background and +1 for the foreground. Note that the size of the given segmentation is allowed to differ from the target size of the function. Positions being undefined in the segmentation are assigned to the background class.
    
    Parameters:
    
    w - Target width of the level set function domain.
    
    h - Target height of the level set function domain.
    
    d - Target depth of the level set function domain.
    
    seg - Initial segmentation.
    
    default_fallback -
  - MTBLevelsetFunctionPDE
```
public MTBLevelsetFunctionPDE(int w,
                              int h,
                              int d,
                              MTBSegmentationInterface seg,
                              boolean default_fallback,
                              int border)
```
    Constructor to build a level set function from a segmentation object.
    The level set function is initialized with value -1 for the background and +1 for the foreground. Note that the size of the given segmentation is allowed to differ from the target size of the function. Positions being undefined in the segmentation are assigned to the background class.
    
    Parameters:
    
    w - Target width of the level set function domain.
    
    h - Target height of the level set function domain.
    
    d - Target depth of the level set function domain.
    
    seg - Initial segmentation.
    
    default_fallback -
    
    border - Width of border to be ignored.
- Method Detail
  - setVisible
```
public boolean setVisible(boolean[][][] mask)
```
    Set visibility of positions.
    
    Parameters:
    
    mask - Visibility mask.
    
    Returns:
    
    True, if successful, otherwise false.
  - get
```
public double get(int x,
                  int y,
                  int z)
```
    get the value of this function at the position of the predecessor of ( x, y, z )
    
    Specified by:
    
    get in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    Returns:
    
    value at position ( x, y, z )
  - getPredecessorOnContour
```
public MTBPoint3D getPredecessorOnContour(int x,
                                          int y,
                                          int z)
```
    gets the value of the nearest contourpoint to point (x,y,z)
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
  - set
```
public void set(int x,
                int y,
                int z,
                double value)
```
    assign a value to the matrix at position ( x, y, z )
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    value - value to save an this position
  - getSizeX
```
public int getSizeX()
```
    Get width of level set function.
    
    Specified by:
    
    getSizeX in interface MTBSegmentationInterface
    
    Returns:
    
    Width of level set function.
  - getSizeY
```
public int getSizeY()
```
    Get height of level set function.
    
    Specified by:
    
    getSizeY in interface MTBSegmentationInterface
    
    Returns:
    
    Height of level set function.
  - getSizeZ
```
public int getSizeZ()
```
    Get depth of level set function.
    
    Specified by:
    
    getSizeZ in interface MTBSegmentationInterface
    
    Returns:
    
    Depth of level set function.
  - getDerivativeX
```
public double getDerivativeX(int x,
                             int y,
                             int z)
```
    retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
    
    Specified by:
    
    getDerivativeX in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - getDerivativeY
```
public double getDerivativeY(int x,
                             int y,
                             int z)
```
    retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
    
    Specified by:
    
    getDerivativeY in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - getDerivativeZ
```
public double getDerivativeZ(int x,
                             int y,
                             int z)
```
    retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
    
    Specified by:
    
    getDerivativeZ in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - forwardDifferencing_X
```
public double forwardDifferencing_X(int x,
                                    int y,
                                    int z,
                                    boolean fallback)
```
    retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    fallback - fall back to other methods at border?
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - forwardDifferencing_Y
```
public double forwardDifferencing_Y(int x,
                                    int y,
                                    int z,
                                    boolean fallback)
```
    retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    fallback - fall back to other methods at border?
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - forwardDifferencing_Z
```
public double forwardDifferencing_Z(int x,
                                    int y,
                                    int z,
                                    boolean fallback)
```
    retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    fallback - fall back to other methods at border?
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - backwardDifferencing_X
```
public double backwardDifferencing_X(int x,
                                     int y,
                                     int z)
```
    retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - backwardDifferencing_Y
```
public double backwardDifferencing_Y(int x,
                                     int y,
                                     int z)
```
    retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - backwardDifferencing_Z
```
public double backwardDifferencing_Z(int x,
                                     int y,
                                     int z)
```
    retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - backwardDifferencing_X
```
public double backwardDifferencing_X(int x,
                                     int y,
                                     int z,
                                     boolean fallback)
```
    retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    fallback - fall back to other methods at border?
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - backwardDifferencing_Y
```
public double backwardDifferencing_Y(int x,
                                     int y,
                                     int z,
                                     boolean fallback)
```
    retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    fallback - fall back to other methods at border?
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - backwardDifferencing_Z
```
public double backwardDifferencing_Z(int x,
                                     int y,
                                     int z,
                                     boolean fallback)
```
    retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
    
    Parameters:
    
    x - position x in matrix
    
    y - position y in matrix
    
    z - position z in matrix
    
    fallback - fall back to other methods at border?
    
    Returns:
    
    derivation at nearest contourpoint to ( x, y, z )
  - getDerivativeXX
```
public double getDerivativeXX(int x,
                              int y,
                              int z)
```
    computes the the derivation in x direction 2 times at nearest contourpoint to (x,y,z)
    
    Specified by:
    
    getDerivativeXX in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
  - getDerivativeYY
```
public double getDerivativeYY(int x,
                              int y,
                              int z)
```
    computes the the derivation in y direction 2 times at nearest contourpoint to (x,y,z)
    
    Specified by:
    
    getDerivativeYY in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
  - getDerivativeZZ
```
public double getDerivativeZZ(int x,
                              int y,
                              int z)
```
    computes the the derivation in z direction 2 times at nearest contourpoint to (x,y,z)
    
    Specified by:
    
    getDerivativeZZ in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
  - getDerivativeXY
```
public double getDerivativeXY(int x,
                              int y,
                              int z)
```
    computes the the derivation in x and y direction at nearest contourpoint to (x,y,z)
    
    Specified by:
    
    getDerivativeXY in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
  - getDerivativeXZ
```
public double getDerivativeXZ(int x,
                              int y,
                              int z)
```
    computes the the derivation in x and z direction at nearest contourpoint to (x,y,z)
    
    Specified by:
    
    getDerivativeXZ in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
  - getDerivativeYZ
```
public double getDerivativeYZ(int x,
                              int y,
                              int z)
```
    computes the the derivation in y and z direction at nearest contourpoint to (x,y,z)
    
    Specified by:
    
    getDerivativeYZ in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
  - getCurvature
```
public double getCurvature(int x,
                           int y,
                           int z)
```
    compute the curvature at at nearest contourpoint to (x,y,z) if x or y are not in the boundaries it returns 0 if z is not in the boundaries it returns the 2d cuvature
    
    Specified by:
    
    getCurvature in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x - x coordinate
    
    y - y coordinate
    
    z - z coordinate
    
    Returns:
    
    curvature at (x, y, z)
  - valid
```
public boolean valid(int x,
                     int y,
                     int z)
```
    is this pixel valid?
    
    Specified by:
    
    valid in class MTBLevelsetFunctionDerivable
    
    Parameters:
    
    x - x coordinate
    
    y - y coordinate
    
    z - z coordinate
    
    Returns:
    
    true if visible and not MAX_VALUE, else false
  - isVisible
```
public boolean isVisible(int x,
                         int y,
                         int z)
```
    is this pixel visible?
    
    Specified by:
    
    isVisible in interface MTBSegmentationInterface
    
    Parameters:
    
    x - x coordinate
    
    y - y coordinate
    
    z - z coordinate
    
    Returns:
    
    true if visible, else false
  - signDistance
```
public void signDistance(double b)
```
    Transform function into signed distance function.
    The transformation can be restricted to a narrow-band around the zero level by setting the width parameter to a value larger or equal to one.
    
    Parameters:
    
    b - Width of narrow-band around zero level.
  - signedExpandation
```
private void signedExpandation(MTBLevelsetFunctionPDE.SortedList<MTBPoint3D> slist,
                               double maximum,
                               double toAdd)
```
    Expand signed distances around zero-level.
    Helper function for method signDistance.
    
    Parameters:
    
    slist - Dynamic sorted list of points to expand.
    
    maximum - Maximal distance value, just for narrow-band.
    
    toAdd - Value to add to next level value, usually 1.
  - sgnSum
```
private double sgnSum(int x,
                      int y,
                      int z)
```
    Computes scaled sign in neighborhood.
    
    Parameters:
    
    x - x coord of point.
    
    y - y coord of point.
    
    z - z coord of point.
    
    Returns:
    
    Scaled sign in neighborhood.
  - clone
```
public MTBLevelsetFunctionPDE clone()
```
    generate a clone of this object
    
    Overrides:
    
    clone in class Object
    
    Returns:
    
    the copy
  - copyTo
```
public void copyTo(MTBLevelsetFunctionPDE two)
```
    copy this object to another one
  - equals
```
public boolean equals(MTBLevelsetFunctionPDE ls2d)
```
    are these two LevelSets equal?
    
    Parameters:
    
    ls2d - LevelSet to check
    
    Returns:
    
    true if this functions equals the other, false otherwise
  - getNarrowIterator
```
public Iterator<MTBPoint3D> getNarrowIterator()
```
    get an iterator through narrow band
    
    Returns:
    
    iterator through narrow band
  - getBinaryMask
```
public MTBImageByte getBinaryMask()
```
    Get a binary mask of the represented segmentation.
    
    Returns:
    
    Binary segmentation mask.
  - getPhiColorImage2D
```
public MTBImageRGB getPhiColorImage2D(MTBImageRGB targetImg)
```
    Get visualization of current level set function in red-blue color map.
    This function only considers the first dimension in z.
    
    Returns:
    
    Image showing level set function.
  - getPhiImage
```
public MTBImageShort getPhiImage()
```
    Get visualization of current level set function.
    
    Returns:
    
    Image showing level set function.
  - getForegroundSum
```
public double getForegroundSum()
```
  - getDimension
```
public MTBSegmentationInterface.SegmentationDimension getDimension()
```
    Description copied from interface: MTBSegmentationInterface
    
    Returns the dimension of the segmentation.
    
    Specified by:
    
    getDimension in interface MTBSegmentationInterface
  - getNumberOfClasses
```
public int getNumberOfClasses()
```
    Description copied from interface: MTBSegmentationInterface
    
    Returns the number of classes represented by the segmentation.
    
    Specified by:
    
    getNumberOfClasses in interface MTBSegmentationInterface
  - getMaxLabel
```
public int getMaxLabel()
```
    Description copied from interface: MTBSegmentationInterface
    
    Returns the maximal label used in the segmentation representation.
    Note that the maximal label is not required to coincide with the number of classes represented by the segmentation. Labels should usually, but do not necessarily need to be positive.
    
    Specified by:
    
    getMaxLabel in interface MTBSegmentationInterface
  - isVisible
```
public boolean isVisible(int x,
                         int y)
```
    Description copied from interface: MTBSegmentationInterface
    
    True, if position (x,y) is visible.
    
    Specified by:
    
    isVisible in interface MTBSegmentationInterface
  - setVisible
```
public void setVisible(int x,
                       int y)
```
    Description copied from interface: MTBSegmentationInterface
    
    Set position (x,y) visible.
    
    Specified by:
    
    setVisible in interface MTBSegmentationInterface
  - setVisible
```
public void setVisible(int x,
                       int y,
                       int z)
```
    Description copied from interface: MTBSegmentationInterface
    
    Set position (x,y,z) visible.
    
    Specified by:
    
    setVisible in interface MTBSegmentationInterface
  - setInvisible
```
public void setInvisible(int x,
                         int y)
```
    Description copied from interface: MTBSegmentationInterface
    
    Set position (x,y) invisible.
    
    Specified by:
    
    setInvisible in interface MTBSegmentationInterface
  - setInvisible
```
public void setInvisible(int x,
                         int y,
                         int z)
```
    Description copied from interface: MTBSegmentationInterface
    
    Set position (x,y,z) invisible.
    
    Specified by:
    
    setInvisible in interface MTBSegmentationInterface
  - getClass
```
public int getClass(int x,
                    int y)
```
    Description copied from interface: MTBSegmentationInterface
    
    Returns the class label of position (x,y).
    
    Specified by:
    
    getClass in interface MTBSegmentationInterface
  - getClass
```
public int getClass(int x,
                    int y,
                    int z)
```
    Description copied from interface: MTBSegmentationInterface
    
    Returns the class label of position (x,y,z).
    
    Specified by:
    
    getClass in interface MTBSegmentationInterface
  - setClass
```
@Deprecated
public void setClass(int x,
                                 int y,
                                 int c)
```
    Deprecated.
    
    Description copied from interface: MTBSegmentationInterface
    
    Set the label of position (x,y) to c.
    
    Specified by:
    
    setClass in interface MTBSegmentationInterface
  - setClass
```
@Deprecated
public void setClass(int x,
                                 int y,
                                 int z,
                                 int c)
```
    Deprecated.
    
    Description copied from interface: MTBSegmentationInterface
    
    Set the label of position (x,y,z) to c.
    
    Specified by:
    
    setClass in interface MTBSegmentationInterface
  - getWeight
```
public double getWeight(int x,
                        int y)
```
    Description copied from interface: MTBSegmentationInterface
    
    Returns the pixel weight of position (x,y).
    
    Specified by:
    
    getWeight in interface MTBSegmentationInterface
  - getWeight
```
public double getWeight(int x,
                        int y,
                        int z)
```
    Description copied from interface: MTBSegmentationInterface
    
    Returns the pixel weight of position (x,y,z).
    
    Specified by:
    
    getWeight in interface MTBSegmentationInterface
  - setWeight
```
public void setWeight(int x,
                      int y,
                      double c)
```
    Description copied from interface: MTBSegmentationInterface
    
    Sets the pixel weight of position (x,y) to c.
    
    Specified by:
    
    setWeight in interface MTBSegmentationInterface
  - setWeight
```
public void setWeight(int x,
                      int y,
                      int z,
                      double c)
```
    Description copied from interface: MTBSegmentationInterface
    
    Sets the pixel weight of position (x,y,z) to c.
    
    Specified by:
    
    setWeight in interface MTBSegmentationInterface
  - getMask
```
public MTBImage getMask(int class_)
```
    Description copied from interface: MTBSegmentationInterface
    
    Gets the mask of the specified class (0 Background, 255 Foreground)
    
    Specified by:
    
    getMask in interface MTBSegmentationInterface

Class MTBLevelsetFunctionPDE

Nested Class Summary

Nested classes/interfaces inherited from interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface

Field Summary

Constructor Summary

Method Summary

Methods inherited from class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable

Methods inherited from class java.lang.Object

Field Detail

MAX_VALUE

phi

visible

height

width

depth

borderDist

narrow

predecessors

helperArray

DEFAULT_FALL_BACK

Constructor Detail

MTBLevelsetFunctionPDE

MTBLevelsetFunctionPDE

MTBLevelsetFunctionPDE

MTBLevelsetFunctionPDE

MTBLevelsetFunctionPDE

MTBLevelsetFunctionPDE

MTBLevelsetFunctionPDE

Method Detail

setVisible

get

getPredecessorOnContour

set

getSizeX

getSizeY

getSizeZ

getDerivativeX

getDerivativeY

getDerivativeZ

forwardDifferencing_X

forwardDifferencing_Y

forwardDifferencing_Z

backwardDifferencing_X

backwardDifferencing_Y

backwardDifferencing_Z

backwardDifferencing_X

backwardDifferencing_Y

backwardDifferencing_Z

getDerivativeXX

getDerivativeYY

getDerivativeZZ

getDerivativeXY

getDerivativeXZ

getDerivativeYZ

getCurvature

valid

isVisible

signDistance

signedExpandation

sgnSum

clone

copyTo

equals

getNarrowIterator

getBinaryMask

getPhiColorImage2D

getPhiImage

getForegroundSum

getDimension

getNumberOfClasses

getMaxLabel

isVisible

setVisible

setVisible

setInvisible

setInvisible

getClass

getClass

setClass

setClass