MTBSnakeEnergyCD_CVRegionFit (mitobo 2.0 API)

java.lang.Object
- de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
- - de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit

All Implemented Interfaces:

MTBActiveContourEnergy, MTBActiveContourEnergyDerivable, MTBSnakeEnergyComputable, MTBSnakeEnergyCoupled, MTBSnakeEnergyDerivable
```
@ALDDerivedClass
 @ALDParametrizedClass
public class MTBSnakeEnergyCD_CVRegionFit
extends MTBActiveContourEnergy_CVRegionFit
implements MTBSnakeEnergyDerivable, MTBSnakeEnergyComputable, MTBSnakeEnergyCoupled
```
Snake energy based on Chan-Vese region fitting.
This energy models the inner and outer regions of a snake by a Gaussian model, i.e. each region is specified by a mean intensity value and deviations from this value are penalized.
The energy can also be used in joint optimization of multiple snakes. In this case the energy over all N snakes is defined as follows:
\begin{eqnarray*} E(C_1,...,C_N) &=& \lambda_{in} \cdot \sum_{i=1}^N \int_{inside(C_i)} (I(x,y) - c_{in,i})^2 dx dy \\ && \hspace*{1cm} + \lambda_{out} \cdot \int_{outside(C_i)\cap...\cap outside(C_N)} (I(x,y) - c_{out})^2 dx dy \end{eqnarray*}

Paper:
- Chan and Vese, Active Contours Without Edges, IEEE Transactions on Image Processing, vol. 10, no. 2, pp. 266-277, 2001.
- C. Zimmer and J.-C. Olivo-Marin, Coupled Parametric Active Contours, IEEE Trans. on PAMI, vol. 27, no. 11, pp. 1838-1842, 2005.
Note that this energy can also be used with multi-channel images, i.e. vectorial pixel data. For details see documentation of the super class or the related paper:
- Chan, Sandberg and Vese, Active Contours without Edges for Vector-Valued Images, Journal of Visual Communications and Image Representation, vol. 11, pp. 130-141, 2000.
Author:

moeller

See Also:

MTBActiveContourEnergy_CVRegionFit

Field Summary

Fields
Modifier and Type	Field and Description
`private SnakeOptimizerCoupled`	`cSnakeOpt` Reference to a coupled snake optimizer.
`private MTBSnake`	`currentSnk` Current snake the energy is based on.
`private double[]`	`energyRange` Interval boundaries of adapted energy interval.
`private boolean[][]`	`excludeMask` Global exclude mask for image to be segmented.
`private int`	`iHeight` Height of working image.
`private int`	`iWidth` Width of working image.
`protected SnakeOptimizerSingle.EnergyNormalizationMode`	`normMode` Mode of normalization.
`private int[][]`	`overlapMask` Current overlap mask for joint optimization of multiple snakes.
`protected double`	`scaleFactor` Scaling factor to rescale image coordinates in range [0,1] or several ranges to the original coordinates range like [1000, 1000] in a image of size 1000 x 1000.

Fields inherited from class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
areas, iChannels, inImg, lambda_in, lambda_out, means

Fields inherited from interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
targetEnergyRange

Constructor Summary

Constructors
Constructor and Description
`MTBSnakeEnergyCD_CVRegionFit()` Default constructor.
`MTBSnakeEnergyCD_CVRegionFit(MTBImage im, double[] lin, double[] lout)` Default constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`calcEnergy(SnakeOptimizerSingle opt)` Calculates the energy of the current snake.
`Jama.Matrix`	`getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc opt)` Updates the fitting term based on new region average values.
`Jama.Matrix`	`getDerivative_VectorPart(SnakeOptimizerSingleVarCalc opt)` Returns the vector part of this energy for snake optimization.
`double`	`getScaleFactor()` Get scaling factor.
`boolean`	`initEnergy(SnakeOptimizerCoupled opt)` Init routine which is called once before the energy is actually used.
`boolean`	`initEnergy(SnakeOptimizerSingle opt)` Init routine which is called once before the energy is actually used.
`boolean`	`requiresCounterClockwiseContourSorting()` Ask energy if contour points need to sorted counter-clockwise.
`boolean`	`requiresOverlapMask()` Ask energy if an overlap mask for all snakes jointly optimized is required.
`void`	`setScaleFactor(double s)` Set the scaling factor.
`String`	`toString()` Get an identifier string for the energy object.
`void`	`updateStatus(SnakeOptimizerCoupled opt)` Update internal state of energy object prior to querying derivatives and so on.
`void`	`updateStatus(SnakeOptimizerSingle opt)` Update internal state of energy object prior to usaging it.

Methods inherited from class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
calcEnergy, calcInteriorEnergy, getDerivative, getEnergyDerivativeMaxVal, getEnergyDerivativeMinVal, getMeans, init, updateParameters

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

- Field Detail
  - energyRange
```
private double[] energyRange
```
    Interval boundaries of adapted energy interval.
    energyRange[0] -> left boundary energyRange[1] -> right boundary energyRange[2] -> interval width
  - iWidth
```
private transient int iWidth
```
    Width of working image.
  - iHeight
```
private transient int iHeight
```
    Height of working image.
  - normMode
```
protected SnakeOptimizerSingle.EnergyNormalizationMode normMode
```
    Mode of normalization.
  - scaleFactor
```
protected transient double scaleFactor
```
    Scaling factor to rescale image coordinates in range [0,1] or several ranges to the original coordinates range like [1000, 1000] in a image of size 1000 x 1000. Default scaling factor is 1.
  - currentSnk
```
private transient MTBSnake currentSnk
```
    Current snake the energy is based on.
  - excludeMask
```
private transient boolean[][] excludeMask
```
    Global exclude mask for image to be segmented.
  - cSnakeOpt
```
private transient SnakeOptimizerCoupled cSnakeOpt
```
    Reference to a coupled snake optimizer.
    This reference is only non-null if the energy is used in conjunction with coupled snake optimization.
  - overlapMask
```
private int[][] overlapMask
```
    Current overlap mask for joint optimization of multiple snakes.
- Constructor Detail
  - MTBSnakeEnergyCD_CVRegionFit
```
public MTBSnakeEnergyCD_CVRegionFit()
```
    Default constructor.
  - MTBSnakeEnergyCD_CVRegionFit
```
public MTBSnakeEnergyCD_CVRegionFit(MTBImage im,
                                    double[] lin,
                                    double[] lout)
```
    Default constructor.
    
    Parameters:
    
    im - Image to work on.
    
    l_in - Weighting factors for inner region fit.
    
    l_out - Weighting factors for outer region fit.
    
    Throws:
    
    de.unihalle.informatik.Alida.exceptions.ALDOperatorException
    
    ALDProcessingDAGException
- Method Detail
  - initEnergy
```
public boolean initEnergy(SnakeOptimizerCoupled opt)
                   throws MTBSnakeException
```
    Description copied from interface: MTBSnakeEnergyCoupled
    
    Init routine which is called once before the energy is actually used.
    In this routine global parameter settings can be handled or other initialization stuff be done. Snake optimizers are supposed to call this routine once before they actual use of the energy. If no stuff needs to be done in advance the routine should at least return true.
    
    Specified by:
    
    initEnergy in interface MTBSnakeEnergyCoupled
    
    Parameters:
    
    opt - Calling snake optimizer.
    
    Returns:
    
    true if init was successful
    
    Throws:
    
    MTBSnakeException
  - initEnergy
```
public boolean initEnergy(SnakeOptimizerSingle opt)
                   throws MTBSnakeException
```
    Description copied from interface: MTBSnakeEnergyDerivable
    
    Init routine which is called once before the energy is actually used.
    In this routine global parameter settings can be handled or other initialization stuff be done. The SnakeOptimizer will call this routine once before the actual use of the energy. If no stuff needs to be done in advance the routine should at least return true.
    
    Specified by:
    
    initEnergy in interface MTBSnakeEnergyComputable
    
    Specified by:
    
    initEnergy in interface MTBSnakeEnergyDerivable
    
    Parameters:
    
    opt - Calling snake optimizer.
    
    Returns:
    
    True if init was successful, otherwise false.
    
    Throws:
    
    MTBSnakeException
  - updateStatus
```
public void updateStatus(SnakeOptimizerCoupled opt)
```
    Description copied from interface: MTBSnakeEnergyCoupled
    
    Update internal state of energy object prior to querying derivatives and so on.
    
    Specified by:
    
    updateStatus in interface MTBSnakeEnergyCoupled
  - updateStatus
```
public void updateStatus(SnakeOptimizerSingle opt)
                  throws MTBSnakeException
```
    Description copied from interface: MTBSnakeEnergyDerivable
    
    Update internal state of energy object prior to usaging it.
    
    Specified by:
    
    updateStatus in interface MTBSnakeEnergyComputable
    
    Specified by:
    
    updateStatus in interface MTBSnakeEnergyDerivable
    
    Throws:
    
    MTBSnakeException
  - getDerivative_MatrixPart
```
public Jama.Matrix getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc opt)
```
    Updates the fitting term based on new region average values.
    
    Specified by:
    
    getDerivative_MatrixPart in interface MTBSnakeEnergyDerivable
    
    Parameters:
    
    opt - Calling snake optimizer.
    
    Returns:
    
    Optimization matrix for this energy object.
  - getDerivative_VectorPart
```
public Jama.Matrix getDerivative_VectorPart(SnakeOptimizerSingleVarCalc opt)
```
    Description copied from interface: MTBSnakeEnergyDerivable
    
    Returns the vector part of this energy for snake optimization.
    
    Specified by:
    
    getDerivative_VectorPart in interface MTBSnakeEnergyDerivable
    
    Parameters:
    
    opt - Calling snake optimizer.
    
    Returns:
    
    Optimization vector for this energy object.
  - calcEnergy
```
public double calcEnergy(SnakeOptimizerSingle opt)
```
    Description copied from interface: MTBSnakeEnergyComputable
    
    Calculates the energy of the current snake.
    
    Specified by:
    
    calcEnergy in interface MTBSnakeEnergyComputable
    
    Parameters:
    
    opt - Calling snake optimizer.
    
    Returns:
    
    Energy of complete snake.
  - setScaleFactor
```
public void setScaleFactor(double s)
```
    Set the scaling factor.
    
    Specified by:
    
    setScaleFactor in interface MTBSnakeEnergyComputable
    
    Specified by:
    
    setScaleFactor in interface MTBSnakeEnergyDerivable
    
    Parameters:
    
    s - new scaling factor.
  - getScaleFactor
```
public double getScaleFactor()
```
    Get scaling factor.
    
    Specified by:
    
    getScaleFactor in interface MTBSnakeEnergyComputable
    
    Specified by:
    
    getScaleFactor in interface MTBSnakeEnergyDerivable
    
    Returns:
    
    Scaling factor.
  - toString
```
public String toString()
```
    Description copied from interface: MTBSnakeEnergyDerivable
    
    Get an identifier string for the energy object.
    When meta parameters are saved to a file, configuration objects need to be converted to strings. Consequently, each snake energy should be associated with a unique and descriptive string for later reference.
    
    Specified by:
    
    toString in interface MTBSnakeEnergyComputable
    
    Specified by:
    
    toString in interface MTBSnakeEnergyDerivable
    
    Overrides:
    
    toString in class MTBActiveContourEnergy_CVRegionFit
    
    Returns:
    
    Identifier string.
  - requiresCounterClockwiseContourSorting
```
public boolean requiresCounterClockwiseContourSorting()
```
    Description copied from interface: MTBSnakeEnergyDerivable
    
    Ask energy if contour points need to sorted counter-clockwise.
    
    Specified by:
    
    requiresCounterClockwiseContourSorting in interface MTBSnakeEnergyComputable
    
    Specified by:
    
    requiresCounterClockwiseContourSorting in interface MTBSnakeEnergyCoupled
    
    Specified by:
    
    requiresCounterClockwiseContourSorting in interface MTBSnakeEnergyDerivable
    
    Returns:
    
    If true, counter-clockwise sorting is expected.
  - requiresOverlapMask
```
public boolean requiresOverlapMask()
```
    Description copied from interface: MTBSnakeEnergyDerivable
    
    Ask energy if an overlap mask for all snakes jointly optimized is required.
    
    Specified by:
    
    requiresOverlapMask in interface MTBSnakeEnergyComputable
    
    Specified by:
    
    requiresOverlapMask in interface MTBSnakeEnergyCoupled
    
    Specified by:
    
    requiresOverlapMask in interface MTBSnakeEnergyDerivable
    
    Returns:
    
    If true, the energy expects an overlap mask to be available.

Class MTBSnakeEnergyCD_CVRegionFit

Field Summary

Fields inherited from class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit

Fields inherited from interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable

Constructor Summary

Method Summary

Methods inherited from class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit

Methods inherited from class java.lang.Object

Field Detail

energyRange

iWidth

iHeight

normMode

scaleFactor

currentSnk

excludeMask

cSnakeOpt

overlapMask

Constructor Detail

MTBSnakeEnergyCD_CVRegionFit

MTBSnakeEnergyCD_CVRegionFit

Method Detail

initEnergy

initEnergy

updateStatus

updateStatus

getDerivative_MatrixPart

getDerivative_VectorPart

calcEnergy

setScaleFactor

getScaleFactor

toString

requiresCounterClockwiseContourSorting

requiresOverlapMask