MTBSnakeEnergyCD_OverlapPenalty (mitobo 2.0 API)

java.lang.Object
- de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty

All Implemented Interfaces:

MTBActiveContourEnergy, MTBActiveContourEnergyDerivable, MTBSnakeEnergyComputable, MTBSnakeEnergyCoupled, MTBSnakeEnergyDerivable
```
@ALDDerivedClass
 @ALDParametrizedClass
public class MTBSnakeEnergyCD_OverlapPenalty
extends Object
implements MTBSnakeEnergyDerivable, MTBSnakeEnergyComputable, MTBSnakeEnergyCoupled
```
Energy to avoid overlaps of snakes in joint optimization of multiple snakes.
This energy is defined as follows for a set of N snakes:
\begin{equation*} E(s_1,\ldots,s_N) = \rho \cdot \sum_{i=1}^N \sum_{j=i+1}^N \int_{s_i \cap s_j} d\sigma \end{equation*}
It basically calculates for each pair of snakes the area of overlap of their interiors. The overall energy value is given by the sum of all pairwise overlap areas. Rho is a weighting factor.
Note that using this energy with a single snake is not reasonable. The energy does not cause a single snake to move anyway, i.e., it strictly requires interaction of multiple snakes.
Paper: C. Zimmer and J.-C. Olivo-Marin, Coupled Parametric Active Contours, IEEE Trans. on PAMI, vol. 27, no. 11, pp. 1838-1842, 2005.

Author:

moeller

Field Summary

Fields
Modifier and Type	Field and Description
`private SnakeOptimizerCoupled`	`cSnakeOpt` Reference to a coupled snake optimizer.
`protected int[][]`	`currentOverlapMask` Overlap mask of current snake configuration, updated in each iteration.
`protected static int[]`	`factorialVals` Pre-computed factorial values.
`protected double`	`maxEnergyVal` Maxmimum value of energy, dependent on number of snakes and rho.
`private double`	`rho` Weighting factor and overlap penalty, respectively.
`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.
`protected int`	`snakeNum` Number of snakes to be optimized.

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

Constructor Summary

Constructors
Constructor and Description
`MTBSnakeEnergyCD_OverlapPenalty()` Default constructor.
`MTBSnakeEnergyCD_OverlapPenalty(double _rho, int snakes)` Default constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`calcEnergy(SnakeOptimizerSingle opt)` Calculates the current energy of the snake.
`Jama.Matrix`	`getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc opt)` Updates the region coupling energy term in matrix A.
`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 o)` Update internal state of energy object prior to querying derivatives and so on.
`void`	`updateStatus(SnakeOptimizerSingle o)` Update internal state of energy object prior to usaging it.

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

- Field Detail
  - rho
```
@ALDClassParameter(label="Weighting Parameter")
private double rho
```
    Weighting factor and overlap penalty, respectively.
  - 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.
  - snakeNum
```
protected transient int snakeNum
```
    Number of snakes to be optimized.
  - maxEnergyVal
```
protected transient double maxEnergyVal
```
    Maxmimum value of energy, dependent on number of snakes and rho.
  - scaleFactor
```
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. Default scaling factor is 1.
  - currentOverlapMask
```
protected int[][] currentOverlapMask
```
    Overlap mask of current snake configuration, updated in each iteration.
  - factorialVals
```
protected static int[] factorialVals
```
    Pre-computed factorial values.
    At position n in this array the following value is stored:
    \begin{equation*} \left( \begin{array}{c} n \\ 2 \end{array} \right) = \frac{n!}{2! \cdot (n-2)!} \;\; \text{for}\;\; n = 0,...,N \end{equation*}
    Here N is the number of snakes simultaneously optimized.
- Constructor Detail
  - MTBSnakeEnergyCD_OverlapPenalty
```
public MTBSnakeEnergyCD_OverlapPenalty()
```
    Default constructor.
  - MTBSnakeEnergyCD_OverlapPenalty
```
public MTBSnakeEnergyCD_OverlapPenalty(double _rho,
                                       int snakes)
```
    Default constructor.
    
    Parameters:
    
    _rho - Overlap penalty coefficient.
- Method Detail
  - 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.
  - initEnergy
```
public boolean initEnergy(SnakeOptimizerCoupled opt)
```
    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
  - initEnergy
```
public boolean initEnergy(SnakeOptimizerSingle opt)
```
    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.
  - updateStatus
```
public void updateStatus(SnakeOptimizerCoupled o)
```
    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 o)
```
    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
  - getDerivative_MatrixPart
```
public Jama.Matrix getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc opt)
```
    Updates the region coupling energy term in matrix A.
    
    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)
```
    Calculates the current energy of the snake.
    The energy is calculated based on the overlap mask of the current configuration of all snakes. In this overlap mask at each pixel position the absolute number of snakes covering that position is stored. For extracting the absolute energy value from this data it is, thus, necessary to derive the number of pairwise overlaps at a certain position. This count is given by the binomial of the number of snakes overlapping at a certain location over 2.
    
    Specified by:
    
    calcEnergy in interface MTBSnakeEnergyComputable
    
    Parameters:
    
    opt - Calling snake optimizer.
    
    Returns:
    
    Energy of complete snake.
  - 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 Object
    
    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_OverlapPenalty

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

rho

cSnakeOpt

snakeNum

maxEnergyVal

scaleFactor

currentOverlapMask

factorialVals

Constructor Detail

MTBSnakeEnergyCD_OverlapPenalty

MTBSnakeEnergyCD_OverlapPenalty

Method Detail

setScaleFactor

getScaleFactor

initEnergy

initEnergy

updateStatus

updateStatus

getDerivative_MatrixPart

getDerivative_VectorPart

calcEnergy

toString

requiresCounterClockwiseContourSorting

requiresOverlapMask