GeodesicActiveContour (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- levelsets.algorithm.SparseFieldLevelSet
- - levelsets.algorithm.LevelSetImplementation
  - - levelsets.algorithm.GeodesicActiveContour

All Implemented Interfaces:

StagedAlgorithm
```
public class GeodesicActiveContour
extends LevelSetImplementation
```
Implementation of the Geodesic active contour algorithm as described by Caselles et.al. (International Journal of Computer Vision 22:61) and implemented in the in the Geodesic Active Contour class of ITK. This class provides the getDeltaPhi function to the SparseFieldLevelSet: deltaPhi = - DELTA_T * (advection * -gradient(g) * ADVECTION_FORCE + propagation * g * PROPAGATION_WEIGHT + curvature * g * CURVATURE_WEIGHT) with: g = 1 / (1 + (gradients[x][y][z]) * 1) advection, curvature from the base functions (upwind scheme and mean curvature) ADVECTION_FORCE, CURVATURE_EPSILON are weights. Geodesic active contours can find Canny-type edges in the region of interest, while also introducing a smoothing term . This is a first effort that is not necessarily feature complete or the entirely correct. Use with caution.

Field Summary

Fields
Modifier and Type	Field and Description
`protected double`	`ALPHA_ADVECTION`
`protected double`	`BETA_PROPAGATION`
`protected double`	`GAMMA_CURVATURE`
`protected double`	`GAMMA_GREYSCALE`
`protected double[][][]`	`grad_gradients`
`protected double[][][]`	`gradients`
`protected double`	`GREY_EPSILON`
`protected double`	`GREY_T`

Fields inherited from class levelsets.algorithm.SparseFieldLevelSet
CONVERGENCE_FACTOR, CONVERGENCE_WEIGHT, DELTA_T, img, init_state, INSIDE, INSIDE_FAR, needInit, OUTSIDE, OUTSIDE_FAR, phi, seed_grey_zero, seed_greyvalue, source, STATE_ZERO, zScale

Constructor Summary

Constructors
Constructor and Description
`GeodesicActiveContour(ImageContainer image, ImageProgressContainer img_progress, StateContainer init_state, double convergence, double advection, double prop, double curve, double grey)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected double[][][]`	`calculateGradients(double[][][] grad_src)` Calculates grey value gradients of an input double array Required for the grad_gradient calculation, taken from ImageContainer
`protected double`	`getAdvectionTerm(int x, int y, int z)`
`protected double`	`getCurvatureTerm(int x, int y, int z)`
`protected double`	`getDeltaPhi(int x, int y, int z)`
`protected double`	`getPropagationTerm(int x, int y, int z)`
`protected void`	`init()`
`protected void`	`updateDeltaT()` Updates the time step for numerical solution.

Methods inherited from class levelsets.algorithm.LevelSetImplementation
cleanup

Methods inherited from class levelsets.algorithm.SparseFieldLevelSet
dumpStateMap, getStateContainer, getStateMap, step

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

Field Detail

gradients
```
protected double[][][] gradients
```

grad_gradients
```
protected double[][][] grad_gradients
```

ALPHA_ADVECTION
```
protected final double ALPHA_ADVECTION
```

BETA_PROPAGATION

protected final double BETA_PROPAGATION

GAMMA_CURVATURE
```
protected final double GAMMA_CURVATURE
```

GAMMA_GREYSCALE
```
protected final double GAMMA_GREYSCALE
```

GREY_EPSILON
```
protected final double GREY_EPSILON
```
See Also:

Constant Field Values

GREY_T
```
protected final double GREY_T
```
See Also:

Constant Field Values

Constructor Detail

GeodesicActiveContour

public GeodesicActiveContour(ImageContainer image,
                             ImageProgressContainer img_progress,
                             StateContainer init_state,
                             double convergence,
                             double advection,
                             double prop,
                             double curve,
                             double grey)

Method Detail

init
```
protected final void init()
```
Overrides:

init in class LevelSetImplementation

getDeltaPhi

protected final double getDeltaPhi(int x,
                                   int y,
                                   int z)

Specified by:: getDeltaPhi in class LevelSetImplementation

updateDeltaT
```
protected final void updateDeltaT()
```
Description copied from class: LevelSetImplementation

Updates the time step for numerical solution. Abstract class forces the derived class to implement it. If default settings are fine, just don't do anything

Specified by:

updateDeltaT in class LevelSetImplementation

getAdvectionTerm

protected final double getAdvectionTerm(int x,
                                        int y,
                                        int z)

getPropagationTerm

protected final double getPropagationTerm(int x,
                                          int y,
                                          int z)

getCurvatureTerm

protected final double getCurvatureTerm(int x,
                                        int y,
                                        int z)

calculateGradients
```
protected final double[][][] calculateGradients(double[][][] grad_src)
```
Calculates grey value gradients of an input double array Required for the grad_gradient calculation, taken from ImageContainer

Returns:

The result array

Class GeodesicActiveContour

Field Summary

Fields inherited from class levelsets.algorithm.SparseFieldLevelSet

Constructor Summary

Method Summary

Methods inherited from class levelsets.algorithm.LevelSetImplementation

Methods inherited from class levelsets.algorithm.SparseFieldLevelSet

Methods inherited from class java.lang.Object

Field Detail

gradients

grad_gradients

ALPHA_ADVECTION

BETA_PROPAGATION

GAMMA_CURVATURE

GAMMA_GREYSCALE

GREY_EPSILON

GREY_T

Constructor Detail

GeodesicActiveContour

Method Detail

init

getDeltaPhi

updateDeltaT

getAdvectionTerm

getPropagationTerm

getCurvatureTerm

calculateGradients