de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE

Class MTBMeijeringFittingEnergyNonPDE

java.lang.Object

de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE

de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE

@ALDParametrizedClass
 @ALDDerivedClass
public class MTBMeijeringFittingEnergyNonPDE
extends MTBGenericEnergyNonPDE

class that implements the energy functional introduced in O. Dzyubachyk, W. Niessen and E. Meijering, "A VARIATIONAL MODEL FOR LEVEL-SET BASED CELL TRACKING IN TIME-LAPSE FLUORESCENCE MICROSCOPY IMAGES", 4th IEEE International Symposium on Biomedical Imaging (ISBI), 2007

Author:

glass

Field Summary

Fields

Modifier and Type	Field and Description
private MTBImage	img Image to be segmented
private double[]	mean
private int	numPhases
private int	sizeX
private int	sizeY
private int	sizeZ
private double[]	var

Fields inherited from class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE

debug, name

Constructor Summary

Constructors

Constructor and Description
MTBMeijeringFittingEnergyNonPDE() constructor
MTBMeijeringFittingEnergyNonPDE(MTBImage img, MTBLevelsetMembership phi) constructor

Method Summary

Modifier and Type	Method and Description
double	deltaE(int x, int y, int z, short newPhase, MTBLevelsetMembership phi) Calculate differences of energy if the pixel/voxel (x,y,z) is changed from its current phase in the level set function phi supplied from current phase to newPhase.
double	E(MTBLevelsetMembership phi) Return the complete energy for the level set function phi.
protected void	estimateParams(MTBLevelsetMembership phi) Estimate internal parameters (if any) for the level set function phi assumed to be associated with this energy object.
MTBGenericEnergyNonPDE	init(MTBImage img, MTBLevelsetMembership phi) Initialize the energy object.
void	print(MTBLevelsetMembership phi, PrintStream out, String indent) Print this energy object - including the value of the energy for phi assumed to be associated with this energy object.
String	toString() Return an ascii representation identifying the energy and internal parameters, but not the state.
void	updateParams(int x, int y, int z, short newPhase, MTBLevelsetMembership phi) Update parameters (if any) of the energy object which depend on the associated level set function.

Methods inherited from class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE

deltaE, getNewIndent, setDebug, updateParams

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

img

@ALDClassParameter(label="Input image")
private MTBImage img

Image to be segmented

numPhases

private int numPhases

mean

private double[] mean

var

private double[] var

sizeX

private int sizeX

sizeY

private int sizeY

sizeZ

private int sizeZ

Constructor Detail

MTBMeijeringFittingEnergyNonPDE

public MTBMeijeringFittingEnergyNonPDE()

constructor

MTBMeijeringFittingEnergyNonPDE

public MTBMeijeringFittingEnergyNonPDE(MTBImage img,
                                       MTBLevelsetMembership phi)

constructor

Parameters:

img -

phi -

Method Detail

init

public MTBGenericEnergyNonPDE init(MTBImage img,
                                   MTBLevelsetMembership phi)

Initialize the energy object.

NOTE: The image provided as argument to this method is only associated with the energy object, if not already set!! This rational behind this is to allow the energy to be supplied generically with the input image and while it is still possible to set an image deviating from this default.

Overrides:

init in class MTBGenericEnergyNonPDE

Parameters:

img - Image to be segmented

phi - Level set function to construct the energy object for

Returns:

The modified or a new energy if initialization was successful, otherwise null.

estimateParams

protected void estimateParams(MTBLevelsetMembership phi)

Description copied from class: MTBGenericEnergyNonPDE

Estimate internal parameters (if any) for the level set function phi assumed to be associated with this energy object.

Overrides:

estimateParams in class MTBGenericEnergyNonPDE

updateParams

public void updateParams(int x,
                         int y,
                         int z,
                         short newPhase,
                         MTBLevelsetMembership phi)

Description copied from class: MTBGenericEnergyNonPDE

Update parameters (if any) of the energy object which depend on the associated level set function.

This method is called to update the parameters if is is intended to change the phase of a pixel/voxel to newPhase.

Note: The level set function phi is still in the old state and is assumed to be to updated subsequently.

Overrides:

updateParams in class MTBGenericEnergyNonPDE

newPhase - new phase to change pixel/voxel to

phi - assumed to be associated with this energy object

deltaE

public double deltaE(int x,
                     int y,
                     int z,
                     short newPhase,
                     MTBLevelsetMembership phi)

Description copied from class: MTBGenericEnergyNonPDE

Calculate differences of energy if the pixel/voxel (x,y,z) is changed from its current phase in the level set function phi supplied from current phase to newPhase.

Specified by:

deltaE in class MTBGenericEnergyNonPDE

newPhase - new phase to change the pixel/voxel to

phi - level set function assumed to be associated with this energy object

Returns:

difference of energy

E

public double E(MTBLevelsetMembership phi)

Description copied from class: MTBGenericEnergyNonPDE

Return the complete energy for the level set function phi.
Note: this may be an expensive operation.

Specified by:

E in class MTBGenericEnergyNonPDE

Parameters:

phi - level set function assumed to be associated with this energy object

Returns:

energy

toString

public String toString()

Description copied from class: MTBGenericEnergyNonPDE

Return an ascii representation identifying the energy and internal parameters, but not the state.

Specified by:

toString in class MTBGenericEnergyNonPDE

print

public void print(MTBLevelsetMembership phi,
                  PrintStream out,
                  String indent)

Description copied from class: MTBGenericEnergyNonPDE

Print this energy object - including the value of the energy for phi assumed to be associated with this energy object. Each line output is prefixed with the string indent. Note: this may be an expensive operation.

Overrides:

print in class MTBGenericEnergyNonPDE

Parameters:

phi - level set function assumed to be associated with this energy object

out - stream to print to

indent - indentation string