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

Class LevelsetSolveNonPDE

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.MiToBo.core.operator.MTBOperator

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

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=NONE)
public class LevelsetSolveNonPDE
extends MTBOperator

Implements a level set solver which may optionally perserve the topology using non PDE optimization. See: Song, B. and Chan, T.: A fast algorithm for level set based optimization, UCLA Cam Report, 2002

Optionally a invalid image may be supplied which defines pixels with nonzero value as invalid and not considered for segmentation.

The resulting image is a short image, where background and invalid pixels have zeros and the obejct compontens/phases values starting from one.

NOTE: if verbose is turned on runtime will typically be increase considerably due to outputting (and consequently computing) the complete energy.

Currently only 2D images are supported.

Author:

Stefan Posch, partially bases on code by Markus Glass

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private class	LevelsetSolveNonPDE.CoordInt3D Just to hold 3D coordinate and nothing else
private class	LevelsetSolveNonPDE.LevelsetIterator Abstract class for iterators of pixels/voxels of the level set function.
private class	LevelsetSolveNonPDE.LevelsetIteratorContourPoints Iterator for all contour pixels/voxels of the level set function excluding invalid pixels/voxels.
private class	LevelsetSolveNonPDE.LevelsetIteratorScan Iterator for all pixels/voxels of the level set function in scanline fashion excluding invalid pixels/voxels.

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
private Integer	debug
private MTBGenericEnergyNonPDE	energy
private static int	FLAG_SOLVER
private static int	FLAG_SOLVER2
private Vector<MTBImageShort>	intermediateLS
private MTBImage	invalidImage
private Integer	maxIterations
private short[]	nbPhases Phases of the 8-neighbors of the current pixel.
private Vector<Short>	nbPhasesNonredundant Non redudant phases in the neighborhood of the current pixel.
private Integer	numIterations
private MTBLevelsetMembership	phi
private Vector<Short>	potentialNewPhases Phases the current pixel is (topologically) allowed to change to.
private Boolean	preserveTopology
private MTBImageShort	resultImage
private Integer	spacingIntermediate
private boolean	verbose

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, versionProvider

Constructor Summary

Constructors

Constructor and Description
LevelsetSolveNonPDE() Constructor
LevelsetSolveNonPDE(MTBGenericEnergyNonPDE energy, MTBLevelsetMembership phi, int maxIter, int spacingIntermediate, MTBImage invalidImg, boolean preserveTopology) Constructor.

Method Summary

Modifier and Type	Method and Description
private void	get8NeighborsPhase(int x, int y, short[] nb) Compute phases of 8 neighbors of (x,y) and store these in the array nb.
Integer	getDebug() Get value of debug.
MTBGenericEnergyNonPDE	getEnergy() Get value of energy.
Vector<MTBImageShort>	getIntermediateLS() Get value of intermediateLS.
MTBImage	getInvalidImage() Get value of invalidImage.
Integer	getMaxIterations() Get value of maxIterations.
Integer	getNumIterations() Get value of numIterations Explanation: Number of iterations performed
MTBLevelsetMembership	getPhi() Get value of phi.
private Vector<Short>	getPotentialNewPhases2D(boolean preserveTopology, int x, int y)
Boolean	getPreserveTopology() Get value of preserveTopology.
MTBImageShort	getResultImage() Get value of resultImage.
Integer	getSpacingIntermediate() Get value of spacingIntermediate.
private boolean	hasForeign4Neighbor(short phase, short[] nbPhases) Check whether there is a different/foreign phase (then phase) in the 4-neighborhood as represented in the 8 neighborhood nbPhases.
private int	numBlockChange(short[] nbPhases, int r) Return number of connected components of different/foreign phase then r in the 8 neighborhood nbPhases, which are 4 connected to the current pixel.
protected void	operate() This function does the actual work, i.e. optimization of the energy.
private void	printNbPhases(short[] nbPhases)
void	setDebug(Integer value) Set value of debug.
void	setMaxIterations(Integer value) Set value of maxIterations.
void	setPreserveTopology(Boolean value) Set value of preserveTopology.
void	setSpacingIntermediate(Integer value) Set value of spacingIntermediate.
private boolean	solve()

Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator

readResolve

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getDocumentation, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

phi

@Parameter(label="phi",
           required=true,
           direction=IN,
           description="Initial levelset function")
private MTBLevelsetMembership phi

invalidImage

@Parameter(label="invalidImage",
           required=false,
           direction=IN,
           description="optional image of invalid pixels (pixels <> 0 are invalid)")
private MTBImage invalidImage

resultImage

@Parameter(label="resultImage",
           direction=OUT,
           description="Result image")
private MTBImageShort resultImage

energy

@Parameter(label="energy",
           required=true,
           direction=IN,
           description="Energy to use for optimization")
private MTBGenericEnergyNonPDE energy

maxIterations

@Parameter(label="maxIterations",
           required=false,
           direction=IN,
           description="Maximal number of iterations")
private Integer maxIterations

preserveTopology

@Parameter(label="preserveTopology",
           required=true,
           direction=IN,
           description="Topology preserving mode?")
private Boolean preserveTopology

debug

@Parameter(label="debug",
           direction=IN,
           supplemental=true,
           description="Additional dubugging informaton")
private Integer debug

spacingIntermediate

@Parameter(label="spacingIntermediate",
           direction=IN,
           supplemental=true,
           description="spacing of intermediate of levelset function returned; 0 = none?")
private Integer spacingIntermediate

intermediateLS

@Parameter(label="intermediateLS",
           direction=IN,
           supplemental=true,
           description="intermediate of levelset functions")
private Vector<MTBImageShort> intermediateLS

numIterations

@Parameter(label="numIterations",
           direction=IN,
           supplemental=true,
           description="Number of iterations performed")
private Integer numIterations

potentialNewPhases

private Vector<Short> potentialNewPhases

Phases the current pixel is (topologically) allowed to change to. This vector is recycled for efficiency.

nbPhasesNonredundant

private Vector<Short> nbPhasesNonredundant

Non redudant phases in the neighborhood of the current pixel. This vector is recycled for efficiency.

nbPhases

private short[] nbPhases

Phases of the 8-neighbors of the current pixel. This array is recycled for efficiency.

verbose

private boolean verbose

FLAG_SOLVER

private static final int FLAG_SOLVER

See Also:

Constant Field Values

FLAG_SOLVER2

private static final int FLAG_SOLVER2

See Also:

Constant Field Values

Constructor Detail

LevelsetSolveNonPDE

public LevelsetSolveNonPDE(MTBGenericEnergyNonPDE energy,
                           MTBLevelsetMembership phi,
                           int maxIter,
                           int spacingIntermediate,
                           MTBImage invalidImg,
                           boolean preserveTopology)
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor.

Parameters:

enery - Energy

ls - initialed level set function of type membership, i.e. LevelsetMembership

maxIter - maximal number of iterations

spacingIntermediate - spacing of intermediate of level set function returned; 0 = none

invalidImg - optional image of invalid pixels (pixels <> 0 are invalid)

preserveTopology -

verbose - output if requested

debug - bit mask for debugging output

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

LevelsetSolveNonPDE

public LevelsetSolveNonPDE()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

This function does the actual work, i.e. optimization of the energy. NOTE: Currently only 2D level set functions are supported NOTE: if debug & FLAG_SOLVER, then for debugging purposes the complete energy is computed in each iteration, which is expensive

Specified by:

operate in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

solve

private boolean solve()
               throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getPotentialNewPhases2D

private Vector<Short> getPotentialNewPhases2D(boolean preserveTopology,
                                              int x,
                                              int y)

hasForeign4Neighbor

private boolean hasForeign4Neighbor(short phase,
                                    short[] nbPhases)

Check whether there is a different/foreign phase (then phase) in the 4-neighborhood as represented in the 8 neighborhood nbPhases.

Parameters:

nbPhases -

Returns:

numBlockChange

private int numBlockChange(short[] nbPhases,
                           int r)

Return number of connected components of different/foreign phase then r in the 8 neighborhood nbPhases, which are 4 connected to the current pixel. Invalid pixels are not considered as another phase This is identical to the topological number T_4(\vec x,fg) n in

Han, X. and Xu, C. and Prince, J.L., A topology preserving level set method for geometric deformable models}, PAMI, pages 755-768, 2003

Parameters:

nbPhases - Phases in the 8 neighborhood of current pixel with pahse r

r - Phase of current pixel

Returns:

Number of components

get8NeighborsPhase

private void get8NeighborsPhase(int x,
                                int y,
                                short[] nb)

Compute phases of 8 neighbors of (x,y) and store these in the array nb. This array is reused for efficiency.

Parameters:

x - x coordinate

y - y coordinate

nb - array in which to store the phases.

printNbPhases

private void printNbPhases(short[] nbPhases)

getMaxIterations

public Integer getMaxIterations()

Get value of maxIterations. Explanation: Maximal number of iterations.

Returns:

value of maxIterations

setMaxIterations

public void setMaxIterations(Integer value)

Set value of maxIterations. Explanation: Maximal number of iterations.

Parameters:

value - New value of maxIterations

getPreserveTopology

public Boolean getPreserveTopology()

Get value of preserveTopology. Explanation: Topology preserving mode?.

Returns:

value of preserveTopology

setPreserveTopology

public void setPreserveTopology(Boolean value)

Set value of preserveTopology. Explanation: Topology preserving mode?.

Parameters:

value - New value of preserveTopology

getEnergy

public MTBGenericEnergyNonPDE getEnergy()

Get value of energy. Explanation: Energy to use for optimization.

Returns:

value of energy

getInvalidImage

public MTBImage getInvalidImage()

Get value of invalidImage. Explanation: optional image of invalid pixels (pixels <> 0 are invalid).

Returns:

value of invalidImage

getPhi

public MTBLevelsetMembership getPhi()

Get value of phi. Explanation: Initial levelset function.

Returns:

value of phi

getResultImage

public MTBImageShort getResultImage()

Get value of resultImage. Explanation: Result image.

Returns:

value of resultImage

getIntermediateLS

public Vector<MTBImageShort> getIntermediateLS()

Get value of intermediateLS. Explanation: Additional dubugging informaton.

Returns:

value of intermediateLS

getDebug

public Integer getDebug()

Get value of debug. Explanation: Additional dubugging informaton.

Returns:

value of debug

setDebug

public void setDebug(Integer value)

Set value of debug. Explanation: Additional dubugging informaton.

Parameters:

value - New value of debug

getNumIterations

public Integer getNumIterations()

Get value of numIterations Explanation: Number of iterations performed

Returns:

value of numIterations

getSpacingIntermediate

public Integer getSpacingIntermediate()

Get value of spacingIntermediate. Explanation: spacing of intermediate of levelset function returned; 0 = none?.

Returns:

value of spacingIntermediate

setSpacingIntermediate

public void setSpacingIntermediate(Integer value)

Set value of spacingIntermediate. Explanation: spacing of intermediate of levelset function returned; 0 = none?.

Parameters:

value - New value of spacingIntermediate