de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver

Class LevelsetSolverPDE

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver

de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives

de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class LevelsetSolverPDE
extends LevelsetSolverDerivatives

Solver for level set segmentation problems based on PDEs.

Author:

Martin Scharm, Michael Schneider, Birgit Moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	LevelsetSolverPDE.VelocityExpansionMode Available modes for expanding zero level velocities.

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
protected int	depth Depth of the input image.
protected int	height Height of the input image.
protected MTBImageRGB	intermediatePhiColorImage Color image to visualize intermediate segmentation results.
protected Vector<MTBImageByte>	intermediateResults List of intermediate result segmentations.
protected int	intermediateResultSamplingRate
protected MTBImageByte	intermediateResultStack
protected MTBPolygon2DSet	invisibleRegionSet
protected int	iteration Iteration counter.
protected int	maxIterations
protected double	narrowBandWidth
private MTBLevelsetFunctionPDE	phi_old Variable to store old level set function for comparison with new one.
protected MTBImageRGB	resultImage
protected MTBImageByte	resultMask
protected boolean	showIntermediateResults
(package private) MTBTopologicalNumber2DN4	topologicalNumber2DN4 Helper object used in topology preservation.
(package private) MTBTopologicalNumber2DN8	topologicalNumber2DN8 Helper object used in topology preservation.
protected boolean	topologyPreservation
protected LevelsetSolverPDE.VelocityExpansionMode	vExpandMode
protected int	width Width of the input image.

Fields inherited from class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives

approxFunction, deltaApproximator, deltaT, energySet, epsilon, phi

Fields inherited from class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver

initGenerator, initialSegmentation, inputImg

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
LevelsetSolverPDE() Default constructor.

Method Summary

Modifier and Type	Method and Description
int	getHeight() Get height of level set function.
int	getMaxIterations() Get maximal number of iterations.
double	getNarrowBandWidth() Get width of narrow band.
MTBImageRGB	getResultImage() Get image with segmentation result overlay.
MTBImageByte	getResultMask() Get binary mask of segmentation result.
int	getWidth() Get width of level set function domain.
protected void	operate() Methode that runs the operator.
void	setInputImg(MTBImage img) Set input image.
void	setNarrowBandWidth(double w) Set width of narrow band.
protected int	sgn(double ka) Returns the sign of a value.
protected boolean	solve() Solve this level set problem.
protected int	step() Do one iteration, update all pixels of levelset function (in narrow band).
void	validateCustom()

Methods inherited from class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives

getDeltaApproximator, getDeltaT, getEnergySet, getEpsilon, getPhi

Methods inherited from class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver

getInitialSegmentation, getInputImg, initSegmentation

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, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

vExpandMode

@Parameter(label="Velocity Expansion Mode",
           required=true,
           direction=IN,
           dataIOOrder=19,
           description="Mode for expansion of contour pixel velocities.")
protected LevelsetSolverPDE.VelocityExpansionMode vExpandMode

maxIterations

@Parameter(label="Max. Iterations",
           required=false,
           direction=IN,
           dataIOOrder=1,
           description="Max. number of iterations in iterative optimization.")
protected int maxIterations

narrowBandWidth

@Parameter(label="Narrow Band Width",
           required=false,
           direction=IN,
           dataIOOrder=2,
           description="Width of narrow band, if zero, all pixels are considered.")
protected double narrowBandWidth

topologyPreservation

@Parameter(label="Preserve Topology",
           required=false,
           direction=IN,
           dataIOOrder=3,
           description="Enables/disables topology preservation.")
protected boolean topologyPreservation

invisibleRegionSet

@Parameter(label="Regions to mask (only 2D)",
           required=false,
           direction=IN,
           dataIOOrder=4,
           description="Optional polygon set to set parts of the image invisible.")
protected MTBPolygon2DSet invisibleRegionSet

showIntermediateResults

@Parameter(label="Show Intermediate Results",
           required=false,
           supplemental=true,
           dataIOOrder=-99,
           direction=IN,
           description="Displays additional, intermediate segmentation results.")
protected boolean showIntermediateResults

intermediateResultSamplingRate

@Parameter(label="Save Intermediate Segmentations, Rate = ",
           required=false,
           supplemental=true,
           dataIOOrder=-98,
           direction=IN,
           description="Sampling rate for intermediate results,\n if zero no stack with intermediate results is generated.")
protected int intermediateResultSamplingRate

resultImage

@Parameter(label="Result Image",
           direction=OUT,
           dataIOOrder=0,
           description="Overlay of contour on input image.")
protected transient MTBImageRGB resultImage

resultMask

@Parameter(label="Result Mask",
           direction=OUT,
           dataIOOrder=1,
           description="Binary segmentation mask.")
protected transient MTBImageByte resultMask

intermediateResultStack

@Parameter(label="Intermediate Results Stack",
           required=false,
           supplemental=true,
           dataIOOrder=2,
           direction=OUT,
           description="Stack with intermediate results.")
protected transient MTBImageByte intermediateResultStack

height

protected int height

Height of the input image.

width

protected int width

Width of the input image.

depth

protected int depth

Depth of the input image.

iteration

protected int iteration

Iteration counter.

phi_old

private transient MTBLevelsetFunctionPDE phi_old

Variable to store old level set function for comparison with new one.

topologicalNumber2DN4

MTBTopologicalNumber2DN4 topologicalNumber2DN4

Helper object used in topology preservation.

topologicalNumber2DN8

MTBTopologicalNumber2DN8 topologicalNumber2DN8

Helper object used in topology preservation.

intermediateResults

protected transient Vector<MTBImageByte> intermediateResults

List of intermediate result segmentations.

intermediatePhiColorImage

protected transient MTBImageRGB intermediatePhiColorImage

Color image to visualize intermediate segmentation results.

Constructor Detail

LevelsetSolverPDE

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

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Overrides:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

operate

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

Methode that runs the operator.

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

solve

protected boolean solve()

Solve this level set problem.

Returns:

True, if a solution could be found, otherwise false.

step

protected int step()

Do one iteration, update all pixels of levelset function (in narrow band).

Returns:

Number of pixels where sign changed.

sgn

protected int sgn(double ka)

Returns the sign of a value.

Parameters:

ka - Value.

Returns:

1 or -1, according to the sign, 0 if value is identical to zero.

getNarrowBandWidth

public double getNarrowBandWidth()

Get width of narrow band.

Returns:

Width of narrow band.

setNarrowBandWidth

public void setNarrowBandWidth(double w)

Set width of narrow band.

Parameters:

w - New width of narrow band.

getWidth

public int getWidth()

Get width of level set function domain.

Returns:

Size of level set function in x.

getMaxIterations

public int getMaxIterations()

Get maximal number of iterations.

Returns:

Maximal number of iterations in optimization.

getHeight

public int getHeight()

Get height of level set function.

Returns:

Size of level set function domain in y.

setInputImg

public void setInputImg(MTBImage img)

Set input image.

Parameters:

img - Image to segment.

getResultMask

public MTBImageByte getResultMask()

Get binary mask of segmentation result.

Returns:

Binary segmentation result.

getResultImage

public MTBImageRGB getResultImage()

Get image with segmentation result overlay.

Returns:

Result image with contour overlay.