de.unihalle.informatik.MiToBo.filters.linear.anisotropic

Class GaussPDxxFilter2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D

de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, Cloneable, EventListener, loci.common.StatusReporter

@ALDDerivedClass
 @ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class GaussPDxxFilter2D
extends OrientedFilter2D

2D filter implementing second partial derivative of Gaussian in x.

This filter is often used in the context of segmenting vessel-like structures, e.g., refer to

Sofka and Stewart, "Retinal Vessel Centerline Extraction Using Multiscale Matched Filters, Confidence and Edge Measures",
IEEE TMI, vol. 25, no. 12, pp. 1531-1546, December 2006

for an example of its application.

Author:

Birgit Moeller

Nested Class Summary

Nested classes/interfaces inherited from class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D

OrientedFilter2D.ApplicationMode

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 Double	gaussStdDev Standard deviation of the Gaussian.
protected Integer	height Height of the filter mask.
protected MTBBooleanData	invertMask Flag to invert filter mask.
private boolean[][]	kernelMask Internal helper mask to mark valid/invalid kernel elements.
protected MTBBooleanData	normalizeMask Flag to normalize sum of kernel elements to zero.

Fields inherited from class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D

angle, inputImg, mode, paddingVariant, resultImg, statusListeners

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
GaussPDxxFilter2D() Default constructor.

Method Summary

Modifier and Type	Method and Description
GaussPDxxFilter2D	clone()
void	disableNormalization() Disable kernel normalization.
void	enableNormalization() Enable kernel normalization.
MTBImageDouble	getKernel(double _angle) Calculates Gaussian derivative kernel for given parameters.
protected boolean[][]	getKernelMask() Get mask of valid kernel elements.
void	setHeight(int h) Specify height of filter mask.
void	setInvertMask(boolean b) Enable/disable inversion of mask.
void	setInvertMask(MTBBooleanData m) Enable or disable mask inversion.
void	setKernelNormalization(MTBBooleanData kn) Enable or disable kernel normalization.
void	setStandardDeviation(double s) Specify standard deviation of Gaussian.
void	validateCustom()

Methods inherited from class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D

addStatusListener, getApplicationMode, getResultImage, notifyListeners, operate, readResolve, removeStatusListener, setAngle, setApplicationMode, setInputImage, setPaddingVariant

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

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

Field Detail

gaussStdDev

@Parameter(label="\u03c3 of Gaussian",
           required=false,
           dataIOOrder=2,
           direction=IN,
           mode=STANDARD,
           description="Std. deviation of Gaussian.")
protected Double gaussStdDev

Standard deviation of the Gaussian.

The mask width is derived from the standard deviation of the Gaussian,
i.e. the width is given by

.
Note that the minimum width is 3.

height

@Parameter(label="Mask Height",
           required=false,
           dataIOOrder=3,
           direction=IN,
           mode=STANDARD,
           description="Height of the filter mask.")
protected Integer height

Height of the filter mask.

Note that the height of the mask must not be smaller than 3.

invertMask

@Parameter(label="Invert Mask",
           required=false,
           dataIOOrder=5,
           direction=IN,
           mode=STANDARD,
           description="If true, filter mask is inverted.")
protected MTBBooleanData invertMask

Flag to invert filter mask.

normalizeMask

@Parameter(label="Normalize Mask",
           required=false,
           dataIOOrder=4,
           direction=IN,
           mode=STANDARD,
           description="If true, mask is normalized to a sum of zero.")
protected MTBBooleanData normalizeMask

Flag to normalize sum of kernel elements to zero.

kernelMask

private boolean[][] kernelMask

Internal helper mask to mark valid/invalid kernel elements.

This variable is mainly used by the corresponding JUnit test class TestGaussPDxxFilter2D.

Constructor Detail

GaussPDxxFilter2D

public GaussPDxxFilter2D()
                  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

clone

public GaussPDxxFilter2D clone()

Specified by:

clone in class OrientedFilter2D

getKernel

public MTBImageDouble getKernel(double _angle)

Calculates Gaussian derivative kernel for given parameters.

Specified by:

getKernel in class OrientedFilter2D

Parameters:

_angle - Rotation angle in degrees.

Returns:

Kernel image.

setInvertMask

public void setInvertMask(boolean b)

Enable/disable inversion of mask.

Parameters:

b - Flag for inversion.

setInvertMask

public void setInvertMask(MTBBooleanData m)

Enable or disable mask inversion.

Using this method with MiToBo wrapper datatypes instead of passing over directly a boolean preserves consistency in the processing history.

Parameters:

m - Value for the mask inversion flag.

enableNormalization

public void enableNormalization()

Enable kernel normalization.

disableNormalization

public void disableNormalization()

Disable kernel normalization.

setKernelNormalization

public void setKernelNormalization(MTBBooleanData kn)

Enable or disable kernel normalization.

Using this method with MiToBo wrapper datatypes instead of passing over directly a boolean preserves consistency in the processing history.

Parameters:

kn - Value for the kernel normalization flag.

setStandardDeviation

public void setStandardDeviation(double s)

Specify standard deviation of Gaussian.

Parameters:

s - Standard deviation sigma.

setHeight

public void setHeight(int h)

Specify height of filter mask.

Parameters:

h - Height of mask.

getKernelMask

protected boolean[][] getKernelMask()

Get mask of valid kernel elements.

Intended to be used for unit testing only.

Returns:

Kernel mask.