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

Class ChaudhuriMatchedFilter2D

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.ChaudhuriMatchedFilter2D

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 ChaudhuriMatchedFilter2D
extends OrientedFilter2D

2D Matched filter.

This filter is mainly used for segmenting vessel-like structures, e.g., refer to

Chaudhuri, S., Chatterjee, S., Katz, N., Nelson, M., and Goldbaum, M.,
"Detection of Blood Vessels in Retinal Images Using 2D Matched Filters",
IEEE Trans. on Medical Imaging, vol. 8, no. 3, September 1989

Target structures are assumed to exhibit a Gaussian-shaped cross-section. This is modeled by a Gaussian kernel with standard deviation .

Contrary to the paper this operator always uses square kernels, i.e. the maximum of the kernel height and is used as kernel size.
In addition, the calculations are done in double precision while the original paper uses integer precision only.

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.
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
ChaudhuriMatchedFilter2D() Default constructor.

Method Summary

Modifier and Type	Method and Description
ChaudhuriMatchedFilter2D	clone()
void	disableNormalization() Disable kernel normalization.
void	enableNormalization() Enable kernel normalization.
MTBImageDouble	getKernel(double _angle) Calculates kernel for given angle and pre-defined sigma and length.
protected Object	readResolve() Init function for deserialized objects.
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, 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.

As defined in the original paper the filter targets at filtering dark structures on bright background.
To detect bright structures on dark background the mask needs to be inverted.

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.

Constructor Detail

ChaudhuriMatchedFilter2D

public ChaudhuriMatchedFilter2D()
                         throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

readResolve

protected Object readResolve()

Description copied from class: MTBOperator

Init function for deserialized objects.

This function is called on an instance of this class being deserialized from file, prior to handing the instance over to the user. It takes care of a proper initialization of transient member variables as they are not initialized to the default values during deserialization.

Overrides:

readResolve in class OrientedFilter2D

Returns:

Updated deserialized object.

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 ChaudhuriMatchedFilter2D clone()

Specified by:

clone in class OrientedFilter2D

getKernel

public MTBImageDouble getKernel(double _angle)

Calculates kernel for given angle and pre-defined sigma and length.

Specified by:

getKernel in class OrientedFilter2D

Parameters:

_angle - Rotation angle in degrees.

Returns:

Kernel image.

setStandardDeviation

public void setStandardDeviation(double s)

Specify standard deviation of Gaussian.

Parameters:

s - Standard deviation .

setHeight

public void setHeight(int h)

Specify height of filter mask.

Parameters:

h - Height of mask.

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.