de.unihalle.informatik.MiToBo.filters.vesselness

Class MFFDOGFilter2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class MFFDOGFilter2D
extends MTBOperator
implements loci.common.StatusReporter

MF-FDOG filter for vessel segmentation.

This filter, the matched filter with first-order derivative of Gaussian, targets at segmenting vessel-like structures. Related publication:

B. Zhang, L. Zhang, L. Zhang and F. Karray, "Retinal vessel extraction by matched filter with first-order derivative of Gaussian",
Comp. in Biology and Medicine, vol. 40 (2010), pp. 438-445.

Author:

Birgit Moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MFFDOGFilter2D.VesselMode Detection scenario mode.

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	angleSampling Angular sampling interval.
protected Double	expectedWidth Expected width of vessels.
protected MTBImage	inputImg Image to process.
protected Integer	length Expected length of vessel segments.
protected int	meanFilterSize Size of mean filter for Gaussian derivative image.
protected MFFDOGFilter2D.VesselMode	mode Mode for detecting vessels.
protected MTBImageByte	resultVesselMap Final vessel map.
protected Vector<loci.common.StatusListener>	statusListeners Vector of installed StatusListeners.
protected double	threshScalingConstant Threshold scaling constant.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
MFFDOGFilter2D() Default constructor.

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener statuslistener)
MTBImageByte	getResultVesselMap() Get result.
void	notifyListeners(loci.common.StatusEvent e)
protected void	operate()
protected Object	readResolve() Init function for deserialized objects.
void	removeStatusListener(loci.common.StatusListener statuslistener)
void	setInputImage(MTBImage img) Specify input image.
void	setLength(Integer l) Specify length of vessels.
void	setSampling(int s) Specify angular sampling.
void	setVesselMode(MFFDOGFilter2D.VesselMode m) Specify detection scenario.
void	setWidth(Double w) Specify width of vessels.

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

statusListeners

protected transient Vector<loci.common.StatusListener> statusListeners

Vector of installed StatusListeners.

inputImg

@Parameter(label="Input Image",
           required=true,
           dataIOOrder=-10,
           direction=IN,
           mode=STANDARD,
           description="Input image.")
protected transient MTBImage inputImg

Image to process.

mode

@Parameter(label="Scenario",
           required=false,
           dataIOOrder=1,
           direction=IN,
           mode=STANDARD,
           description="Relation of vessels to background.")
protected MFFDOGFilter2D.VesselMode mode

Mode for detecting vessels.

expectedWidth

@Parameter(label="Expected Vessel Width",
           required=false,
           dataIOOrder=2,
           direction=IN,
           mode=STANDARD,
           description="Expected size of vessels.")
protected Double expectedWidth

Expected width of vessels.

The width is used to select the standard deviation of the Gaussian, i.e.

.

length

@Parameter(label="Length",
           required=false,
           dataIOOrder=3,
           direction=IN,
           mode=STANDARD,
           description="Length of vessel segments.")
protected Integer length

Expected length of vessel segments.

The length of the vessels is used to set the height of the filter masks.

angleSampling

@Parameter(label="Angular Sampling Steps",
           required=true,
           direction=IN,
           mode=ADVANCED,
           description="Angular sampling step size (in degrees).",
           dataIOOrder=4)
protected int angleSampling

Angular sampling interval.

meanFilterSize

@Parameter(label="Size of Mean Filter",
           required=true,
           direction=IN,
           mode=ADVANCED,
           description="Size of mean filter.",
           dataIOOrder=5)
protected int meanFilterSize

Size of mean filter for Gaussian derivative image.

threshScalingConstant

@Parameter(label="Threshold Scaling Constant",
           required=true,
           direction=IN,
           mode=ADVANCED,
           description="Constant for scaling local threshold, usually from the interval [2,3].",
           dataIOOrder=6)
protected double threshScalingConstant

Threshold scaling constant.

resultVesselMap

@Parameter(label="Result Map",
           dataIOOrder=0,
           direction=OUT,
           description="Resulting vessel map.")
protected transient MTBImageByte resultVesselMap

Final vessel map.

Constructor Detail

MFFDOGFilter2D

public MFFDOGFilter2D()
               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 MTBOperator

Returns:

Updated deserialized object.

operate

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

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

setInputImage

public void setInputImage(MTBImage img)

Specify input image.

Parameters:

img - Image to process.

setVesselMode

public void setVesselMode(MFFDOGFilter2D.VesselMode m)

Specify detection scenario.

Parameters:

m - Mode to assume.

setWidth

public void setWidth(Double w)

Specify width of vessels.

Parameters:

w - Expected width of vessels.

setLength

public void setLength(Integer l)

Specify length of vessels.

Parameters:

l - Length value to apply.

setSampling

public void setSampling(int s)

Specify angular sampling.

Parameters:

s - Size of angular sampling interval.

getResultVesselMap

public MTBImageByte getResultVesselMap()

Get result.

Returns:

Binary vessel map.

addStatusListener

public void addStatusListener(loci.common.StatusListener statuslistener)

Specified by:

addStatusListener in interface loci.common.StatusReporter

notifyListeners

public void notifyListeners(loci.common.StatusEvent e)

Specified by:

notifyListeners in interface loci.common.StatusReporter

removeStatusListener

public void removeStatusListener(loci.common.StatusListener statuslistener)

Specified by:

removeStatusListener in interface loci.common.StatusReporter