de.unihalle.informatik.MiToBo.filters.vesselness

Class MFFDOGMultiScaleFilter2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D

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 MFFDOGMultiScaleFilter2D
extends MTBOperator
implements loci.common.StatusReporter

MF-FDOG multi-scale filter for vessel segmentation.

This operator applies the MFFDOGFilter2D on multiple scales. The results are then combined using a logical OR operation.
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/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 Sampling step size for orientations.
protected MTBImage	inputImg Input image to be processed.
protected MFFDOGFilter2D.VesselMode	mode Scenario for detecting vessels.
private MTBImageByte	responseStack Result stack with binary vessel maps for different scales and lengths.
protected MTBImageByte	resultVesselMap Resulting binary vessel map.
protected Vector<loci.common.StatusListener>	statusListeners Vector of installed StatusListeners.
protected Double[][]	widthLengthTab Table with vessel widths and lengths to apply.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
MFFDOGMultiScaleFilter2D() Default constructor.

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener statuslistener)
void	notifyListeners(loci.common.StatusEvent e)
protected void	operate()
protected Object	readResolve() Init function for deserialized objects.
void	removeStatusListener(loci.common.StatusListener statuslistener)
void	validateCustom()

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

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

Input image to be processed.

mode

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

Scenario for detecting vessels.

widthLengthTab

@Parameter(label="Widths and Lengths",
           required=true,
           dataIOOrder=2,
           direction=IN,
           mode=STANDARD,
           description="Widths and lengths to apply.")
protected Double[][] widthLengthTab

Table with vessel widths and lengths to apply.

The operator expects an array with two columns. The first column refers to the widths to be applied, the second column refers to related vessel length. Note that both columns need to have the same length.

The widths determine the standard deviation of the Gaussian kernel, i.e. sigma = w / 2.0.

angleSampling

@Parameter(label="Angular Sampling Steps",
           required=true,
           direction=IN,
           mode=ADVANCED,
           description="Angular sampling step size (in degrees).",
           dataIOOrder=3)
protected int angleSampling

Sampling step size for orientations.

resultVesselMap

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

Resulting binary vessel map.

responseStack

@Parameter(label="Filter Response Stack",
           dataIOOrder=1,
           direction=OUT,
           description="Filter response stack.")
private transient MTBImageByte responseStack

Result stack with binary vessel maps for different scales and lengths.

Constructor Detail

MFFDOGMultiScaleFilter2D

public MFFDOGMultiScaleFilter2D()
                         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.

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

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

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