de.unihalle.informatik.MiToBo.apps.cellMorphology.paceQuant

Class PaCeQuant.SkeletonPostprocessor

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.cellMorphology.paceQuant.PaCeQuant.SkeletonPostprocessor

All Implemented Interfaces:

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

Enclosing class:

PaCeQuant

private class PaCeQuant.SkeletonPostprocessor
extends MTBOperator

Helper operator to post-process border skeletons.

This operator mainly removes spines from the border skeletons and eliminates regions including very long intrusions, i.e. spines which are longer than the given threshold or even branch.

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
private boolean	allowBranchPointsInSpines Flag to enable/disable check for branch points in spines.
private MTBImageByte	inputImg Input skeleton image to process.
private double	maxSpineLength Maximal allowed length of a branch to be accepted as spine.
private static String	opID Identifier string for this operator class.
private MTBImageByte	postprocessedImg Postprocessed skeleton image.
private PaCeQuant.SpineLengthDefine	spineLengthDefine Spine length interpretation.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
SkeletonPostprocessor() Default constructor.

Method Summary

Modifier and Type	Method and Description
void	allowBranchPointsInSpines(boolean flag) Allow/deny branch points in spines.
MTBImageByte	getResultImage() Returns postprocessed skeleton image.
protected void	operate()
void	setInputImage(MTBImageByte img) Set input image to process.
void	setMaximalSpineLength(double maxLength) Set maximal length of spines.
void	setSpineLengthDefine(PaCeQuant.SpineLengthDefine sld) Set interpretation mode for maximal length of spines.

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, 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

opID

private static final String opID

Identifier string for this operator class.

See Also:

Constant Field Values

inputImg

@Parameter(label="Input Image",
           required=true,
           direction=IN,
           description="Input image.",
           dataIOOrder=0)
private transient MTBImageByte inputImg

Input skeleton image to process.

The operator expects a binary image with the skeleton pixels having black color on a white background.

spineLengthDefine

@Parameter(label="Interpretation Mode for Spine Length",
           required=true,
           direction=IN,
           dataIOOrder=10,
           description="Interpretation of spine length.")
private PaCeQuant.SpineLengthDefine spineLengthDefine

Spine length interpretation.

maxSpineLength

@Parameter(label="Maximal Length of Spines",
           required=true,
           direction=IN,
           description="Max. spine length.",
           dataIOOrder=11)
private double maxSpineLength

Maximal allowed length of a branch to be accepted as spine.

The interpretation of the provided values depends on the settings of the parameter spineLengthDefine, i.e., has to be either in absolute pixel values or as a relative value with regard to the region perimeter (measured in terms of the number of border pixels).

allowBranchPointsInSpines

@Parameter(label="Allow Branch Points in Spines?",
           required=true,
           direction=IN,
           description="Flag to enable/disable check for branch points in spines.",
           dataIOOrder=12)
private boolean allowBranchPointsInSpines

Flag to enable/disable check for branch points in spines.

postprocessedImg

@Parameter(label="Postprocessed Image",
           dataIOOrder=0,
           direction=OUT,
           description="Postprocessed skeleton image.")
private transient MTBImageByte postprocessedImg

Postprocessed skeleton image.

Constructor Detail

SkeletonPostprocessor

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

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown on instantiation failures.

Method Detail

setInputImage

public void setInputImage(MTBImageByte img)

Set input image to process.

Expecting skeleton to be black on white background.

Parameters:

img - Input skeleton image.

setSpineLengthDefine

public void setSpineLengthDefine(PaCeQuant.SpineLengthDefine sld)

Set interpretation mode for maximal length of spines.

Parameters:

sld - Spine length interpretation mode (see PaCeQuant.SpineLengthDefine).

setMaximalSpineLength

public void setMaximalSpineLength(double maxLength)

Set maximal length of spines.

Parameters:

maxLength - Maximal length of spines.

allowBranchPointsInSpines

public void allowBranchPointsInSpines(boolean flag)

Allow/deny branch points in spines.

Often branch points within spines are indicators for peculiar intensity structures and it might be better to remove regions with such spines.

Parameters:

flag - If true branch points in spines are tolerated.

getResultImage

public MTBImageByte getResultImage()

Returns postprocessed skeleton image.

Returns:

Result image.

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