de.unihalle.informatik.MiToBo.apps.biofilms

Class TexturalParameterExtractor

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class TexturalParameterExtractor
extends MTBOperator

operator for calculating textural parameters from biofilm images as described in Yang et al., Quantifying biofilm structure using image analysis. Journal of Microbiological Methods 39 (2000) 109–119. input image should be a 8-bit gray scale image

Author:

glass

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 MTBDoubleData	angularSecondMoment
private boolean	calcASM
private boolean	calcEntropy
private boolean	calcIDM
private MTBImage	inImg
private MTBDoubleData	inverseDifferenceMoment
private int	outDigits
private MTBTableModel	resultsTable
private MTBDoubleData	texturalEntropy

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
TexturalParameterExtractor()
TexturalParameterExtractor(MTBImage inImg)

Method Summary

Modifier and Type	Method and Description
private double	calcAngularSecondMoment(Double[][] P)
private double	calcInverseDifferenceMoment(Double[][] P)
private Double[][]	calcNormSpatialDependenceMatrix(MTBImage image)
private double	calcTexturalEntropy(Double[][] P)
private MTBTableModel	makeTable()
protected void	operate()
private void	printMatrix(Double[][] matrix)

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

inImg

@Parameter(label="input image",
           required=true,
           direction=IN,
           supplemental=false,
           description="input image (should be 8 bit gray scale)",
           dataIOOrder=0)
private transient MTBImage inImg

calcEntropy

@Parameter(label="calculate textural entropy",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the textural entropy of the image be calculated",
           dataIOOrder=3)
private boolean calcEntropy

calcASM

@Parameter(label="calculate angular second moment",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the angular second moment of the image be calculated",
           dataIOOrder=4)
private boolean calcASM

calcIDM

@Parameter(label="calculate inverse difference moment",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the inverse difference moment of the image be calculated",
           dataIOOrder=4)
private boolean calcIDM

outDigits

@Parameter(label="result value digits",
           required=false,
           direction=IN,
           supplemental=false,
           description="number of digits for output values",
           mode=ADVANCED,
           dataIOOrder=9)
private int outDigits

texturalEntropy

private MTBDoubleData texturalEntropy

angularSecondMoment

private MTBDoubleData angularSecondMoment

inverseDifferenceMoment

private MTBDoubleData inverseDifferenceMoment

resultsTable

@Parameter(label="results table",
           required=true,
           direction=OUT,
           supplemental=false,
           description="table containing the resulting values")
private MTBTableModel resultsTable

Constructor Detail

TexturalParameterExtractor

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

TexturalParameterExtractor

public TexturalParameterExtractor(MTBImage inImg)
                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

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

calcNormSpatialDependenceMatrix

private Double[][] calcNormSpatialDependenceMatrix(MTBImage image)

Parameters:

image - 8 bit grayscale image

Returns:

normalized spatial dependence matrix

calcTexturalEntropy

private double calcTexturalEntropy(Double[][] P)

Parameters:

P - normalized spatial dependence matrix

Returns:

textural entropy of the input image

calcAngularSecondMoment

private double calcAngularSecondMoment(Double[][] P)

Parameters:

P - normalized spatial dependence matrix

Returns:

angular second moment of the input image

calcInverseDifferenceMoment

private double calcInverseDifferenceMoment(Double[][] P)

Parameters:

P - normalized spatial dependence matrix

Returns:

inverse difference moment of the input image

makeTable

private MTBTableModel makeTable()

printMatrix

private void printMatrix(Double[][] matrix)