de.unihalle.informatik.MiToBo.apps.biofilms

Class ArealParameterExtractor

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor

All Implemented Interfaces:

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

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

operator for calculating areal 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	arealPorosity
private MTBDoubleData	avgDiffusionDist
private MTBDoubleData	avgHorizontalRunLength
private MTBDoubleData	avgVerticalRunLength
private boolean	calcAvgDiffusionDistance
private boolean	calcAvgHorizontalRunLength
private boolean	calcAvgVerticalRunLength
private boolean	calcDilationAreas
private boolean	calcMaxDiffusionDistance
private boolean	calcPorosity
private Vector<MTBIntegerData>	dilationAreas
private MTBImage	inImg
private MTBDoubleData	maxDiffusionDist
private int	maxDilMaskSize
private int	minDilMaskSize
private int	outDigits
private MTBTableModel	resultsTable

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
ArealParameterExtractor()
ArealParameterExtractor(MTBImage inImg)

Method Summary

Modifier and Type	Method and Description
private double	calcArealPorosity(MTBImage img)
private double	calcAverageDiffusionDistance(MTBImage distImg)
private double	calcAvgHorizontalRunLength(MTBImage img)
private double	calcAvgVerticalRunLength(MTBImage img)
private Vector<MTBIntegerData>	calcDilationAreas(MTBImage img, int minSize, int maxSize)
private double	calcMaximumDiffusionDistance(MTBImage distImg)
private MTBImage	getDistanceImage(MTBImage img)
private MTBTableModel	makeTable()
protected void	operate()

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

calcPorosity

@Parameter(label="calculate areal porosity",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the areal porosity of the image be calculated",
           dataIOOrder=1)
private boolean calcPorosity

calcAvgHorizontalRunLength

@Parameter(label="calculate avg. horizontal run lengths",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the average length of horizontal runs of the image be calculated",
           dataIOOrder=2)
private boolean calcAvgHorizontalRunLength

calcAvgVerticalRunLength

@Parameter(label="calculate avg. vertical run lengths",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the average length of vertical runs of the image be calculated",
           dataIOOrder=3)
private boolean calcAvgVerticalRunLength

calcAvgDiffusionDistance

@Parameter(label="calculate avg. diffusion distance",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the average diffusion of the image be calculated",
           dataIOOrder=4)
private boolean calcAvgDiffusionDistance

calcMaxDiffusionDistance

@Parameter(label="calculate max. diffusion distance",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the maximum diffusion of the image be calculated",
           dataIOOrder=5)
private boolean calcMaxDiffusionDistance

calcDilationAreas

@Parameter(label="calculate dilation areas",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the maximum diffusion of the image be calculated",
           dataIOOrder=6)
private boolean calcDilationAreas

minDilMaskSize

@Parameter(label="minimum dilation mask diameter",
           required=false,
           direction=IN,
           supplemental=false,
           description="the minimum diameter of dilation mask used for calculating dilation areas",
           dataIOOrder=7)
private int minDilMaskSize

maxDilMaskSize

@Parameter(label="maximum dilation mask diameter",
           required=false,
           direction=IN,
           supplemental=false,
           description="the maximum diameter of dilation mask used for calculating dilation areas",
           dataIOOrder=8)
private int maxDilMaskSize

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

arealPorosity

private MTBDoubleData arealPorosity

avgHorizontalRunLength

private MTBDoubleData avgHorizontalRunLength

avgVerticalRunLength

private MTBDoubleData avgVerticalRunLength

avgDiffusionDist

private MTBDoubleData avgDiffusionDist

maxDiffusionDist

private MTBDoubleData maxDiffusionDist

dilationAreas

private Vector<MTBIntegerData> dilationAreas

resultsTable

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

Constructor Detail

ArealParameterExtractor

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ArealParameterExtractor

public ArealParameterExtractor(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

calcArealPorosity

private double calcArealPorosity(MTBImage img)

Parameters:

img - binary input image

Returns:

areal porosity of the input image

calcAvgHorizontalRunLength

private double calcAvgHorizontalRunLength(MTBImage img)

Parameters:

img - binary input image

Returns:

average length of horizontal foreground runs (i.e., consecutive pixels in a row with value != 0)

calcAvgVerticalRunLength

private double calcAvgVerticalRunLength(MTBImage img)

Parameters:

img - binary input image

Returns:

average length of vertical foreground runs (i.e., consecutive pixels in a column with value != 0)

getDistanceImage

private MTBImage getDistanceImage(MTBImage img)
                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Parameters:

img - binary input image

Returns:

distance transform (euclidean) of the input image

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

calcAverageDiffusionDistance

private double calcAverageDiffusionDistance(MTBImage distImg)

Parameters:

distImg - distance transform image

Returns:

average diffusion distance

calcMaximumDiffusionDistance

private double calcMaximumDiffusionDistance(MTBImage distImg)

Parameters:

distImg - distance transform image

Returns:

maximum diffusion image

calcDilationAreas

private Vector<MTBIntegerData> calcDilationAreas(MTBImage img,
                                                 int minSize,
                                                 int maxSize)
                                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                 de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Parameters:

img - binary input image

minSize - minimum diameter of the circular dilation mask

maxSize - maximum diameter of the circular dilation mask

Returns:

dilation areas for the used dilation mask diameters

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

makeTable

private MTBTableModel makeTable()