de.unihalle.informatik.MiToBo.apps.scratchAssay

Class ScratchAssaySegmenter

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=SWING,
              level=STANDARD,
              shortDescription="Segments the wound area of a scratch assay image.")
public class ScratchAssaySegmenter
extends MTBOperator

class for segmenting the wound area of a scratch assay image

First the image is smoothed.
Subsequently, the shannon entropy for every pixel is calculated.
Then a 2-phase topology preserving levelset segmentation is performed on the
entropy image to separate the cells from the scratch area.
Finally, the resulting scratch area is measured.

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 Integer	closingMaskSize
private Integer	entropyFilterSize
private MTBImage	entropyImg
private MTBImage	inImg
private MTBImage	initMask
private Boolean	isHorizontal
private Integer	maxIter
private String	modelFile
private Boolean	noCheck
private Integer	numIterations
private MTBImage	resultImg
private Long	runtime
private Double	scratchArea
private double[]	scratchFeatures
private Integer	sigma
private int	sizeX
private int	sizeY
private de.unihalle.informatik.Alida.datatypes.ALDFileString	svmFile
private Boolean	useExternalSVM

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
ScratchAssaySegmenter()
ScratchAssaySegmenter(MTBImage inImg, int sigma, int entropyFilterSize, boolean isHorizontal, boolean noCheck, int maxIter)

Method Summary

Modifier and Type	Method and Description
private double	classify(MTBImage entropyImg, MTBImage scratchMask, String modelFile) decide, whether the given entropy image contains an open scratch or not
private MTBImage	createInitBar(boolean horizontal) create rectangular shaped bar as initialization for the scratch
private double	getBhattacharyyaCoefficient(MTBImage entropyImg, MTBImage scratchMask)
String	getDocumentation()
MTBImage	getEntropyImage()
private double	getEntropyMeanDifference(MTBImage entropyImg, MTBImage scratchMask)
private double	getKolmogorovSmirnovStatistic(MTBImage entropyImg, MTBImage scratchMask)
Integer	getNumIterations()
MTBImage	getResultImage()
Long	getRuntime()
Double	getScratchArea()
double[]	getScratchFeatures()
private double	measure() measures the scratch area, i.e. number of pixels that don't have value 0
protected void	operate()
void	setInitMask(MTBImage initMask)
void	setSVMFile(String path)
void	useExternalSVM(boolean useExternalSVM)

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, 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",
           mode=STANDARD,
           dataIOOrder=0)
private transient MTBImage inImg

initMask

@Parameter(label="initialization mask",
           required=false,
           direction=IN,
           supplemental=false,
           description="initialization mask",
           mode=ADVANCED,
           dataIOOrder=1)
private transient MTBImage initMask

isHorizontal

@Parameter(label="horizontal scratch",
           required=true,
           direction=IN,
           supplemental=false,
           description="horizontally or vertically oriented scratch",
           mode=STANDARD,
           dataIOOrder=2)
private Boolean isHorizontal

sigma

@Parameter(label="\u03c3",
           required=true,
           direction=IN,
           supplemental=false,
           description="standard deviation of gauss filter",
           mode=STANDARD,
           dataIOOrder=3)
private Integer sigma

entropyFilterSize

@Parameter(label="entropy filter size",
           required=true,
           direction=IN,
           supplemental=false,
           description="size of entropy filter mask",
           mode=STANDARD,
           dataIOOrder=4)
private Integer entropyFilterSize

maxIter

@Parameter(label="maximum iterations",
           required=false,
           direction=IN,
           supplemental=false,
           description="maximum number of iterations of level set segmentation",
           mode=ADVANCED,
           dataIOOrder=5)
private Integer maxIter

noCheck

@Parameter(label="don\'t check for scratch presence",
           required=false,
           direction=IN,
           supplemental=false,
           description="don\'t check for scratch presence prior to segmentation",
           mode=STANDARD,
           dataIOOrder=6)
private Boolean noCheck

useExternalSVM

@Parameter(label="use external svm file",
           required=false,
           direction=IN,
           supplemental=false,
           description="should an external svm file be used for classification",
           mode=ADVANCED,
           dataIOOrder=7)
private Boolean useExternalSVM

svmFile

@Parameter(label="external svm file",
           required=false,
           direction=IN,
           supplemental=false,
           description="absolute path to external svm model file",
           mode=ADVANCED,
           dataIOOrder=8)
private de.unihalle.informatik.Alida.datatypes.ALDFileString svmFile

scratchArea

@Parameter(label="scratch area",
           required=true,
           direction=OUT,
           supplemental=false,
           description="detected scratch area")
private Double scratchArea

resultImg

@Parameter(label="result image",
           required=true,
           direction=OUT,
           supplemental=false,
           description="resulting segmented image")
private transient MTBImage resultImg

numIterations

@Parameter(label="number of iterations",
           required=false,
           direction=OUT,
           supplemental=true,
           description="number of iterations required for the segmentation")
private Integer numIterations

runtime

@Parameter(label="runtime",
           required=false,
           direction=OUT,
           supplemental=true,
           description="time required to perform the segmentation")
private Long runtime

entropyImg

@Parameter(label="entropy image",
           required=false,
           direction=OUT,
           supplemental=true,
           description="entropy image")
private transient MTBImage entropyImg

sizeX

private int sizeX

sizeY

private int sizeY

scratchFeatures

private double[] scratchFeatures

modelFile

private String modelFile

closingMaskSize

private Integer closingMaskSize

Constructor Detail

ScratchAssaySegmenter

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ScratchAssaySegmenter

public ScratchAssaySegmenter(MTBImage inImg,
                             int sigma,
                             int entropyFilterSize,
                             boolean isHorizontal,
                             boolean noCheck,
                             int maxIter)
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Parameters:

inImg - input image

sigma - variance of gauss filter

entropyFilterSize - size of mask for entropy filtering

isHorizontal - is scratch horizontally oriented (assumed to be vertically oriented else)

noCheck - don't check for scratch presence prior to segmentation

maxIter - maximum number of iterations

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

getResultImage

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

Returns:

the resulting image

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getScratchArea

public Double getScratchArea()
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Returns:

the measured scratch area

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getNumIterations

public Integer getNumIterations()

Returns:

the number of iterations required for the level set segmentation

getRuntime

public Long getRuntime()

Returns:

time in sec required for the segmentation

getEntropyImage

public MTBImage getEntropyImage()

Returns:

entropy filter image

useExternalSVM

public void useExternalSVM(boolean useExternalSVM)

setSVMFile

public void setSVMFile(String path)

setInitMask

public void setInitMask(MTBImage initMask)

getScratchFeatures

public double[] getScratchFeatures()
                            throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                   de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Returns:

array containing features extracted from the histogram of the segmented scratch area from the entropy image

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

measure

private double measure()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

measures the scratch area, i.e. number of pixels that don't have value 0

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

createInitBar

private MTBImage createInitBar(boolean horizontal)

create rectangular shaped bar as initialization for the scratch

Parameters:

horizontal - should the craeted bar be horizontally oriented

Returns:

Image containing a rectangular bar in the middle of the image

classify

private double classify(MTBImage entropyImg,
                        MTBImage scratchMask,
                        String modelFile)
                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                        de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

decide, whether the given entropy image contains an open scratch or not

Parameters:

entropyImg -

scratchMask -

modelFile -

Returns:

1, if a scratch is present; -1, if not

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getEntropyMeanDifference

private double getEntropyMeanDifference(MTBImage entropyImg,
                                        MTBImage scratchMask)
                                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                        de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Parameters:

entropyImg -

scratchMask -

Returns:

the difference between the mean entropies of the segmented scratch and cell areas

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getBhattacharyyaCoefficient

private double getBhattacharyyaCoefficient(MTBImage entropyImg,
                                           MTBImage scratchMask)
                                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                           de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Parameters:

entropyImg -

scratchMask -

Returns:

Bhattacharyya coefficient of histograms for segmented scratch area and the rest of the image (cell area)

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getKolmogorovSmirnovStatistic

private double getKolmogorovSmirnovStatistic(MTBImage entropyImg,
                                             MTBImage scratchMask)
                                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                             de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Parameters:

entropyImg -

scratchMask -

Returns:

Kolmogorov-Smirnov statistic of histograms for segmented scratch area and the rest of the image (cell area)

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getDocumentation

public String getDocumentation()

Overrides:

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