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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
@ALDAOperator(genericExecutionMode=SWING, level=STANDARD) public class ScratchAssaySegmenter
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.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode |
Field Summary |
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Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider |
Constructor Summary | |
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ScratchAssaySegmenter()
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ScratchAssaySegmenter(MTBImage inImg,
int sigma,
int entropyFilterSize,
boolean isHorizontal,
boolean noCheck,
int maxIter)
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Method Summary | |
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MTBImage |
getEntropyImage()
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Integer |
getNumIterations()
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MTBImage |
getResultImage()
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Long |
getRuntime()
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Double |
getScratchArea()
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double[] |
getScratchFeatures()
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protected void |
operate()
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void |
setInitMask(MTBImage initMask)
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void |
setSVMFile(String path)
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void |
useExternalSVM(boolean useExternalSVM)
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Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator |
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readResolve |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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addOperatorExecutionProgressEventListener, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getHidingMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, runOp, runOp, runOp, setConstructionMode, setHidingMode, setName, setParameter, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ScratchAssaySegmenter() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public ScratchAssaySegmenter(MTBImage inImg, int sigma, int entropyFilterSize, boolean isHorizontal, boolean noCheck, int maxIter) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
inImg
- input imagesigma
- variance of gauss filterentropyFilterSize
- size of mask for entropy filteringisHorizontal
- is scratch horizontally oriented (assumed to be vertically oriented else)noCheck
- don't check for scratch presence prior to segmentationmaxIter
- maximum number of iterations
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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protected void operate() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
operate
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
public MTBImage getResultImage() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public Double getScratchArea() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public Integer getNumIterations()
public Long getRuntime()
public MTBImage getEntropyImage()
public void useExternalSVM(boolean useExternalSVM)
public void setSVMFile(String path)
public void setInitMask(MTBImage initMask)
public double[] getScratchFeatures() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
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