de.unihalle.informatik.MiToBo.apps.cells2D
Class Mica2D

java.lang.Object
  extended by de.unihalle.informatik.Alida.operator.ALDOperator
      extended by de.unihalle.informatik.Alida.operator.ALDOperatorControllable
          extended by de.unihalle.informatik.MiToBo.core.operator.MTBOperatorControllable
              extended by de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
All Implemented Interfaces:
de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventListener, de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventReporter, de.unihalle.informatik.Alida.operator.events.ALDControlEventListener, de.unihalle.informatik.Alida.operator.events.ALDControlEventReporter, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class Mica2D
extends MTBOperatorControllable

Operator for integrated cell image analysis.

Given a multi-channel input image this operator detects nuclei, particles and the cell boundary and integrates all results to complete cell statistics.

Author:
moeller

Nested Class Summary
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorControlStatus, de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorExecutionStatus
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
 
Field Summary
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
configurationEventlistenerList, controlEventlistenerList, notifyListenersRecursively, operatorExecStatus, operatorStatus, stepSize, stepWiseExecution
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider
 
Constructor Summary
Mica2D()
          Default constructor.
Mica2D(MTBImage img, int nc, int cc)
          Default constructor.
 
Method Summary
 SegResult_Complete getResultData()
          Returns result data object.
 String getSaveIntermediateResultPath()
          Returns path where to save intermediate results.
protected  void operate()
          Invokes analysis procedure on given image.
 void saveIntermediateResults(boolean flag)
          Set flag to save intermediate results.
 void setChannelsToCopy(int[] carray)
          Specify list of channels to copy to result stack.
 void setDoGauss(boolean _doGauss)
          Specify if cell channel is to be smoothed prior to detection.
 void setGaussSigma(double _gaussSigma)
          Specify sigma for Gaussian smoothing.
 void setInitialSnakes(MTBPolygon2DSet f)
          Specify set of initial snakes.
 void setMeasureUnits(SegResultEnums.MeasureUnit mu)
          Specify how to measure lengths and areas.
 void setSaveIntermediateResultPath(String sIntermediateResultPath)
          Set path where to save intermediate results.
 void showIntermediateResults(boolean flag)
          Set flag to display intermediate results.
 void showMasksOnly(boolean flag)
          Set flag indicating whether to show masks or overlays in result stack.
 boolean supportsStepWiseExecution()
           
 
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
addALDConfigurationEventListener, addALDControlEventListener, fireALDConfigurationEvent, fireALDControlEvent, getExecutionStatus, handleALDConfigurationEvent, handleALDControlEvent, removeALDConfigurationEventListener, removeALDControlEventListener, setNotifyRecursiveFlag
 
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
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, readResolve, 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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Mica2D

public Mica2D()
       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Default constructor.

Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Mica2D

public Mica2D(MTBImage img,
              int nc,
              int cc)
       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Default constructor.

Parameters:
img - Input multi-layer image to be processed.
nc - Nuclei channel.
cc - Cytoplasm channel.
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail

supportsStepWiseExecution

public boolean supportsStepWiseExecution()
Specified by:
supportsStepWiseExecution in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable

setInitialSnakes

public void setInitialSnakes(MTBPolygon2DSet f)
Specify set of initial snakes.


showIntermediateResults

public void showIntermediateResults(boolean flag)
Set flag to display intermediate results.


saveIntermediateResults

public void saveIntermediateResults(boolean flag)
Set flag to save intermediate results.


getSaveIntermediateResultPath

public String getSaveIntermediateResultPath()
Returns path where to save intermediate results.


setSaveIntermediateResultPath

public void setSaveIntermediateResultPath(String sIntermediateResultPath)
Set path where to save intermediate results.


setChannelsToCopy

public void setChannelsToCopy(int[] carray)
Specify list of channels to copy to result stack.


showMasksOnly

public void showMasksOnly(boolean flag)
Set flag indicating whether to show masks or overlays in result stack.


setMeasureUnits

public void setMeasureUnits(SegResultEnums.MeasureUnit mu)
Specify how to measure lengths and areas.


setDoGauss

public void setDoGauss(boolean _doGauss)
Specify if cell channel is to be smoothed prior to detection.


setGaussSigma

public void setGaussSigma(double _gaussSigma)
Specify sigma for Gaussian smoothing.


getResultData

public SegResult_Complete getResultData()
Returns result data object.


operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
Invokes analysis procedure on given image.

Specified by:
operate in class de.unihalle.informatik.Alida.operator.ALDOperator
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException


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