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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperatorControllable
de.unihalle.informatik.MiToBo.core.operator.MTBOperatorControllable
de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
@ALDAOperator(genericExecutionMode=ALL, level=APPLICATION) public class Mica2D
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.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable |
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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 |
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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.ALDOperatorControllable |
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configurationEventlistenerList, controlEventlistenerList, notifyListenersRecursively, operatorExecStatus, operatorStatus, stepSize, stepWiseExecution |
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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Mica2D()
Default constructor. |
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Mica2D(MTBImage img,
int nc,
int cc)
Default constructor. |
Method Summary | |
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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()
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Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable |
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addALDConfigurationEventListener, addALDControlEventListener, fireALDConfigurationEvent, fireALDControlEvent, getExecutionStatus, handleALDConfigurationEvent, handleALDControlEvent, removeALDConfigurationEventListener, removeALDControlEventListener, setNotifyRecursiveFlag |
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, 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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Mica2D() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public Mica2D(MTBImage img, int nc, int cc) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
img
- Input multi-layer image to be processed.nc
- Nuclei channel.cc
- Cytoplasm channel.
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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public boolean supportsStepWiseExecution()
supportsStepWiseExecution
in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
public void setInitialSnakes(MTBPolygon2DSet f)
public void showIntermediateResults(boolean flag)
public void saveIntermediateResults(boolean flag)
public String getSaveIntermediateResultPath()
public void setSaveIntermediateResultPath(String sIntermediateResultPath)
public void setChannelsToCopy(int[] carray)
public void showMasksOnly(boolean flag)
public void setMeasureUnits(SegResultEnums.MeasureUnit mu)
public void setDoGauss(boolean _doGauss)
public void setGaussSigma(double _gaussSigma)
public SegResult_Complete getResultData()
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
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