de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
Class FluorescentCellSegmenter
java.lang.Object
de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
- All Implemented Interfaces:
- de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator
@ALDAOperator(genericExecutionMode=ALL,
level=STANDARD)
public class FluorescentCellSegmenter
- extends CellSegmenter
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode |
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
completeDAG, name, portHashAccess, verbose, versionProvider |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
deserializeFromXmlFile, fieldContained, getALDPortHashAccessKey, getConstructionMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, isConfigured, parametersToXmlObject, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, runOp, runOp, runOp, serializeToXmlFile, setConstructionMode, setName, setParameter, setParametersFromXml, setParametersFromXml, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory, writeParametersToXml |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
gamma
@Parameter(label=" \u03b3",
required=false,
direction=IN,
supplemental=false,
description="value for \u03b3-correction for emphasizing cells",
mode=ADVANCED)
private java.lang.Double gamma
maxIter
@Parameter(label="maximum number of iterations",
required=false,
direction=IN,
supplemental=false,
description="maximum number of iterations for level set evolution",
mode=ADVANCED)
private java.lang.Integer maxIter
medianRadius
@Parameter(label="median filter radius",
required=false,
direction=IN,
supplemental=false,
description="radius of median filter mask")
private java.lang.Integer medianRadius
FluorescentCellSegmenter
public FluorescentCellSegmenter()
throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
- Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
FluorescentCellSegmenter
public FluorescentCellSegmenter(MTBImage inImg)
throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
- Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
getResultImage
public MTBImage getResultImage()
- Overrides:
getResultImage
in class CellSegmenter
- Returns:
- segmentation result
getSeedPoints
protected MTBImage getSeedPoints(MTBImage frame)
throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
- coarse segmentation of input frame to localize cells
- Specified by:
getSeedPoints
in class CellSegmenter
- Parameters:
frame
-
- Returns:
- image containing seed points for the given frame
- Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
preprocess
protected MTBImage preprocess(MTBImage frame)
throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
- Specified by:
preprocess
in class CellSegmenter
- Parameters:
frame
-
- Returns:
- preprocessed frame
- Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
segment
protected MTBImage segment(MTBImage frame,
MTBImage seedFrame)
throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
- Description copied from class:
CellSegmenter
- segment cells in a single frame of the input image
- Specified by:
segment
in class CellSegmenter
- Parameters:
frame
- input frame
- Returns:
- segmented frame
- Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
setGamma
public void setGamma(double gamma)
- Parameters:
gamma
-
setMaxIteration
public void setMaxIteration(int maxIter)
- Parameters:
maxIter
-
setMedianMaskSize
public void setMedianMaskSize(int size)
- Parameters:
size
-