de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
Class CellSegmenter

java.lang.Object
  extended by de.unihalle.informatik.Alida.operator.ALDOperator
      extended by de.unihalle.informatik.MiToBo.core.operator.MTBOperator
          extended by de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
All Implemented Interfaces:
de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator
Direct Known Subclasses:
FluorescentCellSegmenter

public abstract class CellSegmenter
extends MTBOperator

base class for cell segmentation

Author:
glass

Nested Class Summary
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
 
Field Summary
protected  MTBImage inImg
           
protected  java.lang.Integer minSeedSize
           
protected  MTBImage resultImg
           
protected  MTBImage seedImg
           
protected  int sizeT
           
protected  int sizeX
           
protected  int sizeY
           
protected  int sizeZ
           
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, portHashAccess, verbose, versionProvider
 
Constructor Summary
protected CellSegmenter()
           
  CellSegmenter(MTBImage inImg)
           
 
Method Summary
 MTBImage getResultImage()
           
protected abstract  MTBImage getSeedPoints(MTBImage frame)
          coarse segementation of input frame to localize cells
protected  void operate()
           
protected abstract  MTBImage preprocess(MTBImage frame)
           
protected abstract  MTBImage segment(MTBImage frame, MTBImage seedFrame)
          segment cells in a single frame of the input image
 void setMinSeedSize(int minSize)
           
 void setSeedPointImage(MTBImage seedImg)
           
protected  void verbosePrintln(java.lang.String s)
          prints the given text if the verbose flag is set
 
Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator
readResolve
 
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
 

Field Detail

inImg

@Parameter(label="input image",
           required=true,
           direction=IN,
           supplemental=false,
           description="input image")
protected transient MTBImage inImg

minSeedSize

@Parameter(label="minimum seed size",
           required=false,
           direction=IN,
           supplemental=false,
           description="minimum size for seeds to be not discarded")
protected java.lang.Integer minSeedSize

resultImg

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

seedImg

@Parameter(label="seed image",
           required=false,
           direction=IN,
           supplemental=false,
           description="seed point image")
protected transient MTBImage seedImg

sizeT

protected int sizeT

sizeX

protected int sizeX

sizeY

protected int sizeY

sizeZ

protected int sizeZ
Constructor Detail

CellSegmenter

protected CellSegmenter()
                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

CellSegmenter

public CellSegmenter(MTBImage inImg)
              throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail

getResultImage

public MTBImage getResultImage()
Returns:
result image

getSeedPoints

protected abstract MTBImage getSeedPoints(MTBImage frame)
                                   throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                          de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
coarse segementation of input frame to localize cells

Parameters:
frame -
Returns:
image containing seed points for the given frame
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

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

preprocess

protected abstract MTBImage preprocess(MTBImage frame)
                                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
Parameters:
frame -
Returns:
preprocessed frame
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

segment

protected abstract MTBImage segment(MTBImage frame,
                                    MTBImage seedFrame)
                             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                    de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
segment cells in a single frame of the input image

Parameters:
frame - input frame
seedFrame -
Returns:
segmented frame
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

setMinSeedSize

public void setMinSeedSize(int minSize)
Parameters:
minSize -

setSeedPointImage

public void setSeedPointImage(MTBImage seedImg)
Parameters:
seedImg -

verbosePrintln

protected void verbosePrintln(java.lang.String s)
prints the given text if the verbose flag is set

Parameters:
s - text to print