de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
Class CellSegmenter
java.lang.Object
de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
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 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 |
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
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
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 frameseedFrame
-
- 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