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, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

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, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
protected Integer	channel
protected MTBImage	inImg
protected Integer	minSeedSize
protected MTBImage	resultImg
protected MTBImage	seedImg
protected int	sizeC
protected int	sizeT
protected int	sizeX
protected int	sizeY
protected int	sizeZ

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	CellSegmenter()
	CellSegmenter(MTBImage inImg)

Method Summary

Modifier and Type	Method and Description
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	setChannel(int channel)
void	setMinSeedSize(int minSize)
void	setSeedPointImage(MTBImage seedImg)
void	validateCustom()
protected void	verbosePrintln(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

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getDocumentation, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateGeneric, writeHistory, writeHistory, writeHistory

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

channel

@Parameter(label="channel",
           required=false,
           direction=IN,
           supplemental=false,
           description="channel used for segmentation")
protected Integer channel

seedImg

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

minSeedSize

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

resultImg

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

sizeX

protected int sizeX

sizeY

protected int sizeY

sizeZ

protected int sizeZ

sizeT

protected int sizeT

sizeC

protected int sizeC

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

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Overrides:

validateCustom in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

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

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

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

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

getResultImage

public MTBImage getResultImage()

Returns:

result image

setChannel

public void setChannel(int channel)

Parameters:

channel -

setMinSeedSize

public void setMinSeedSize(int minSize)

Parameters:

minSize -

setSeedPointImage

public void setSeedPointImage(MTBImage seedImg)

Parameters:

seedImg -

verbosePrintln

protected void verbosePrintln(String s)

prints the given text if the verbose flag is set

Parameters:

s - text to print