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 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, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, runOp, runOp, runOp, setConstructionMode, setHidingMode, setName, setParameter, 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 |
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
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
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 frameseedFrame
-
- 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
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