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

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.MigrationAnalyzer
All Implemented Interfaces:
de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator

@ALDAOperator(genericExecutionMode=ALL,
              level=STANDARD)
public class MigrationAnalyzer
extends MTBOperator


Nested Class Summary
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
 
Field Summary
private  java.lang.Boolean analyzeIntensities
           
private  java.lang.Boolean analyzeShapes
           
private  java.lang.Boolean analyzeTrajectories
           
private  java.lang.Double deltaT
           
private  java.lang.Double deltaX
           
private  java.lang.Double deltaY
           
private  java.lang.Boolean include
           
private  MTBImage intImg
           
private  MTBImage labelImg
           
private  MTBImage maskImg
           
private  java.lang.Integer minTrackLength
           
private  java.lang.Boolean showOverlayImage
           
private  java.lang.Boolean showTrajectoryMap
           
private  java.lang.String unitT
           
private  java.lang.String unitXY
           
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, portHashAccess, verbose, versionProvider
 
Constructor Summary
MigrationAnalyzer()
           
MigrationAnalyzer(MTBImage labelImg)
           
MigrationAnalyzer(MTBImage labelImg, MTBImage maskImg)
           
 
Method Summary
 void analyzeIntensities(boolean analyzeIntensities)
           
 void analyzeShapes(boolean analyzeShapes)
           
 void analyzeTrajectories(boolean analyzeTrajectories)
           
 void IncludeMask(boolean include)
           
 void operate()
           
 void setDeltaT(double deltaT)
           
 void setDeltaX(double deltaX)
           
 void setDeltaY(double deltaY)
           
 void setIntensityImage(MTBImage intImg)
           
 void setMinTrackLength(int minTrackLength)
           
 void setUnitT(java.lang.String unitT)
           
 void setUnitXY(java.lang.String unitXY)
           
 void showOverlayImage(boolean showOverlay)
           
 void showTrajectoryMap(boolean showTrajectories)
           
 
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

analyzeIntensities

@Parameter(label="analyze intensities",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the objects\' intensities be analyzed",
           dataIOOrder=7)
private java.lang.Boolean analyzeIntensities

analyzeShapes

@Parameter(label="analyze shapes",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the objects\' shapes be analyzed",
           dataIOOrder=7)
private java.lang.Boolean analyzeShapes

analyzeTrajectories

@Parameter(label="analyze trajectories",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the objects\' trajectories be analyzed",
           dataIOOrder=7)
private java.lang.Boolean analyzeTrajectories

deltaT

@Parameter(label="time between frames",
           required=false,
           direction=IN,
           supplemental=false,
           description="time between frames",
           dataIOOrder=4)
private java.lang.Double deltaT

deltaX

@Parameter(label="pixel length, x-direction",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in x-direction",
           dataIOOrder=1)
private java.lang.Double deltaX

deltaY

@Parameter(label="pixel length, y-direction",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in y-direction",
           dataIOOrder=2)
private java.lang.Double deltaY

include

@Parameter(label="include mask",
           required=false,
           direction=IN,
           supplemental=false,
           description="include tracks that have corresponding signals in mask image (otherwise these tracks are excluded)")
private java.lang.Boolean include

intImg

@Parameter(label="intensity image",
           required=false,
           direction=IN,
           supplemental=false,
           description="additional intensity image",
           dataIOOrder=0)
private transient MTBImage intImg

labelImg

@Parameter(label="label image",
           required=true,
           direction=IN,
           supplemental=false,
           description="labeled input image",
           dataIOOrder=0)
private transient MTBImage labelImg

maskImg

@Parameter(label="binary mask image",
           required=false,
           direction=IN,
           supplemental=false,
           description="binary mask image")
private transient MTBImage maskImg

minTrackLength

@Parameter(label="minimum track length",
           required=false,
           direction=IN,
           supplemental=false,
           description="minimum track length to be considered",
           dataIOOrder=6)
private java.lang.Integer minTrackLength

showOverlayImage

@Parameter(label="show overlay image",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the extracted trajectories be shown overlayed on the cells",
           dataIOOrder=7)
private java.lang.Boolean showOverlayImage

showTrajectoryMap

@Parameter(label="show trajectory map",
           required=false,
           direction=IN,
           supplemental=false,
           description="should a 2D map of the extracted trajectories be shown",
           dataIOOrder=7)
private java.lang.Boolean showTrajectoryMap

unitT

@Parameter(label="unit time",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit time",
           dataIOOrder=5)
private java.lang.String unitT

unitXY

@Parameter(label="unit x/y",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit x/y",
           dataIOOrder=3)
private java.lang.String unitXY
Constructor Detail

MigrationAnalyzer

public MigrationAnalyzer()
                  throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

MigrationAnalyzer

public MigrationAnalyzer(MTBImage labelImg)
                  throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

MigrationAnalyzer

public MigrationAnalyzer(MTBImage labelImg,
                         MTBImage maskImg)
                  throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail

analyzeIntensities

public void analyzeIntensities(boolean analyzeIntensities)
Parameters:
analyzeIntensities -

analyzeShapes

public void analyzeShapes(boolean analyzeShapes)
Parameters:
analyzeShapes -

analyzeTrajectories

public void analyzeTrajectories(boolean analyzeTrajectories)
Parameters:
analyzeTrajectories -

IncludeMask

public void IncludeMask(boolean include)

operate

public 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

setDeltaT

public void setDeltaT(double deltaT)
Parameters:
deltaT -

setDeltaX

public void setDeltaX(double deltaX)
Parameters:
deltaX -

setDeltaY

public void setDeltaY(double deltaY)
Parameters:
deltaY -

setIntensityImage

public void setIntensityImage(MTBImage intImg)
Parameters:
intImg -

setMinTrackLength

public void setMinTrackLength(int minTrackLength)
Parameters:
minTrackLength -

setUnitT

public void setUnitT(java.lang.String unitT)
Parameters:
unitT -

setUnitXY

public void setUnitXY(java.lang.String unitXY)
Parameters:
unitXY -

showOverlayImage

public void showOverlayImage(boolean showOverlay)
Parameters:
showOverlay -

showTrajectoryMap

public void showTrajectoryMap(boolean showTrajectories)
Parameters:
showTrajectories -