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