de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
Class SingleCellMigrationAnalyzer
java.lang.Object
de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
- All Implemented Interfaces:
- de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator
@ALDAOperator(genericExecutionMode=ALL,
level=APPLICATION,
allowBatchMode=false)
public class SingleCellMigrationAnalyzer
- extends MTBOperator
- 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 |
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
gamma
@Parameter(label=" \u03b3",
required=false,
direction=IN,
supplemental=false,
description="value for \u03b3-correction for emphasizing cells",
mode=ADVANCED)
private java.lang.Double gamma
inImg
@Parameter(label="input image",
required=true,
direction=IN,
supplemental=false,
description="input image")
private transient MTBImage inImg
labelResult
@Parameter(label="label result",
required=true,
direction=OUT,
supplemental=true,
description="resulting label image")
private transient MTBImage labelResult
maxAreaChange
@Parameter(label="maximum area change",
required=false,
direction=IN,
supplemental=false,
description="maximum change in area (fraction) for two objects to be assigned to each other")
private java.lang.Double maxAreaChange
maxDist
@Parameter(label="maximum distance (pixels)",
required=false,
direction=IN,
supplemental=false,
description="maximum distance for two objects to be assigned to each other",
mode=ADVANCED)
private java.lang.Double maxDist
maxIter
@Parameter(label="maximum number of iterations",
required=false,
direction=IN,
supplemental=false,
description="maximum number of iterations for level set evolution",
mode=ADVANCED)
private java.lang.Integer maxIter
medianRadius
@Parameter(label="median filter radius",
required=false,
direction=IN,
supplemental=false,
description="radius of median filter mask")
private java.lang.Integer medianRadius
minArea
@Parameter(label="minimum area (pixels)",
required=false,
direction=IN,
supplemental=false,
description="minimum area (number of pixels) an object should have")
private java.lang.Integer minArea
minSeedSize
@Parameter(label="minimum seed size",
required=false,
direction=IN,
supplemental=false,
description="minimum size for seeds to be not discarded",
mode=ADVANCED)
private java.lang.Integer minSeedSize
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
removeBorderObjects
@Parameter(label="remove border touching objects",
required=false,
direction=IN,
supplemental=false,
description="should border touching objects be removed")
private java.lang.Boolean removeBorderObjects
segmentationResult
@Parameter(label="segmentation result",
required=true,
direction=OUT,
supplemental=false,
description="resulting segmentation image")
private transient MTBImage segmentationResult
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
useAutoDistance
@Parameter(label="determine gating distance automatically",
required=false,
direction=IN,
supplemental=false,
description="determine gating distance automatically",
mode=ADVANCED)
private java.lang.Boolean useAutoDistance
SingleCellMigrationAnalyzer
public SingleCellMigrationAnalyzer()
throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
- Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
SingleCellMigrationAnalyzer
public SingleCellMigrationAnalyzer(MTBImage img)
throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
- Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
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